Citrus Sinensis ID: 042541

---

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
MAAAFVGGALLGAVFGELLKAVSEEKDKAVTFKDRLEQLESTLRNSIPWIEEIEKLNQVLDRPKQETENLVRMMEQVEQLVRKCSKVKWNCFKRYVYAKKIIKLDTSISDFFRTSLPLQHARDGKLIMVEVKEIHTMVRRMSGNGNINGWMSNQVGDCCSAPDPPVISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSESLLQKLGFQLPDYKILVTSRSEFPQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGGSLCGKHEVFWQRMVKECSRGESVFQSKNDILDCLGSSLDVLNNEVKECYLDLCSFPEDQRIPITALIDMWMELYELVDDVFAITNLHELSSQNLVDRVVTRKTAGDYGCYNDDFVMQHDLLRELTICRSKSEPINQRKRLVVEISGNNFPKWWMDQKQHPNNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPEGI
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccHHHHHHHHHHHccccEEEEEEEcccccHHHHHHHHHccccccccccccEEEEEEcccccHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHcccccEEEEEEccccccHHHHHHHcccccccEEEEEccccccccccEEEcccccHHHHHHHHHHHcccccccccccHHHHHHHHHHHccccHHHHHHHHHHcccccHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHccccccccccccccEEEcHHHHHHHHHHHccccccccccEEEEEcccccccccccccccccccEEEEEEccccccccccccccccEEEEEEEcccccccccccccccccccEEEEccccccccccccccccccccccccccccccccccccHHcccccccEEEcccccccccccccccccccccccccEEEEccccccccccccccccccccEEEEccccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccEEcccccHHHHHHHHHccccEEEEEEccccccHHHHHHHHHccHHHHHHcccEEEEEEEcccccHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHccccEEEEEEccccccHHHHHHccccccccEEEEEEccccccccccEEcccccHHHHHHHHHHHHccccccccccHHHHHHHHHHHHcccHHHHHHHHHHHHcccHHHHHHHHHHHHcccccccccccHHHHHHHHHHHccHHHHHHHHHHHcccccccccHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHccccccccccccccEEEHHHHHHHHHHHHcccccHHHHHHcEEEccccccccccccccccccEEEEEEEEccccccccccccccccHEEEEEccccccccccHHHHHccccEEEEEEccccccccccccHHHHcHHHHEcccccEEccccccccccHHHccEEEcccccHHHccHHHccHHHHccccccEEEEcccccHHHccccHHccccccEEEccccccHccccccc
Coil and Loop (DISEMBL)
MAAAFVGGALLGAVFGELLKAVSEEKDKAVTFKDRLEQLESTLRNSIPWIEEIEKLNQVLDRPKQETENLVRMMEQVEQLVRKCSKVKWNCFKRYVYAKKIIKLDTSIsdffrtslplqhardgkLIMVEVKEIHTMVRRMsgngningwmsnqvgdccsapdppvispgldvplKELKMELFKDGRQFIvvsapggygktTLVQRLckddqvqgkfkddIFYVTVSKNPNVKAIVQKVlhhkgypvpefqtdeAAINDLERFFKQMRIEAILLVLDDVWPGSESLLQKLgfqlpdykilvtsrsefpqfgsvhylkplTYEAARTLFLHsanlqdgnsyipdenIVSKILRACkgcplalkvvggslcgkHEVFWQRMVKECsrgesvfqskNDILDCLGSSLDVLNNEVKECYLdlcsfpedqripITALIDMWMELYELVDDVFAITNlhelssqnLVDRVVTrktagdygcynddfvmQHDLLRELTicrsksepinqRKRLVVEIsgnnfpkwwmdqkqhpnnasllsistdetfssnwpdmqgpeVKVVVLNIRtkkyvlpdflQKMDELKVLIVTNygfspaelnNFRVLSALSKLKKIRLEHVSLPNSLATVRMNHLQKVSLVMCNVgqvfrnstfrisdafpNLLEMDIDYCNDlielpdglcdivsmeklritnchrlsalpegi
Flexible Loop (DISEMBL)
maaafvggALLGAVFGELLKAVSEEKDKAVTFKDRLEQLestlrnsipwieeIEKLNQVLDRPKQETENLVRMMEQVEQLVrkcskvkwncFKRYVYAKKIIKLDTSISDFFRtslplqhardgklIMVEVKEIHTMVRRMSGNGNINGWMSNQVGDCCSAPDPPVISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSESLLQKLGFQLPDYKILVTSRSEFPQFGSVHYLKPLTYEAARTLFLHSAnlqdgnsyiPDENIVSKILRACKGCPLALKVVGGSLCGKHEVFWQRMVKECSRGESVFQSKNDILDCLGSSLDVLNNEVKECYLDLCSFPEDQRIPITALIDMWMELYELVDDVFAITNLhelssqnlvdrVVTRKTAGDYGCYNDDFVMQHDLLRELTIcrsksepinqrkrLVVEISGNNFPKWWMDQKQHPNNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITnchrlsalpegi
Low Complexity Region (SEG)
MaaafvggallgavfgELLKAVSEEKDKAVTFKDRLEQLESTLRNSIPWIEEIEKLNQVLDRPKQETENLVRMMEQVEQLVRKCSKVKWNCFKRYVYAKKIIKLDTSISDFFRTSLPLQHARDGKLIMVEVKEIHTMVRRMSGNGNINGWMSNQVGDCCSAPDPPVISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSESLLQKLGFQLPDYKILVTSRSEFPQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGGSLCGKHEVFWQRMVKECSRGESVFQSKNDILDCLGSSLDVLNNEVKECYLDLCSFPEDQRIPITALIDMWMELYELVDDVFAITNLHELSSQNLVDRVVTRKTAGDYGCYNDDFVMQHDLLRELTICRSKSEPINQRKRLVVEISGNNFPKWWMDQKQHPNNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPEGI
Disordered region (IsUnstruct)
***AFVGGALLGAVFGELLKAVSEEKDKAVTFKDRLEQLESTLRNSIPWIEEIEKLNQVL********NLVRMMEQVEQLVRKCSKVKWNCFKRYVYAKKIIKLDTSISDFFRTSLPLQHARDGKLIMVEVKEIHTMVRRMSGNGNINGWMSNQVGDCCSAPDPPVISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSESLLQKLGFQLPDYKILVTSRSEFPQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGGSLCGKHEVFWQRMVKECSRGESVFQSKNDILDCLGSSLDVLNNEVKECYLDLCSFPEDQRIPITALIDMWMELYELVDDVFAITNLHELSSQNLVDRVVTRKTAGDYGCYNDDFVMQHDLLRELTICRSKSEPINQRKRLVVEISGNNFPKWWMD**********************WPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRL*******
Disordered Region (DISOPRED)
MAAAFVGGALLGAVFGELLKAVSEEKDKAVTFKDRLEQLESTLRNSIPWIEEIEKLNQVLDRPKQETENLVRMMEQVEQLVRKCSKVKWN******************SDFFRTSLPLQHARD*****V*************************************ISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGY**************LE**FKQMRIEAILLVLDDVWPGSESLLQKLGFQLPDYKILVTSRSEFPQFGSVHYLKPLTYEAARTLFLHSANL*****YI**ENIVSKILRACKGCPLALKVVGGSLCGKHEVFWQRMVKEC**********NDILDCLGSSLDVLNNEVKECYLDLCSFPEDQRIPITALIDMWMELYELVDDVFAITNLHELSSQNLVDRVVTRKTAGDYGCYNDDFVMQHDLLRELTICRSKSEPINQRKRLVVEISGNN***********PNNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPE**
Disordered Region (DISEMBL)
MAAAFVGGALLGAVFGELLKAVSEEKDKAVTFKDRLEQLESTLRNSIPWIEEIEKLNQVLDRPKQETENLVRMMEQVEQLVRKCSKVKWNCFKRYVYAKKIIKLDTSISDFFRTSLPLQHARDGKLIMVEVKEIHTMVRRMSGNGNINGWMSNQVGDCCSAPDPPVISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSESLLQKLGFQLPDYKILVTSRSEFPQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGGSLCGKHEVFWQRMVKECSRGESVFQSKNDILDCLGSSLDVLNNEVKECYLDLCSFPEDQRIPITALIDMWMELYELVDDVFAITNLHELSSQNLVDRVVTRKTAGDYGCYNDDFVMQHDLLRELTICRSKSEPINQRKRLVVEISGNNFPKWWMDQKQHPNNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPEGI
Disordered Region (DISPRO)
MAAAFVGGALLGAVFGELLKAVSEEKDKAVTFKDRLEQLESTLRNSIPWIEEIEKLNQVLDRPKQETENLVRMMEQVEQLVRKCSKVKWNCFKRYVYAKKIIKLDTSISDFFRTSLPLQHARDGKLIMVEVKEIHTMVRRMSG*****************APDPPVISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSESLLQKLGFQLPDYKILVTSRSEFPQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGGSLCGKHEVFWQRMVKECSRGESVFQSKNDILDCLGSSLDVLNNEVKECYLDLCSFPEDQRIPITALIDMWMELYELVDDVFAITNLHELSSQNLVDRVVTRKTAGDYGCYNDDFVMQHDLLRELTICRSKSEPINQRKRLVVEISGNNFPKWWMDQKQHPNNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALP***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooohhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAAAFVGGALLGAVFGELLKAxxxxxxxxxxxxxxxxxxxxxLRNSIPWIEEIEKLNQVLDRPKQETENLVRMMEQVEQLVRKCSKVKWNCFKRYVYAKKIIKLDTSISDFFRTSLPLQHARDGKLIMVEVKEIHTMVRRMSGNGNINGWMSNQVGDCCSAPDPPVISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSESLLQKLGFQLPDYKILVTSRSEFPQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGGSLCGKHEVFWQRMVKECSRGESVFQSKNDILDCLGSSLDVLNNEVKECYLDLCSFPEDQRIPITALIDMWMELYELVDDVFAITNLHELSSQNLVDRVVTRKTAGDYGCYNDDFVMQHDLLRELTICRSKSEPINQRKRLVVEISGNNFPKWWMDQKQHPNNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPEGI
Positional Conservation
no confident homologs detected

---

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	695	2.2.26 [Sep-21-2011]
Q9FKZ1	809	Probable disease resistan	yes	no	0.985	0.846	0.413	1e-135
Q9FKZ0	815	Probable disease resistan	no	no	0.958	0.817	0.395	1e-123
Q9SZA7	816	Probable disease resistan	no	no	0.952	0.811	0.312	1e-90
Q9LZ25	811	Probable disease resistan	no	no	0.955	0.818	0.291	1e-82
Q9FW44	787	Disease resistance protei	no	no	0.941	0.831	0.300	6e-80
Q9LVT1	623	Putative disease resistan	no	no	0.710	0.792	0.312	3e-72
Q9FKZ2	415	Probable disease resistan	no	no	0.414	0.693	0.407	3e-53
Q84WJ0	702	Protein DA1-related 5 OS=	no	no	0.585	0.579	0.334	8e-53
P0C8S1	906	Probable disease resistan	no	no	0.461	0.354	0.294	1e-20
Q8W3K3	910	Putative disease resistan	no	no	0.663	0.506	0.254	1e-20

>sp|Q9FKZ1|DRL42_ARATH Probable disease resistance protein At5g66900 OS=Arabidopsis thaliana GN=At5g66900 PE=3 SV=1

 Score =  481 bits (1237), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 288/697 (41%), Positives = 415/697 (59%), Gaps = 12/697 (1%)

Query: 3   AAFVGGALLGAVFGELLKAVSEEKDKAVTFKDRLEQLESTLRNSIPWIEEIEKLNQVLDR 62
           A+   G++  AVF +LLK V +E  K   FK   + L ST+    P  ++I+ + + LD 
Sbjct: 5   ASLGIGSIGEAVFSKLLKVVIDEAKKFKAFKPLSKDLVSTMEILFPLTQKIDSMQKELDF 64

Query: 63  PKQETENLVRMMEQVEQLVRKCSKVKWNCFKRYVYAKKIIKLDTSISDFFRTSLPLQHAR 122
             +E + L   +E+ +  VRK  +VKW  +++  Y +KI +++  +  F +  L L   R
Sbjct: 65  GVKELKELRDTIERADVAVRKFPRVKW--YEKSKYTRKIERINKDMLKFCQIDLQLLQHR 122

Query: 123 DGKLIMVEVKEIHTMVRRMSGNGNINGWMSNQVGDCCSAPDPPVISPGLDVPLKELKMEL 182
           +   ++     +   V  +S   ++    +    D CS P    +  GLD PL ELK  L
Sbjct: 123 NQLTLLGLTGNLVNSVDGLSKRMDLLSVPAPVFRDLCSVPKLDKVIVGLDWPLGELKKRL 182

Query: 183 FKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHH 242
             D    +VVSAP G GKTTLV RLC D  ++GKFK  IF+  VS  PN + IVQ +L H
Sbjct: 183 LDDSVVTLVVSAPPGCGKTTLVSRLCDDPDIKGKFKH-IFFNVVSNTPNFRVIVQNLLQH 241

Query: 243 KGYPVPEFQTDEAAINDLERFFKQMRIEA-ILLVLDDVWPGSESLLQKLGFQLPDYKILV 301
            GY    F+ D  A   L +  ++++    ILLVLDDVW G++S LQK   +LP+YKILV
Sbjct: 242 NGYNALTFENDSQAEVGLRKLLEELKENGPILLVLDDVWRGADSFLQKFQIKLPNYKILV 301

Query: 302 TSRSEFPQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLAL 361
           TSR +FP F S + LKPL  + AR L +H A+     S    E+++ KIL+ C G P+ +
Sbjct: 302 TSRFDFPSFDSNYRLKPLEDDDARALLIHWASRPCNTSPDEYEDLLQKILKRCNGFPIVI 361

Query: 362 KVVGGSLCGKHEVFWQRMVKECSRGESVF-QSKNDILDCLGSSLDVLNNEVKECYLDLCS 420
           +VVG SL G+    W+  V+  S GE +  +    +L+CL  S D L+  +KEC+LD+ S
Sbjct: 362 EVVGVSLKGRSLNTWKGQVESWSEGEKILGKPYPTVLECLQPSFDALDPNLKECFLDMGS 421

Query: 421 FPEDQRIPITALIDMWMELYELVDDVFAITNLHELSSQNLVDRVVTRKTAGDYGCYNDDF 480
           F EDQ+I  + +IDMW+ELY     +  +  L +L+SQNL+  V       + G YND  
Sbjct: 422 FLEDQKIRASVIIDMWVELYGKGSSILYMY-LEDLASQNLLKLVPLGTNEHEDGFYNDFL 480

Query: 481 VMQHDLLRELTICRSKSEPINQRKRLVVEISGNNFPKWWMDQKQHPNNASLLSISTDETF 540
           V QHD+LREL IC+S+ +   +RKRL +EI  N FP W ++      NASLLSISTD+ F
Sbjct: 481 VTQHDILRELAICQSEFKENLERKRLNLEILENTFPDWCLNTI----NASLLSISTDDLF 536

Query: 541 SSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSAL 600
           SS W +M  P V+ +VLN+ +  Y LP F+  M +LKVL +TN+GF PA L+NF  LS+L
Sbjct: 537 SSKWLEMDCPNVEALVLNLSSSDYALPSFISGMKKLKVLTITNHGFYPARLSNFSCLSSL 596

Query: 601 SKLKKIRLEHVSLP-NSLATVRMNHLQKVSLVMCNVGQVFRNST-FRISDAFPNLLEMDI 658
             LK+IRLE VS+    +  ++++ L+K+SLVMC+ G+VF ++    +S+A   L E+DI
Sbjct: 597 PNLKRIRLEKVSITLLDIPQLQLSSLKKLSLVMCSFGEVFYDTEDIVVSNALSKLQEIDI 656

Query: 659 DYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPEGI 695
           DYC DL ELP  + +IVS++ L ITNC++LS LPE I
Sbjct: 657 DYCYDLDELPYWISEIVSLKTLSITNCNKLSQLPEAI 693

Probable disease resistance protein.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9FKZ0|DRL43_ARATH Probable disease resistance protein At5g66910 OS=Arabidopsis thaliana GN=At5g66910 PE=2 SV=1

 Score =  441 bits (1135), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 281/710 (39%), Positives = 411/710 (57%), Gaps = 44/710 (6%)

Query: 8   GALLGAVFGELLKAVSEEKDKAVTFKDRLEQLESTLRNSIPWIEEIEKLNQVLDRPKQET 67
           G++ GA+  E LK +  E  K + FK    +L ST+ + +P I+EIE +   +     E 
Sbjct: 12  GSVAGALVSEGLKVLISEAKKVLAFKSVSNELASTMESLLPVIKEIESMQDGM-----EL 66

Query: 68  ENLVRMMEQVEQLVRKCSKV-KWNCFKRYVYAKKIIKLDTSISDFFRTSLPLQHARDGKL 126
           ++L   +++   LV KCS V KWN   +  Y +K+ +++  +  F +  L L   R+   
Sbjct: 67  QDLKDTIDKALLLVEKCSHVEKWNIILKSKYTRKVEEINRKMLKFCQVQLQLLLFRN--- 123

Query: 127 IMVEVKEIHTMVRRMSGN-GNINGWMSNQVGDCCSAPDPPVISP-------------GLD 172
              ++K + +M   ++    NIN  +    G    +P PP++S              GLD
Sbjct: 124 ---QLKSMPSMEAILNNYFQNINKKLDRLSG----SPAPPLVSKRCSVPKLDNMVLVGLD 176

Query: 173 VPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNV 232
            PL ELK +L  +    +VVS P G GKTTLV +LC D +++G+FK  IFY  VS  PN 
Sbjct: 177 WPLVELKKKLLDNS--VVVVSGPPGCGKTTLVTKLCDDPEIEGEFKK-IFYSVVSNTPNF 233

Query: 233 KAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEA-ILLVLDDVWPGSESLLQKLG 291
           +AIVQ +L   G     F  D  A   L    +++  +  ILLVLDDVW GSE LL+K  
Sbjct: 234 RAIVQNLLQDNGCGAITFDDDSQAETGLRDLLEELTKDGRILLVLDDVWQGSEFLLRKFQ 293

Query: 292 FQLPDYKILVTSRSEFPQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKIL 351
             LPDYKILVTS+ +F      ++L PL YE AR+L +  A+     S    E+++ KIL
Sbjct: 294 IDLPDYKILVTSQFDFTSLWPTYHLVPLKYEYARSLLIQWASPPLHTSPDEYEDLLQKIL 353

Query: 352 RACKGCPLALKVVGGSLCGKHEVFWQRMVKECSRGESVFQSKN-DILDCLGSSLDVLNNE 410
           + C G PL ++VVG SL G+    W+  V+  S GE++  + N  +   L  S +VL   
Sbjct: 354 KRCNGFPLVIEVVGISLKGQALYLWKGQVESWSEGETILGNANPTVRQRLQPSFNVLKPH 413

Query: 411 VKECYLDLCSFPEDQRIPITALIDMWMELY---ELVDDVFAITNLHELSSQNLVDRVVTR 467
           +KEC++D+ SF +DQ+I  + +ID+WMELY       + F +  L+EL+SQNL+  V   
Sbjct: 414 LKECFMDMGSFLQDQKIRASLIIDIWMELYGRGSSSTNKFMLY-LNELASQNLLKLVHLG 472

Query: 468 KTAGDYGCYNDDFVMQHDLLRELTICRSKSEPINQRKRLVVEISGNNFPKWWMDQKQHPN 527
               + G YN+  V QH++LREL I +S+ EPI QRK+L +EI  +NFP   ++Q   P 
Sbjct: 473 TNKREDGFYNELLVTQHNILRELAIFQSELEPIMQRKKLNLEIREDNFPDECLNQ---PI 529

Query: 528 NASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFS 587
           NA LLSI TD+ FSS W +M  P V+ +VLNI +  Y LP F+ +M +LKVL + N+GF 
Sbjct: 530 NARLLSIYTDDLFSSKWLEMDCPNVEALVLNISSLDYALPSFIAEMKKLKVLTIANHGFY 589

Query: 588 PAELNNFRVLSALSKLKKIRLEHVSLP-NSLATVRMNHLQKVSLVMCNVGQVFRNST-FR 645
           PA L+NF  LS+L  LK+IR E VS+    +  +++  L+K+S  MC+ G+VF ++    
Sbjct: 590 PARLSNFSCLSSLPNLKRIRFEKVSVTLLDIPQLQLGSLKKLSFFMCSFGEVFYDTEDID 649

Query: 646 ISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPEGI 695
           +S A  NL E+DIDYC DL ELP  + ++VS++ L ITNC++LS LPE I
Sbjct: 650 VSKALSNLQEIDIDYCYDLDELPYWIPEVVSLKTLSITNCNKLSQLPEAI 699

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SZA7|DRL29_ARATH Probable disease resistance protein At4g33300 OS=Arabidopsis thaliana GN=At4g33300 PE=2 SV=3

 Score =  334 bits (857), Expect = 1e-90,   Method: Compositional matrix adjust.
 Identities = 223/714 (31%), Positives = 387/714 (54%), Gaps = 52/714 (7%)

Query: 12  GAVFGELLKAVSEEKDKAVTFKDRLEQLESTLRNSIPWIEEIEKLNQVLDRPKQ-ETENL 70
           G +  ELLK +      A  +K+  +QL + + +  P I+EI+     L   +Q +   L
Sbjct: 9   GEIATELLKQLFTISTTAWRYKNTAKQLLTLIDSIRPTIKEIQYSGVELPAHRQAQIGML 68

Query: 71  VRMMEQVEQLVRKC-SKVKWNCFKRYVYAKKIIKLDTSISDFFRTSL------PLQHARD 123
              +E+ ++L  K  S  +WN +++   A+K+ KL+ +IS+F +  +       + H R 
Sbjct: 69  FDTLEKGKKLTDKVLSSKRWNLYRQLTLARKMEKLEKTISNFLKNEVFTHILADVHHLRA 128

Query: 124 GKLIMVE---------VKEIHTMVRRMSGNGNINGWMSN-QVGDCCSAPDPPVISPGLDV 173
              + ++         ++++ +M  ++ G G I+  M   +  +  +  D      GL++
Sbjct: 129 DTSVRLDRVDMSLDRVIQQVGSM--KIGGGGLISEAMKRAEAMEIETNDDSEKFGVGLEL 186

Query: 174 PLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVK 233
              ++K  +F+       +S  GG GKTTL + L +D +VQ  F++ I ++TVS++P ++
Sbjct: 187 GKVKVKKMMFESQGGVFGISGMGGVGKTTLAKELQRDHEVQCHFENRILFLTVSQSPLLE 246

Query: 234 AIVQKVLH-----HKGYPVPE--FQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSESL 286
            + + +         G PVP+  F  D A                 L++LDDVW  +++L
Sbjct: 247 ELRELIWGFLSGCEAGNPVPDCNFPFDGARK---------------LVILDDVWT-TQAL 290

Query: 287 LQKLGFQLPDYKILVTSRSEFPQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIP---D 343
            +   F+ P    LV SRS+  +    + ++ L+ + A +LF   A    G   IP    
Sbjct: 291 DRLTSFKFPGCTTLVVSRSKLTEPKFTYDVEVLSEDEAISLFCLCAF---GQKSIPLGFC 347

Query: 344 ENIVSKILRACKGCPLALKVVGGSLCGKHEVFWQRMVKECSRGESVFQS-KNDILDCLGS 402
           +++V ++   CKG PLALKV G SL GK E++W+ +++  S+GE    S ++ +L  + +
Sbjct: 348 KDLVKQVANECKGLPLALKVTGASLNGKPEMYWKGVLQRLSKGEPADDSHESRLLRQMEA 407

Query: 403 SLDVLNNEVKECYLDLCSFPEDQRIPITALIDMWMELYELVDDVFAITNLHELSSQNLVD 462
           SLD L+   K+C+LDL +FPED++IP+  LI++W+EL++ +D+  A   L +LS +NL+ 
Sbjct: 408 SLDNLDQTTKDCFLDLGAFPEDRKIPLDVLINIWIELHD-IDEGNAFAILVDLSHKNLLT 466

Query: 463 RVVTRKTAGDYGCYNDDFVMQHDLLRELTICRSKSEPINQRKRLVVEISGNNFPKWWMDQ 522
                +    Y  + D FV QHD+LR+L +  S +  +N+RKRL++     + P  W   
Sbjct: 467 LGKDPRLGSLYASHYDIFVTQHDVLRDLALHLSNAGKVNRRKRLLMPKRELDLPGDWERN 526

Query: 523 KQHPNNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVT 582
                 A ++SI T E     W DM+ P+ ++++LN  + KYVLP F+ KM  LKVL++ 
Sbjct: 527 NDEHYIAQIVSIHTGEMNEMQWFDMEFPKAEILILNFSSDKYVLPPFISKMSRLKVLVII 586

Query: 583 NYGFSPAELNNFRVLSALSKLKKIRLEHVSLPN-SLATVRMNHLQKVSLVMCNVGQVFRN 641
           N G SPA L++F + + LSKL+ + LE V +P  S +T  + +L K+SL++C + + F  
Sbjct: 587 NNGMSPAVLHDFSIFAHLSKLRSLWLERVHVPQLSNSTTPLKNLHKMSLILCKINKSFDQ 646

Query: 642 STFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPEGI 695
           +   ++D FP L ++ ID+C+DL+ LP  +C + S+  L ITNC RL  LP+ +
Sbjct: 647 TGLDVADIFPKLGDLTIDHCDDLVALPSSICGLTSLSCLSITNCPRLGELPKNL 700

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LZ25|DRL30_ARATH Probable disease resistance protein At5g04720 OS=Arabidopsis thaliana GN=At5g04720 PE=2 SV=1

 Score =  308 bits (789), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 207/709 (29%), Positives = 367/709 (51%), Gaps = 45/709 (6%)

Query: 12  GAVFGELLKAVSEEKDKAVTFKDRLEQLESTLRNSIPWIEEIEKLNQVLDRPKQETENLV 71
           G V  EL++ +     K +  +   + L + +    P I+EI+     L   +Q     +
Sbjct: 7   GEVVTELVRQLYAVSQKTLRCRGIAKNLATMIDGLQPTIKEIQYSGVELTPHRQAQ---L 63

Query: 72  RMMEQVEQLVRKCSK-----VKWNCFKRYVYAKKIIKLDTSISDFFRTSL------PLQH 120
           RM  +     RK ++      +WN  ++ ++ +K+  L + +S F    L       + H
Sbjct: 64  RMFSETLDKCRKLTEKVLKSSRWNMVRQLLHVRKMENLQSKVSSFLNGQLLVHVLADVHH 123

Query: 121 AR-DGKLIMVEVKEIHTMVRRMSGNGNINGWMSNQVGDCCSAPDPPV---------ISPG 170
            R D +     +      +    G+  + G  S  + +     +  V         +  G
Sbjct: 124 VRADSEFRFDRIDRKVDSLNEKLGSMKLRG--SESLREALKTAEATVEMVTTDGADLGVG 181

Query: 171 LDVPLKELKMELFK--DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSK 228
           LD+  +++K  LFK  DG + I +S   G GKTTL + L +D++V+G F + + ++TVS+
Sbjct: 182 LDLGKRKVKEMLFKSIDGERLIGISGMSGSGKTTLAKELARDEEVRGHFGNKVLFLTVSQ 241

Query: 229 NPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSESLLQ 288
           +PN++ +     H  G+      + EA +         +     L++LDDVW   ESL Q
Sbjct: 242 SPNLEELRA---HIWGF----LTSYEAGVG------ATLPESRKLVILDDVWT-RESLDQ 287

Query: 289 KLGFQLPDYKILVTSRSEFPQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVS 348
            +   +P    LV SRS+       + ++ L    A  LF  S   Q        +++V 
Sbjct: 288 LMFENIPGTTTLVVSRSKLADSRVTYDVELLNEHEATALFCLSVFNQKLVPSGFSQSLVK 347

Query: 349 KILRACKGCPLALKVVGGSLCGKHEVFWQRMVKECSRGESVFQS-KNDILDCLGSSLDVL 407
           +++  CKG PL+LKV+G SL  + E +W+  V+  SRGE   ++ ++ +   + ++L+ L
Sbjct: 348 QVVGECKGLPLSLKVIGASLKERPEKYWEGAVERLSRGEPADETHESRVFAQIEATLENL 407

Query: 408 NNEVKECYLDLCSFPEDQRIPITALIDMWMELYELVDDVFAITNLHELSSQNLVDRVVTR 467
           + + ++C+L L +FPED++IP+  LI++ +EL++L +D  A   + +L+++NL+  V   
Sbjct: 408 DPKTRDCFLVLGAFPEDKKIPLDVLINVLVELHDL-EDATAFAVIVDLANRNLLTLVKDP 466

Query: 468 KTAGDYGCYNDDFVMQHDLLRELTICRSKSEPINQRKRLVVEISGNNFPKWWMDQKQHPN 527
           +    Y  Y D FV QHD+LR++ +  S    +N R+RL++    +  P+ W      P 
Sbjct: 467 RFGHMYTSYYDIFVTQHDVLRDVALRLSNHGKVNNRERLLMPKRESMLPREWERNNDEPY 526

Query: 528 NASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFS 587
            A ++SI T E    +W DM+ P+ +V++L+  + KYVLP F+ KM +L  L++ N G S
Sbjct: 527 KARVVSIHTGEMTQMDWFDMELPKAEVLILHFSSDKYVLPPFIAKMGKLTALVIINNGMS 586

Query: 588 PAELNNFRVLSALSKLKKIRLEHVSLPN-SLATVRMNHLQKVSLVMCNVGQVFRNSTFRI 646
           PA L++F + + L+KLK + L+ V +P  S +TV + +L K+SL+ C +      +   I
Sbjct: 587 PARLHDFSIFTNLAKLKSLWLQRVHVPELSSSTVPLQNLHKLSLIFCKINTSLDQTELDI 646

Query: 647 SDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPEGI 695
           +  FP L ++ ID+C+DL+ELP  +C I S+  + ITNC R+  LP+ +
Sbjct: 647 AQIFPKLSDLTIDHCDDLLELPSTICGITSLNSISITNCPRIKELPKNL 695

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FW44|ADR1_ARATH Disease resistance protein ADR1 OS=Arabidopsis thaliana GN=ADR1 PE=2 SV=2

 Score =  299 bits (765), Expect = 6e-80,   Method: Compositional matrix adjust.
 Identities = 213/709 (30%), Positives = 366/709 (51%), Gaps = 55/709 (7%)

Query: 3   AAFVGGALLGAVFGELLKAVSEEKDKAVTFKDRLEQLESTLRNSIPWIEEIEKLNQVLDR 62
           A+F+     G +  +LLK ++   +   + K   E+L + +R+  P I EI+     L  
Sbjct: 2   ASFID-LFAGDITTQLLKLLALVANTVYSCKGIAERLITMIRDVQPTIREIQYSGAELSN 60

Query: 63  PKQETENLVRMMEQVEQLVRKCSKV----KWNCFKRYVYAKKIIKLDTSISDFFRTSLPL 118
             Q    L    E +E+  + C KV    +WN  K   +A K+  L+  IS F  + + L
Sbjct: 61  HHQT--QLGVFYEILEKARKLCEKVLRCNRWN-LKHVYHANKMKDLEKQISRFLNSQILL 117

Query: 119 QHARDGKLIMVEVKEIHTMVRRMSGNGNINGWMSNQVGDCCSAPDP---------PVISP 169
                   ++ EV  +     R+  N +    +  +  D  S P+          P I  
Sbjct: 118 -------FVLAEVCHLRVNGDRIERNMD---RLLTERNDSLSFPETMMEIETVSDPEIQT 167

Query: 170 GLDVPLKELKMELFK-DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSK 228
            L++  K++K  +FK        +S   G GKTTL   L KDD V+G FK+ + ++TVS+
Sbjct: 168 VLELGKKKVKEMMFKFTDTHLFGISGMSGSGKTTLAIELSKDDDVRGLFKNKVLFLTVSR 227

Query: 229 NPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSESLLQ 288
           +PN                  F+  E+ I +   F      +  L++LDDVW  +   L 
Sbjct: 228 SPN------------------FENLESCIRE---FLYDGVHQRKLVILDDVW--TRESLD 264

Query: 289 KLGFQLPDYKILVTSRSEFPQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVS 348
           +L  ++     LV SRS+     + + ++ L  + A +L    A  Q       ++ +V 
Sbjct: 265 RLMSKIRGSTTLVVSRSKLADPRTTYNVELLKKDEAMSLLCLCAFEQKSPPSPFNKYLVK 324

Query: 349 KILRACKGCPLALKVVGGSLCGKHEVFWQRMVKECSRGESVFQS-KNDILDCLGSSLDVL 407
           +++  CKG PL+LKV+G SL  K E +W+ +VK   RGE+  ++ ++ +   +  SL+ L
Sbjct: 325 QVVDECKGLPLSLKVLGASLKNKPERYWEGVVKRLLRGEAADETHESRVFAHMEESLENL 384

Query: 408 NNEVKECYLDLCSFPEDQRIPITALIDMWMELYELVDDVFAITNLHELSSQNLVDRVVTR 467
           + ++++C+LD+ +FPED++IP+  L  +W+E ++ +D+  A + +  L+ +NL+  V   
Sbjct: 385 DPKIRDCFLDMGAFPEDKKIPLDLLTSVWVERHD-IDEETAFSFVLRLADKNLLTIVNNP 443

Query: 468 KTAGDYGCYNDDFVMQHDLLRELTICRSKSEPINQRKRLVVEISGNNFPKWWMDQKQHPN 527
           +    +  Y D FV QHD+LR+L +  S    +N+R+RL++  +    P+ W   K  P 
Sbjct: 444 RFGDVHIGYYDVFVTQHDVLRDLALHMSNRVDVNRRERLLMPKTEPVLPREWEKNKDEPF 503

Query: 528 NASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFS 587
           +A ++S+ T E    NW DM  P+ +V++LN  +  YVLP F+ KM  L+VL++ N G S
Sbjct: 504 DAKIVSLHTGEMDEMNWFDMDLPKAEVLILNFSSDNYVLPPFIGKMSRLRVLVIINNGMS 563

Query: 588 PAELNNFRVLSALSKLKKIRLEHVSLPN-SLATVRMNHLQKVSLVMCNVGQVFRNSTFRI 646
           PA L+ F + + L+KL+ + L+ V +P  +  T+ + +L K+ L+ C V   F  ++F I
Sbjct: 564 PARLHGFSIFANLAKLRSLWLKRVHVPELTSCTIPLKNLHKIHLIFCKVKNSFVQTSFDI 623

Query: 647 SDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPEGI 695
           S  FP+L ++ ID+C+DL+EL   +  I S+  L ITNC R+  LP+ +
Sbjct: 624 SKIFPSLSDLTIDHCDDLLEL-KSIFGITSLNSLSITNCPRILELPKNL 671

Disease resistance (R) protein that mediates resistance against Hyaloperonospora parasitica in a salicylic acid-dependent manner. Also mediates resistance against Erysiphe cichoracearum is both salicylic acid-dependent and partially NPR1-dependent. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via an indirect interaction with this avirulence protein. That triggers a defense system including the hypersensitive response, which restricts the pathogen growth.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LVT1|DRL39_ARATH Putative disease resistance protein At5g47280 OS=Arabidopsis thaliana GN=At5g47280 PE=3 SV=1

 Score =  273 bits (699), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 163/522 (31%), Positives = 289/522 (55%), Gaps = 28/522 (5%)

Query: 183 FKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNV---KAIVQKV 239
             D  + I +S   G GKT L + L +D++V+G F + + ++TVS++PN+   +++++  
Sbjct: 5   LNDEARIIGISGMIGSGKTILAKELARDEEVRGHFANRVLFLTVSQSPNLEELRSLIRDF 64

Query: 240 L--HHKGY--PVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSESLLQKLGFQLP 295
           L  H  G+   +PE      ++    +          L++LDDV   +   L +L F +P
Sbjct: 65  LTGHEAGFGTALPE------SVGHTRK----------LVILDDV--RTRESLDQLMFNIP 106

Query: 296 DYKILVTSRSEFPQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACK 355
               LV S+S+     + + ++ L    A +LF  SA  Q        +++V +++   K
Sbjct: 107 GTTTLVVSQSKLVDPRTTYDVELLNEHDATSLFCLSAFNQKSVPSGFSKSLVKQVVGESK 166

Query: 356 GCPLALKVVGGSLCGKHEVFWQRMVKECSRGESVFQS-KNDILDCLGSSLDVLNNEVKEC 414
           G PL+LKV+G SL  + E +W   V+  SRGE V ++ ++ +   + ++L+ L+ + KEC
Sbjct: 167 GLPLSLKVLGASLNDRPETYWAIAVERLSRGEPVDETHESKVFAQIEATLENLDPKTKEC 226

Query: 415 YLDLCSFPEDQRIPITALIDMWMELYELVDDVFAITNLHELSSQNLVDRVVTRKTAGDYG 474
           +LD+ +FPE ++IP+  LI+M +++++L +D  A   L +L+++NL+  V          
Sbjct: 227 FLDMGAFPEGKKIPVDVLINMLVKIHDL-EDAAAFDVLVDLANRNLLTLVKDPTFVAMGT 285

Query: 475 CYNDDFVMQHDLLRELTICRSKSEPINQRKRLVVEISGNNFPKWWMDQKQHPNNASLLSI 534
            Y D FV QHD+LR++ +  +    +++R RL++       P  W      P NA ++SI
Sbjct: 286 SYYDIFVTQHDVLRDVALHLTNRGKVSRRDRLLMPKRETMLPSEWERSNDEPYNARVVSI 345

Query: 535 STDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNF 594
            T E    +W DM  P+ +V+++N  +  YVLP F+ KM  L+V ++ N G SPA L++F
Sbjct: 346 HTGEMTEMDWFDMDFPKAEVLIVNFSSDNYVLPPFIAKMGMLRVFVIINNGTSPAHLHDF 405

Query: 595 RVLSALSKLKKIRLEHVSLPN-SLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNL 653
            + ++L+ L+ + LE V +P  S + + + +L K+ L++C +   F  +   I+  FP L
Sbjct: 406 PIPTSLTNLRSLWLERVHVPELSSSMIPLKNLHKLYLIICKINNSFDQTAIDIAQIFPKL 465

Query: 654 LEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPEGI 695
            ++ IDYC+DL ELP  +C I S+  + ITNC  +  LP+ I
Sbjct: 466 TDITIDYCDDLAELPSTICGITSLNSISITNCPNIKELPKNI 507

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FKZ2|DRL41_ARATH Probable disease resistance protein At5g66890 OS=Arabidopsis thaliana GN=At5g66890 PE=3 SV=1

 Score =  210 bits (535), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 121/297 (40%), Positives = 182/297 (61%), Gaps = 9/297 (3%)

Query: 403 SLDVLNNEVKECYLDLCSFPEDQRIPITALIDMWMELYELVDDVFAITNLHELSSQNLVD 462
           S D L + ++EC+LD+ SF EDQRI  + +ID+W   Y        + NL +L+S+NL+ 
Sbjct: 8   SFDALPHNLRECFLDMASFLEDQRIIASTIIDLWSASY----GKEGMNNLQDLASRNLLK 63

Query: 463 RVVTRKTAGDYGCYNDDFVMQHDLLRELTI--CRSKSEPINQRKRLVVEISGNNFPKWWM 520
            +   +   + G YN+  V Q ++LRE  I  C  +S  I +RKRL +EI  N FP W +
Sbjct: 64  LLPIGRNEYEDGFYNELLVKQDNVLREFAINQCLKESSSIFERKRLNLEIQDNKFPNWCL 123

Query: 521 DQKQH-PNNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVL 579
           + KQ    NASL SISTD++F+S+W +M  P V+ +VLNI +  Y LP+F+  M ELKV+
Sbjct: 124 NPKQPIVINASLFSISTDDSFASSWFEMDCPNVEALVLNISSSNYALPNFIATMKELKVV 183

Query: 580 IVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLP-NSLATVRMNHLQKVSLVMCNVGQV 638
           I+ N+G  PA+L N   LS+L  LK+IR E VS+    +  + +  L+K+SL  C+V   
Sbjct: 184 IIINHGLEPAKLTNLSCLSSLPNLKRIRFEKVSISLLDIPKLGLKSLEKLSLWFCHVVDA 243

Query: 639 FRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPEGI 695
             N    +S+   +L E++IDYC +L ELP  +  +VS++KL +TNC++L  + E I
Sbjct: 244 L-NELEDVSETLQSLQEIEIDYCYNLDELPYWISQVVSLKKLSVTNCNKLCRVIEAI 299

Possible disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q84WJ0|DAR5_ARATH Protein DA1-related 5 OS=Arabidopsis thaliana GN=DAR5 PE=2 SV=2

 Score =  209 bits (531), Expect = 8e-53,   Method: Compositional matrix adjust.
 Identities = 151/452 (33%), Positives = 228/452 (50%), Gaps = 45/452 (9%)

Query: 3   AAFVGGALLGAVFGELLKAVSEEKDKAVTFKDRLEQLESTLRNSIPWIEEIEKLNQVLDR 62
           A+ VGGA LGA   E+ K V EE  K   FK   + L ST+   +P   EI+ + Q  +R
Sbjct: 7   ASLVGGAALGAPLSEIFKLVIEEAKKVKDFKPLSQDLASTMERLVPIFNEIDMMQQGSNR 66

Query: 63  PKQETENLVRMMEQVEQLVRKCSKVKW-NCFKRYVYAKKIIKLDTSISDFFRTSLPLQHA 121
              E + L   ME+  ++V KCS+++W +  K+ +Y ++I  ++     F +  L L   
Sbjct: 67  GTSELKVLTETMERAGEMVHKCSRIQWYSIAKKALYTREIKAINQDFLKFCQIELQLIQH 126

Query: 122 RDGKLIMVEVKEIHTM-VRRMSGNGNINGWMSNQVGDCCSAPDPPVISP-GLDVPLKELK 179
           R+      +++ + +M +  +S   ++   + N+    C    P V++   L  PL ELK
Sbjct: 127 RN------QLQYMRSMGMASVSTKADLLSDIGNEFSKLCLVAQPEVVTKFWLKRPLMELK 180

Query: 180 MELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKV 239
             LF+DG   +VVSAP   GKTTLV +LC D  V+ KFK  IF+++VSK PNV+ I  K+
Sbjct: 181 KMLFEDGVVTVVVSAPYALGKTTLVTKLCHDADVKEKFKQ-IFFISVSKFPNVRLIGHKL 239

Query: 240 LHHKGYPVPEFQTDEAAINDLERFFKQM-RIEAILLVLDDVWPGSESLLQKLGFQLPDYK 298
           L H G    E++ D  A+  +++  KQ+ R  +ILLVLDDVW   ESLLQK   QLPDYK
Sbjct: 240 LEHIGCKANEYENDLDAMLYIQQLLKQLGRNGSILLVLDDVWAEEESLLQKFLIQLPDYK 299

Query: 299 ILVTSRSEFPQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCP 358
           ILVTSR EF  FG   +LKPL  +      +   +  + N  +P+   V+  L  C GC 
Sbjct: 300 ILVTSRFEFTSFGPTFHLKPLIDDE-----VECRDEIEENEKLPE---VNPPLSMCGGCN 351

Query: 359 LALKVVGGSLCGKHE-------VFWQR---MVKECSRGESVFQSKNDILDCLGSSLDVLN 408
            A+         KHE       V W       + C +  ++ + +N + +  G       
Sbjct: 352 SAV---------KHEESVNILGVLWHPGCFCCRSCDKPIAIHELENHVSNSRGKFH---- 398

Query: 409 NEVKECYLDLCSFPEDQRIPITALIDMWMELY 440
              K CY   C   +++++    +   W E Y
Sbjct: 399 ---KSCYERYCYVCKEKKMKTYNIHPFWEERY 427

Arabidopsis thaliana (taxid: 3702)

>sp|P0C8S1|RP8L2_ARATH Probable disease resistance RPP8-like protein 2 OS=Arabidopsis thaliana GN=RPP8L2 PE=1 SV=1

 Score =  102 bits (254), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 103/350 (29%), Positives = 165/350 (47%), Gaps = 29/350 (8%)

Query: 170 GLDVPLKELKMELFK-DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSK 228
           GLD  ++EL   L + D  Q + VS  GG GKTTL +++   D V+  F D   +V VS+
Sbjct: 165 GLDQSVEELVDHLVENDSVQVVSVSGMGGIGKTTLARQVFHHDIVRRHF-DGFSWVCVSQ 223

Query: 229 NPNVKAIVQKVLHH-KGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSESLL 287
               K + Q++L   + Y     Q DE  +      F+ +     LLVLDDVW   E   
Sbjct: 224 QFTRKDVWQRILQDLRPYDEGIIQMDEYTLQG--ELFELLESGRYLLVLDDVW--KEEDW 279

Query: 288 QKLGFQLPD---YKILVTSRSEFPQFG---SVHYLKP--LTYEAARTLFLH-SANLQDGN 338
            ++    P    +K+L+TSR+E        +    +P  LT E +  LF    ++ +D  
Sbjct: 280 DRIKAVFPHKRGWKMLLTSRNEGLGLHADPTCFAFRPRILTPEQSWKLFERIVSSRRDKT 339

Query: 339 SYIPDENIVSKILRACKGCPLALKVVGGSLCGKHEVF-WQRMVKECSR---GESVFQ--S 392
            +  DE +  +++  C G PLA+KV+GG L  KH V  W+R+         G+S     +
Sbjct: 340 EFKVDEAMGKEMVTYCGGLPLAVKVLGGLLAKKHTVLEWKRVHSNIVTHIVGKSGLSDDN 399

Query: 393 KNDILDCLGSSLDVLNNEVKECYLDLCSFPEDQRIPITALIDMWME--LYELVDDVFAIT 450
            N +   L  S + L  ++K C+  L  FPED +I +  L + W+   +     D   I 
Sbjct: 400 SNSVYRVLSLSYEDLPMQLKHCFFYLAHFPEDYKIDVKILFNYWVAEGIITPFHDGSTIQ 459

Query: 451 NLHELSSQNLVDR--VVTRKTAGDYGCYNDDFVMQHDLLRELTICRSKSE 498
           +  E   + LV R  VV  ++   Y     ++   HD++RE+ + ++K E
Sbjct: 460 DTGESYLEELVRRNMVVVEES---YLTSRIEYCQMHDMMREVCLSKAKEE 506

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8W3K3|DRL8_ARATH Putative disease resistance protein At1g58400 OS=Arabidopsis thaliana GN=At1g58400 PE=3 SV=1

 Score =  102 bits (254), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 139/547 (25%), Positives = 245/547 (44%), Gaps = 86/547 (15%)

Query: 170 GLDVPLKELKMELFK-DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSK 228
           GL+V +K+L   L + D  Q + V+  GG GKTTL +++   + V+ +F D + +V VS+
Sbjct: 166 GLEVNVKKLVGYLVEEDDIQIVSVTGMGGLGKTTLARQVFNHEDVKHQF-DRLAWVCVSQ 224

Query: 229 NPNVKAIVQKVLHH---KGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSE- 284
               K + Q +L +   +       Q +EA ++D    F+ +     L+V DD+W   + 
Sbjct: 225 EFTRKNVWQMILQNLTSRETKDEILQMEEAELHD--ELFQLLETSKSLIVFDDIWKEEDW 282

Query: 285 SLLQKLGFQLPDYKILVTSRSE-FPQFGSVHYL--KP--LTYEAARTLFLHSANLQ-DGN 338
            L+  +      +K+L+TSR+E     G+  Y+  KP  LT   +  LF   A  + D +
Sbjct: 283 GLINPIFPPKKGWKVLITSRTETIAMHGNRRYVNFKPECLTILESWILFQRIAMPRVDES 342

Query: 339 SYIPD---ENIVSKILRACKGCPLALKVVGGSLCGKHEVF-WQRMVKECS---RGESVFQ 391
            +  D   E +  ++++ C G PLA+KV+GG L  K+    W+R+ +       G + F 
Sbjct: 343 EFKVDKEMEMMGKQMIKYCGGLPLAVKVLGGLLAAKYTFHDWKRLSENIGCHIVGRTDFS 402

Query: 392 SKND--ILDCLGSSLDVLNNEVKECYLDLCSFPEDQRIPITALIDMWME---------LY 440
             N+  +   L  S + L + +K C+L L  FPED  I +  L   W             
Sbjct: 403 DGNNSSVYHVLSLSFEELPSYLKHCFLYLAHFPEDHNIKVEKLSYCWAAEGILEPRHYHG 462

Query: 441 ELVDDVFAITNLHELSSQNLV--DRVVTRKTAGDYGCYNDDFVMQHDLLRELTICRSKSE 498
           + + DV   + + EL  +N+V  +R VT  T     C+       HD++RE+ + ++K E
Sbjct: 463 QTIRDV-GESYIEELVRRNMVIAERDVT--TLRFEACH------LHDMMREVCLLKAKEE 513

Query: 499 PINQRKRLVVEISGNNFPKWWMDQKQHPNNASLLSISTDETFSSNWPDMQGPEVKVVVLN 558
              Q   ++   + + +P     ++    N + L +S D     N P +Q     ++V  
Sbjct: 514 NFVQIASILPPTANSQYPG--TSRRFVSQNPTTLHVSRD----INNPKLQSL---LIVWE 564

Query: 559 IRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSLA 618
            R K + L                  G S   L   RVL     L K + E  +LP+ + 
Sbjct: 565 NRRKSWKL-----------------LGSSFIRLELLRVLD----LYKAKFEGRNLPSGIG 603

Query: 619 TVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPN---LLEMDIDYCNDLIELPDGLCDIV 675
             ++ HL+ ++L +  V         R+  +  N   L+ +DI+ C   + +P+ L  + 
Sbjct: 604 --KLIHLRYLNLDLARVS--------RLPSSLGNLRLLIYLDINVCTKSLFVPNCLMGMH 653

Query: 676 SMEKLRI 682
            +  LR+
Sbjct: 654 ELRYLRL 660

Potential disease resistance protein.

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	695
224096806	804	cc-nbs-lrr resistance protein [Populus t	0.975	0.843	0.522	0.0
225463693	823	PREDICTED: probable disease resistance p	0.991	0.837	0.508	0.0
359480461	801	PREDICTED: probable disease resistance p	0.974	0.845	0.511	0.0
359480459	814	PREDICTED: probable disease resistance p	0.987	0.842	0.515	0.0
359496922	815	PREDICTED: probable disease resistance p	0.988	0.842	0.509	0.0
345104748	822	disease resistance protein [Vitis pseudo	0.987	0.834	0.5	0.0
359480455	1175	PREDICTED: probable disease resistance p	0.988	0.584	0.504	0.0
359480457	797	PREDICTED: probable disease resistance p	0.958	0.835	0.499	0.0
359480445	803	PREDICTED: probable disease resistance p	0.971	0.840	0.498	0.0
189096590	798	VRP1-1 [Vitis hybrid cultivar]	0.955	0.832	0.486	1e-180

>gi|224096806|ref|XP_002310744.1| cc-nbs-lrr resistance protein [Populus trichocarpa] gi|222853647|gb|EEE91194.1| cc-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  701 bits (1810), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 366/701 (52%), Positives = 495/701 (70%), Gaps = 23/701 (3%)

Query: 1   MAAAFVGGALLGAVFGELLKAVSEEKDKAVTFKDRLEQLESTLRNSIPWIEEIEKLNQVL 60
           MAA  +GGA    VFGELLK +     KA+ FK +L+Q++ TL ++IP ++EI++L++ L
Sbjct: 1   MAAELLGGA----VFGELLKVIENVAQKALVFKTKLKQIQETLESNIPILDEIKQLDEEL 56

Query: 61  DRPKQETENLVRMMEQVEQLVRKCSKVKW-NCFKRYVYAKKIIKLDTSISDFFRTSLPLQ 119
           DR  +E E L+ ++   E LV +CSK++W +C++R  Y  K+I+L+ SI+ FF+T +P Q
Sbjct: 57  DRRNEEIEKLMEVIRNGETLVLECSKIRWYHCWRRPKYTDKLIELERSINQFFQTVMPAQ 116

Query: 120 HARDGKLIMVEVKEIHTMVRRMSG-NGNINGWMSNQVGDCCSAPDPPVISPGLDVPLKEL 178
            ARD K I++EV+      R+ SG NG I+G   +     C+ P+  V   GL V + EL
Sbjct: 117 IARDTKEILLEVRG-----RKGSGSNGTIDGRDVS-----CAVPESLVNPVGLQVAIGEL 166

Query: 179 KMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQK 238
           KM+LFKDG   +V+SAP G GKTTL + LC D +V+ KFKD+IFYV VSKN N++ IV+ 
Sbjct: 167 KMKLFKDGVSIVVLSAPPGCGKTTLARLLCHDKEVEEKFKDNIFYVIVSKNTNMEGIVRA 226

Query: 239 VLHHKGY-PVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSESLLQKLGFQLPDY 297
           + +HKG  P  +F++DE  +  LE+F   +    ILLVLDDVWP SES L+K  FQ+ DY
Sbjct: 227 LFNHKGQKPPSDFRSDEDIVYRLEQFLNSIGPSPILLVLDDVWPESESFLEKFMFQIKDY 286

Query: 298 KILVTSRSEFPQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGC 357
           KILVTSRS F +FGS + LKPL YE + TLF  SA L   +  IPD+N+VSKI++ CKG 
Sbjct: 287 KILVTSRSVFRRFGSTYELKPLNYEDSLTLFRSSAFLPHQSQDIPDKNVVSKIVKGCKGF 346

Query: 358 PLALKVVGGSLCGKHEVFWQRMVKECSRGESVFQSKNDILDCLGSSLDVLNNEV--KECY 415
           PLALKVVG SLCG+ E  W+    E S+  S+F+   D+L+ L  SLD L+N+V  KEC+
Sbjct: 347 PLALKVVGSSLCGEPEEIWKTRAMELSKVGSIFEY-TDLLNSLQKSLDTLDNKVILKECF 405

Query: 416 LDLCSFPEDQRIPITALIDMWMELYELVDDVFAITNLHELSSQNLVDRVVTRKTAGDYGC 475
           +DLCSFPEDQRIP+ AL+DMWMELY L ++ +A+  L EL ++NLVD VVT   A   GC
Sbjct: 406 IDLCSFPEDQRIPVNALVDMWMELYNLDEEAYAVAKLQELCNRNLVDLVVTGNVAS--GC 463

Query: 476 YNDDFVMQHDLLRELTICRSKSEPINQRKRLVVEISGNNFPKWWMDQKQHPNNASLLSIS 535
           YN  F MQHDLLREL IC+S SE I +RKRL++EIS NN P WWM+QKQ   +  LLSIS
Sbjct: 464 YNQQFAMQHDLLRELAICQSDSESIERRKRLILEISANNVPAWWMEQKQPNISCRLLSIS 523

Query: 536 TDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFR 595
           TDE FSS+W  +Q PEV+V+VLN+R+K + LP+F++KM++LKVLIV NYGF P ELNNF 
Sbjct: 524 TDEKFSSSWCFIQAPEVEVLVLNVRSKNHTLPEFIKKMEKLKVLIVENYGFFPTELNNFL 583

Query: 596 VLSALSKLKKIRLEHVSLPN-SLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLL 654
           +L  ++ LK+IRLE VS+P  +  TV++  LQK++L MCN+ Q F  ST  +S+A PN++
Sbjct: 584 LLGYVTNLKRIRLERVSIPPFAFTTVKLEILQKLTLYMCNISQAFSTSTILVSEALPNIM 643

Query: 655 EMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPEGI 695
           E++I+Y NDLIELP  +C +  ++KL I NCH+L ALP+ I
Sbjct: 644 EINIEYSNDLIELPVEICLLTKLKKLSIINCHKLVALPKEI 684

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225463693|ref|XP_002276590.1| PREDICTED: probable disease resistance protein At5g66900 isoform 1 [Vitis vinifera]

 Score =  684 bits (1766), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 364/716 (50%), Positives = 493/716 (68%), Gaps = 27/716 (3%)

Query: 1   MAAAFVGGALLGAVFGELLKAVSEEKDKAVTFKDRLEQLESTLRNSIPWIEEIEKLNQVL 60
           MA   VGG +L  V GEL+K   +   K   F D L++++S ++   P + +I+KL+  L
Sbjct: 1   MALETVGGVVLDKVIGELIKPFVDGGKKQAAFGDILQRVKSIIKLIGPTVRQIKKLSAEL 60

Query: 61  DRPKQETENLVRMMEQVEQLVRKCSKVKWNCFKRYVYAKKIIKLDTSISDFFRTSLPLQH 120
           DRPK+E+ENL+++ ++ E+L++KCSK+ W    R+ YA K+     S+  FF+  +PLQ 
Sbjct: 61  DRPKEESENLIQLFDEGEKLIQKCSKLNWWMPNRWKYANKLTAFYESLLRFFQFHMPLQQ 120

Query: 121 ARDGKLIMVEVKEIHTMVRRMSGNGNINGWM----------SNQVG--DCCSAPDPPVIS 168
                 I+      H   +   G G ++G M          S ++G  D C+APDPP   
Sbjct: 121 FMTNMEILA-----HLQSQFRYGTGGVSGQMGYLGSGGSRVSGEIGYLDPCNAPDPPDFM 175

Query: 169 PGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSK 228
            GLDVPLKE+K  LFKD    IVVSAPGG GKTTLVQ+LC+D  V+  FKD+IFYVTVSK
Sbjct: 176 VGLDVPLKEVKKRLFKDDTSVIVVSAPGGCGKTTLVQKLCQDPDVKENFKDNIFYVTVSK 235

Query: 229 NPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFK-QMRIEAILLVLDDVWPGSESLL 287
             N+K IV+K+  H G+ VPEFQTDE AIN LE+  K Q R   ILLVLDDVW   E  L
Sbjct: 236 VHNLKLIVRKLFEHNGFRVPEFQTDEDAINQLEQLLKNQARKAPILLVLDDVWKEPEFPL 295

Query: 288 QKLGFQLPDYKILVTSRSEFPQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIP----D 343
           QK  F++P+Y+ILVTSR EFP FGS + LK L  E A  LF HSA L DG+ ++P    D
Sbjct: 296 QKFAFKIPEYRILVTSRYEFPSFGSTYKLKLLNDEDAMKLFRHSAFLTDGD-FMPDEDFD 354

Query: 344 ENIVSKILRACKGCPLALKVVGGSLCGKHEVFWQRMVKECSRGESVFQSKNDILDCLGSS 403
           E++V++I++ C G PLAL+V+GGSLCG+    W+  + E S+G+S+F S   +LDCL  S
Sbjct: 355 EDLVNEIVKRCGGFPLALQVIGGSLCGQPVEIWKSRLMEFSKGQSIFDSGKRLLDCLQLS 414

Query: 404 LDVLNNEVKECYLDLCSFPEDQRIPITALIDMWMELYEL-VDDVFAITNLHELSSQNLVD 462
           L  L+ E KE ++DL SFPEDQ+IP+TALIDMW ELY+L  + V AI+NLH+LS QNL+ 
Sbjct: 415 LTSLDGEQKERFMDLGSFPEDQKIPVTALIDMWAELYKLDKNGVQAISNLHKLSLQNLLK 474

Query: 463 RVVTRKTAGDY-GCYNDDFVMQHDLLRELTICRSKSEPINQRKRLVVEISGNNFPKWWMD 521
            VVTRK A +  G Y++ FV+QHDLLR+L +  S  EP+ QRKRL++++SGN  P+WW +
Sbjct: 475 LVVTRKDATEVDGYYDEAFVLQHDLLRDLAMHESSQEPMEQRKRLILDLSGNKLPEWWTE 534

Query: 522 QKQHPNNASLLSISTDETFSSNWPDMQGPEVKVVVLNIR-TKKYVLPDFLQKMDELKVLI 580
           +KQ    A L+SISTD+ FSS+W +MQ PEV+V++LN + T+ Y  P+F+++MD LKVLI
Sbjct: 535 EKQPCFKARLMSISTDQMFSSSWCNMQVPEVEVLILNFQATENYTFPNFMKQMDNLKVLI 594

Query: 581 VTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSLAT-VRMNHLQKVSLVMCNVGQVF 639
           VTNYG S AEL NF VL +LS+LK+IRLE VS+P    T V + +++K+SLVMC + Q F
Sbjct: 595 VTNYGSSAAELINFSVLGSLSRLKRIRLEQVSIPTLCDTMVELKNVEKISLVMCKINQAF 654

Query: 640 RNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPEGI 695
            +   +IS+  PNLLE++I YC+DL+ LP+GLCD+V ++KL I+NCH+LSALP GI
Sbjct: 655 NSCAIQISNMLPNLLEINISYCSDLVGLPEGLCDLVHLKKLSISNCHKLSALPGGI 710

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359480461|ref|XP_002268207.2| PREDICTED: probable disease resistance protein At5g66900-like [Vitis vinifera]

 Score =  680 bits (1755), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 359/702 (51%), Positives = 486/702 (69%), Gaps = 25/702 (3%)

Query: 1   MAAAFVGGALLGAVFGELLKAVSEEKDKAVTFKDRLEQLESTLRNSIPWIEEIEKLNQVL 60
           MA   +G  ++  + GEL+KA+ +E  KA  F+   ++L+STL +  P I+EIE+LN+  
Sbjct: 1   MALELIGETVVETLIGELIKAILDEGKKAAEFQAIFDRLQSTLISIGPTIQEIERLNKES 60

Query: 61  DRPKQETENLVRMMEQVEQLVRKCSKVKW-NCFKRYVYAKKIIKLDTSISDFFRTSLPLQ 119
           DR K ETE LV+M++  ++L++KCSKV W +  K++ Y+ K++ LD S+  FF+  + +Q
Sbjct: 61  DRSK-ETEQLVQMLKDGKELIQKCSKVTWWHYHKKWKYSNKLLDLDESLLRFFQVDMAVQ 119

Query: 120 HARDGKLIMVEVKEIHTMVRRMSGNGNINGWMSNQVGDCCSAPDPPVISPGLDVPLKELK 179
             RD K I +  ++ + +                ++G C  APDPP ++ GLD+PL+ELK
Sbjct: 120 GFRDIKEIKLGQRDPYHL----------------KLGPC-QAPDPPPLTVGLDIPLQELK 162

Query: 180 MELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKV 239
           M LF+D    IVVSAPGG GKTTL + LC D QV+ KFK++IFYVTVSK  N+ AIVQ +
Sbjct: 163 MRLFRDDSSVIVVSAPGGCGKTTLAKMLCHDHQVKEKFKNNIFYVTVSKAFNLNAIVQSL 222

Query: 240 LHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSESLLQKLGFQLPDYKI 299
             H G+ V  FQ DE A+N LER   Q+    ILLVLDDVW GSESLL    F++P+YKI
Sbjct: 223 FQHNGHGVRVFQNDEDAVNQLERLLNQIAPAPILLVLDDVWGGSESLLDNFVFKIPNYKI 282

Query: 300 LVTSRSEFPQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPL 359
           LVTSR EFP+FGS + L  L  E A TLF  SA  QDG SY+PDE++V KI++ CKG PL
Sbjct: 283 LVTSRFEFPRFGSTYKLPLLKDEDAMTLFRSSAFQQDGRSYMPDEDLVEKIVKGCKGFPL 342

Query: 360 ALKVVGGSLCGKHEVFWQRMVKECSRGESVFQSKNDILDCLGSSLDVLNNE--VKECYLD 417
           AL+VVG SLCG+    W+  +   S G+S+F S +D+L CL SSLD L ++  +KEC++D
Sbjct: 343 ALRVVGRSLCGQPAEAWESRLLTWSEGQSIFSSDSDLLLCLQSSLDALADKGILKECFMD 402

Query: 418 LCSFPEDQRIPITALIDMWMELYEL-VDDVFAITNLHELSSQNLVDRVVTRKTAGDY-GC 475
           L SFPEDQ+IP TALIDMW ELY+L    VFAI NL ELS +NL+  V  RK   D  GC
Sbjct: 403 LGSFPEDQKIPATALIDMWAELYKLHTGGVFAINNLQELSFRNLLSLVDARKDESDVDGC 462

Query: 476 YNDDFVMQHDLLRELTICRSKSEPINQRKRLVVEISGNNFPKWWMDQKQHPNNASLLSIS 535
           YND +VM HDLLREL I +S  EPI QRKRL+V++SG+  P WW    Q P  A LLSIS
Sbjct: 463 YNDTYVMLHDLLRELAIYQSSQEPIEQRKRLIVDLSGDKVPNWWTQDNQQPFGARLLSIS 522

Query: 536 TDETFSSNWPDMQGPEVKVVVLNIRTKK-YVLPDFLQKMDELKVLIVTNYGFSPAELNNF 594
           TDE FSS+W ++Q PE++V++LN ++K+ Y LP+F+++M++LKVL++TN G SPA+L NF
Sbjct: 523 TDELFSSSWCNIQTPELEVLILNFQSKENYTLPEFIKQMEKLKVLVLTNNGPSPAQLINF 582

Query: 595 RVLSALSKLKKIRLEHVSLPNSL-ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNL 653
            VL +L  LK+IR E V +P     T    +L+K+SLVMC + +   N + +IS+ FPNL
Sbjct: 583 SVLGSLPSLKRIRFEQVRIPPLCNTTAEFKNLEKISLVMCKISEALSNRSIQISNMFPNL 642

Query: 654 LEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPEGI 695
           +E++IDYCNDL+EL +GLCD+V ++KL I+NC +LSALP+GI
Sbjct: 643 VELNIDYCNDLVELLEGLCDLVELKKLSISNCPKLSALPKGI 684

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359480459|ref|XP_002265449.2| PREDICTED: probable disease resistance protein At5g66900-like [Vitis vinifera] gi|302144172|emb|CBI23299.3| unnamed protein product [Vitis vinifera]

 Score =  679 bits (1751), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 365/708 (51%), Positives = 498/708 (70%), Gaps = 22/708 (3%)

Query: 1   MAAAFVGGALLGAVFGELLKAVSEEKDKAVTFKDRLEQLESTLRNSIPWIEEIEKLNQVL 60
           MA   VGGA LGAVF +L  AV +  +KA  F+  L++LE TL++  P I E++KLN  L
Sbjct: 1   MALELVGGAALGAVFEKLFAAVVDASNKATQFESSLKKLEETLKSINPSILEMKKLNDEL 60

Query: 61  DRPKQETENLVRMMEQVEQLVRKCSKVKW-NCFKRYVYAKKIIKLDTSISDFFRTSLPLQ 119
           DRPK+E E L+++++  E+L+ KCSKV   +CFK++ YA KI  L+ S+ +FF+  L  Q
Sbjct: 61  DRPKEEMEKLIQILKDGEKLIHKCSKVSCCSCFKKWRYANKIEALEDSLLNFFQVELQAQ 120

Query: 120 HARDGKLIMVEVKEIHTMVRRMSGNGNINGWMSNQVGDCCSAPDPPVISPGLDVPLKELK 179
             R+   I+V +K     +     + N     S      C A DPP    GLDVPLKELK
Sbjct: 121 LGRNNVEILVMLKSNRFSLSNRGVSDNFENLGS------CEATDPPAFMVGLDVPLKELK 174

Query: 180 MELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKV 239
             LF DG   IVVSAPGG GKTTL +RLC D QV+  F D I YVTVSK  ++  I++K+
Sbjct: 175 RWLFTDGESRIVVSAPGGCGKTTLAKRLCHDQQVKEYFTD-ICYVTVSKACDLIGIIKKL 233

Query: 240 LHHKGYPVPEFQTDEAAINDLERFFKQMRIEA--ILLVLDDVWPGSESLLQKLGFQLPDY 297
             H    VP FQ +E A+N LER  K+ ++E+  ILLVLDDVW GSES+L K   ++  Y
Sbjct: 234 FWHNDEQVPSFQNEEDAVNQLERMLKR-KVESGRILLVLDDVWSGSESVLAKFK-KISGY 291

Query: 298 KILVTSRSEFPQFGSVHYLKPLTYEAARTLFLHSANLQDGN-SYIPDENIVSKILRACKG 356
           K+LVTSR+EFP+FGS ++LK L+ E A+TLF HSA  +DG+ S +P E++V+ I+R CKG
Sbjct: 292 KVLVTSRNEFPEFGSTYHLKLLSEEDAKTLFRHSAIPEDGSGSSMPSEDLVNTIVRCCKG 351

Query: 357 CPLALKVVGGSLCGKHEVFWQRMVKECSRGESVFQSKNDILDCLGSSLDVLNNE---VKE 413
            PLAL+VVG SL G+    W+  + + S G+S+  S++++ +CL SSLD L+++   +KE
Sbjct: 352 FPLALEVVGRSLHGQPVEIWRSTLMKLSEGQSIVNSEDELRNCLQSSLDALDDKDIMLKE 411

Query: 414 CYLDLCSFPEDQRIPITALIDMWMELYEL-VDDVFAITNLHELSSQNLVDRVVTRKTAGD 472
           C++DL SFPEDQ+IP TALIDMW EL++L    ++AI+NL +L S+NL++ VVTR  A +
Sbjct: 412 CFMDLGSFPEDQKIPATALIDMWAELHKLDKGGIYAISNLQKLCSRNLLNLVVTRNDANE 471

Query: 473 Y-GCYNDDFVMQHDLLRELTICRSKSEPINQRKRLVVEISGNNFPKWWMDQKQHPNNASL 531
             GCYND FVMQHDLLR+L I +S+ EPI +RKRL+V+++GN  P+WW  +KQ  ++A L
Sbjct: 472 IDGCYNDAFVMQHDLLRDLAIYQSEQEPIEKRKRLIVDLTGNRLPEWWTKEKQPRSSARL 531

Query: 532 LSISTDETFSSNWPDMQGPEVKVVVLNIRT--KKYVLPDFLQKMDELKVLIVTNYGFSPA 589
           +SISTDE FSS+W +MQ PE +V++LN     KKY LP+F+++MDELKVL+VTNYGF  A
Sbjct: 532 VSISTDEMFSSSWCNMQLPEAEVLILNFNQTEKKYELPEFMKQMDELKVLVVTNYGFCTA 591

Query: 590 ELNNFRVLSALSKLKKIRLEHVSLPNSLAT-VRMNHLQKVSLVMCN-VGQVFRNSTFRIS 647
           EL NF VL +LS LK+IRLE VS+P    T + + +L+K+SLVMC+ +GQ F +ST +I 
Sbjct: 592 ELTNFSVLGSLSNLKRIRLEQVSIPTLCNTSMELKNLEKLSLVMCHKIGQAFASSTIQIP 651

Query: 648 DAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPEGI 695
           +  PNL E++IDYCNDL+ELP+G CD+V + KL I NCH+LS+LPEGI
Sbjct: 652 EMLPNLREINIDYCNDLVELPEGFCDLVQLNKLSIGNCHKLSSLPEGI 699

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359496922|ref|XP_003635372.1| PREDICTED: probable disease resistance protein At5g66900-like [Vitis vinifera]

 Score =  669 bits (1725), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 361/708 (50%), Positives = 487/708 (68%), Gaps = 21/708 (2%)

Query: 1   MAAAFVGGALLGAVFGELLKAVSEEKDKAVTFKDRLEQLESTLRNSIPWIEEIEKLNQVL 60
           MA   VGGA LGAVF +L  AV + + KA  F   L++LE TL++  P I E++++N  L
Sbjct: 1   MALELVGGAALGAVFEKLFAAVEDARTKATKFYSSLKKLEETLKSINPSILEMKRMNDQL 60

Query: 61  DRPKQETENLVRMMEQVEQLVRKCSKVKW-NCFKRYVYAKKIIKLDTSISDFFRTSLPLQ 119
           DRPK+E E L+++++  E+L+ KCSKV   N FK++ YA +I  L+ S+   F+  L  Q
Sbjct: 61  DRPKEEMEKLIQILKDGEKLIHKCSKVSCRNYFKKWRYANEIEALEDSLRKIFQVELQAQ 120

Query: 120 HARDGKLIMVEVKEIHTMVRRMSGNGNINGWMSNQVGDCCSAPDPPVISPGLDVPLKELK 179
            +R+   I+V +K       R S +          +G C  A DPP    GLDVPLKELK
Sbjct: 121 LSRNNMQILVLLKS-----NRFSWSNKGVSVKYESLGSC-EATDPPAFMVGLDVPLKELK 174

Query: 180 MELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKV 239
             LF DG   IVVSAPGG GKTTL +RLC D QV+  F+  IFYVTVSK  N+  I++K+
Sbjct: 175 RWLFTDGESRIVVSAPGGCGKTTLAKRLCHDQQVKEYFQH-IFYVTVSKTFNLIGIIKKL 233

Query: 240 LHHKGYPVPEFQTDEAAINDLERFFKQMRIEA--ILLVLDDVWPGSESLLQKLGFQLPDY 297
             H    VP FQ +E A+N LE   K+ ++E+  ILLVLDDVW GSES L K  FQ+   
Sbjct: 234 FWHSDEQVPGFQNEEDAVNQLELMLKR-KVESGRILLVLDDVWSGSESFLTKFNFQISGC 292

Query: 298 KILVTSRSEFPQFGSVHYLKPLTYEAARTLFLHSANLQDGN-SYIPDENIVSKILRACKG 356
           K+L+TSR+EFP+FGS + LK L+ E A+TLF HSA  +DG+ S +P E++V+ I+R CKG
Sbjct: 293 KVLITSRNEFPKFGSTYNLKLLSEEDAKTLFRHSAIPEDGSGSSMPGEDLVNTIVRRCKG 352

Query: 357 CPLALKVVGGSLCGKHEVFWQRMVKECSRGESVFQSKNDILDCLGSSLDVLNNE---VKE 413
            PLAL+VVG SL G+    W+  + + S GES+  S++++ +CL SSLD L ++   +KE
Sbjct: 353 FPLALEVVGRSLHGQPVEIWRSTLMKLSEGESIVNSEDELRNCLQSSLDALADKDIMLKE 412

Query: 414 CYLDLCSFPEDQRIPITALIDMWMELYEL-VDDVFAITNLHELSSQNLVDRVVTRKTAGD 472
           C++DL SFPEDQ+IP TALIDMW EL++L  D ++A+ NL  L SQNL++ VVTR  A +
Sbjct: 413 CFMDLGSFPEDQKIPATALIDMWAELHKLDKDGIYAVINLQNLCSQNLLNLVVTRNDANE 472

Query: 473 YG-CYNDDFVMQHDLLRELTICRSKSEPINQRKRLVVEISGNNFPKWWMDQKQHPNNASL 531
            G CY D FVMQHDLLR+L I +S  EPI +RKRL+V+++GN  P+WW  + Q   +A L
Sbjct: 473 IGWCYKDAFVMQHDLLRDLAIYQSNQEPIEKRKRLIVDLTGNRLPEWWTKENQPQLSARL 532

Query: 532 LSISTDETFSSNWPDMQGPEVKVVVLNIRT--KKYVLPDFLQKMDELKVLIVTNYGFSPA 589
           +SISTDE FSSNW +MQ PE + ++LN      KY LP+F+++MD+LKVL+VTNYGF  A
Sbjct: 533 VSISTDEMFSSNWCNMQLPEAEALILNFNQTENKYELPEFMKQMDKLKVLVVTNYGFCAA 592

Query: 590 ELNNFRVLSALSKLKKIRLEHVSLPNSLAT-VRMNHLQKVSLVMCN-VGQVFRNSTFRIS 647
           EL NF VL +LS LK+IRLE VS+P    T + + +L+K+SLVMC+ +GQ F +ST +I 
Sbjct: 593 ELTNFSVLGSLSNLKRIRLEQVSIPRLCNTSMELKNLEKLSLVMCHKIGQAFASSTIQIP 652

Query: 648 DAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPEGI 695
           +  PNL E++IDYCNDL+ELP+G CD+V + KL I+NCH+LSALPEGI
Sbjct: 653 EMLPNLREINIDYCNDLVELPEGFCDLVQLNKLSISNCHKLSALPEGI 700

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|345104748|gb|AEN71144.1| disease resistance protein [Vitis pseudoreticulata]

 Score =  664 bits (1712), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 359/718 (50%), Positives = 492/718 (68%), Gaps = 32/718 (4%)

Query: 1   MAAAFVGGALLGAVFGELLKAVSEEKDKAVTFKDRLEQLESTLRNSIPWIEEIEKLNQVL 60
           MA   VGG +L  V GEL+K + +   K   F D L++++S ++   P + +I+KL+  L
Sbjct: 1   MALETVGGVVLDKVIGELIKPIVDGGKKQAAFGDILQRVKSIIKLIGPTVRQIKKLSAEL 60

Query: 61  DRPKQETENLVRMMEQVEQLVRKCSKVKWNCFKRYVYAKKIIKLDTSISDFFRTSLPLQH 120
           DRPK+E+ENL+++ ++ E+L++KCSK+ W    R+ YA K+     S+  FF+  +PLQ 
Sbjct: 61  DRPKEESENLIQLFDEGEKLIQKCSKLNWWMPNRWKYANKLTAFYESLLRFFQFHMPLQQ 120

Query: 121 ARDGKLIMVEVKEIHTMVRRMSGNGNINGWM----------SNQVG--DCCSAPDPPVI- 167
                 I+      H   +  SG G ++G M          S ++G  D    P  P+I 
Sbjct: 121 FMTNMEILA-----HLQSQFRSGTGGVSGQMGYLGSGGSRVSGEIGYLDPLQMPLTPLIF 175

Query: 168 SPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVS 227
             GLDVPLKE+K  LFKD    IVVSAPGG GKTTLVQ+LC+D  V+ KFKD+IFYVTVS
Sbjct: 176 MVGLDVPLKEVKKRLFKDDTSVIVVSAPGGCGKTTLVQKLCQDPDVKEKFKDNIFYVTVS 235

Query: 228 KNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFK-QMRIEAILLVLDDVWPGSESL 286
           K  N+K IV+K+  H G+ VPEFQTDE AIN LE+  K Q R   ILL+LDDVW   E  
Sbjct: 236 KVHNLKLIVRKLFEHNGFRVPEFQTDEDAINQLEQLLKSQARKAPILLILDDVWKEPEFP 295

Query: 287 LQKLGFQLPDYKILVTSRSEFPQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDEN- 345
           LQK  F++P+YKILVTSR EFP FGS + L+ L  + A  LF HSA L DG+ ++PDE+ 
Sbjct: 296 LQKFAFKIPEYKILVTSRYEFPSFGSTYKLELLNDKDAMKLFRHSAFLTDGD-FMPDEDF 354

Query: 346 ---IVSKILRACKGCPLALKVVGGSLCGKHEVFWQRMVKECSRGESVFQSKND-ILDCLG 401
              +V++I++ C G PLAL+V+GGSLCG+    W+ ++ E S+G+S+F S    +LDCL 
Sbjct: 355 DEELVNEIVKRCGGFPLALQVIGGSLCGQPVEIWKSILMELSKGQSIFDSAGKRVLDCLQ 414

Query: 402 SSLDVLNNEVKECYLDLCSFPEDQRIPITALIDMWMELYEL-VDDVFAITNLHELSSQNL 460
            SL  L+ E KEC++DL SFPEDQ+IP+T LIDMW ELY+L  + V AI+NLH+LS QNL
Sbjct: 415 LSLTSLDGEQKECFMDLGSFPEDQKIPVTTLIDMWAELYKLDKNGVQAISNLHKLSLQNL 474

Query: 461 VDRVVTRKTAGDY-GCYNDDFVMQHDLLRELTICRSKSEPINQRKRLVVEISGNNFPKWW 519
           +  VVTRK A +  G Y++ FV+QHDLLR+L I +S  EP+   +RL++++SGN  P+WW
Sbjct: 475 LKLVVTRKDASEVDGYYDEAFVLQHDLLRDLAIHQSSQEPM---ERLILDLSGNKLPEWW 531

Query: 520 MDQKQHPNNASLLSISTDETFSSNWPDMQGPEVKVVVLNIR-TKKYVLPDFLQKMDELKV 578
            ++KQ    A LLSISTD+ FSS+W +MQ PEV+V++LN + T+ Y  P F+++MD LKV
Sbjct: 532 TEEKQPCFKARLLSISTDQMFSSSWCNMQVPEVEVLILNFQATENYTFPKFMKQMDNLKV 591

Query: 579 LIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSLAT-VRMNHLQKVSLVMCNVGQ 637
           LIVTNYG S AEL NF VL +LS+LK+IRLE VS+P    T V + +++K+SLVMC + Q
Sbjct: 592 LIVTNYGSSAAELINFSVLGSLSRLKRIRLEQVSIPTLCDTMVELKNVEKISLVMCKINQ 651

Query: 638 VFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPEGI 695
            F +   +IS+  PNL+E++I+YCNDL+ LP+ LCD+V ++KL I+NCH+LSALP GI
Sbjct: 652 AFNSCAIQISNMLPNLMEININYCNDLVGLPEELCDLVHLKKLSISNCHKLSALPGGI 709

Source: Vitis pseudoreticulata

Species: Vitis pseudoreticulata

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359480455|ref|XP_003632465.1| PREDICTED: probable disease resistance protein At5g66900-like [Vitis vinifera]

 Score =  660 bits (1702), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 357/708 (50%), Positives = 490/708 (69%), Gaps = 21/708 (2%)

Query: 1    MAAAFVGGALLGAVFGELLKAVSEEKDKAVTFKDRLEQLESTLRNSIPWIEEIEKLNQVL 60
            MA   VGGA LGAVF +L  AV + + KA  F   L++LE TL++  P I E++++N  L
Sbjct: 361  MALELVGGAALGAVFEKLFAAVEDARTKATKFDSSLKKLEETLKSINPSILEMKRMNDQL 420

Query: 61   DRPKQETENLVRMMEQVEQLVRKCSKVKW-NCFKRYVYAKKIIKLDTSISDFFRTSLPLQ 119
            DR K++ E L+++++  E+L+ KCSKV   N FK++ YA +I  L+ S+   F+  L  Q
Sbjct: 421  DRSKEDMEKLIQILKDGEKLIHKCSKVSCCNYFKKWRYANEIEALEDSLLKIFQVELQAQ 480

Query: 120  HARDGKLIMVEVKEIHTMVRRMSGNGNINGWMSNQVGDCCSAPDPPVISPGLDVPLKELK 179
             +R+   I+V +K       R S +          +G C  A DPP    GLDVPLKELK
Sbjct: 481  LSRNNMQILVLLKS-----NRFSWSNKGVSVKYESLGSC-EATDPPAFMVGLDVPLKELK 534

Query: 180  MELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKV 239
              LF DG   IVVSAPGG GKTTL +RLC D QV+  F+  IFYVTVSK  N+  I++K+
Sbjct: 535  RWLFTDGESRIVVSAPGGCGKTTLAKRLCHDQQVKEYFQH-IFYVTVSKTFNLIGIIKKL 593

Query: 240  LHHKGYPVPEFQTDEAAINDLERFFKQMRIEA--ILLVLDDVWPGSESLLQKLGFQLPDY 297
              H    VP FQ +E A+N LE   K+ ++E+  +LLVLDDVW GSES L K  FQ+   
Sbjct: 594  FWHSDEQVPGFQNEEDAVNQLELMLKR-KVESGRLLLVLDDVWSGSESFLTKFNFQISGC 652

Query: 298  KILVTSRSEFPQFGSVHYLKPLTYEAARTLFLHSANLQDGN-SYIPDENIVSKILRACKG 356
            K+L+TSR+EFP+FGS + LK L+ E A+TLF HSA  +DG+ S +P E++V+ I+R CKG
Sbjct: 653  KVLITSRNEFPKFGSTYNLKLLSEEDAKTLFRHSAIPEDGSGSSMPGEDLVNTIVRRCKG 712

Query: 357  CPLALKVVGGSLCGKHEVFWQRMVKECSRGESVFQSKNDILDCLGSSLDVLNNE---VKE 413
             PLAL+VVG SL G+    W+  + + S G+S+  S++++ +CL SSLD L+++   +KE
Sbjct: 713  FPLALEVVGRSLHGQPVEIWRSTLMKLSEGQSIVNSEDELRNCLQSSLDALDDKDIMLKE 772

Query: 414  CYLDLCSFPEDQRIPITALIDMWMELYEL-VDDVFAITNLHELSSQNLVDRVVTRKTAGD 472
            C++DL SFPEDQ+IP TALIDMW EL++L  D ++AI+NL +L S+NL++ VVTR  A +
Sbjct: 773  CFMDLGSFPEDQKIPATALIDMWAELHKLDKDGIYAISNLQKLCSRNLLNLVVTRNDANE 832

Query: 473  YG-CYNDDFVMQHDLLRELTICRSKSEPINQRKRLVVEISGNNFPKWWMDQKQHPNNASL 531
               CYND FVMQHDLLR+L I +S  EPI +RKRL+V+++GN  P+WW  + Q   +A L
Sbjct: 833  IDWCYNDAFVMQHDLLRDLAIYQSNQEPIEKRKRLIVDLTGNRLPEWWTKENQPQLSARL 892

Query: 532  LSISTDETFSSNWPDMQGPEVKVVVLNIRT--KKYVLPDFLQKMDELKVLIVTNYGFSPA 589
            +SISTDE FSS+W +MQ PE + ++LN      KY LP+F+++MD+LKVL+VTNYGF  A
Sbjct: 893  VSISTDEMFSSSWCNMQLPEAEALILNFNQTENKYELPEFMKQMDKLKVLVVTNYGFCAA 952

Query: 590  ELNNFRVLSALSKLKKIRLEHVSLPNSLAT-VRMNHLQKVSLVMCN-VGQVFRNSTFRIS 647
            EL NF VLS+LS LK+IRLE VS+P    T + + +L+K+SLVMC+ +GQ F +ST +I 
Sbjct: 953  ELTNFSVLSSLSNLKRIRLEQVSIPTLCNTSMELKNLEKLSLVMCHKIGQAFASSTIQIP 1012

Query: 648  DAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPEGI 695
            +  PNL E++IDYCNDL+ELP+G CD+V + KL I+NCH+LSALPEGI
Sbjct: 1013 EMLPNLREINIDYCNDLVELPEGFCDLVQLNKLSISNCHKLSALPEGI 1060

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359480457|ref|XP_002265331.2| PREDICTED: probable disease resistance protein At5g66900-like [Vitis vinifera]

 Score =  656 bits (1692), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 355/711 (49%), Positives = 485/711 (68%), Gaps = 45/711 (6%)

Query: 1   MAAAFVGGALLGAVFGELLKAVSEEKDKAVTFKDRLEQLESTLRNSIPWIEEIEKLNQVL 60
           MA   VGGA LGAVF +L  AV + + KA  F   L++LE TL++  P I E++++N  L
Sbjct: 1   MALELVGGAALGAVFKKLFVAVEDARTKATKFDSSLKKLEETLKSINPSILEMKRMNDQL 60

Query: 61  DRPKQETENLVRMMEQVEQLVRKCSKVKW-NCFKRYVYAKKIIKLDTSISDFFRTSLPLQ 119
           D PK+E E L+++++  E+L+ KCSKV   N FK+  YA +I  L+ S+   F+  L  Q
Sbjct: 61  DHPKEEMEKLIQILKDGEKLIHKCSKVSCCNYFKKGRYANEIKALEDSLLKIFQVELQAQ 120

Query: 120 HARDGKLIMVEVKEIHTMVRRMSGNGNINGWMS---NQVGDCCSAPDPPVISPGLDVPLK 176
            +R+                          W+S     +G C  A DPP    GLDVPLK
Sbjct: 121 LSRN--------------------------WVSVKYESLGSC-EATDPPAFMVGLDVPLK 153

Query: 177 ELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIV 236
           ELK  LF DG   IVVSAPGG GKTTL +RLC D QV+  F+  IFYVTVSK  N+  I+
Sbjct: 154 ELKRWLFTDGESRIVVSAPGGCGKTTLAKRLCHDQQVKEYFQH-IFYVTVSKTFNLIGII 212

Query: 237 QKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEA--ILLVLDDVWPGSESLLQKLGFQL 294
           +K+  H    VP FQ +E A+N LE   K+ ++E+  ILLVLDDVW GSES L K  FQ+
Sbjct: 213 KKLFWHSDEQVPGFQNEEDAVNQLELMLKR-KVESGRILLVLDDVWSGSESFLTKFNFQI 271

Query: 295 PDYKILVTSRSEFPQFGSVHYLKPLTYEAARTLFLHSANLQDGN-SYIPDENIVSKILRA 353
              K+L+TSR+EFP+FGS +YLK L+ E A+TLF HSA  +DG+ S +P E++V+ I+R 
Sbjct: 272 SGCKVLITSRNEFPKFGSTYYLKLLSEEDAKTLFRHSAIPEDGSGSSMPGEDLVNTIVRR 331

Query: 354 CKGCPLALKVVGGSLCGKHEVFWQRMVKECSRGESVFQSKNDILDCLGSSLDVLNNE--- 410
           CKG PLAL+VVG SL G+    W+  + + S G+S+  S++++ +CL SSLD L+++   
Sbjct: 332 CKGFPLALEVVGRSLHGQPVEIWRSTLMKLSEGQSIVNSEDELRNCLQSSLDALDDKDIM 391

Query: 411 VKECYLDLCSFPEDQRIPITALIDMWMELYEL-VDDVFAITNLHELSSQNLVDRVVTRKT 469
           +KEC++DL SFPEDQ+IP TALIDMW EL++L  D ++AI+NLH+L S+NL++ VVTR  
Sbjct: 392 LKECFMDLGSFPEDQKIPATALIDMWAELHKLDKDGIYAISNLHKLCSRNLLNLVVTRND 451

Query: 470 AGDYG-CYNDDFVMQHDLLRELTICRSKSEPINQRKRLVVEISGNNFPKWWMDQKQHPNN 528
           A +   CYND FVMQHDLLR+L I +S  E I +RKRL+++++GN  P+WW  + Q   +
Sbjct: 452 ANEIDWCYNDAFVMQHDLLRDLAIYQSNQESIEKRKRLIMDLTGNRLPEWWTKENQPQLS 511

Query: 529 ASLLSISTDETFSSNWPDMQGPEVKVVVLNIRT--KKYVLPDFLQKMDELKVLIVTNYGF 586
           A L+SISTDE FSS+W +M+ PE + ++LN      KY LP+F+++MD+LKVL+VTNYGF
Sbjct: 512 ARLVSISTDEMFSSSWCNMELPEAEALILNFNQTENKYELPEFMKQMDKLKVLVVTNYGF 571

Query: 587 SPAELNNFRVLSALSKLKKIRLEHVSLPNSLAT-VRMNHLQKVSLVMCN-VGQVFRNSTF 644
             AEL NF VLS+LS LK+IRLE VS+P    T + + +L+K+SLVMC+ +GQ F +ST 
Sbjct: 572 CAAELTNFSVLSSLSNLKRIRLEQVSIPTLCNTSMELKNLEKLSLVMCHKIGQAFASSTI 631

Query: 645 RISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPEGI 695
           +I +  PNL E++IDYCNDL+ELP+G CD+V + KL I+NCH+LSALPEGI
Sbjct: 632 QIPEMLPNLREINIDYCNDLVELPEGFCDLVQLNKLSISNCHKLSALPEGI 682

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359480445|ref|XP_003632464.1| PREDICTED: probable disease resistance protein At5g66900-like [Vitis vinifera]

 Score =  651 bits (1679), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 353/708 (49%), Positives = 483/708 (68%), Gaps = 33/708 (4%)

Query: 1   MAAAFVGGALLGAVFGELLKAVSEEKDKAVTFKDRLEQLESTLRNSIPWIEEIEKLNQVL 60
           MA   VGGA LGAVF  L  AV +  +KA  F+  L++LE TL++  P I E++KLN  L
Sbjct: 1   MALELVGGAALGAVFETLFTAVVDASNKATQFESSLKKLEETLKSINPSILEMKKLNDQL 60

Query: 61  DRPKQETENLVRMMEQVEQLVRKCSKVKW-NCFKRYVYAKKIIKLDTSISDFFRTSLPLQ 119
           D PK+E E L+++++  E+L+ +CSKV   N FK++ YA KI  LD S+ +FF+  L   
Sbjct: 61  DHPKEELEKLIQILKDGEKLIHECSKVSCCNYFKKWRYANKIKALDGSLLNFFQVELQAI 120

Query: 120 HARDGKLIMVEVKEIHTMVRRMSGNGNINGWMSNQVGDCCSAPDPPVISPGLDVPLKELK 179
             R    ++V +K      ++ S                C A DPP    GLDVPLKELK
Sbjct: 121 LLRSSTQVLVLLKS-----KKFSLGS-------------CEATDPPAFMVGLDVPLKELK 162

Query: 180 MELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKV 239
             LF DG   IVVSAPGG GKTTL +RLC D QV+  F D I YVTVSK  ++  I++K+
Sbjct: 163 RRLFTDGESRIVVSAPGGCGKTTLAKRLCHDQQVKEYFTD-ICYVTVSKTCDLIGIIKKL 221

Query: 240 LHHKGYPVPEFQTDEAAINDLERFFKQMRIEA--ILLVLDDVWPGSESLLQKLGFQLPDY 297
             +    V  FQ++E A+N LE   K+ ++E+  ILLVLDDVW GS+S+  K  FQ+  +
Sbjct: 222 FWYNAERVQGFQSEEDAVNQLELMLKR-KVESGRILLVLDDVWSGSKSVPDKFKFQISKF 280

Query: 298 KILVTSRSEFPQFGSVHYLKPLTYEAARTLFLHSANLQDGNSY-IPDENIVSKILRACKG 356
           K+LVTSR EFP FGS + LK L+ E A+TLF HSA  +DG+S  +P E +V+ I+R CKG
Sbjct: 281 KVLVTSRDEFPGFGSTYNLKLLSEEDAKTLFCHSAIPEDGSSSSMPSEELVNGIVRRCKG 340

Query: 357 CPLALKVVGGSLCGKHEVFWQRMVKECSRGESVFQSKNDILDCLGSSLDVLNNE---VKE 413
            PLAL+VVG SL  +    W+  + + S GES+  S++++ +CL SSLD L+++   +KE
Sbjct: 341 FPLALEVVGRSLHEQPVEIWRSTLMKLSEGESIVNSEDELRNCLQSSLDALDDKDIMLKE 400

Query: 414 CYLDLCSFPEDQRIPITALIDMWMELYEL-VDDVFAITNLHELSSQNLVDRVVTRKTAGD 472
           C++DL SFPEDQ+IP TALIDMW EL++L    ++AI+NLH+L  +NL++ VVTR  A +
Sbjct: 401 CFMDLGSFPEDQKIPATALIDMWAELHKLDKGGIYAISNLHKLCFRNLLNLVVTRNDANE 460

Query: 473 YG-CYNDDFVMQHDLLRELTICRSKSEPINQRKRLVVEISGNNFPKWWMDQKQHPNNASL 531
              CYND FVMQHDLLR+L I +SK EPI +RKRL+V+++GN  P+WW  +KQ  ++A L
Sbjct: 461 IDRCYNDAFVMQHDLLRDLAIYQSKQEPIEKRKRLIVDLTGNRLPEWWTKEKQPRSSARL 520

Query: 532 LSISTDETFSSNWPDMQGPEVKVVVLNIRT--KKYVLPDFLQKMDELKVLIVTNYGFSPA 589
           +SISTDE FSS+W  MQ PE + ++LN     KKY LP+F+++MDELKVL+VTNYGF  A
Sbjct: 521 VSISTDEMFSSSWCSMQLPEAEALILNFNQTEKKYELPEFMKQMDELKVLVVTNYGFCTA 580

Query: 590 ELNNFRVLSALSKLKKIRLEHVSLPNSLAT-VRMNHLQKVSLVMCN-VGQVFRNSTFRIS 647
           EL NF +L +L  LK+IRLE VS+P    T + + +L+K+SLVMC+ +GQ F +ST +I 
Sbjct: 581 ELTNFSILGSLLNLKRIRLEKVSIPTLCKTSIELKNLEKLSLVMCHKIGQAFASSTIQIP 640

Query: 648 DAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPEGI 695
           +  PNL E++IDYCNDL+ELP+G CD++ + KL I+NCH+LS+LPEGI
Sbjct: 641 EMLPNLREINIDYCNDLVELPEGFCDLIQLNKLSISNCHKLSSLPEGI 688

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|189096590|gb|ACD76093.1| VRP1-1 [Vitis hybrid cultivar]

 Score =  639 bits (1648), Expect = e-180,   Method: Compositional matrix adjust.
 Identities = 348/716 (48%), Positives = 474/716 (66%), Gaps = 52/716 (7%)

Query: 1   MAAAFVGGALLGAVFGELLKAVSEEKDKAVTFKDRLEQLESTLRNSIPWIEEIEKLNQVL 60
           MA   VGG +L  V GEL+K   +   K   F D L++++S ++   P + +I+KL+  L
Sbjct: 1   MALETVGGVVLDKVIGELIKPFVDGGKKQAAFGDILQRVKSIIKLIGPTVRQIKKLSAEL 60

Query: 61  DRPKQETENLVRMMEQVEQLVRKCSKVKWNCFKRYVYAKKIIKLDTSISDFFRTSLPLQH 120
           DRPK+E+ENL+++ ++ E+L++KCSK+ W    R+ YA K+     S+  FF+  +PLQ 
Sbjct: 61  DRPKEESENLIQLFDEGEKLIQKCSKLNWWMPNRWKYANKLTAFYESLLRFFQFHMPLQQ 120

Query: 121 ARDGKLIMVEVKEIHTMVRRMSGNGNINGWM----------SNQVG--DCCSAPDPPVIS 168
                 I+      H   +  SG G ++G M          S ++G  D C+APDPP   
Sbjct: 121 FMTNMEILA-----HLQSQFRSGTGGVSGQMGYLGSGGSRVSGEIGYLDPCNAPDPPDFM 175

Query: 169 PGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSK 228
            GLDVPLKE+K  LFKD    IVVSAPGG GKTTLVQ+LC+D  V+  FKD+IFYVTVSK
Sbjct: 176 VGLDVPLKEVKKRLFKDDTSVIVVSAPGGCGKTTLVQKLCQDPDVKENFKDNIFYVTVSK 235

Query: 229 NPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFK-QMRIEAILLVLDDVWPGSESLL 287
             N+K IV+K+  H G+ VPEFQTDE AIN LE+  K Q R   ILLVLDDVW   E  L
Sbjct: 236 VHNLKLIVRKLFEHNGFRVPEFQTDEDAINQLEQLLKNQARKAPILLVLDDVWKEPEFPL 295

Query: 288 QKLGFQLPDYKILVTSRSEFPQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDEN-- 345
           QK  F++P+Y+ILVTSR EFP FGS + LK L  E A  LF HSA L DG+ ++PDE+  
Sbjct: 296 QKFAFKIPEYRILVTSRYEFPSFGSTYKLKLLNDEDAMKLFRHSAFLTDGD-FMPDEDFD 354

Query: 346 --IVSKILRACKGCPLALKVVGGSLCGKHEVFWQRMVKECSRGESVFQSKNDILDCLGSS 403
             +V++I++ C G PLAL+V+GGSLCG+    W+  + E S+G+S+F S   +LDCL  S
Sbjct: 355 EDLVNEIVKRCGGFPLALQVIGGSLCGQPVEIWKSRLMEFSKGQSIFDSGKRLLDCLQLS 414

Query: 404 LDVLNNEVKECYLDLCSFPEDQRIPITALIDMWMELYEL-VDDVFAITNLHELSSQNLVD 462
           L                         T+L DMW ELY+L  + V AI+NLH+LS QNL+ 
Sbjct: 415 L-------------------------TSLDDMWAELYKLDKNGVQAISNLHKLSLQNLLK 449

Query: 463 RVVTRKTAGDY-GCYNDDFVMQHDLLRELTICRSKSEPINQRKRLVVEISGNNFPKWWMD 521
            VVTRK A +  G Y++ FV+QHDLLR+L +  S  EP+ QRKRL++++SGN  P+WW +
Sbjct: 450 LVVTRKDATEVDGYYDEAFVLQHDLLRDLAMHESSQEPMEQRKRLILDLSGNKLPEWWTE 509

Query: 522 QKQHPNNASLLSISTDETFSSNWPDMQGPEVKVVVLNIR-TKKYVLPDFLQKMDELKVLI 580
           +KQ    A L+SISTD+ FSS+W +MQ PEV+V++LN + T+ Y  P+F+++MD LKVLI
Sbjct: 510 EKQPCFKARLMSISTDQMFSSSWCNMQVPEVEVLILNFQATENYTFPNFMKQMDNLKVLI 569

Query: 581 VTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSLAT-VRMNHLQKVSLVMCNVGQVF 639
           VTNYG S AEL NF VL +LS+LK+IRLE VS+P    T V + +++K+SLVMC + Q F
Sbjct: 570 VTNYGSSAAELINFSVLGSLSRLKRIRLEQVSIPTLCDTMVELKNVEKISLVMCKINQAF 629

Query: 640 RNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPEGI 695
            +   +IS+  PNL+E++I YC+DL+ LP+GLCD+V ++KL I+NCH+LSALP GI
Sbjct: 630 NSCAIQISNMLPNLMEINISYCSDLVGLPEGLCDLVHLKKLSISNCHKLSALPGGI 685

Source: Vitis hybrid cultivar

Species: Vitis hybrid cultivar

Genus: Vitis

Family: Vitaceae

Order: Vitales

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	695
TAIR|locus:2175019	809	AT5G66900 [Arabidopsis thalian	0.962	0.826	0.416	1.8e-126
TAIR|locus:2174944	815	AT5G66910 [Arabidopsis thalian	0.956	0.815	0.399	8.2e-115
TAIR|locus:2119196	816	ADR1-L1 "ADR1-like 1" [Arabido	0.943	0.803	0.321	5.4e-86
TAIR|locus:2175433	811	ADR1-L2 "ADR1-like 2" [Arabido	0.946	0.811	0.292	4.7e-80
TAIR|locus:2171479	623	ADR1-L3 "ADR1-like 3" [Arabido	0.715	0.797	0.326	4.4e-68
TAIR|locus:2006932	787	ADR1 "ACTIVATED DISEASE RESIST	0.667	0.589	0.331	8.2e-67
TAIR|locus:2175009	415	AT5G66890 "AT5G66890" [Arabido	0.414	0.693	0.407	3e-53
TAIR|locus:2154890	702	DAR5 "DA1-related protein 5" [	0.574	0.568	0.328	5.2e-49
TAIR|locus:2078012	852	ZAR1 "HOPZ-ACTIVATED RESISTANC	0.706	0.576	0.256	5.8e-22
TAIR|locus:2037639	907	AT1G58390 "AT1G58390" [Arabido	0.618	0.474	0.268	2.2e-21

TAIR|locus:2175019 AT5G66900 [Arabidopsis thaliana (taxid:3702)]

 Score = 1242 (442.3 bits), Expect = 1.8e-126, P = 1.8e-126
 Identities = 285/685 (41%), Positives = 409/685 (59%)

Query:    17 ELLKAVSEEKDKAVTFKDRLEQLESTLRNSIPWIEEIEKLNQVLDRPKQETENLVRMMEQ 76
             +LLK V +E  K   FK   + L ST+    P  ++I+ + + LD   +E + L   +E+
Sbjct:    19 KLLKVVIDEAKKFKAFKPLSKDLVSTMEILFPLTQKIDSMQKELDFGVKELKELRDTIER 78

Query:    77 VEQLVRKCSKVKWNCFKRYVYAKKIIKLDTSISDFFRTSLPLQHARDGKLIMVEVKEIHT 136
              +  VRK  +VKW  +++  Y +KI +++  +  F +  L L   R+   ++     +  
Sbjct:    79 ADVAVRKFPRVKW--YEKSKYTRKIERINKDMLKFCQIDLQLLQHRNQLTLLGLTGNLVN 136

Query:   137 MVRRMSGNGNINGWMSNQVGDCCSAPDPPVISPGLDVPLKELKMELFKDGRQFIVVSAPG 196
              V  +S   ++    +    D CS P    +  GLD PL ELK  L  D    +VVSAP 
Sbjct:   137 SVDGLSKRMDLLSVPAPVFRDLCSVPKLDKVIVGLDWPLGELKKRLLDDSVVTLVVSAPP 196

Query:   197 GYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAA 256
             G GKTTLV RLC D  ++GKFK  IF+  VS  PN + IVQ +L H GY    F+ D  A
Sbjct:   197 GCGKTTLVSRLCDDPDIKGKFKH-IFFNVVSNTPNFRVIVQNLLQHNGYNALTFENDSQA 255

Query:   257 INDLERFFKQMRIEA-ILLVLDDVWPGSESLLQKLGFQLPDYKILVTSRSEFPQFGSVHY 315
                L +  ++++    ILLVLDDVW G++S LQK   +LP+YKILVTSR +FP F S + 
Sbjct:   256 EVGLRKLLEELKENGPILLVLDDVWRGADSFLQKFQIKLPNYKILVTSRFDFPSFDSNYR 315

Query:   316 LKPLTYEAARTLFLHSANLQDGNSYIPDE--NIVSKILRACKGCPLALKVVGGSLCGKHE 373
             LKPL  + AR L +H A+     S  PDE  +++ KIL+ C G P+ ++VVG SL G+  
Sbjct:   316 LKPLEDDDARALLIHWASRPCNTS--PDEYEDLLQKILKRCNGFPIVIEVVGVSLKGRSL 373

Query:   374 VFWQRMVKECSRGESVF-QSKNDILDCLGSSLDVLNNEVKECYLDLCSFPEDQRIPITAL 432
               W+  V+  S GE +  +    +L+CL  S D L+  +KEC+LD+ SF EDQ+I  + +
Sbjct:   374 NTWKGQVESWSEGEKILGKPYPTVLECLQPSFDALDPNLKECFLDMGSFLEDQKIRASVI 433

Query:   433 IDMWMELYELVDDVFAITNLHELSSQNLVDRVVTRKTAGDYGCYNDDFVMQHDLLRELTI 492
             IDMW+ELY     +  +  L +L+SQNL+  V       + G YND  V QHD+LREL I
Sbjct:   434 IDMWVELYGKGSSILYMY-LEDLASQNLLKLVPLGTNEHEDGFYNDFLVTQHDILRELAI 492

Query:   493 CRSKSEPINQRKRLVVEISGNNFPKWWMDQKQHPNNASLLSISTDETFSSNWPDMQGPEV 552
             C+S+ +   +RKRL +EI  N FP W ++      NASLLSISTD+ FSS W +M  P V
Sbjct:   493 CQSEFKENLERKRLNLEILENTFPDWCLNTI----NASLLSISTDDLFSSKWLEMDCPNV 548

Query:   553 KVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVS 612
             + +VLN+ +  Y LP F+  M +LKVL +TN+GF PA L+NF  LS+L  LK+IRLE VS
Sbjct:   549 EALVLNLSSSDYALPSFISGMKKLKVLTITNHGFYPARLSNFSCLSSLPNLKRIRLEKVS 608

Query:   613 LPN-SLATVRMNHLQKVSLVMCNVGQVFRNST-FRISDAFPNLLEMDIDYCNDLIELPDG 670
             +    +  ++++ L+K+SLVMC+ G+VF ++    +S+A   L E+DIDYC DL ELP  
Sbjct:   609 ITLLDIPQLQLSSLKKLSLVMCSFGEVFYDTEDIVVSNALSKLQEIDIDYCYDLDELPYW 668

Query:   671 LCDIVSMEKLRITNCHRLSALPEGI 695
             + +IVS++ L ITNC++LS LPE I
Sbjct:   669 ISEIVSLKTLSITNCNKLSQLPEAI 693

GO:0005634 "nucleus" evidence=ISM

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2174944 AT5G66910 [Arabidopsis thaliana (taxid:3702)]

 Score = 1132 (403.5 bits), Expect = 8.2e-115, P = 8.2e-115
 Identities = 277/693 (39%), Positives = 405/693 (58%)

Query:    17 ELLKAVSEEKDKAVTFKDRLEQLESTLRNSIPWIEEIEKLNQVLDRPKQETENLVRMMEQ 76
             E LK +  E  K + FK    +L ST+ + +P I+EIE +   +     E ++L   +++
Sbjct:    21 EGLKVLISEAKKVLAFKSVSNELASTMESLLPVIKEIESMQDGM-----ELQDLKDTIDK 75

Query:    77 VEQLVRKCSKV-KWNCFKRYVYAKKIIKLDTSISDFFRTSLPLQHARDGKLIMVEVKEI- 134
                LV KCS V KWN   +  Y +K+ +++  +  F +  L L   R+    M  ++ I 
Sbjct:    76 ALLLVEKCSHVEKWNIILKSKYTRKVEEINRKMLKFCQVQLQLLLFRNQLKSMPSMEAIL 135

Query:   135 HTMVRRMSGN-GNINGWMSNQ-VGDCCSAPD-PPVISPGLDVPLKELKMELFKDGRQFIV 191
             +   + ++     ++G  +   V   CS P    ++  GLD PL ELK +L  +    +V
Sbjct:   136 NNYFQNINKKLDRLSGSPAPPLVSKRCSVPKLDNMVLVGLDWPLVELKKKLLDNS--VVV 193

Query:   192 VSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQ 251
             VS P G GKTTLV +LC D +++G+FK  IFY  VS  PN +AIVQ +L   G     F 
Sbjct:   194 VSGPPGCGKTTLVTKLCDDPEIEGEFKK-IFYSVVSNTPNFRAIVQNLLQDNGCGAITFD 252

Query:   252 TDEAAINDLERFFKQMRIEA-ILLVLDDVWPGSESLLQKLGFQLPDYKILVTSRSEFPQF 310
              D  A   L    +++  +  ILLVLDDVW GSE LL+K    LPDYKILVTS+ +F   
Sbjct:   253 DDSQAETGLRDLLEELTKDGRILLVLDDVWQGSEFLLRKFQIDLPDYKILVTSQFDFTSL 312

Query:   311 GSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDE--NIVSKILRACKGCPLALKVVGGSL 368
                ++L PL YE AR+L +  A+     S  PDE  +++ KIL+ C G PL ++VVG SL
Sbjct:   313 WPTYHLVPLKYEYARSLLIQWASPPLHTS--PDEYEDLLQKILKRCNGFPLVIEVVGISL 370

Query:   369 CGKHEVFWQRMVKECSRGESVFQSKND-ILDCLGSSLDVLNNEVKECYLDLCSFPEDQRI 427
              G+    W+  V+  S GE++  + N  +   L  S +VL   +KEC++D+ SF +DQ+I
Sbjct:   371 KGQALYLWKGQVESWSEGETILGNANPTVRQRLQPSFNVLKPHLKECFMDMGSFLQDQKI 430

Query:   428 PITALIDMWMELY---ELVDDVFAITNLHELSSQNLVDRVVTRKTAGDYGCYNDDFVMQH 484
               + +ID+WMELY       + F +  L+EL+SQNL+  V       + G YN+  V QH
Sbjct:   431 RASLIIDIWMELYGRGSSSTNKFMLY-LNELASQNLLKLVHLGTNKREDGFYNELLVTQH 489

Query:   485 DLLRELTICRSKSEPINQRKRLVVEISGNNFPKWWMDQKQHPNNASLLSISTDETFSSNW 544
             ++LREL I +S+ EPI QRK+L +EI  +NFP   ++Q   P NA LLSI TD+ FSS W
Sbjct:   490 NILRELAIFQSELEPIMQRKKLNLEIREDNFPDECLNQ---PINARLLSIYTDDLFSSKW 546

Query:   545 PDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLK 604
              +M  P V+ +VLNI +  Y LP F+ +M +LKVL + N+GF PA L+NF  LS+L  LK
Sbjct:   547 LEMDCPNVEALVLNISSLDYALPSFIAEMKKLKVLTIANHGFYPARLSNFSCLSSLPNLK 606

Query:   605 KIRLEHVSLPN-SLATVRMNHLQKVSLVMCNVGQVFRNST-FRISDAFPNLLEMDIDYCN 662
             +IR E VS+    +  +++  L+K+S  MC+ G+VF ++    +S A  NL E+DIDYC 
Sbjct:   607 RIRFEKVSVTLLDIPQLQLGSLKKLSFFMCSFGEVFYDTEDIDVSKALSNLQEIDIDYCY 666

Query:   663 DLIELPDGLCDIVSMEKLRITNCHRLSALPEGI 695
             DL ELP  + ++VS++ L ITNC++LS LPE I
Sbjct:   667 DLDELPYWIPEVVSLKTLSITNCNKLSQLPEAI 699

GO:0005634 "nucleus" evidence=ISM

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2119196 ADR1-L1 "ADR1-like 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 860 (307.8 bits), Expect = 5.4e-86, P = 5.4e-86
 Identities = 228/710 (32%), Positives = 388/710 (54%)

Query:    17 ELLKAVSEEKDKAVTFKDRLEQLESTLRNSI-PWIEEIEKLNQVLDRPKQ-ETENLVRMM 74
             ELLK +      A  +K+  +QL  TL +SI P I+EI+     L   +Q +   L   +
Sbjct:    14 ELLKQLFTISTTAWRYKNTAKQL-LTLIDSIRPTIKEIQYSGVELPAHRQAQIGMLFDTL 72

Query:    75 EQVEQLVRKC-SKVKWNCFKRYVYAKKIIKLDTSISDFFRTSL------PLQHARDGKLI 127
             E+ ++L  K  S  +WN +++   A+K+ KL+ +IS+F +  +       + H R    +
Sbjct:    73 EKGKKLTDKVLSSKRWNLYRQLTLARKMEKLEKTISNFLKNEVFTHILADVHHLRADTSV 132

Query:   128 MVE---------VKEIHTMVRRMSGNGNINGWMSN-QVGDCCSAPDPPVISPGLDVPLKE 177
              ++         ++++ +M  ++ G G I+  M   +  +  +  D      GL++   +
Sbjct:   133 RLDRVDMSLDRVIQQVGSM--KIGGGGLISEAMKRAEAMEIETNDDSEKFGVGLELGKVK 190

Query:   178 LKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP---NVKA 234
             +K  +F+       +S  GG GKTTL + L +D +VQ  F++ I ++TVS++P    ++ 
Sbjct:   191 VKKMMFESQGGVFGISGMGGVGKTTLAKELQRDHEVQCHFENRILFLTVSQSPLLEELRE 250

Query:   235 IVQKVLH--HKGYPVPE--FQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSESLLQKL 290
             ++   L     G PVP+  F  D A         K       L++LDDVW  +++L +  
Sbjct:   251 LIWGFLSGCEAGNPVPDCNFPFDGAR--------K-------LVILDDVWT-TQALDRLT 294

Query:   291 GFQLPDYKILVTSRSEFPQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIP---DENIV 347
              F+ P    LV SRS+  +    + ++ L+ + A +LF   A    G   IP    +++V
Sbjct:   295 SFKFPGCTTLVVSRSKLTEPKFTYDVEVLSEDEAISLFCLCAF---GQKSIPLGFCKDLV 351

Query:   348 SKILRACKGCPLALKVVGGSLCGKHEVFWQRMVKECSRGESVFQS-KNDILDCLGSSLDV 406
              ++   CKG PLALKV G SL GK E++W+ +++  S+GE    S ++ +L  + +SLD 
Sbjct:   352 KQVANECKGLPLALKVTGASLNGKPEMYWKGVLQRLSKGEPADDSHESRLLRQMEASLDN 411

Query:   407 LNNEVKECYLDLCSFPEDQRIPITALIDMWMELYELVDDVFAITNLHELSSQNLVDRVVT 466
             L+   K+C+LDL +FPED++IP+  LI++W+EL++ +D+  A   L +LS +NL+     
Sbjct:   412 LDQTTKDCFLDLGAFPEDRKIPLDVLINIWIELHD-IDEGNAFAILVDLSHKNLLTLGKD 470

Query:   467 RKTAGDYGCYNDDFVMQHDLLRELTICRSKSEPINQRKRLVVEISGNNFPKWWMDQKQHP 526
              +    Y  + D FV QHD+LR+L +  S +  +N+RKRL++     + P  W       
Sbjct:   471 PRLGSLYASHYDIFVTQHDVLRDLALHLSNAGKVNRRKRLLMPKRELDLPGDWERNNDEH 530

Query:   527 NNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGF 586
               A ++SI T E     W DM+ P+ ++++LN  + KYVLP F+ KM  LKVL++ N G 
Sbjct:   531 YIAQIVSIHTGEMNEMQWFDMEFPKAEILILNFSSDKYVLPPFISKMSRLKVLVIINNGM 590

Query:   587 SPAELNNFRVLSALSKLKKIRLEHVSLPN-SLATVRMNHLQKVSLVMCNVGQVFRNSTFR 645
             SPA L++F + + LSKL+ + LE V +P  S +T  + +L K+SL++C + + F  +   
Sbjct:   591 SPAVLHDFSIFAHLSKLRSLWLERVHVPQLSNSTTPLKNLHKMSLILCKINKSFDQTGLD 650

Query:   646 ISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPEGI 695
             ++D FP L ++ ID+C+DL+ LP  +C + S+  L ITNC RL  LP+ +
Sbjct:   651 VADIFPKLGDLTIDHCDDLVALPSSICGLTSLSCLSITNCPRLGELPKNL 700

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

GO:0048046 "apoplast" evidence=IDA

GO:0042742 "defense response to bacterium" evidence=IGI

GO:0006612 "protein targeting to membrane" evidence=RCA

GO:0009963 "positive regulation of flavonoid biosynthetic process" evidence=RCA

GO:0010363 "regulation of plant-type hypersensitive response" evidence=RCA

GO:0031348 "negative regulation of defense response" evidence=RCA

TAIR|locus:2175433 ADR1-L2 "ADR1-like 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 804 (288.1 bits), Expect = 4.7e-80, P = 4.7e-80
 Identities = 206/705 (29%), Positives = 374/705 (53%)

Query:    17 ELLKAVSEEKDKAVTFKDRLEQLESTLRNSIPWIEEIEKLNQVLDRPKQ-ETENLVRMME 75
             EL++ +     K +  +   + L + +    P I+EI+     L   +Q +       ++
Sbjct:    12 ELVRQLYAVSQKTLRCRGIAKNLATMIDGLQPTIKEIQYSGVELTPHRQAQLRMFSETLD 71

Query:    76 QVEQLVRKCSKV-KWNCFKRYVYAKKIIKLDTSISDFFRTSL------PLQHAR-DGKLI 127
             +  +L  K  K  +WN  ++ ++ +K+  L + +S F    L       + H R D +  
Sbjct:    72 KCRKLTEKVLKSSRWNMVRQLLHVRKMENLQSKVSSFLNGQLLVHVLADVHHVRADSEFR 131

Query:   128 MVEV-KEIHTMVRRMSGNGNINGWMSNQVGDCCSAPDPPV---------ISPGLDVPLKE 177
                + +++ ++  ++ G+  + G  S  + +     +  V         +  GLD+  ++
Sbjct:   132 FDRIDRKVDSLNEKL-GSMKLRG--SESLREALKTAEATVEMVTTDGADLGVGLDLGKRK 188

Query:   178 LKMELFK--DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAI 235
             +K  LFK  DG + I +S   G GKTTL + L +D++V+G F + + ++TVS++PN++ +
Sbjct:   189 VKEMLFKSIDGERLIGISGMSGSGKTTLAKELARDEEVRGHFGNKVLFLTVSQSPNLEEL 248

Query:   236 VQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSESLLQKLGFQLP 295
                  H  G+      + EA +        + R    L++LDDVW   ESL Q +   +P
Sbjct:   249 RA---HIWGF----LTSYEAGVGAT---LPESRK---LVILDDVWT-RESLDQLMFENIP 294

Query:   296 DYKILVTSRSEFPQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPD---ENIVSKILR 352
                 LV SRS+       + ++ L    A  LF  S   Q     +P    +++V +++ 
Sbjct:   295 GTTTLVVSRSKLADSRVTYDVELLNEHEATALFCLSVFNQ---KLVPSGFSQSLVKQVVG 351

Query:   353 ACKGCPLALKVVGGSLCGKHEVFWQRMVKECSRGESVFQS-KNDILDCLGSSLDVLNNEV 411
              CKG PL+LKV+G SL  + E +W+  V+  SRGE   ++ ++ +   + ++L+ L+ + 
Sbjct:   352 ECKGLPLSLKVIGASLKERPEKYWEGAVERLSRGEPADETHESRVFAQIEATLENLDPKT 411

Query:   412 KECYLDLCSFPEDQRIPITALIDMWMELYELVDDVFAITNLHELSSQNLVDRVVTRKTAG 471
             ++C+L L +FPED++IP+  LI++ +EL++L +D  A   + +L+++NL+  V   +   
Sbjct:   412 RDCFLVLGAFPEDKKIPLDVLINVLVELHDL-EDATAFAVIVDLANRNLLTLVKDPRFGH 470

Query:   472 DYGCYNDDFVMQHDLLRELTICRSKSEPINQRKRLVVEISGNNFPKWWMDQKQHPNNASL 531
              Y  Y D FV QHD+LR++ +  S    +N R+RL++    +  P+ W      P  A +
Sbjct:   471 MYTSYYDIFVTQHDVLRDVALRLSNHGKVNNRERLLMPKRESMLPREWERNNDEPYKARV 530

Query:   532 LSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAEL 591
             +SI T E    +W DM+ P+ +V++L+  + KYVLP F+ KM +L  L++ N G SPA L
Sbjct:   531 VSIHTGEMTQMDWFDMELPKAEVLILHFSSDKYVLPPFIAKMGKLTALVIINNGMSPARL 590

Query:   592 NNFRVLSALSKLKKIRLEHVSLPN-SLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAF 650
             ++F + + L+KLK + L+ V +P  S +TV + +L K+SL+ C +      +   I+  F
Sbjct:   591 HDFSIFTNLAKLKSLWLQRVHVPELSSSTVPLQNLHKLSLIFCKINTSLDQTELDIAQIF 650

Query:   651 PNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPEGI 695
             P L ++ ID+C+DL+ELP  +C I S+  + ITNC R+  LP+ +
Sbjct:   651 PKLSDLTIDHCDDLLELPSTICGITSLNSISITNCPRIKELPKNL 695

GO:0000166 "nucleotide binding" evidence=IEA

GO:0006952 "defense response" evidence=IEA;ISS

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

GO:0043531 "ADP binding" evidence=IEA

GO:0042742 "defense response to bacterium" evidence=IGI

GO:0006499 "N-terminal protein myristoylation" evidence=RCA

GO:0006612 "protein targeting to membrane" evidence=RCA

GO:0009627 "systemic acquired resistance" evidence=RCA

GO:0009697 "salicylic acid biosynthetic process" evidence=RCA

GO:0009963 "positive regulation of flavonoid biosynthetic process" evidence=RCA

GO:0010363 "regulation of plant-type hypersensitive response" evidence=RCA

TAIR|locus:2171479 ADR1-L3 "ADR1-like 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 691 (248.3 bits), Expect = 4.4e-68, P = 4.4e-68
 Identities = 168/515 (32%), Positives = 287/515 (55%)

Query:   185 DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKG 244
             D  + I +S   G GKT L + L +D++V+G F + + ++TVS++PN++ +  + L    
Sbjct:     7 DEARIIGISGMIGSGKTILAKELARDEEVRGHFANRVLFLTVSQSPNLEEL--RSL---- 60

Query:   245 YPVPEFQTD-EAAIND-LERFFKQMRIEAILLVLDDVWPGSESLLQKLGFQLPDYKILVT 302
               + +F T  EA     L       R    L++LDDV    ESL Q L F +P    LV 
Sbjct:    61 --IRDFLTGHEAGFGTALPESVGHTRK---LVILDDVRT-RESLDQ-LMFNIPGTTTLVV 113

Query:   303 SRSEFPQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALK 362
             S+S+     + + ++ L    A +LF  SA  Q        +++V +++   KG PL+LK
Sbjct:   114 SQSKLVDPRTTYDVELLNEHDATSLFCLSAFNQKSVPSGFSKSLVKQVVGESKGLPLSLK 173

Query:   363 VVGGSLCGKHEVFWQRMVKECSRGESVFQS-KNDILDCLGSSLDVLNNEVKECYLDLCSF 421
             V+G SL  + E +W   V+  SRGE V ++ ++ +   + ++L+ L+ + KEC+LD+ +F
Sbjct:   174 VLGASLNDRPETYWAIAVERLSRGEPVDETHESKVFAQIEATLENLDPKTKECFLDMGAF 233

Query:   422 PEDQRIPITALIDMWMELYELVDDVFAITNLHELSSQNLVDRVVTRKTAGDYGCYNDDFV 481
             PE ++IP+  LI+M +++++L +D  A   L +L+++NL+  V           Y D FV
Sbjct:   234 PEGKKIPVDVLINMLVKIHDL-EDAAAFDVLVDLANRNLLTLVKDPTFVAMGTSYYDIFV 292

Query:   482 MQHDLLRELTICRSKSEPINQRKRLVVEISGNNFPKWWMDQKQHPNNASLLSISTDETFS 541
              QHD+LR++ +  +    +++R RL++       P  W      P NA ++SI T E   
Sbjct:   293 TQHDVLRDVALHLTNRGKVSRRDRLLMPKRETMLPSEWERSNDEPYNARVVSIHTGEMTE 352

Query:   542 SNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALS 601
              +W DM  P+ +V+++N  +  YVLP F+ KM  L+V ++ N G SPA L++F + ++L+
Sbjct:   353 MDWFDMDFPKAEVLIVNFSSDNYVLPPFIAKMGMLRVFVIINNGTSPAHLHDFPIPTSLT 412

Query:   602 KLKKIRLEHVSLPN-SLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDY 660
              L+ + LE V +P  S + + + +L K+ L++C +   F  +   I+  FP L ++ IDY
Sbjct:   413 NLRSLWLERVHVPELSSSMIPLKNLHKLYLIICKINNSFDQTAIDIAQIFPKLTDITIDY 472

Query:   661 CNDLIELPDGLCDIVSMEKLRITNCHRLSALPEGI 695
             C+DL ELP  +C I S+  + ITNC  +  LP+ I
Sbjct:   473 CDDLAELPSTICGITSLNSISITNCPNIKELPKNI 507

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0006952 "defense response" evidence=IEA;ISS

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2006932 ADR1 "ACTIVATED DISEASE RESISTANCE 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 679 (244.1 bits), Expect = 8.2e-67, P = 8.2e-67
 Identities = 158/476 (33%), Positives = 273/476 (57%)

Query:   224 VTVSKNPNVKAIVQ-KVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPG 282
             + +SK+ +V+ + + KVL       P F+  E+ I +   F      +  L++LDDVW  
Sbjct:   204 IELSKDDDVRGLFKNKVLFLTVSRSPNFENLESCIRE---FLYDGVHQRKLVILDDVWT- 259

Query:   283 SESLLQKLGFQLPDYKILVTSRSEFPQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIP 342
              ESL  +L  ++     LV SRS+     + + ++ L  + A +L    A  Q       
Sbjct:   260 RESL-DRLMSKIRGSTTLVVSRSKLADPRTTYNVELLKKDEAMSLLCLCAFEQKSPPSPF 318

Query:   343 DENIVSKILRACKGCPLALKVVGGSLCGKHEVFWQRMVKECSRGESVFQS-KNDILDCLG 401
             ++ +V +++  CKG PL+LKV+G SL  K E +W+ +VK   RGE+  ++ ++ +   + 
Sbjct:   319 NKYLVKQVVDECKGLPLSLKVLGASLKNKPERYWEGVVKRLLRGEAADETHESRVFAHME 378

Query:   402 SSLDVLNNEVKECYLDLCSFPEDQRIPITALIDMWMELYELVDDVFAITNLHELSSQNLV 461
              SL+ L+ ++++C+LD+ +FPED++IP+  L  +W+E ++ +D+  A + +  L+ +NL+
Sbjct:   379 ESLENLDPKIRDCFLDMGAFPEDKKIPLDLLTSVWVERHD-IDEETAFSFVLRLADKNLL 437

Query:   462 DRVVTRKTAGDYGC-YNDDFVMQHDLLRELTICRSKSEPINQRKRLVVEISGNNFPKWWM 520
               +V     GD    Y D FV QHD+LR+L +  S    +N+R+RL++  +    P+ W 
Sbjct:   438 T-IVNNPRFGDVHIGYYDVFVTQHDVLRDLALHMSNRVDVNRRERLLMPKTEPVLPREWE 496

Query:   521 DQKQHPNNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLI 580
               K  P +A ++S+ T E    NW DM  P+ +V++LN  +  YVLP F+ KM  L+VL+
Sbjct:   497 KNKDEPFDAKIVSLHTGEMDEMNWFDMDLPKAEVLILNFSSDNYVLPPFIGKMSRLRVLV 556

Query:   581 VTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPN-SLATVRMNHLQKVSLVMCNVGQVF 639
             + N G SPA L+ F + + L+KL+ + L+ V +P  +  T+ + +L K+ L+ C V   F
Sbjct:   557 IINNGMSPARLHGFSIFANLAKLRSLWLKRVHVPELTSCTIPLKNLHKIHLIFCKVKNSF 616

Query:   640 RNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPEGI 695
               ++F IS  FP+L ++ ID+C+DL+EL   +  I S+  L ITNC R+  LP+ +
Sbjct:   617 VQTSFDISKIFPSLSDLTIDHCDDLLELKS-IFGITSLNSLSITNCPRILELPKNL 671

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

GO:0016301 "kinase activity" evidence=TAS

GO:0051707 "response to other organism" evidence=IEP

GO:0009414 "response to water deprivation" evidence=IMP

GO:0080167 "response to karrikin" evidence=IEP

GO:0042742 "defense response to bacterium" evidence=IGI

TAIR|locus:2175009 AT5G66890 "AT5G66890" [Arabidopsis thaliana (taxid:3702)]

 Score = 551 (199.0 bits), Expect = 3.0e-53, P = 3.0e-53
 Identities = 121/297 (40%), Positives = 182/297 (61%)

Query:   403 SLDVLNNEVKECYLDLCSFPEDQRIPITALIDMWMELYELVDDVFAITNLHELSSQNLVD 462
             S D L + ++EC+LD+ SF EDQRI  + +ID+W   Y        + NL +L+S+NL+ 
Sbjct:     8 SFDALPHNLRECFLDMASFLEDQRIIASTIIDLWSASYGKE----GMNNLQDLASRNLLK 63

Query:   463 RVVTRKTAGDYGCYNDDFVMQHDLLRELTI--CRSKSEPINQRKRLVVEISGNNFPKWWM 520
              +   +   + G YN+  V Q ++LRE  I  C  +S  I +RKRL +EI  N FP W +
Sbjct:    64 LLPIGRNEYEDGFYNELLVKQDNVLREFAINQCLKESSSIFERKRLNLEIQDNKFPNWCL 123

Query:   521 DQKQH-PNNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVL 579
             + KQ    NASL SISTD++F+S+W +M  P V+ +VLNI +  Y LP+F+  M ELKV+
Sbjct:   124 NPKQPIVINASLFSISTDDSFASSWFEMDCPNVEALVLNISSSNYALPNFIATMKELKVV 183

Query:   580 IVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPN-SLATVRMNHLQKVSLVMCNVGQV 638
             I+ N+G  PA+L N   LS+L  LK+IR E VS+    +  + +  L+K+SL  C+V   
Sbjct:   184 IIINHGLEPAKLTNLSCLSSLPNLKRIRFEKVSISLLDIPKLGLKSLEKLSLWFCHVVDA 243

Query:   639 FRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPEGI 695
               N    +S+   +L E++IDYC +L ELP  +  +VS++KL +TNC++L  + E I
Sbjct:   244 L-NELEDVSETLQSLQEIEIDYCYNLDELPYWISQVVSLKKLSVTNCNKLCRVIEAI 299

GO:0006952 "defense response" evidence=ISS

TAIR|locus:2154890 DAR5 "DA1-related protein 5" [Arabidopsis thaliana (taxid:3702)]

 Score = 511 (184.9 bits), Expect = 5.2e-49, P = 5.2e-49
 Identities = 142/432 (32%), Positives = 220/432 (50%)

Query:    17 ELLKAVSEEKDKAVTFKDRLEQLESTLRNSIPWIEEIEKLNQVLDRPKQETENLVRMMEQ 76
             E+ K V EE  K   FK   + L ST+   +P   EI+ + Q  +R   E + L   ME+
Sbjct:    21 EIFKLVIEEAKKVKDFKPLSQDLASTMERLVPIFNEIDMMQQGSNRGTSELKVLTETMER 80

Query:    77 VEQLVRKCSKVKW-NCFKRYVYAKKIIKLDTSISDFFRTSLPLQHARDGKLIMVEVKEIH 135
               ++V KCS+++W +  K+ +Y ++I  ++     F +  L L   R+      +++ + 
Sbjct:    81 AGEMVHKCSRIQWYSIAKKALYTREIKAINQDFLKFCQIELQLIQHRN------QLQYMR 134

Query:   136 TM-VRRMSGNGNINGWMSNQVGDCCSAPDPPVISP-GLDVPLKELKMELFKDGRQFIVVS 193
             +M +  +S   ++   + N+    C    P V++   L  PL ELK  LF+DG   +VVS
Sbjct:   135 SMGMASVSTKADLLSDIGNEFSKLCLVAQPEVVTKFWLKRPLMELKKMLFEDGVVTVVVS 194

Query:   194 APGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTD 253
             AP   GKTTLV +LC D  V+ KFK  IF+++VSK PNV+ I  K+L H G    E++ D
Sbjct:   195 APYALGKTTLVTKLCHDADVKEKFKQ-IFFISVSKFPNVRLIGHKLLEHIGCKANEYEND 253

Query:   254 EAAINDLERFFKQM-RIEAILLVLDDVWPGSESLLQKLGFQLPDYKILVTSRSEFPQFGS 312
               A+  +++  KQ+ R  +ILLVLDDVW   ESLLQK   QLPDYKILVTSR EF  FG 
Sbjct:   254 LDAMLYIQQLLKQLGRNGSILLVLDDVWAEEESLLQKFLIQLPDYKILVTSRFEFTSFGP 313

Query:   313 VHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGG-SLCGK 371
               +LKPL  +           +++ N  +P+   V+  L  C GC  A+K     ++ G 
Sbjct:   314 TFHLKPLIDDEVEC----RDEIEE-NEKLPE---VNPPLSMCGGCNSAVKHEESVNILG- 364

Query:   372 HEVFWQR---MVKECSRGESVFQSKNDILDCLGSSLDVLNNEVKECYLDLCSFPEDQRIP 428
               V W       + C +  ++ + +N + +  G          K CY   C   +++++ 
Sbjct:   365 --VLWHPGCFCCRSCDKPIAIHELENHVSNSRGKFH-------KSCYERYCYVCKEKKMK 415

Query:   429 ITALIDMWMELY 440
                +   W E Y
Sbjct:   416 TYNIHPFWEERY 427

GO:0008270 "zinc ion binding" evidence=IEA

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2078012 ZAR1 "HOPZ-ACTIVATED RESISTANCE 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 273 (101.2 bits), Expect = 5.8e-22, Sum P(2) = 5.8e-22
 Identities = 144/561 (25%), Positives = 254/561 (45%)

Query:    22 VSEEKDKAVT-FKDRLEQLESTLRNSIPWIEEIEKLNQVLDRPKQETENLVRMMEQVEQL 80
             + EEK + V+ ++ +LE L+S L+    ++++ E       R K+  E L  ++  + +L
Sbjct:    16 ILEEKGRTVSDYRKQLEDLQSELKYMQSFLKDAE-------RQKRTNETLRTLVADLREL 68

Query:    81 VRKCSKVKWNC-FKRYVYAKKIIKLDTSISDFFRTSLPLQHARDGKL--IMVEVKEIHTM 137
             V +   +  +C         +    +  +S      +PLQ+ +  +L  I   + +I + 
Sbjct:    69 VYEAEDILVDCQLADGDDGNEQRSSNAWLSRLHPARVPLQYKKSKRLQEINERITKIKSQ 128

Query:   138 VRRM------SGNGNING---WMSNQVGDCCSAPDPPVISPGLDVPLKELKMELFKDGRQ 188
             V         S  G  NG   W S+ V D        V+  GL+   +++K  LF+    
Sbjct:   129 VEPYFEFITPSNVGRDNGTDRW-SSPVYD-----HTQVV--GLEGDKRKIKEWLFRSNDS 180

Query:   189 FIVVSA---PGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGY 245
              +++ A    GG GKTT+ Q +  D +++ +F+  I +V+VS+    + I++ +L + G 
Sbjct:   181 QLLIMAFVGMGGLGKTTIAQEVFNDKEIEHRFERRI-WVSVSQTFTEEQIMRSILRNLG- 238

Query:   246 PVPEFQTDEAAINDLERFFKQMRI-EAILLVLDDVWPGSESLLQKLGFQLPDYK---ILV 301
                    D+  I  L R  +Q  + +  L+V+DDVW  + S   K+   LP  +   ++V
Sbjct:   239 --DASVGDD--IGTLLRKIQQYLLGKRYLIVMDDVWDKNLSWWDKIYQGLPRGQGGSVIV 294

Query:   302 TSRSEF------PQFGSVHYLKPLTYEAARTLFLHSA-NLQDGNSYIPD-ENIVSKILRA 353
             T+RSE        +    H  + L+ + +  LF + A    DG    P+ E++  +I+  
Sbjct:   295 TTRSESVAKRVQARDDKTHRPELLSPDNSWLLFCNVAFAANDGTCERPELEDVGKEIVTK 354

Query:   354 CKGCPLALKVVGGSLCGKHEVF--WQRMVKECS---RGESVFQSKNDILDCLGSSLDVLN 408
             CKG PL +K VGG L  K  V+  W+R+ +      RG +     ++++  L  S D L 
Sbjct:   355 CKGLPLTIKAVGGLLLCKDHVYHEWRRIAEHFQDELRGNT--SETDNVMSSLQLSYDELP 412

Query:   409 NEVKECYLDLCSFPEDQRIPITALIDMWM-ELYELVDDVFAITNLHELSSQNLVDRVVTR 467
             + +K C L L  +PED  IP   L+  W+ E + +  +  + T   E     L +R +  
Sbjct:   413 SHLKSCILTLSLYPEDCVIPKQQLVHGWIGEGFVMWRNGRSATESGEDCFSGLTNRCLIE 472

Query:   468 KTAGDY-GCYNDDFVMQHDLLRELTICRSKSEPINQRKRLVVE---ISGNNFPKWWMDQK 523
                  Y G      +  HD++R+L I  +K +  +  + L      ISGN       D+K
Sbjct:   473 VVDKTYSGTIITCKI--HDMVRDLVIDIAKKDSFSNPEGLNCRHLGISGN------FDEK 524

Query:   524 QHPNNASLLSI-STDETFSSN 543
             Q   N  L  + ST +T   N
Sbjct:   525 QIKVNHKLRGVVSTTKTGEVN 545

GO:0005634 "nucleus" evidence=ISM

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2037639 AT1G58390 "AT1G58390" [Arabidopsis thaliana (taxid:3702)]

 Score = 280 (103.6 bits), Expect = 2.2e-21, Sum P(2) = 2.2e-21
 Identities = 132/492 (26%), Positives = 233/492 (47%)

Query:   170 GLDVPLKELKMELF-KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSK 228
             GL+V +K+L   L  ++  Q + ++  GG GKTTL +++   + V+ +F D + +V VS+
Sbjct:   165 GLEVNVKKLVGYLVDEENVQVVSITGMGGLGKTTLARQVFNHEDVKHQF-DRLAWVCVSQ 223

Query:   229 NPNVKAIVQKVLHHKGYPVPE---FQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSE- 284
                 K + Q +L +      +    Q +EA ++D  + F+ +     L+V DD+W   + 
Sbjct:   224 EFTRKNVWQMILQNLTSREKKDEILQMEEAELHD--KLFQLLETSKSLIVFDDIWKDEDW 281

Query:   285 SLLQKLGFQLPDYKILVTSRSEFPQF-GSVHYL--KP--LTYEAARTLFLHSA-NLQDGN 338
              L++ +      +K+L+TS++E     G + YL  KP  L  E + TLF   A   +D +
Sbjct:   282 DLIKPIFPPNKGWKVLLTSQNESVAVRGDIKYLNFKPECLAIEDSWTLFQRIAFPKKDAS 341

Query:   339 SYIPDENIVS---KILRACKGCPLALKVVGGSLCGKHEVF-WQRMVKECSRGESVF--QS 392
                 DE +     ++L+ C G PLA+KV+GG L  K+ +  W+R+    + G  +    S
Sbjct:   342 ESKVDEEMEDMGKQMLKHCGGLPLAIKVLGGLLAAKYTMHDWERL--SVNIGSDIVGRTS 399

Query:   393 KND--ILDCLGSSLDVLNNEVKECYLDLCSFPEDQRIPITALIDMWM-------ELY--- 440
              N+  I   L  S + L + +K C+L L  FPED +I +  L   W        E Y   
Sbjct:   400 SNNSSIYHVLSMSFEELPSYLKHCFLYLAHFPEDHKINVEKLSYCWAAEGISTAEDYHNG 459

Query:   441 ELVDDVFAITNLHELSSQNLVDRVVTRK-TAGDYG-CYNDDFVMQHDLLRELTICRSKSE 498
             E + DV   + L EL  +N++  +  R  TA  +G C+       HD++RE+ + ++K E
Sbjct:   460 ETIQDV-GQSYLEELVRRNMI--IWERDATASRFGTCH------LHDMMREVCLFKAKEE 510

Query:   499 PINQRKRLVVEISGNNFPKWWMDQKQHPNNASLLSISTDETFSSNWPDMQGPEVK-VVVL 557
                Q     V ++ ++         Q P  +  L      T      D+  P+++ +VVL
Sbjct:   511 NFLQIAVKSVGVTSSS-----TGNSQSPCRSRRLVYQCPTTLHVE-RDINNPKLRSLVVL 564

Query:   558 --NIRTKKY-VLPDFLQKMDELKVLIVTNYGFS----PAELNNFRVLSALSKLKKIRLEH 610
               ++  + + +L     ++  L+VL +    F     P  + N   L  LS L+  ++ H
Sbjct:   565 WHDLWVENWKLLGTSFTRLKLLRVLDLFYVDFEGMKLPFGIGNLIHLRYLS-LQDAKVSH 623

Query:   611 VSLPNSLATVRM 622
               LP+SL  + +
Sbjct:   624 --LPSSLGNLML 633

GO:0005575 "cellular_component" evidence=ND

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9FKZ1	DRL42_ARATH	No assigned EC number	0.4131	0.9856	0.8467	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

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	695
pfam00931	285	pfam00931, NB-ARC, NB-ARC domain	2e-32
pfam05659	147	pfam05659, RPW8, Arabidopsis broad-spectrum mildew	1e-23
pfam13401	124	pfam13401, AAA_22, AAA domain	6e-07
pfam13191	154	pfam13191, AAA_16, AAA ATPase domain	0.002

>gnl|CDD|216202 pfam00931, NB-ARC, NB-ARC domain

 Score =  126 bits (318), Expect = 2e-32
 Identities = 80/265 (30%), Positives = 128/265 (48%), Gaps = 16/265 (6%)

Query: 184 KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHK 243
            D    + +   GG GKTTL +++  DD V G F D + +V VSK      + + +L   
Sbjct: 16  SDNLGVVGIVGMGGVGKTTLAKQIYNDDSVGGHF-DSVAWVVVSKTYTEFRLQKDILQEL 74

Query: 244 GYPVPEFQTDEAAINDL-ERFFKQMRIEAILLVLDDVWPGSESLLQKLGFQLPDY----K 298
           G  + +    E   ++L  +  + +  +  LLVLDDVW   ++   K+G   PD     +
Sbjct: 75  G--LDDSDWVEKNESELAVKIKEALLRKRFLLVLDDVW--EKNDWDKIGVPFPDGENGSR 130

Query: 299 ILVTSRSE----FPQFGS-VHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRA 353
           ++VT+RSE         S  H ++ L  E +  LF +    ++       E +  +I+  
Sbjct: 131 VIVTTRSESVAGRMGGTSKPHEVESLEPEESWELFSNKVFEKELPPCPELEEVAKEIVEK 190

Query: 354 CKGCPLALKVVGGSLCGKHEV-FWQRMVKECSRGESVFQSKNDILDCLGSSLDVLNNEVK 412
           CKG PLALKV+GG L  K  V  W+ ++++ +   +     N++L  L  S D L   +K
Sbjct: 191 CKGLPLALKVLGGLLAFKSTVQEWEHVLEQLNNELAGRDGLNEVLSILSLSYDNLPMHLK 250

Query: 413 ECYLDLCSFPEDQRIPITALIDMWM 437
            C+L L  FPED  I    LI +W+
Sbjct: 251 RCFLYLALFPEDYNIRKEQLIKLWI 275

Length = 285

>gnl|CDD|203301 pfam05659, RPW8, Arabidopsis broad-spectrum mildew resistance protein RPW8

 Score = 97.1 bits (242), Expect = 1e-23
 Identities = 44/138 (31%), Positives = 80/138 (57%), Gaps = 2/138 (1%)

Query: 1   MAAAFVGGALLGAVFGELLKAVSEEKDKAVTFKDRLEQLESTLRNSIPWIEEIEKLNQVL 60
             A    GA LG     L KAV + KDK++T +  L++L++T+ +  P  ++I+KL++  
Sbjct: 1   PIAELAAGAALGLALQVLHKAVIKAKDKSLTTRCILQRLDATIESITPLFDQIDKLSKES 60

Query: 61  DRP-KQETENLVRMMEQVEQLVRKCSKVKW-NCFKRYVYAKKIIKLDTSISDFFRTSLPL 118
           D P ++  E+L R++E+   LV K ++++  N  K+Y Y +KI +L+ S+  F    + +
Sbjct: 61  DDPFRKVIEDLKRLLEKAVSLVEKYAELRRRNLLKKYRYKRKIKELEASLRWFCDVDVQV 120

Query: 119 QHARDGKLIMVEVKEIHT 136
              RD K +M ++ E+ T
Sbjct: 121 NQWRDIKELMAKMSEMST 138

This family consists of several broad-spectrum mildew resistance proteins from Arabidopsis thaliana. Plant disease resistance (R) genes control the recognition of specific pathogens and activate subsequent defence responses. The Arabidopsis thaliana locus Resistance To Powdery Mildew 8 (RPW8) contains two naturally polymorphic, dominant R genes, RPW8.1 and RPW8.2, which individually control resistance to a broad range of powdery mildew pathogens. They induce localised, salicylic acid-dependent defences similar to those induced by R genes that control specific resistance. Apparently, broad-spectrum resistance mediated by RPW8 uses the same mechanisms as specific resistance. Length = 147

>gnl|CDD|222104 pfam13401, AAA_22, AAA domain

 Score = 48.4 bits (116), Expect = 6e-07
 Identities = 22/95 (23%), Positives = 38/95 (40%), Gaps = 8/95 (8%)

Query: 185 DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKG 244
            G    V++   G GKTTL++RL +           + YV        K +++K+L   G
Sbjct: 2   RGAGIGVLTGESGSGKTTLLRRLARQLP-----NRRVVYVEAPSLGTPKDLLRKILRALG 56

Query: 245 YPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDV 279
            P     T    +  +    K+      LL++D+ 
Sbjct: 57  LP-LSGGTTAELLEAILDALKRRGRP--LLIIDEA 88

Length = 124

>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain

 Score = 39.1 bits (91), Expect = 0.002
 Identities = 28/131 (21%), Positives = 55/131 (41%), Gaps = 15/131 (11%)

Query: 186 GRQFIVVSAPGGYGKTTLVQRLCKD-DQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKG 244
           G   ++++ P G GKT+L++ L +      GK          + +  ++ +++++L    
Sbjct: 23  GPPSVLLTGPSGTGKTSLLRELLEGLLVAAGKCDQAERNPPYAFSQALRELLRQLLRELA 82

Query: 245 YPVPEFQTDEAAI---------NDLERFFKQM--RIEAILLVLDDV-W--PGSESLLQKL 290
             +   +    A           DL    +++  R   ++LVLDD+ W    S  LL  L
Sbjct: 83  AELLLLREALLAALGAELIEGLQDLVELLERLLARARPLVLVLDDLQWADEESLDLLAAL 142

Query: 291 GFQLPDYKILV 301
             +L    +LV
Sbjct: 143 LRRLERLPLLV 153

This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Length = 154

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	695
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	100.0
PLN03210	1153	Resistant to P. syringae 6; Provisional	100.0
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	100.0
PRK04841	903	transcriptional regulator MalT; Provisional	99.62
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	99.53
KOG0617	264	consensus Ras suppressor protein (contains leucine	99.38
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	99.31
PRK00411	394	cdc6 cell division control protein 6; Reviewed	99.31
PLN00113	968	leucine-rich repeat receptor-like protein kinase;	99.29
PLN00113	968	leucine-rich repeat receptor-like protein kinase;	99.23
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	99.23
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	99.21
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	99.18
KOG0617	264	consensus Ras suppressor protein (contains leucine	99.17
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	99.13
PF05659	147	RPW8: Arabidopsis broad-spectrum mildew resistance	99.08
COG3903	414	Predicted ATPase [General function prediction only	99.07
PTZ00112	1164	origin recognition complex 1 protein; Provisional	99.01
KOG0444	1255	consensus Cytoskeletal regulator Flightless-I (con	99.01
KOG0444	1255	consensus Cytoskeletal regulator Flightless-I (con	99.01
PLN03210	1153	Resistant to P. syringae 6; Provisional	98.99
PF05729	166	NACHT: NACHT domain	98.96
PTZ00202	550	tuzin; Provisional	98.9
COG3899	849	Predicted ATPase [General function prediction only	98.89
KOG0472	565	consensus Leucine-rich repeat protein [Function un	98.81
KOG4194	873	consensus Membrane glycoprotein LIG-1 [Signal tran	98.76
PRK13342	413	recombination factor protein RarA; Reviewed	98.76
PF14580	175	LRR_9: Leucine-rich repeat; PDB: 2JE1_D 2JE0_A 2JQ	98.73
PRK12402	337	replication factor C small subunit 2; Reviewed	98.73
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	98.71
KOG0472	565	consensus Leucine-rich repeat protein [Function un	98.71
KOG4194	873	consensus Membrane glycoprotein LIG-1 [Signal tran	98.69
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	98.69
COG2256	436	MGS1 ATPase related to the helicase subunit of the	98.68
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	98.62
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	98.62
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	98.61
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.6
PRK06893	229	DNA replication initiation factor; Validated	98.59
PLN03025	319	replication factor C subunit; Provisional	98.58
PRK00440	319	rfc replication factor C small subunit; Reviewed	98.57
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	98.57
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	98.57
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	98.54
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	98.52
PLN03150	623	hypothetical protein; Provisional	98.52
PF13855	61	LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RF	98.51
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	98.5
PF14580	175	LRR_9: Leucine-rich repeat; PDB: 2JE1_D 2JE0_A 2JQ	98.5
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	98.49
PRK07471	365	DNA polymerase III subunit delta'; Validated	98.49
PRK09112	351	DNA polymerase III subunit delta'; Validated	98.48
PF13173	128	AAA_14: AAA domain	98.48
PRK15387	788	E3 ubiquitin-protein ligase SspH2; Provisional	98.48
PLN03150	623	hypothetical protein; Provisional	98.47
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	98.47
KOG0532	722	consensus Leucine-rich repeat (LRR) protein, conta	98.47
KOG1259	490	consensus Nischarin, modulator of integrin alpha5	98.47
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	98.46
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	98.45
PRK04195	482	replication factor C large subunit; Provisional	98.45
PRK05564	313	DNA polymerase III subunit delta'; Validated	98.42
PRK08727	233	hypothetical protein; Validated	98.42
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	98.41
PRK15370	754	E3 ubiquitin-protein ligase SlrP; Provisional	98.41
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	98.41
PRK07940	394	DNA polymerase III subunit delta'; Validated	98.41
PF14516	331	AAA_35: AAA-like domain	98.4
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	98.39
PRK13341	725	recombination factor protein RarA/unknown domain f	98.39
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	98.37
KOG2028	554	consensus ATPase related to the helicase subunit o	98.37
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	98.36
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	98.35
KOG0618	1081	consensus Serine/threonine phosphatase 2C containi	98.35
PF13855	61	LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RF	98.32
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	98.32
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	98.32
cd01128	249	rho_factor Transcription termination factor rho is	98.3
PRK08084	235	DNA replication initiation factor; Provisional	98.29
PRK15370	754	E3 ubiquitin-protein ligase SlrP; Provisional	98.29
cd00116	319	LRR_RI Leucine-rich repeats (LRRs), ribonuclease i	98.29
PRK15387	788	E3 ubiquitin-protein ligase SspH2; Provisional	98.28
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	98.28
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	98.28
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	98.27
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	98.25
KOG0618	1081	consensus Serine/threonine phosphatase 2C containi	98.24
PRK08903	227	DnaA regulatory inactivator Hda; Validated	98.24
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	98.23
PRK05642	234	DNA replication initiation factor; Validated	98.19
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	98.18
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	98.17
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	98.16
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	98.15
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	98.15
PRK09376	416	rho transcription termination factor Rho; Provisio	98.15
PRK14087	450	dnaA chromosomal replication initiation protein; P	98.15
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	98.15
PRK09087	226	hypothetical protein; Validated	98.14
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	98.13
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	98.12
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	98.11
cd00116	319	LRR_RI Leucine-rich repeats (LRRs), ribonuclease i	98.11
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	98.11
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	98.1
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	98.09
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	98.05
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	98.04
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	98.04
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	98.03
PHA02544	316	44 clamp loader, small subunit; Provisional	98.03
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	98.0
KOG1259	490	consensus Nischarin, modulator of integrin alpha5	98.0
PF12799	44	LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_	97.99
KOG3207	505	consensus Beta-tubulin folding cofactor E [Posttra	97.99
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	97.98
KOG0532	722	consensus Leucine-rich repeat (LRR) protein, conta	97.98
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	97.96
PRK07399	314	DNA polymerase III subunit delta'; Validated	97.96
PRK14088	440	dnaA chromosomal replication initiation protein; P	97.94
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	97.93
PRK03992	389	proteasome-activating nucleotidase; Provisional	97.93
TIGR00767	415	rho transcription termination factor Rho. Members	97.93
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	97.92
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	97.9
PRK06620	214	hypothetical protein; Validated	97.88
PRK00149	450	dnaA chromosomal replication initiation protein; R	97.88
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	97.86
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	97.86
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	97.84
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	97.84
KOG4237	498	consensus Extracellular matrix protein slit, conta	97.83
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	97.82
PRK08769	319	DNA polymerase III subunit delta'; Validated	97.8
KOG3665	699	consensus ZYG-1-like serine/threonine protein kina	97.79
PRK05707	328	DNA polymerase III subunit delta'; Validated	97.79
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	97.78
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	97.77
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	97.74
KOG3207	505	consensus Beta-tubulin folding cofactor E [Posttra	97.72
PF10443	431	RNA12: RNA12 protein; InterPro: IPR018850 Mitochon	97.72
CHL00095	821	clpC Clp protease ATP binding subunit	97.71
PRK10865	857	protein disaggregation chaperone; Provisional	97.7
CHL00181	287	cbbX CbbX; Provisional	97.67
PRK12422	445	chromosomal replication initiation protein; Provis	97.67
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	97.67
KOG3665	699	consensus ZYG-1-like serine/threonine protein kina	97.64
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	97.63
PF12799	44	LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_	97.63
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	97.62
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	97.62
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	97.6
COG4886	394	Leucine-rich repeat (LRR) protein [Function unknow	97.59
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	97.59
PRK08116	268	hypothetical protein; Validated	97.59
PRK14086	617	dnaA chromosomal replication initiation protein; P	97.58
smart00382	148	AAA ATPases associated with a variety of cellular	97.58
PF00004	132	AAA: ATPase family associated with various cellula	97.57
PRK08058	329	DNA polymerase III subunit delta'; Validated	97.57
PRK10536	262	hypothetical protein; Provisional	97.56
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	97.53
PRK12608	380	transcription termination factor Rho; Provisional	97.52
PRK06871	325	DNA polymerase III subunit delta'; Validated	97.51
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	97.51
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	97.5
PRK15386	426	type III secretion protein GogB; Provisional	97.49
PRK06090	319	DNA polymerase III subunit delta'; Validated	97.49
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	97.48
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	97.48
PRK07993	334	DNA polymerase III subunit delta'; Validated	97.47
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	97.47
COG4886	394	Leucine-rich repeat (LRR) protein [Function unknow	97.44
KOG1514	767	consensus Origin recognition complex, subunit 1, a	97.44
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	97.44
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	97.43
KOG1859	1096	consensus Leucine-rich repeat proteins [General fu	97.43
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	97.42
KOG1859	1096	consensus Leucine-rich repeat proteins [General fu	97.4
CHL00176	638	ftsH cell division protein; Validated	97.4
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	97.4
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	97.36
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	97.36
KOG4237	498	consensus Extracellular matrix protein slit, conta	97.36
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	97.34
PTZ00494	664	tuzin-like protein; Provisional	97.33
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	97.31
KOG2739	260	consensus Leucine-rich acidic nuclear protein [Cel	97.31
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	97.26
KOG2035	351	consensus Replication factor C, subunit RFC3 [Cell	97.25
PRK08118	167	topology modulation protein; Reviewed	97.22
PRK10865	857	protein disaggregation chaperone; Provisional	97.19
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	97.17
KOG0531	414	consensus Protein phosphatase 1, regulatory subuni	97.17
COG0593	408	DnaA ATPase involved in DNA replication initiation	97.16
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	97.15
CHL00095	821	clpC Clp protease ATP binding subunit	97.15
PRK15386	426	type III secretion protein GogB; Provisional	97.11
PRK13531	498	regulatory ATPase RavA; Provisional	97.08
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	97.06
KOG4579	177	consensus Leucine-rich repeat (LRR) protein associ	97.05
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	97.05
KOG1909	382	consensus Ran GTPase-activating protein [RNA proce	97.03
PRK04132	846	replication factor C small subunit; Provisional	97.0
PRK06964	342	DNA polymerase III subunit delta'; Validated	97.0
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	97.0
PRK06921	266	hypothetical protein; Provisional	97.0
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	97.0
CHL00195	489	ycf46 Ycf46; Provisional	96.99
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	96.99
PRK12377	248	putative replication protein; Provisional	96.98
PRK08181	269	transposase; Validated	96.98
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	96.97
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	96.96
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	96.96
PRK04296	190	thymidine kinase; Provisional	96.93
KOG2120	419	consensus SCF ubiquitin ligase, Skp2 component [Po	96.92
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	96.92
KOG4579	177	consensus Leucine-rich repeat (LRR) protein associ	96.92
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	96.91
PHA00729	226	NTP-binding motif containing protein	96.89
KOG1909	382	consensus Ran GTPase-activating protein [RNA proce	96.88
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	96.86
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	96.83
PRK06526	254	transposase; Provisional	96.83
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	96.82
PRK09183	259	transposase/IS protein; Provisional	96.82
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	96.8
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	96.76
PHA02244	383	ATPase-like protein	96.75
TIGR02237	209	recomb_radB DNA repair and recombination protein R	96.72
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	96.7
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	96.69
PRK08699	325	DNA polymerase III subunit delta'; Validated	96.68
TIGR02236	310	recomb_radA DNA repair and recombination protein R	96.65
PRK08939	306	primosomal protein DnaI; Reviewed	96.65
PRK07261	171	topology modulation protein; Provisional	96.65
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	96.64
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	96.63
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	96.61
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	96.6
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	96.59
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	96.58
KOG2123	388	consensus Uncharacterized conserved protein [Funct	96.56
PRK06696	223	uridine kinase; Validated	96.56
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	96.56
KOG1969	877	consensus DNA replication checkpoint protein CHL12	96.48
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	96.48
KOG2739	260	consensus Leucine-rich acidic nuclear protein [Cel	96.47
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	96.47
PRK00771	437	signal recognition particle protein Srp54; Provisi	96.46
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	96.46
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	96.44
PRK05541	176	adenylylsulfate kinase; Provisional	96.43
KOG0531	414	consensus Protein phosphatase 1, regulatory subuni	96.42
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	96.41
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	96.4
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	96.39
COG1484	254	DnaC DNA replication protein [DNA replication, rec	96.38
cd01394	218	radB RadB. The archaeal protein radB shares simila	96.37
cd03115	173	SRP The signal recognition particle (SRP) mediates	96.33
PRK07952	244	DNA replication protein DnaC; Validated	96.32
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	96.29
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	96.28
PRK15455	644	PrkA family serine protein kinase; Provisional	96.28
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	96.26
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	96.23
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	96.22
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	96.17
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	96.16
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	96.15
PRK10867	433	signal recognition particle protein; Provisional	96.15
cd00983	325	recA RecA is a bacterial enzyme which has roles in	96.14
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	96.13
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	96.13
PRK06835	329	DNA replication protein DnaC; Validated	96.12
PRK09270	229	nucleoside triphosphate hydrolase domain-containin	96.12
PRK14974	336	cell division protein FtsY; Provisional	96.11
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	96.11
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	96.11
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	96.11
KOG1644	233	consensus U2-associated snRNP A' protein [RNA proc	96.08
PRK06547	172	hypothetical protein; Provisional	96.07
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	96.07
PTZ00035	337	Rad51 protein; Provisional	96.03
PRK05022	509	anaerobic nitric oxide reductase transcription reg	96.01
PRK07667	193	uridine kinase; Provisional	96.01
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	96.01
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	96.01
PRK09354	349	recA recombinase A; Provisional	95.98
TIGR00959	428	ffh signal recognition particle protein. This mode	95.98
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	95.96
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	95.95
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	95.94
PRK04301	317	radA DNA repair and recombination protein RadA; Va	95.91
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	95.9
PRK00409	782	recombination and DNA strand exchange inhibitor pr	95.9
KOG1644	233	consensus U2-associated snRNP A' protein [RNA proc	95.89
PRK07132	299	DNA polymerase III subunit delta'; Validated	95.86
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	95.85
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	95.82
TIGR00064	272	ftsY signal recognition particle-docking protein F	95.77
KOG2120	419	consensus SCF ubiquitin ligase, Skp2 component [Po	95.76
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	95.75
KOG0736	953	consensus Peroxisome assembly factor 2 containing	95.74
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	95.73
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	95.73
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	95.69
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	95.66
PF12061	402	DUF3542: Protein of unknown function (DUF3542); In	95.66
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	95.65
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	95.65
PF10236	309	DAP3: Mitochondrial ribosomal death-associated pro	95.62
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	95.62
PRK11608	326	pspF phage shock protein operon transcriptional ac	95.6
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	95.59
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	95.58
COG0541	451	Ffh Signal recognition particle GTPase [Intracellu	95.57
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	95.57
PRK05480	209	uridine/cytidine kinase; Provisional	95.56
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	95.55
PTZ00301	210	uridine kinase; Provisional	95.55
PRK08233	182	hypothetical protein; Provisional	95.53
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	95.52
cd01135	276	V_A-ATPase_B V/A-type ATP synthase (non-catalytic)	95.5
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	95.5
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	95.5
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	95.5
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	95.49
TIGR00235	207	udk uridine kinase. Model contains a number of lon	95.49
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	95.49
KOG2982	418	consensus Uncharacterized conserved protein [Funct	95.48
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	95.48
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	95.46
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	95.46
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	95.43
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	95.42
PRK08533	230	flagellar accessory protein FlaH; Reviewed	95.4
PRK06762	166	hypothetical protein; Provisional	95.4
COG1121	254	ZnuC ABC-type Mn/Zn transport systems, ATPase comp	95.32
cd03283	199	ABC_MutS-like MutS-like homolog in eukaryotes. The	95.3
PRK14527	191	adenylate kinase; Provisional	95.3
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	95.29
COG3640	255	CooC CO dehydrogenase maturation factor [Cell divi	95.25
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	95.24
PRK12597	461	F0F1 ATP synthase subunit beta; Provisional	95.23
COG1428	216	Deoxynucleoside kinases [Nucleotide transport and	95.2
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	95.18
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	95.17
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	95.17
TIGR00554	290	panK_bact pantothenate kinase, bacterial type. Sho	95.16
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	95.16
PRK09280	463	F0F1 ATP synthase subunit beta; Validated	95.14
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	95.14
cd03282	204	ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS	95.13
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	95.12
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	95.11
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	95.11
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	95.11
PTZ00088	229	adenylate kinase 1; Provisional	95.08
PF00006	215	ATP-synt_ab: ATP synthase alpha/beta family, nucle	95.08
KOG2123	388	consensus Uncharacterized conserved protein [Funct	95.07
PRK10463	290	hydrogenase nickel incorporation protein HypB; Pro	95.07
cd03230	173	ABC_DR_subfamily_A This family of ATP-binding prot	95.05
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	95.03
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	95.01
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	95.01
COG0572	218	Udk Uridine kinase [Nucleotide transport and metab	95.01
PRK12678	672	transcription termination factor Rho; Provisional	94.99
PRK03839	180	putative kinase; Provisional	94.99
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	94.98
cd03246	173	ABCC_Protease_Secretion This family represents the	94.98
KOG2982	418	consensus Uncharacterized conserved protein [Funct	94.97
PF00560	22	LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Le	94.97
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	94.96
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	94.96
TIGR03575	340	selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryoti	94.95
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	94.95
PRK04040	188	adenylate kinase; Provisional	94.95
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	94.94
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	94.93
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	94.89
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	94.88
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	94.88
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	94.87
cd03216	163	ABC_Carb_Monos_I This family represents the domain	94.85
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	94.83
PRK07276	290	DNA polymerase III subunit delta'; Validated	94.83
TIGR01039	461	atpD ATP synthase, F1 beta subunit. The sequences	94.83
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	94.82
PRK06002	450	fliI flagellum-specific ATP synthase; Validated	94.81
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	94.81
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	94.8
PRK08972	444	fliI flagellum-specific ATP synthase; Validated	94.77
PRK06067	234	flagellar accessory protein FlaH; Validated	94.77
PRK06217	183	hypothetical protein; Validated	94.76
PF00154	322	RecA: recA bacterial DNA recombination protein; In	94.76
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	94.73
PRK00625	173	shikimate kinase; Provisional	94.72
PF13245	76	AAA_19: Part of AAA domain	94.71
PRK00131	175	aroK shikimate kinase; Reviewed	94.7
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	94.69
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	94.68
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	94.64
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	94.63
COG4618	580	ArpD ABC-type protease/lipase transport system, AT	94.6
COG0055	468	AtpD F0F1-type ATP synthase, beta subunit [Energy	94.6
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	94.6
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	94.58
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	94.56
PF03193	161	DUF258: Protein of unknown function, DUF258; Inter	94.55
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	94.54
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	94.51
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	94.5
PHA02774	613	E1; Provisional	94.49
cd01132	274	F1_ATPase_alpha F1 ATP synthase alpha, central dom	94.49
PRK05439	311	pantothenate kinase; Provisional	94.49
PRK04328	249	hypothetical protein; Provisional	94.47
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	94.47
PF07726	131	AAA_3: ATPase family associated with various cellu	94.47
PRK05917	290	DNA polymerase III subunit delta'; Validated	94.46
PRK00889	175	adenylylsulfate kinase; Provisional	94.45
TIGR01351	210	adk adenylate kinases. Adenylate kinase (EC 2.7.4.	94.45
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	94.45
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	94.44
COG0714	329	MoxR-like ATPases [General function prediction onl	94.43
PRK14528	186	adenylate kinase; Provisional	94.41
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	94.4
TIGR00041	195	DTMP_kinase thymidylate kinase. Function: phosphor	94.4
TIGR03305	449	alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit	94.38
COG0378	202	HypB Ni2+-binding GTPase involved in regulation of	94.38
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	94.38
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	94.37
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	94.34
TIGR00073	207	hypB hydrogenase accessory protein HypB. HypB is i	94.34
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	94.34
cd03285	222	ABC_MSH2_euk MutS2 homolog in eukaryotes. The MutS	94.33
PRK08927	442	fliI flagellum-specific ATP synthase; Validated	94.33
COG0003	322	ArsA Predicted ATPase involved in chromosome parti	94.33
PRK10416	318	signal recognition particle-docking protein FtsY;	94.3
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	94.29
PRK13947	171	shikimate kinase; Provisional	94.27
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	94.26
PRK10751	173	molybdopterin-guanine dinucleotide biosynthesis pr	94.25
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	94.21
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	94.21
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	94.2
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	94.2
) proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF06309">PF06309	127	Torsin: Torsin; InterPro: IPR010448 This family co	94.19
cd01136	326	ATPase_flagellum-secretory_path_III Flagellum-spec	94.18
PF12780	268	AAA_8: P-loop containing dynein motor region D4; I	94.17
COG0194	191	Gmk Guanylate kinase [Nucleotide transport and met	94.17
cd00820	107	PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPC	94.16
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	94.16
PF00560	22	LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Le	94.16
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	94.16
PRK00279	215	adk adenylate kinase; Reviewed	94.13
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	94.13
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	94.12
COG1703	323	ArgK Putative periplasmic protein kinase ArgK and	94.1
PRK13765	637	ATP-dependent protease Lon; Provisional	94.1
PRK00300	205	gmk guanylate kinase; Provisional	94.07
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	94.07
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	94.07
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	94.06
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	94.05
PRK14737	186	gmk guanylate kinase; Provisional	94.04
PF00625	183	Guanylate_kin: Guanylate kinase; InterPro: IPR0081	94.03
PF08477	119	Miro: Miro-like protein; InterPro: IPR013684 Mitoc	94.03
PRK14529	223	adenylate kinase; Provisional	94.02
PRK08149	428	ATP synthase SpaL; Validated	94.02
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	94.01
COG2019	189	AdkA Archaeal adenylate kinase [Nucleotide transpo	94.0
PRK09099	441	type III secretion system ATPase; Provisional	94.0
COG0529	197	CysC Adenylylsulfate kinase and related kinases [I	93.99
PF03308	266	ArgK: ArgK protein; InterPro: IPR005129 Bacterial	93.99
COG2274	709	SunT ABC-type bacteriocin/lantibiotic exporters, c	93.99
PRK03846	198	adenylylsulfate kinase; Provisional	93.98
cd03287	222	ABC_MSH3_euk MutS3 homolog in eukaryotes. The MutS	93.94
KOG1532	366	consensus GTPase XAB1, interacts with DNA repair p	93.94
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	93.93
CHL00060	494	atpB ATP synthase CF1 beta subunit	93.93
PRK10875	615	recD exonuclease V subunit alpha; Provisional	93.93
PRK09519	790	recA DNA recombination protein RecA; Reviewed	93.91
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	93.89
PRK13949	169	shikimate kinase; Provisional	93.88
PRK13948	182	shikimate kinase; Provisional	93.85
PF02374	305	ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_	93.81
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	93.79
PRK12339	197	2-phosphoglycerate kinase; Provisional	93.76
PRK05922	434	type III secretion system ATPase; Validated	93.74
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	93.72
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	93.71
PRK14530	215	adenylate kinase; Provisional	93.7
PRK14738	206	gmk guanylate kinase; Provisional	93.68
PRK09302	509	circadian clock protein KaiC; Reviewed	93.67
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	93.63
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	93.61
PRK06793	432	fliI flagellum-specific ATP synthase; Validated	93.59
TIGR03497	413	FliI_clade2 flagellar protein export ATPase FliI.	93.58

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=100.00  E-value=4.6e-74  Score=649.70  Aligned_cols=650  Identities=19%  Similarity=0.205  Sum_probs=481.9

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhhhchHHHHHHHHHHHhhhHHHHHHHHhhhccCCChHHHHHHHHHHHHHHHHHHhccccc
Q 042541            9 ALLGAVFGELLKAVSEEKDKAVTFKDRLEQLESTLRNSIPWIEEIEKLNQVLDRPKQETENLVRMMEQVEQLVRKCSKVK   88 (695)
Q Consensus         9 a~~~~v~~kl~~~l~~~~~~~~~~~~~l~~L~~~L~~i~~~l~~ae~~~~~~~~~~~wl~~l~~~~~d~ed~ld~~~~~~   88 (695)
                      +.++..++++.+.+.+++....+.++.+..|++.|..++++++|++.++........|.+.+++++|+++|.++.|... 
T Consensus         3 ~~~s~~~~~~~~~l~~~~~~~~~~~~~i~~Lk~~L~~l~~~l~d~~a~~~~~~~~~~~~e~~~~~~~~~e~~~~~~~v~-   81 (889)
T KOG4658|consen    3 ACVSFGVEKLDQLLNRESECLDGKDNYILELKENLKALQSALEDLDAKRDDLERRVNWEEDVGDLVYLAEDIIWLFLVE-   81 (889)
T ss_pred             eEEEEehhhHHHHHHHHHHHHhchHHHHHHHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHH-
Confidence            4566678889999999999999999999999999999999999999998888888999999999999999999999862 


Q ss_pred             hhhhcchhhHHHHHHHHHhhhhHhhccchhhhhhhhhhHHHHHHHHHHHH-hccCCCCCcCCcc-CCccCCCCCCCCCC-
Q 042541           89 WNCFKRYVYAKKIIKLDTSISDFFRTSLPLQHARDGKLIMVEVKEIHTMV-RRMSGNGNINGWM-SNQVGDCCSAPDPP-  165 (695)
Q Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~l~~~~~~~-~~~~~~~~~~~~~-~~~~~~~~~~~~~~-  165 (695)
                        ...+. ....+.+......+.+-.........++..+..++.++.+.+ .++.+..-..... ..+.......|..+ 
T Consensus        82 --~~~~~-~~~~l~~~~~~~~~~c~~~~~~~~~~~~~~~~~rv~~~l~~ve~l~~~~~~~~~~~~~~~~~~~e~~~~~~~  158 (889)
T KOG4658|consen   82 --EIERK-ANDLLSTRSVERQRLCLCGFCSKNVSDSYKYGKRVSKVLREVESLGSKGVFEVVGESLDPREKVETRPIQSE  158 (889)
T ss_pred             --HHHHH-HhHHhhhhHHHHHHHhhhhhHhHhhhhhHhHHHHHHHHHHHHHHhccccceecccccccchhhcccCCCCcc
Confidence              21110 111111110011111111233455555666666666666665 4443321111111 11111112222222 


Q ss_pred             CCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhcccc-ccccCCCcEEEEEeCCCCCHHHHHHHHHHhcC
Q 042541          166 VISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQ-VQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKG  244 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~-~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~  244 (695)
                      .. ||.+..++++.+.|..++..+++|+||||+||||||+.++|+.. ++.+|+. ++||.||+.++...++.+|+..++
T Consensus       159 ~~-VG~e~~~~kl~~~L~~d~~~iv~i~GMGGvGKTTL~~qi~N~~~~v~~~Fd~-~iWV~VSk~f~~~~iq~~Il~~l~  236 (889)
T KOG4658|consen  159 SD-VGLETMLEKLWNRLMEDDVGIVGIYGMGGVGKTTLARQIFNKFDEVGNHFDG-VIWVVVSKEFTTRKIQQTILERLG  236 (889)
T ss_pred             cc-ccHHHHHHHHHHHhccCCCCEEEEECCCcccHHHHHHHHhcccchhcccCce-EEEEEEcccccHHhHHHHHHHHhc
Confidence            23 99999999999999988889999999999999999999999977 9999998 889999999999999999999998


Q ss_pred             CCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCChHH--HhhhccCCCCCEEEEEcCCCCCC---C--CCeEec
Q 042541          245 YPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGSESL--LQKLGFQLPDYKILVTSRSEFPQ---F--GSVHYL  316 (695)
Q Consensus       245 ~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~~~~--~~~l~~~~~gs~iivTtR~~~~~---~--~~~~~l  316 (695)
                      ...+......  .+.++..+ +.|+++||+|||||||+..+|.  -.+++....||||++|||+..++   +  ...+++
T Consensus       237 ~~~~~~~~~~--~~~~~~~i~~~L~~krfllvLDDIW~~~dw~~I~~~~p~~~~g~KvvlTTRs~~V~~~~m~~~~~~~v  314 (889)
T KOG4658|consen  237 LLDEEWEDKE--EDELASKLLNLLEGKRFLLVLDDIWEEVDWDKIGVPFPSRENGSKVVLTTRSEEVCGRAMGVDYPIEV  314 (889)
T ss_pred             cCCcccchhh--HHHHHHHHHHHhccCceEEEEecccccccHHhcCCCCCCccCCeEEEEEeccHhhhhccccCCccccc
Confidence            7544322221  14455555 7889999999999999998742  23334444589999999999542   2  348999


Q ss_pred             CCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHHHhhCCC-CHHHHHHHHHHhcCC-CCc-cCch
Q 042541          317 KPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGGSLCGK-HEVFWQRMVKECSRG-ESV-FQSK  393 (695)
Q Consensus       317 ~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~~~L~~~-~~~~w~~~l~~~~~~-~~~-~~~~  393 (695)
                      +.|+++|||+||.+.++.......+..+++|++|+++|+|+|||+.++|+.|+.+ +..+|++++..+... ... .+..
T Consensus       315 ~~L~~~eaW~LF~~~v~~~~~~~~~~i~~lak~v~~kC~GLPLAl~viG~~ma~K~t~~eW~~~~~~l~s~~~~~~~~~~  394 (889)
T KOG4658|consen  315 ECLTPEEAWDLFQKKVGPNTLGSHPDIEELAKEVAEKCGGLPLALNVLGGLLACKKTVQEWRRALNVLKSSLAADFSGME  394 (889)
T ss_pred             cccCccccHHHHHHhhccccccccccHHHHHHHHHHHhCChHHHHHHHHHHhcCCCcHHHHHHHHccccccccCCCCchh
Confidence            9999999999999999887554444479999999999999999999999999998 578999888766443 111 2235


Q ss_pred             hhHHHHHHHHHHhccHHHHHHHhhhcccCCCcccChHHHHHHHHHhhCCChh-------HHHHHHHHHHhhccccchhhc
Q 042541          394 NDILDCLGSSLDVLNNEVKECYLDLCSFPEDQRIPITALIDMWMELYELVDD-------VFAITNLHELSSQNLVDRVVT  466 (695)
Q Consensus       394 ~~i~~~l~~s~~~L~~~~k~cf~~ls~fp~~~~i~~~~Li~~W~~~~~~~~~-------~~~~~~l~~L~~~sLl~~~~~  466 (695)
                      +.+..++.+||+.||+++|.||+|||+||+||.|+++.|+.+|+|+|++.+.       ++|.+|+++|++++|++....
T Consensus       395 ~~i~~iLklSyd~L~~~lK~CFLycalFPED~~I~~e~Li~yWiaEGfi~~~~~~~~~~d~G~~~i~~LV~~~Ll~~~~~  474 (889)
T KOG4658|consen  395 ESILPILKLSYDNLPEELKSCFLYCALFPEDYEIKKEKLIEYWIAEGFIDPLDGGETAEDVGYDYIEELVRASLLIEERD  474 (889)
T ss_pred             hhhHHhhhccHhhhhHHHHHHHHhhccCCcccccchHHHHHHHHhccCcCccccccchhcchHHHHHHHHHHHHHhhccc
Confidence            6899999999999999999999999999999999999999999999988662       589999999999999997432


Q ss_pred             cccCCCCCCCCCcceehhHHHHHHHHHhccCCCcccccceeeeccCCCCchhhhhccCCCccceEEeeecCCcccCCCCC
Q 042541          467 RKTAGDYGCYNDDFVMQHDLLRELTICRSKSEPINQRKRLVVEISGNNFPKWWMDQKQHPNNASLLSISTDETFSSNWPD  546 (695)
Q Consensus       467 ~~~~~~~~~~~~~~~~mHdlv~~~a~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~l~~~~~~~~~~~~~~  546 (695)
                              .++..+|.|||+|||+|.+++++....... .++..+.+ ..+  ..+.......|++++.+++.. .....
T Consensus       475 --------~~~~~~~kmHDvvRe~al~ias~~~~~~e~-~iv~~~~~-~~~--~~~~~~~~~~rr~s~~~~~~~-~~~~~  541 (889)
T KOG4658|consen  475 --------EGRKETVKMHDVVREMALWIASDFGKQEEN-QIVSDGVG-LSE--IPQVKSWNSVRRMSLMNNKIE-HIAGS  541 (889)
T ss_pred             --------ccceeEEEeeHHHHHHHHHHhccccccccc-eEEECCcC-ccc--cccccchhheeEEEEeccchh-hccCC
Confidence                    135678999999999999999943332222 22322111 110  012234467899998876542 23345


Q ss_pred             CCCCceEEEEEEccCc-cccCC-hhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc-cccccc
Q 042541          547 MQGPEVKVVVLNIRTK-KYVLP-DFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL-ATVRMN  623 (695)
Q Consensus       547 ~~~~~l~~L~l~~~~~-~~~~p-~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp-~i~~l~  623 (695)
                      ..++++++|.+..+.. ...++ ++|..|+.||+|||++|.- ...+  +..+++|-+||||+|+++.++++| ++++|+
T Consensus       542 ~~~~~L~tLll~~n~~~l~~is~~ff~~m~~LrVLDLs~~~~-l~~L--P~~I~~Li~LryL~L~~t~I~~LP~~l~~Lk  618 (889)
T KOG4658|consen  542 SENPKLRTLLLQRNSDWLLEISGEFFRSLPLLRVLDLSGNSS-LSKL--PSSIGELVHLRYLDLSDTGISHLPSGLGNLK  618 (889)
T ss_pred             CCCCccceEEEeecchhhhhcCHHHHhhCcceEEEECCCCCc-cCcC--ChHHhhhhhhhcccccCCCccccchHHHHHH
Confidence            6788999999988852 34444 4689999999999998533 2333  344899999999999999999999 999999


Q ss_pred             cccEEeeccccCCcccccchhhhcccCCCccEEeccccc-cc-ccCchhhcCCCCCceeeccccc
Q 042541          624 HLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCN-DL-IELPDGLCDIVSMEKLRITNCH  686 (695)
Q Consensus       624 ~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~-~l-~~lP~~i~~L~~L~~L~l~~~~  686 (695)
                      +|.|||+..+.....++.+..    .|++|++|.+-.-. .. ...=..+.+|.+|+.|.++.++
T Consensus       619 ~L~~Lnl~~~~~l~~~~~i~~----~L~~Lr~L~l~~s~~~~~~~~l~el~~Le~L~~ls~~~~s  679 (889)
T KOG4658|consen  619 KLIYLNLEVTGRLESIPGILL----ELQSLRVLRLPRSALSNDKLLLKELENLEHLENLSITISS  679 (889)
T ss_pred             hhheeccccccccccccchhh----hcccccEEEeeccccccchhhHHhhhcccchhhheeecch
Confidence            999999999975555666665    69999999987532 11 1111234555566655555433

>PLN03210 Resistant to P

Probab=100.00  E-value=3.8e-50  Score=480.08  Aligned_cols=481  Identities=17%  Similarity=0.232  Sum_probs=332.1

Q ss_pred             CCCCCCCCcchHHHHHHHHH--cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEe---CCC---------
Q 042541          164 PPVISPGLDVPLKELKMELF--KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTV---SKN---------  229 (695)
Q Consensus       164 ~~~~~vGr~~~~~~l~~~L~--~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~---~~~---------  229 (695)
                      ..+.+|||+..++++..+|.  .+++++|+|+||||+||||||+++|+  ++..+|+. .+|+.-   +..         
T Consensus       182 ~~~~~vG~~~~l~~l~~lL~l~~~~~~vvgI~G~gGiGKTTLA~~l~~--~l~~~F~g-~vfv~~~~v~~~~~~~~~~~~  258 (1153)
T PLN03210        182 DFEDFVGIEDHIAKMSSLLHLESEEVRMVGIWGSSGIGKTTIARALFS--RLSRQFQS-SVFIDRAFISKSMEIYSSANP  258 (1153)
T ss_pred             ccccccchHHHHHHHHHHHccccCceEEEEEEcCCCCchHHHHHHHHH--HHhhcCCe-EEEeeccccccchhhcccccc
Confidence            34568999999999998886  45689999999999999999999999  78889987 446532   111         


Q ss_pred             --CC-HHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH--HHhhhccCCCCCEEEEEcC
Q 042541          230 --PN-VKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES--LLQKLGFQLPDYKILVTSR  304 (695)
Q Consensus       230 --~~-~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~--~~~~l~~~~~gs~iivTtR  304 (695)
                        .+ ...+..+++..+.........      .+..+.+.++++++||||||||+...+  +.....+..+||+||||||
T Consensus       259 ~~~~~~~~l~~~~l~~il~~~~~~~~------~~~~~~~~L~~krvLLVLDdv~~~~~l~~L~~~~~~~~~GsrIIiTTr  332 (1153)
T PLN03210        259 DDYNMKLHLQRAFLSEILDKKDIKIY------HLGAMEERLKHRKVLIFIDDLDDQDVLDALAGQTQWFGSGSRIIVITK  332 (1153)
T ss_pred             cccchhHHHHHHHHHHHhCCCCcccC------CHHHHHHHHhCCeEEEEEeCCCCHHHHHHHHhhCccCCCCcEEEEEeC
Confidence              01 123344444443221110000      011222556899999999999986543  2222334468999999999


Q ss_pred             CCCC----CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHHHhhCCCCHHHHHHHH
Q 042541          305 SEFP----QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGGSLCGKHEVFWQRMV  380 (695)
Q Consensus       305 ~~~~----~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~~~L~~~~~~~w~~~l  380 (695)
                      ++..    .....|+++.+++++||+||+++||+... .+....+++++|+++|+|+||||+++|+.|++++.++|+..+
T Consensus       333 d~~vl~~~~~~~~~~v~~l~~~ea~~LF~~~Af~~~~-~~~~~~~l~~~iv~~c~GLPLAl~vlgs~L~~k~~~~W~~~l  411 (1153)
T PLN03210        333 DKHFLRAHGIDHIYEVCLPSNELALEMFCRSAFKKNS-PPDGFMELASEVALRAGNLPLGLNVLGSYLRGRDKEDWMDML  411 (1153)
T ss_pred             cHHHHHhcCCCeEEEecCCCHHHHHHHHHHHhcCCCC-CcHHHHHHHHHHHHHhCCCcHHHHHHHHHHcCCCHHHHHHHH
Confidence            9832    23458999999999999999999997644 233467899999999999999999999999999999999999


Q ss_pred             HHhcCCCCccCchhhHHHHHHHHHHhccH-HHHHHHhhhcccCCCcccChHHHHHHHHHhhCCChhHHHHHHHHHHhhcc
Q 042541          381 KECSRGESVFQSKNDILDCLGSSLDVLNN-EVKECYLDLCSFPEDQRIPITALIDMWMELYELVDDVFAITNLHELSSQN  459 (695)
Q Consensus       381 ~~~~~~~~~~~~~~~i~~~l~~s~~~L~~-~~k~cf~~ls~fp~~~~i~~~~Li~~W~~~~~~~~~~~~~~~l~~L~~~s  459 (695)
                      .++...     .+..+..+|++||+.|++ ..|.||+++|+|+.+..++   .+..|.+.+..+.    +..++.|+++|
T Consensus       412 ~~L~~~-----~~~~I~~~L~~SYd~L~~~~~k~~Fl~ia~ff~~~~~~---~v~~~l~~~~~~~----~~~l~~L~~ks  479 (1153)
T PLN03210        412 PRLRNG-----LDGKIEKTLRVSYDGLNNKKDKAIFRHIACLFNGEKVN---DIKLLLANSDLDV----NIGLKNLVDKS  479 (1153)
T ss_pred             HHHHhC-----ccHHHHHHHHHhhhccCccchhhhhheehhhcCCCCHH---HHHHHHHhcCCCc----hhChHHHHhcC
Confidence            887652     245799999999999987 5999999999999887653   4667777665543    34589999999


Q ss_pred             ccchhhccccCCCCCCCCCcceehhHHHHHHHHHhccCCC--cccccceeeeccCCCCchhhhhccCCCccceEEeeecC
Q 042541          460 LVDRVVTRKTAGDYGCYNDDFVMQHDLLRELTICRSKSEP--INQRKRLVVEISGNNFPKWWMDQKQHPNNASLLSISTD  537 (695)
Q Consensus       460 Ll~~~~~~~~~~~~~~~~~~~~~mHdlv~~~a~~~~~~e~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~l~~~~~  537 (695)
                      ||+..             ...++|||++|++|+.++.++.  +.++.+++-.   .++..... .......++.+++..+
T Consensus       480 Li~~~-------------~~~~~MHdLl~~~~r~i~~~~~~~~~~r~~l~~~---~di~~vl~-~~~g~~~v~~i~l~~~  542 (1153)
T PLN03210        480 LIHVR-------------EDIVEMHSLLQEMGKEIVRAQSNEPGEREFLVDA---KDICDVLE-DNTGTKKVLGITLDID  542 (1153)
T ss_pred             CEEEc-------------CCeEEhhhHHHHHHHHHHHhhcCCCCcceeEeCH---HHHHHHHH-hCcccceeeEEEeccC
Confidence            99852             1358999999999999987664  2233333211   01111111 1223456677766544


Q ss_pred             CcccCCC---CCCCCCceEEEEEEccC------ccccCChhhcCCC-CCcEEEEcccCCCCcccCcccccccCCCCcEEE
Q 042541          538 ETFSSNW---PDMQGPEVKVVVLNIRT------KKYVLPDFLQKMD-ELKVLIVTNYGFSPAELNNFRVLSALSKLKKIR  607 (695)
Q Consensus       538 ~~~~~~~---~~~~~~~l~~L~l~~~~------~~~~~p~~~~~l~-~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~  607 (695)
                      +......   ....+++|+.|.+..+.      ....+|..+..++ +||+|.+.++...  .+   |.-..+.+|+.|+
T Consensus       543 ~~~~~~i~~~aF~~m~~L~~L~~~~~~~~~~~~~~~~lp~~~~~lp~~Lr~L~~~~~~l~--~l---P~~f~~~~L~~L~  617 (1153)
T PLN03210        543 EIDELHIHENAFKGMRNLLFLKFYTKKWDQKKEVRWHLPEGFDYLPPKLRLLRWDKYPLR--CM---PSNFRPENLVKLQ  617 (1153)
T ss_pred             ccceeeecHHHHhcCccccEEEEecccccccccceeecCcchhhcCcccEEEEecCCCCC--CC---CCcCCccCCcEEE
Confidence            3211111   11257778888775431      2345666666654 5888888776432  11   1122456777788


Q ss_pred             eccCCCCCcc-cccccccccEEeecccc-CCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccc
Q 042541          608 LEHVSLPNSL-ATVRMNHLQKVSLVMCN-VGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNC  685 (695)
Q Consensus       608 L~~~~l~~lp-~i~~l~~L~~L~l~~~~-i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~  685 (695)
                      |.++.+..+| ++..+++|++|+|++|. +..+ |...     .+++|++|+|++|..+..+|.++++|++|+.|++++|
T Consensus       618 L~~s~l~~L~~~~~~l~~Lk~L~Ls~~~~l~~i-p~ls-----~l~~Le~L~L~~c~~L~~lp~si~~L~~L~~L~L~~c  691 (1153)
T PLN03210        618 MQGSKLEKLWDGVHSLTGLRNIDLRGSKNLKEI-PDLS-----MATNLETLKLSDCSSLVELPSSIQYLNKLEDLDMSRC  691 (1153)
T ss_pred             CcCccccccccccccCCCCCEEECCCCCCcCcC-Cccc-----cCCcccEEEecCCCCccccchhhhccCCCCEEeCCCC
Confidence            8777777777 77777778888887764 4443 3333     6777777777777777777777777777777777777


Q ss_pred             cCCCCCCCC
Q 042541          686 HRLSALPEG  694 (695)
Q Consensus       686 ~~l~~lP~~  694 (695)
                      +.++.+|.+
T Consensus       692 ~~L~~Lp~~  700 (1153)
T PLN03210        692 ENLEILPTG  700 (1153)
T ss_pred             CCcCccCCc
Confidence            777777764

syringae 6; Provisional

>PF00931 NB-ARC: NB-ARC domain; InterPro: IPR002182 This is the NB-ARC domain, a novel signalling motif found in bacteria and eukaryotes, shared by plant resistance gene products and regulators of cell death in animals []

Probab=100.00  E-value=2.3e-41  Score=347.78  Aligned_cols=271  Identities=28%  Similarity=0.459  Sum_probs=209.1

Q ss_pred             CcchHHHHHHHHHc--CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCC
Q 042541          171 LDVPLKELKMELFK--DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVP  248 (695)
Q Consensus       171 r~~~~~~l~~~L~~--~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~  248 (695)
                      ||.++++|.+.|..  ++.++|+|+||||+||||||++++++..++.+|+. ++|++++...+...++..|+.+++....
T Consensus         1 re~~~~~l~~~L~~~~~~~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~-v~wv~~~~~~~~~~~~~~i~~~l~~~~~   79 (287)
T PF00931_consen    1 REKEIEKLKDWLLDNSNEVRVVAIVGMGGIGKTTLARQVARDLRIKNRFDG-VIWVSLSKNPSLEQLLEQILRQLGEPDS   79 (287)
T ss_dssp             -HHHHHHHHHHHHTTTTSSEEEEEEESTTSSHHHHHHHHHCHHHHCCCCTE-EEEEEEES-SCCHHHHHHHHHHHTCC-S
T ss_pred             CHHHHHHHHHHhhCCCCCeEEEEEEcCCcCCcceeeeeccccccccccccc-cccccccccccccccccccccccccccc
Confidence            78899999999997  77999999999999999999999997679999976 8999999999999999999999987744


Q ss_pred             CC---CChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH--HHhhhccCCCCCEEEEEcCCCCCCC-----CCeEecCC
Q 042541          249 EF---QTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES--LLQKLGFQLPDYKILVTSRSEFPQF-----GSVHYLKP  318 (695)
Q Consensus       249 ~~---~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~--~~~~l~~~~~gs~iivTtR~~~~~~-----~~~~~l~~  318 (695)
                      ..   .+.......+.   +.+.++++||||||||+...+  +...+.....|++||||||+.....     ...+++++
T Consensus        80 ~~~~~~~~~~~~~~l~---~~L~~~~~LlVlDdv~~~~~~~~l~~~~~~~~~~~kilvTTR~~~v~~~~~~~~~~~~l~~  156 (287)
T PF00931_consen   80 SISDPKDIEELQDQLR---ELLKDKRCLLVLDDVWDEEDLEELREPLPSFSSGSKILVTTRDRSVAGSLGGTDKVIELEP  156 (287)
T ss_dssp             TSSCCSSHHHHHHHHH---HHHCCTSEEEEEEEE-SHHHH-------HCHHSS-EEEEEESCGGGGTTHHSCEEEEECSS
T ss_pred             ccccccccccccccch---hhhccccceeeeeeecccccccccccccccccccccccccccccccccccccccccccccc
Confidence            32   22233333333   667889999999999987643  2233344456899999999984321     34799999


Q ss_pred             CChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHHHhhCCC-CHHHHHHHHHHhcCCCC-ccCchhhH
Q 042541          319 LTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGGSLCGK-HEVFWQRMVKECSRGES-VFQSKNDI  396 (695)
Q Consensus       319 L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~~~L~~~-~~~~w~~~l~~~~~~~~-~~~~~~~i  396 (695)
                      |+.++|++||.+.++..........++.+++|+++|+|+||||+++|++|+.+ +..+|+..++++..... ..+....+
T Consensus       157 L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~~i~~~c~glPLal~~~a~~l~~~~~~~~w~~~~~~l~~~~~~~~~~~~~~  236 (287)
T PF00931_consen  157 LSEEEALELFKKRAGRKESESPEDLEDLAKEIVEKCGGLPLALKLIASYLRSKSTVDEWEEALEELENSLRESRDYDRSV  236 (287)
T ss_dssp             --HHHHHHHHHHHHTSHS----TTSCTHHHHHHHHTTT-HHHHHHHHHHHHHHHSSSSHHHHHHHHHHCHTCSSGSCHHH
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            99999999999998876622334457789999999999999999999999654 67889888877654332 12245789


Q ss_pred             HHHHHHHHHhccHHHHHHHhhhcccCCCcccChHHHHHHHHHhhCCChh
Q 042541          397 LDCLGSSLDVLNNEVKECYLDLCSFPEDQRIPITALIDMWMELYELVDD  445 (695)
Q Consensus       397 ~~~l~~s~~~L~~~~k~cf~~ls~fp~~~~i~~~~Li~~W~~~~~~~~~  445 (695)
                      ..++..||+.||+++|+||+|||+||+++.|+.+.|+++|++++++.+.
T Consensus       237 ~~~l~~s~~~L~~~~~~~f~~L~~f~~~~~i~~~~li~lW~~e~~i~~~  285 (287)
T PF00931_consen  237 FSALELSYDSLPDELRRCFLYLSIFPEGVPIPRERLIRLWVAEGFISSK  285 (287)
T ss_dssp             HHHHHHHHHSSHTCCHHHHHHGGGSGTTS-EEHHHHHHHHTT-HHTC--
T ss_pred             cccceechhcCCccHHHHHhhCcCCCCCceECHHHHHHHHHHCCCCccc
Confidence            9999999999999999999999999999999999999999999888753

This domain has been structurally characterised in the human protein apoptotic protease-activating factor 1 (Apaf-1) []. It contains the three-layered alpha-beta fold and subsequent short alpha-helical region characteristic of the AAA+ ATPase domain superfamily. While this domain is thought to bind and hyrolyse ATP, only ADP binding has been experimentally verified. It is proposed that binding and hydrolysis of ATP by this domain induces conformational changes the the overall protein, leading to formation of the apoptosome.; GO: 0043531 ADP binding; PDB: 3IZA_E 1Z6T_D 3SFZ_A 3SHF_A 1VT4_M 3IZ8_G 3LQR_A 2A5Y_C 3LQQ_A.

>PRK04841 transcriptional regulator MalT; Provisional

Probab=99.62  E-value=8.7e-14  Score=166.32  Aligned_cols=297  Identities=14%  Similarity=0.179  Sum_probs=187.5

Q ss_pred             CCCCCCCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeC-CCCCHHHHHHHH
Q 042541          161 APDPPVISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVS-KNPNVKAIVQKV  239 (695)
Q Consensus       161 ~~~~~~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~-~~~~~~~~~~~i  239 (695)
                      +|..+..+|-|..-.+.+..   ....+++.|+|++|.||||++..+.+.      ++. +.|+++. .+.++..+...+
T Consensus         9 ~p~~~~~~~~R~rl~~~l~~---~~~~~~~~v~apaG~GKTtl~~~~~~~------~~~-~~w~~l~~~d~~~~~f~~~l   78 (903)
T PRK04841          9 RPVRLHNTVVRERLLAKLSG---ANNYRLVLVTSPAGYGKTTLISQWAAG------KNN-LGWYSLDESDNQPERFASYL   78 (903)
T ss_pred             CCCCccccCcchHHHHHHhc---ccCCCeEEEECCCCCCHHHHHHHHHHh------CCC-eEEEecCcccCCHHHHHHHH
Confidence            44455666777755544432   235789999999999999999998752      233 7899996 445667777777


Q ss_pred             HHhcCCCCCCC-C---------ChHHHHHHHHHHHHhcC--CCcEEEEEeCCCCCChH----HHhhhccC-CCCCEEEEE
Q 042541          240 LHHKGYPVPEF-Q---------TDEAAINDLERFFKQMR--IEAILLVLDDVWPGSES----LLQKLGFQ-LPDYKILVT  302 (695)
Q Consensus       240 ~~~l~~~~~~~-~---------~~~~~~~~l~~~~~~l~--~~~~LlVlDdv~~~~~~----~~~~l~~~-~~gs~iivT  302 (695)
                      +..++...+.. .         ........+..++..+.  +.+++|||||+...++.    .+..+... .++.++|||
T Consensus        79 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~lvlDD~h~~~~~~~~~~l~~l~~~~~~~~~lv~~  158 (903)
T PRK04841         79 IAALQQATNGHCSKSEALAQKRQYASLSSLFAQLFIELADWHQPLYLVIDDYHLITNPEIHEAMRFFLRHQPENLTLVVL  158 (903)
T ss_pred             HHHHHHhcCcccchhhhhhccCCcCCHHHHHHHHHHHHhcCCCCEEEEEeCcCcCCChHHHHHHHHHHHhCCCCeEEEEE
Confidence            77764221111 0         00111122333343332  68999999999776522    33344443 346788899


Q ss_pred             cCCCCCC-------CCCeEecC----CCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHHHhhCCC
Q 042541          303 SRSEFPQ-------FGSVHYLK----PLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGGSLCGK  371 (695)
Q Consensus       303 tR~~~~~-------~~~~~~l~----~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~~~L~~~  371 (695)
                      ||.....       .+....+.    +|+.+|+.++|....+..      ...+.+.+|.+.|+|+|+++..++..++..
T Consensus       159 sR~~~~~~~~~l~~~~~~~~l~~~~l~f~~~e~~~ll~~~~~~~------~~~~~~~~l~~~t~Gwp~~l~l~~~~~~~~  232 (903)
T PRK04841        159 SRNLPPLGIANLRVRDQLLEIGSQQLAFDHQEAQQFFDQRLSSP------IEAAESSRLCDDVEGWATALQLIALSARQN  232 (903)
T ss_pred             eCCCCCCchHhHHhcCcceecCHHhCCCCHHHHHHHHHhccCCC------CCHHHHHHHHHHhCChHHHHHHHHHHHhhC
Confidence            9985321       12244555    999999999998765322      235678899999999999999998776543


Q ss_pred             CHHHHHHHHHHhcCCCCccCchhhHHHHHH-HHHHhccHHHHHHHhhhcccCCCcccChHHHHHHHHHhhCCChhHHHHH
Q 042541          372 HEVFWQRMVKECSRGESVFQSKNDILDCLG-SSLDVLNNEVKECYLDLCSFPEDQRIPITALIDMWMELYELVDDVFAIT  450 (695)
Q Consensus       372 ~~~~w~~~l~~~~~~~~~~~~~~~i~~~l~-~s~~~L~~~~k~cf~~ls~fp~~~~i~~~~Li~~W~~~~~~~~~~~~~~  450 (695)
                      +... ......+..     .....+...+. ..++.||++.+..+...|+++.   ++.+.+-.      ..+.+ .+.+
T Consensus       233 ~~~~-~~~~~~~~~-----~~~~~~~~~l~~~v~~~l~~~~~~~l~~~a~~~~---~~~~l~~~------l~~~~-~~~~  296 (903)
T PRK04841        233 NSSL-HDSARRLAG-----INASHLSDYLVEEVLDNVDLETRHFLLRCSVLRS---MNDALIVR------VTGEE-NGQM  296 (903)
T ss_pred             CCch-hhhhHhhcC-----CCchhHHHHHHHHHHhcCCHHHHHHHHHhccccc---CCHHHHHH------HcCCC-cHHH
Confidence            2100 001111110     01234555443 3489999999999999999973   33332211      11222 5678


Q ss_pred             HHHHHhhccccchhhccccCCCCCCCCCcceehhHHHHHHHHHhccCC
Q 042541          451 NLHELSSQNLVDRVVTRKTAGDYGCYNDDFVMQHDLLRELTICRSKSE  498 (695)
Q Consensus       451 ~l~~L~~~sLl~~~~~~~~~~~~~~~~~~~~~mHdlv~~~a~~~~~~e  498 (695)
                      .+++|.+.+++....         ..+..+|++|+++++++......+
T Consensus       297 ~L~~l~~~~l~~~~~---------~~~~~~yr~H~L~r~~l~~~l~~~  335 (903)
T PRK04841        297 RLEELERQGLFIQRM---------DDSGEWFRYHPLFASFLRHRCQWE  335 (903)
T ss_pred             HHHHHHHCCCeeEee---------cCCCCEEehhHHHHHHHHHHHHhc
Confidence            999999999975311         123357899999999998775433

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=99.53  E-value=1.7e-12  Score=141.25  Aligned_cols=326  Identities=17%  Similarity=0.192  Sum_probs=209.7

Q ss_pred             CCCCCCCCCCCcchHHHHHHHHHc-CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCC-CCCHHHHHHH
Q 042541          161 APDPPVISPGLDVPLKELKMELFK-DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSK-NPNVKAIVQK  238 (695)
Q Consensus       161 ~~~~~~~~vGr~~~~~~l~~~L~~-~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~-~~~~~~~~~~  238 (695)
                      .|..+...|-|.    ++.+.|.. .+.+++.|..|+|.|||||+..+..  +....-  .|.|.++++ +.++..+...
T Consensus        14 ~P~~~~~~v~R~----rL~~~L~~~~~~RL~li~APAGfGKttl~aq~~~--~~~~~~--~v~Wlslde~dndp~rF~~y   85 (894)
T COG2909          14 RPVRPDNYVVRP----RLLDRLRRANDYRLILISAPAGFGKTTLLAQWRE--LAADGA--AVAWLSLDESDNDPARFLSY   85 (894)
T ss_pred             CCCCcccccccH----HHHHHHhcCCCceEEEEeCCCCCcHHHHHHHHHH--hcCccc--ceeEeecCCccCCHHHHHHH
Confidence            344445556555    56666664 4689999999999999999999875  333332  378999975 4578899999


Q ss_pred             HHHhcCCCCCCCCChHH----------HHHHHHHHHHhcC--CCcEEEEEeCCCCCChH----HHhhhc-cCCCCCEEEE
Q 042541          239 VLHHKGYPVPEFQTDEA----------AINDLERFFKQMR--IEAILLVLDDVWPGSES----LLQKLG-FQLPDYKILV  301 (695)
Q Consensus       239 i~~~l~~~~~~~~~~~~----------~~~~l~~~~~~l~--~~~~LlVlDdv~~~~~~----~~~~l~-~~~~gs~iiv  301 (695)
                      ++..++...+...+...          ...-+..++..+.  .+++++||||..-..+.    -+..|. ...++-.+||
T Consensus        86 Li~al~~~~p~~~~~a~~l~q~~~~~~l~~l~~~L~~Ela~~~~pl~LVlDDyHli~~~~l~~~l~fLl~~~P~~l~lvv  165 (894)
T COG2909          86 LIAALQQATPTLGDEAQTLLQKHQYVSLESLLSSLLNELASYEGPLYLVLDDYHLISDPALHEALRFLLKHAPENLTLVV  165 (894)
T ss_pred             HHHHHHHhCccccHHHHHHHHhcccccHHHHHHHHHHHHHhhcCceEEEeccccccCcccHHHHHHHHHHhCCCCeEEEE
Confidence            99988754443322111          1112233333332  56899999998655432    233333 3445889999


Q ss_pred             EcCCCCCCCCC-------eEecC----CCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHHHhhCC
Q 042541          302 TSRSEFPQFGS-------VHYLK----PLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGGSLCG  370 (695)
Q Consensus       302 TtR~~~~~~~~-------~~~l~----~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~~~L~~  370 (695)
                      |||+...-.-.       .++++    .|+.+|+.++|......      +-.+..++.+.+..+|.+-|+..++=.+++
T Consensus       166 ~SR~rP~l~la~lRlr~~llEi~~~~Lrf~~eE~~~fl~~~~~l------~Ld~~~~~~L~~~teGW~~al~L~aLa~~~  239 (894)
T COG2909         166 TSRSRPQLGLARLRLRDELLEIGSEELRFDTEEAAAFLNDRGSL------PLDAADLKALYDRTEGWAAALQLIALALRN  239 (894)
T ss_pred             EeccCCCCcccceeehhhHHhcChHhhcCChHHHHHHHHHcCCC------CCChHHHHHHHhhcccHHHHHHHHHHHccC
Confidence            99998532211       33333    68999999999876422      223567899999999999999999888884


Q ss_pred             C-CHHHHHHHHHHhcCCCCccCchhhHHH-HHHHHHHhccHHHHHHHhhhcccCCCcccChHHHHHHHHHhhCCChhHHH
Q 042541          371 K-HEVFWQRMVKECSRGESVFQSKNDILD-CLGSSLDVLNNEVKECYLDLCSFPEDQRIPITALIDMWMELYELVDDVFA  448 (695)
Q Consensus       371 ~-~~~~w~~~l~~~~~~~~~~~~~~~i~~-~l~~s~~~L~~~~k~cf~~ls~fp~~~~i~~~~Li~~W~~~~~~~~~~~~  448 (695)
                      . +.+.-   +..+..      ....+.. ...-.++.||+++|..++.||+++.-    -..|+..-     ... +.+
T Consensus       240 ~~~~~q~---~~~LsG------~~~~l~dYL~eeVld~Lp~~l~~FLl~~svl~~f----~~eL~~~L-----tg~-~ng  300 (894)
T COG2909         240 NTSAEQS---LRGLSG------AASHLSDYLVEEVLDRLPPELRDFLLQTSVLSRF----NDELCNAL-----TGE-ENG  300 (894)
T ss_pred             CCcHHHH---hhhccc------hHHHHHHHHHHHHHhcCCHHHHHHHHHHHhHHHh----hHHHHHHH-----hcC-CcH
Confidence            3 33221   111111      1122222 34557899999999999999999752    13343321     122 267


Q ss_pred             HHHHHHHhhccccchhhccccCCCCCCCCCcceehhHHHHHHHHHhccCCCcccccceeeeccCCCCchhhhhccCCCcc
Q 042541          449 ITNLHELSSQNLVDRVVTRKTAGDYGCYNDDFVMQHDLLRELTICRSKSEPINQRKRLVVEISGNNFPKWWMDQKQHPNN  528 (695)
Q Consensus       449 ~~~l~~L~~~sLl~~~~~~~~~~~~~~~~~~~~~mHdlv~~~a~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  528 (695)
                      ...+++|.+++|+-..-         ..+..+|+.|.++.||.+.....+.......+.     ....+||.+..-....
T Consensus       301 ~amLe~L~~~gLFl~~L---------dd~~~WfryH~LFaeFL~~r~~~~~~~~~~~lH-----~~Aa~w~~~~g~~~eA  366 (894)
T COG2909         301 QAMLEELERRGLFLQRL---------DDEGQWFRYHHLFAEFLRQRLQRELAARLKELH-----RAAAEWFAEHGLPSEA  366 (894)
T ss_pred             HHHHHHHHhCCCceeee---------cCCCceeehhHHHHHHHHhhhccccCCchhHHH-----HHHHHHHHhCCChHHH
Confidence            78999999999887522         345689999999999999887775443211111     1235688766555555


Q ss_pred             ceEEe
Q 042541          529 ASLLS  533 (695)
Q Consensus       529 ~r~l~  533 (695)
                      +.|..
T Consensus       367 I~hAl  371 (894)
T COG2909         367 IDHAL  371 (894)
T ss_pred             HHHHH
Confidence            55543

>KOG0617 consensus Ras suppressor protein (contains leucine-rich repeats) [Signal transduction mechanisms]

Probab=99.38  E-value=1.2e-14  Score=127.66  Aligned_cols=156  Identities=19%  Similarity=0.217  Sum_probs=122.8

Q ss_pred             cceEEeeecCCcccCCCCCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEE
Q 042541          528 NASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIR  607 (695)
Q Consensus       528 ~~r~l~~~~~~~~~~~~~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~  607 (695)
                      .+-++.+++++...-.+--.++.+|++|.+..+ ....+|.+++.+++||.|++.-|.+.  .  .+..+|+++-|++|+
T Consensus        34 ~ITrLtLSHNKl~~vppnia~l~nlevln~~nn-qie~lp~~issl~klr~lnvgmnrl~--~--lprgfgs~p~levld  108 (264)
T KOG0617|consen   34 NITRLTLSHNKLTVVPPNIAELKNLEVLNLSNN-QIEELPTSISSLPKLRILNVGMNRLN--I--LPRGFGSFPALEVLD  108 (264)
T ss_pred             hhhhhhcccCceeecCCcHHHhhhhhhhhcccc-hhhhcChhhhhchhhhheecchhhhh--c--CccccCCCchhhhhh
Confidence            344555555443222222236778888887655 44678889999999999998876542  1  122388999999999


Q ss_pred             eccCCCC--Ccc-cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeeccc
Q 042541          608 LEHVSLP--NSL-ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITN  684 (695)
Q Consensus       608 L~~~~l~--~lp-~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~  684 (695)
                      |..|++.  .+| .+..|..|+-|.|+.|.+.-+|+++.     +|++||.|.+..| .+-++|..+|.|+.|+.|++++
T Consensus       109 ltynnl~e~~lpgnff~m~tlralyl~dndfe~lp~dvg-----~lt~lqil~lrdn-dll~lpkeig~lt~lrelhiqg  182 (264)
T KOG0617|consen  109 LTYNNLNENSLPGNFFYMTTLRALYLGDNDFEILPPDVG-----KLTNLQILSLRDN-DLLSLPKEIGDLTRLRELHIQG  182 (264)
T ss_pred             ccccccccccCCcchhHHHHHHHHHhcCCCcccCChhhh-----hhcceeEEeeccC-chhhCcHHHHHHHHHHHHhccc
Confidence            9999986  789 88889999999999999999999888     8999999999995 6789999999999999999999


Q ss_pred             ccCCCCCCCCC
Q 042541          685 CHRLSALPEGI  695 (695)
Q Consensus       685 ~~~l~~lP~~i  695 (695)
                      | .+..+|+++
T Consensus       183 n-rl~vlppel  192 (264)
T KOG0617|consen  183 N-RLTVLPPEL  192 (264)
T ss_pred             c-eeeecChhh
Confidence            5 599999874

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=99.31  E-value=1e-09  Score=116.82  Aligned_cols=288  Identities=15%  Similarity=0.103  Sum_probs=166.5

Q ss_pred             CCCCCCCcchHHHHHHHHHc----CCceEEEEEcCCCCcHHHHHHHHhccccc-ccc--CCCcEEEEEeCCCCCHHHHHH
Q 042541          165 PVISPGLDVPLKELKMELFK----DGRQFIVVSAPGGYGKTTLVQRLCKDDQV-QGK--FKDDIFYVTVSKNPNVKAIVQ  237 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~----~~~~vv~I~G~gGiGKTtLa~~~~~~~~~-~~~--f~~~~~wv~~~~~~~~~~~~~  237 (695)
                      |+.++||+.++++|..+|..    ...+.+.|+|++|+|||++++.+++...- ...  ....++|+++....+...++.
T Consensus        14 p~~l~gRe~e~~~l~~~l~~~~~~~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~~~~~~~~~~~   93 (365)
T TIGR02928        14 PDRIVHRDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLYQVLV   93 (365)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECCCCCCHHHHHH
Confidence            45789999999999999872    34568999999999999999999974211 011  113366888888778889999


Q ss_pred             HHHHhcC---CCCCCC-CChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCC---hHHHhhhcc-----CCCC--CEEEEEc
Q 042541          238 KVLHHKG---YPVPEF-QTDEAAINDLERFFKQMRIEAILLVLDDVWPGS---ESLLQKLGF-----QLPD--YKILVTS  303 (695)
Q Consensus       238 ~i~~~l~---~~~~~~-~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~---~~~~~~l~~-----~~~g--s~iivTt  303 (695)
                      .|+.++.   ...+.. .+..+....+...+.. .+++++||||+++...   ...+..+..     ..++  ..+|.+|
T Consensus        94 ~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~-~~~~~vlvIDE~d~L~~~~~~~L~~l~~~~~~~~~~~~~v~lI~i~  172 (365)
T TIGR02928        94 ELANQLRGSGEEVPTTGLSTSEVFRRLYKELNE-RGDSLIIVLDEIDYLVGDDDDLLYQLSRARSNGDLDNAKVGVIGIS  172 (365)
T ss_pred             HHHHHHhhcCCCCCCCCCCHHHHHHHHHHHHHh-cCCeEEEEECchhhhccCCcHHHHhHhccccccCCCCCeEEEEEEE
Confidence            9999883   322211 1222222333322211 3668999999997662   222222211     1222  3444444


Q ss_pred             CCCC----------CCC-CCeEecCCCChHHHHHHHHHhccCCC--CCCCCCchHHHHHHHHhcCCchhHHHHHH-Hhh-
Q 042541          304 RSEF----------PQF-GSVHYLKPLTYEAARTLFLHSANLQD--GNSYIPDENIVSKILRACKGCPLALKVVG-GSL-  368 (695)
Q Consensus       304 R~~~----------~~~-~~~~~l~~L~~~ea~~Lf~~~~~~~~--~~~~~~~~~~~~~I~~~c~G~PLai~~~~-~~L-  368 (695)
                      ....          ... ...+.+++++.++..+++..++....  ........+.+..++..+.|.|..+..+. .+. 
T Consensus       173 n~~~~~~~l~~~~~s~~~~~~i~f~p~~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~  252 (365)
T TIGR02928       173 NDLKFRENLDPRVKSSLCEEEIIFPPYDAEELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGE  252 (365)
T ss_pred             CCcchHhhcCHHHhccCCcceeeeCCCCHHHHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            3321          011 23688999999999999998764211  11111122344556667778875443222 111 


Q ss_pred             ---C-CC---CHHHHHHHHHHhcCCCCccCchhhHHHHHHHHHHhccHHHHHHHhhhcccC--CCcccChHHHHHHHH--
Q 042541          369 ---C-GK---HEVFWQRMVKECSRGESVFQSKNDILDCLGSSLDVLNNEVKECYLDLCSFP--EDQRIPITALIDMWM--  437 (695)
Q Consensus       369 ---~-~~---~~~~w~~~l~~~~~~~~~~~~~~~i~~~l~~s~~~L~~~~k~cf~~ls~fp--~~~~i~~~~Li~~W~--  437 (695)
                         . +.   +.+..+.++...            -.....-++..||.+.+..+..++..-  ++..+....+...+-  
T Consensus       253 ~a~~~~~~~it~~~v~~a~~~~------------~~~~~~~~i~~l~~~~~~~l~ai~~~~~~~~~~~~~~~~~~~y~~~  320 (365)
T TIGR02928       253 IAEREGAERVTEDHVEKAQEKI------------EKDRLLELIRGLPTHSKLVLLAIANLAANDEDPFRTGEVYEVYKEV  320 (365)
T ss_pred             HHHHcCCCCCCHHHHHHHHHHH------------HHHHHHHHHHcCCHHHHHHHHHHHHHHhcCCCCccHHHHHHHHHHH
Confidence               1 11   233333333321            123344567889988886665544221  344466666666443  


Q ss_pred             -HhhCCChh--HHHHHHHHHHhhccccchhh
Q 042541          438 -ELYELVDD--VFAITNLHELSSQNLVDRVV  465 (695)
Q Consensus       438 -~~~~~~~~--~~~~~~l~~L~~~sLl~~~~  465 (695)
                       ....+.+-  ....++++.|...|||+...
T Consensus       321 ~~~~~~~~~~~~~~~~~l~~l~~~gli~~~~  351 (365)
T TIGR02928       321 CEDIGVDPLTQRRISDLLNELDMLGLVEAEE  351 (365)
T ss_pred             HHhcCCCCCcHHHHHHHHHHHHhcCCeEEEE
Confidence             22122111  47889999999999999744

Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=99.31  E-value=8.9e-10  Score=118.50  Aligned_cols=286  Identities=14%  Similarity=0.131  Sum_probs=168.3

Q ss_pred             CCCCCCCCcchHHHHHHHHH----cCCceEEEEEcCCCCcHHHHHHHHhccccccccC-CCcEEEEEeCCCCCHHHHHHH
Q 042541          164 PPVISPGLDVPLKELKMELF----KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKF-KDDIFYVTVSKNPNVKAIVQK  238 (695)
Q Consensus       164 ~~~~~vGr~~~~~~l~~~L~----~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f-~~~~~wv~~~~~~~~~~~~~~  238 (695)
                      .|+.++||++++++|...|.    ......+.|+|++|+|||++++.++++  ..... ...++++++....+...++..
T Consensus        28 ~P~~l~~Re~e~~~l~~~l~~~~~~~~~~~~lI~G~~GtGKT~l~~~v~~~--l~~~~~~~~~v~in~~~~~~~~~~~~~  105 (394)
T PRK00411         28 VPENLPHREEQIEELAFALRPALRGSRPLNVLIYGPPGTGKTTTVKKVFEE--LEEIAVKVVYVYINCQIDRTRYAIFSE  105 (394)
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHH--HHHhcCCcEEEEEECCcCCCHHHHHHH
Confidence            45678999999999999885    234567889999999999999999984  32222 223567777777788899999


Q ss_pred             HHHhcCCC-CCC-CCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCC----hHHHhhhc---cCCCCCE--EEEEcCCCC
Q 042541          239 VLHHKGYP-VPE-FQTDEAAINDLERFFKQMRIEAILLVLDDVWPGS----ESLLQKLG---FQLPDYK--ILVTSRSEF  307 (695)
Q Consensus       239 i~~~l~~~-~~~-~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~----~~~~~~l~---~~~~gs~--iivTtR~~~  307 (695)
                      ++.++... .+. ..+.......+...+.. .++..+||||+++...    ...+..+.   ...++++  +|.++....
T Consensus       106 i~~~l~~~~~~~~~~~~~~~~~~~~~~l~~-~~~~~viviDE~d~l~~~~~~~~l~~l~~~~~~~~~~~v~vI~i~~~~~  184 (394)
T PRK00411        106 IARQLFGHPPPSSGLSFDELFDKIAEYLDE-RDRVLIVALDDINYLFEKEGNDVLYSLLRAHEEYPGARIGVIGISSDLT  184 (394)
T ss_pred             HHHHhcCCCCCCCCCCHHHHHHHHHHHHHh-cCCEEEEEECCHhHhhccCCchHHHHHHHhhhccCCCeEEEEEEECCcc
Confidence            99998752 221 11223333333333321 3567899999997643    22222221   1223433  455544331


Q ss_pred             -----------CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhc----CCchhHHHHHHHhh----
Q 042541          308 -----------PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRAC----KGCPLALKVVGGSL----  368 (695)
Q Consensus       308 -----------~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c----~G~PLai~~~~~~L----  368 (695)
                                 ......+.+++++.++..+++..++...... ..-..+.++.|++.+    |..+.|+.++-.+.    
T Consensus       185 ~~~~l~~~~~s~~~~~~i~f~py~~~e~~~il~~r~~~~~~~-~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~  263 (394)
T PRK00411        185 FLYILDPRVKSVFRPEEIYFPPYTADEIFDILKDRVEEGFYP-GVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAE  263 (394)
T ss_pred             hhhhcCHHHHhcCCcceeecCCCCHHHHHHHHHHHHHhhccc-CCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHH
Confidence                       0112367899999999999998876432111 111234455555554    55777777664321    


Q ss_pred             -CCC---CHHHHHHHHHHhcCCCCccCchhhHHHHHHHHHHhccHHHHHHHhhhcccC--CCcccChHHHHHHHHH---h
Q 042541          369 -CGK---HEVFWQRMVKECSRGESVFQSKNDILDCLGSSLDVLNNEVKECYLDLCSFP--EDQRIPITALIDMWME---L  439 (695)
Q Consensus       369 -~~~---~~~~w~~~l~~~~~~~~~~~~~~~i~~~l~~s~~~L~~~~k~cf~~ls~fp--~~~~i~~~~Li~~W~~---~  439 (695)
                       ++.   +.+....++...            -.....-.+..||.+.|..+..++..-  +...+....+...-..   .
T Consensus       264 ~~~~~~I~~~~v~~a~~~~------------~~~~~~~~~~~L~~~~k~~L~ai~~~~~~~~~~~~~~~i~~~y~~l~~~  331 (394)
T PRK00411        264 REGSRKVTEEDVRKAYEKS------------EIVHLSEVLRTLPLHEKLLLRAIVRLLKKGGDEVTTGEVYEEYKELCEE  331 (394)
T ss_pred             HcCCCCcCHHHHHHHHHHH------------HHHHHHHHHhcCCHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHH
Confidence             111   234444344332            122345568899998887766554332  1133555555433221   1


Q ss_pred             hCCCh--hHHHHHHHHHHhhccccchhh
Q 042541          440 YELVD--DVFAITNLHELSSQNLVDRVV  465 (695)
Q Consensus       440 ~~~~~--~~~~~~~l~~L~~~sLl~~~~  465 (695)
                      ..+.+  .....+++++|...|+|+...
T Consensus       332 ~~~~~~~~~~~~~~l~~L~~~glI~~~~  359 (394)
T PRK00411        332 LGYEPRTHTRFYEYINKLDMLGIINTRY  359 (394)
T ss_pred             cCCCcCcHHHHHHHHHHHHhcCCeEEEE
Confidence            12222  136778999999999998643

>PLN00113 leucine-rich repeat receptor-like protein kinase; Provisional

Probab=99.29  E-value=8.3e-12  Score=150.27  Aligned_cols=142  Identities=16%  Similarity=0.164  Sum_probs=86.5

Q ss_pred             CCCceEEEEEEccCccccCChhh-cCCCCCcEEEEcccCCCCcc-------------------cCcccccccCCCCcEEE
Q 042541          548 QGPEVKVVVLNIRTKKYVLPDFL-QKMDELKVLIVTNYGFSPAE-------------------LNNFRVLSALSKLKKIR  607 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~~~-~~l~~Lr~L~l~~~~~~~~~-------------------~~~~~~l~~l~~L~~L~  607 (695)
                      .+++|+.|.|+.+...+.+|..+ ..+++|++|++++|.+....                   -..+..++++++|++|+
T Consensus        91 ~l~~L~~L~Ls~n~~~~~ip~~~~~~l~~L~~L~Ls~n~l~~~~p~~~l~~L~~L~Ls~n~~~~~~p~~~~~l~~L~~L~  170 (968)
T PLN00113         91 RLPYIQTINLSNNQLSGPIPDDIFTTSSSLRYLNLSNNNFTGSIPRGSIPNLETLDLSNNMLSGEIPNDIGSFSSLKVLD  170 (968)
T ss_pred             CCCCCCEEECCCCccCCcCChHHhccCCCCCEEECcCCccccccCccccCCCCEEECcCCcccccCChHHhcCCCCCEEE
Confidence            44555555555554444455432 25555555555554432100                   00112356677777777


Q ss_pred             eccCCCC-Ccc-cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccc
Q 042541          608 LEHVSLP-NSL-ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNC  685 (695)
Q Consensus       608 L~~~~l~-~lp-~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~  685 (695)
                      |++|.+. .+| .++++++|++|+|++|.+....|..+.    .+++|++|++++|...+.+|..++++++|++|++++|
T Consensus       171 L~~n~l~~~~p~~~~~l~~L~~L~L~~n~l~~~~p~~l~----~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L~L~~n  246 (968)
T PLN00113        171 LGGNVLVGKIPNSLTNLTSLEFLTLASNQLVGQIPRELG----QMKSLKWIYLGYNNLSGEIPYEIGGLTSLNHLDLVYN  246 (968)
T ss_pred             CccCcccccCChhhhhCcCCCeeeccCCCCcCcCChHHc----CcCCccEEECcCCccCCcCChhHhcCCCCCEEECcCc
Confidence            7777765 566 777777777777777776655554444    6777777777777666677777777777777777777


Q ss_pred             cCCCCCCC
Q 042541          686 HRLSALPE  693 (695)
Q Consensus       686 ~~l~~lP~  693 (695)
                      +..+.+|.
T Consensus       247 ~l~~~~p~  254 (968)
T PLN00113        247 NLTGPIPS  254 (968)
T ss_pred             eeccccCh
Confidence            65556664

>PLN00113 leucine-rich repeat receptor-like protein kinase; Provisional

Probab=99.23  E-value=1.7e-11  Score=147.61  Aligned_cols=139  Identities=17%  Similarity=0.190  Sum_probs=82.2

Q ss_pred             CCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCC-Ccc-cccccccc
Q 042541          548 QGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLP-NSL-ATVRMNHL  625 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~-~lp-~i~~l~~L  625 (695)
                      .+++|++|.++.|...+.+|..++++++|++|++++|.+... +  +..++.+++|++|++++|.+. .+| .++++++|
T Consensus       186 ~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L~L~~n~l~~~-~--p~~l~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L  262 (968)
T PLN00113        186 NLTSLEFLTLASNQLVGQIPRELGQMKSLKWIYLGYNNLSGE-I--PYEIGGLTSLNHLDLVYNNLTGPIPSSLGNLKNL  262 (968)
T ss_pred             hCcCCCeeeccCCCCcCcCChHHcCcCCccEEECcCCccCCc-C--ChhHhcCCCCCEEECcCceeccccChhHhCCCCC
Confidence            455566666655555555565666666666666665544211 1  122556666666666666665 555 66666666


Q ss_pred             cEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccccCCCCCCC
Q 042541          626 QKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPE  693 (695)
Q Consensus       626 ~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~~l~~lP~  693 (695)
                      ++|++++|.+.+..|..+.    .+++|++|++++|...+.+|..++++++|+.|++++|...+.+|.
T Consensus       263 ~~L~L~~n~l~~~~p~~l~----~l~~L~~L~Ls~n~l~~~~p~~~~~l~~L~~L~l~~n~~~~~~~~  326 (968)
T PLN00113        263 QYLFLYQNKLSGPIPPSIF----SLQKLISLDLSDNSLSGEIPELVIQLQNLEILHLFSNNFTGKIPV  326 (968)
T ss_pred             CEEECcCCeeeccCchhHh----hccCcCEEECcCCeeccCCChhHcCCCCCcEEECCCCccCCcCCh
Confidence            6666666666544443333    566677777776655556666667777777777776665444443

>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP

Probab=99.23  E-value=5e-11  Score=118.36  Aligned_cols=189  Identities=20%  Similarity=0.250  Sum_probs=100.1

Q ss_pred             CCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccc-cCCCcEEEEEeCCCCCHHHHHHH--------
Q 042541          168 SPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQG-KFKDDIFYVTVSKNPNVKAIVQK--------  238 (695)
Q Consensus       168 ~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~-~f~~~~~wv~~~~~~~~~~~~~~--------  238 (695)
                      |+||+.++++|.+++..+..+.+.|+|+.|+|||+|++.+.+  ..+. .+ . ++|+...+......+...        
T Consensus         1 F~gR~~el~~l~~~l~~~~~~~~~l~G~rg~GKTsLl~~~~~--~~~~~~~-~-~~y~~~~~~~~~~~~~~~~~~~~~~~   76 (234)
T PF01637_consen    1 FFGREKELEKLKELLESGPSQHILLYGPRGSGKTSLLKEFIN--ELKEKGY-K-VVYIDFLEESNESSLRSFIEETSLAD   76 (234)
T ss_dssp             S-S-HHHHHHHHHCHHH--SSEEEEEESTTSSHHHHHHHHHH--HCT--EE-C-CCHHCCTTBSHHHHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHHHhhcCcEEEEEcCCcCCHHHHHHHHHH--HhhhcCC-c-EEEEecccchhhhHHHHHHHHHHHHH
Confidence            799999999999999887788999999999999999999998  3422 22 2 345555444332221111        


Q ss_pred             -HHHhcCCCCCC----------CCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCC------hHHHhhh----cc--CCC
Q 042541          239 -VLHHKGYPVPE----------FQTDEAAINDLERFFKQMRIEAILLVLDDVWPGS------ESLLQKL----GF--QLP  295 (695)
Q Consensus       239 -i~~~l~~~~~~----------~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~------~~~~~~l----~~--~~~  295 (695)
                       +.+.+....+.          ..........+...+.. .+++++||+||+....      ......+    ..  ...
T Consensus        77 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~-~~~~~iiviDe~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  155 (234)
T PF01637_consen   77 ELSEALGISIPSITLEKISKDLSEDSFSALERLLEKLKK-KGKKVIIVIDEFQYLAIASEEDKDFLKSLRSLLDSLLSQQ  155 (234)
T ss_dssp             HCHHHHHHHCCTSTTEEEECTS-GG-G--HHHHHHHHHH-CHCCEEEEEETGGGGGBCTTTTHHHHHHHHHHHHH----T
T ss_pred             HHHHHHhhhcccccchhhhhcchhhHHHHHHHHHHHHHh-cCCcEEEEEecHHHHhhcccchHHHHHHHHHHHhhccccC
Confidence             11112111110          01112223333333322 3445999999985544      1211111    11  122


Q ss_pred             C-CEEEEEcCCC---------CC--CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHH
Q 042541          296 D-YKILVTSRSE---------FP--QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKV  363 (695)
Q Consensus       296 g-s~iivTtR~~---------~~--~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~  363 (695)
                      + +.|+++|...         ..  .....+.+++|+.+++++++....... ... ....+..++|+..+||+|..|..
T Consensus       156 ~~~~v~~~S~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~e~~~~~~~~~~~~-~~~-~~~~~~~~~i~~~~gG~P~~l~~  233 (234)
T PF01637_consen  156 NVSIVITGSSDSLMEEFLDDKSPLFGRFSHIELKPLSKEEAREFLKELFKEL-IKL-PFSDEDIEEIYSLTGGNPRYLQE  233 (234)
T ss_dssp             TEEEEEEESSHHHHHHTT-TTSTTTT---EEEE----HHHHHHHHHHHHHCC--------HHHHHHHHHHHTT-HHHHHH
T ss_pred             CceEEEECCchHHHHHhhcccCccccccceEEEeeCCHHHHHHHHHHHHHHh-hcc-cCCHHHHHHHHHHhCCCHHHHhc
Confidence            3 4444444421         11  111269999999999999999865433 211 12466789999999999998764

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=99.21  E-value=1.3e-09  Score=110.78  Aligned_cols=188  Identities=22%  Similarity=0.270  Sum_probs=119.5

Q ss_pred             HHHHHHHH---cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCC
Q 042541          176 KELKMELF---KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQT  252 (695)
Q Consensus       176 ~~l~~~L~---~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~  252 (695)
                      +++...+.   ..+.+++.|+|++|+|||||++.+++.... .  ...+.|+ +....+..+++..++..++.+... ..
T Consensus        29 ~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~~~l~~~l~~-~--~~~~~~~-~~~~~~~~~~l~~i~~~lG~~~~~-~~  103 (269)
T TIGR03015        29 KRAMAYLEYGLSQREGFILITGEVGAGKTTLIRNLLKRLDQ-E--RVVAAKL-VNTRVDAEDLLRMVAADFGLETEG-RD  103 (269)
T ss_pred             HHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHHHHHHHhcCC-C--CeEEeee-eCCCCCHHHHHHHHHHHcCCCCCC-CC
Confidence            34444443   344578999999999999999999984221 1  1112233 233457778999999998775432 22


Q ss_pred             hHHHHHHHHHHH-H-hcCCCcEEEEEeCCCCCChHHHhhh---ccC----CCCCEEEEEcCCCC----C---------CC
Q 042541          253 DEAAINDLERFF-K-QMRIEAILLVLDDVWPGSESLLQKL---GFQ----LPDYKILVTSRSEF----P---------QF  310 (695)
Q Consensus       253 ~~~~~~~l~~~~-~-~l~~~~~LlVlDdv~~~~~~~~~~l---~~~----~~gs~iivTtR~~~----~---------~~  310 (695)
                      .......+...+ . ...+++.++|+||++......+..+   ...    .....|++|.....    .         ..
T Consensus       104 ~~~~~~~l~~~l~~~~~~~~~~vliiDe~~~l~~~~~~~l~~l~~~~~~~~~~~~vvl~g~~~~~~~l~~~~~~~l~~r~  183 (269)
T TIGR03015       104 KAALLRELEDFLIEQFAAGKRALLVVDEAQNLTPELLEELRMLSNFQTDNAKLLQIFLVGQPEFRETLQSPQLQQLRQRI  183 (269)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCeEEEEECcccCCHHHHHHHHHHhCcccCCCCeEEEEEcCCHHHHHHHcCchhHHHHhhe
Confidence            233344454444 2 2368889999999998775433332   221    12235556654331    0         11


Q ss_pred             CCeEecCCCChHHHHHHHHHhccCCCCCCC-CCchHHHHHHHHhcCCchhHHHHHHHhh
Q 042541          311 GSVHYLKPLTYEAARTLFLHSANLQDGNSY-IPDENIVSKILRACKGCPLALKVVGGSL  368 (695)
Q Consensus       311 ~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~-~~~~~~~~~I~~~c~G~PLai~~~~~~L  368 (695)
                      ...+.+++++.+|..+++...+........ .-..+..+.|++.|+|.|..|..++..+
T Consensus       184 ~~~~~l~~l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~  242 (269)
T TIGR03015       184 IASCHLGPLDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRL  242 (269)
T ss_pred             eeeeeCCCCCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHH
Confidence            236789999999999999877643322111 1246889999999999999999988764

Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=99.18  E-value=1.8e-09  Score=111.85  Aligned_cols=264  Identities=15%  Similarity=0.102  Sum_probs=145.1

Q ss_pred             CCCCCcchHHHHHHHHH-----cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHH
Q 042541          167 ISPGLDVPLKELKMELF-----KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLH  241 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~-----~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~  241 (695)
                      .|||++..+++|..++.     ......+.++|++|+|||+||+.+++  .....    ...+..+.......+ ...+.
T Consensus         5 ~~iG~~~~~~~l~~~l~~~~~~~~~~~~~ll~Gp~G~GKT~la~~ia~--~~~~~----~~~~~~~~~~~~~~l-~~~l~   77 (305)
T TIGR00635         5 EFIGQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIAN--EMGVN----LKITSGPALEKPGDL-AAILT   77 (305)
T ss_pred             HHcCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHH--HhCCC----EEEeccchhcCchhH-HHHHH
Confidence            57999999999988887     23356788999999999999999988  33222    222222211122222 22223


Q ss_pred             hcCCCC----CCCC-ChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChHHHhhhccCCC-CCEEEEEcCCCCC------C
Q 042541          242 HKGYPV----PEFQ-TDEAAINDLERFFKQMRIEAILLVLDDVWPGSESLLQKLGFQLP-DYKILVTSRSEFP------Q  309 (695)
Q Consensus       242 ~l~~~~----~~~~-~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~~~~~l~~~~~-gs~iivTtR~~~~------~  309 (695)
                      .++...    ++.. -.....+.+.   ..+.+.+..+|+|+..+...     +....+ .+-|..||+....      .
T Consensus        78 ~~~~~~vl~iDEi~~l~~~~~e~l~---~~~~~~~~~~v~~~~~~~~~-----~~~~~~~~~li~~t~~~~~l~~~l~sR  149 (305)
T TIGR00635        78 NLEEGDVLFIDEIHRLSPAVEELLY---PAMEDFRLDIVIGKGPSARS-----VRLDLPPFTLVGATTRAGMLTSPLRDR  149 (305)
T ss_pred             hcccCCEEEEehHhhhCHHHHHHhh---HHHhhhheeeeeccCccccc-----eeecCCCeEEEEecCCccccCHHHHhh
Confidence            332111    0000 0001111111   33344455566665433321     111112 3445556665421      2


Q ss_pred             CCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHHHhhCCCCHHHHHHHHHHhcCCCCc
Q 042541          310 FGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGGSLCGKHEVFWQRMVKECSRGESV  389 (695)
Q Consensus       310 ~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~~~L~~~~~~~w~~~l~~~~~~~~~  389 (695)
                      .+..+.+++++.++..+++.+.+.....   .-.++.+..|++.|+|.|..+..++..+       |.  ..........
T Consensus       150 ~~~~~~l~~l~~~e~~~il~~~~~~~~~---~~~~~al~~ia~~~~G~pR~~~~ll~~~-------~~--~a~~~~~~~i  217 (305)
T TIGR00635       150 FGIILRLEFYTVEELAEIVSRSAGLLNV---EIEPEAALEIARRSRGTPRIANRLLRRV-------RD--FAQVRGQKII  217 (305)
T ss_pred             cceEEEeCCCCHHHHHHHHHHHHHHhCC---CcCHHHHHHHHHHhCCCcchHHHHHHHH-------HH--HHHHcCCCCc
Confidence            3447899999999999999988764322   2246778999999999997765554422       11  1000110000


Q ss_pred             c-CchhhHHHHHHHHHHhccHHHHHHHh-hhcccCCCcccChHHHHHHHHHhhCCChhHHHHHHHH-HHhhccccch
Q 042541          390 F-QSKNDILDCLGSSLDVLNNEVKECYL-DLCSFPEDQRIPITALIDMWMELYELVDDVFAITNLH-ELSSQNLVDR  463 (695)
Q Consensus       390 ~-~~~~~i~~~l~~s~~~L~~~~k~cf~-~ls~fp~~~~i~~~~Li~~W~~~~~~~~~~~~~~~l~-~L~~~sLl~~  463 (695)
                      . +.-......+...|..|+++.+..+. .++.++.+ .+..+.+...    -..+.. .++..++ .|++++||+.
T Consensus       218 t~~~v~~~l~~l~~~~~~l~~~~~~~L~al~~~~~~~-~~~~~~ia~~----lg~~~~-~~~~~~e~~Li~~~li~~  288 (305)
T TIGR00635       218 NRDIALKALEMLMIDELGLDEIDRKLLSVLIEQFQGG-PVGLKTLAAA----LGEDAD-TIEDVYEPYLLQIGFLQR  288 (305)
T ss_pred             CHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHhCCC-cccHHHHHHH----hCCCcc-hHHHhhhHHHHHcCCccc
Confidence            0 00012222245567788888777666 45666544 4444444332    234443 7888888 6999999974

RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.

>KOG0617 consensus Ras suppressor protein (contains leucine-rich repeats) [Signal transduction mechanisms]

Probab=99.17  E-value=1.2e-12  Score=115.15  Aligned_cols=138  Identities=19%  Similarity=0.260  Sum_probs=113.3

Q ss_pred             CCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc-cccccccc
Q 042541          547 MQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL-ATVRMNHL  625 (695)
Q Consensus       547 ~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp-~i~~l~~L  625 (695)
                      +++++++.|.|+.+.. ..+|+.+..+.+|.+|++++|++.  .  .+.++++|+.|+.|++.-|.+..+| ++|.++-|
T Consensus        30 f~~s~ITrLtLSHNKl-~~vppnia~l~nlevln~~nnqie--~--lp~~issl~klr~lnvgmnrl~~lprgfgs~p~l  104 (264)
T KOG0617|consen   30 FNMSNITRLTLSHNKL-TVVPPNIAELKNLEVLNLSNNQIE--E--LPTSISSLPKLRILNVGMNRLNILPRGFGSFPAL  104 (264)
T ss_pred             cchhhhhhhhcccCce-eecCCcHHHhhhhhhhhcccchhh--h--cChhhhhchhhhheecchhhhhcCccccCCCchh
Confidence            3556677777766643 566778999999999999998773  2  2345899999999999999999999 99999999


Q ss_pred             cEEeeccccCCc-ccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccccCCCCCCCCC
Q 042541          626 QKVSLVMCNVGQ-VFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPEGI  695 (695)
Q Consensus       626 ~~L~l~~~~i~~-~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~~l~~lP~~i  695 (695)
                      +.|||+.|++.. ..|+.|.    .++.|+.|+|++| ...-+|..+|+|++|+.|.+++|. +-++|.+|
T Consensus       105 evldltynnl~e~~lpgnff----~m~tlralyl~dn-dfe~lp~dvg~lt~lqil~lrdnd-ll~lpkei  169 (264)
T KOG0617|consen  105 EVLDLTYNNLNENSLPGNFF----YMTTLRALYLGDN-DFEILPPDVGKLTNLQILSLRDND-LLSLPKEI  169 (264)
T ss_pred             hhhhccccccccccCCcchh----HHHHHHHHHhcCC-CcccCChhhhhhcceeEEeeccCc-hhhCcHHH
Confidence            999999997643 3344443    8999999999994 689999999999999999999966 77888753

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=99.13  E-value=4e-09  Score=109.97  Aligned_cols=272  Identities=17%  Similarity=0.138  Sum_probs=147.1

Q ss_pred             CCCCCCCCCCcchHHHHHHHHH-----cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHH
Q 042541          162 PDPPVISPGLDVPLKELKMELF-----KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIV  236 (695)
Q Consensus       162 ~~~~~~~vGr~~~~~~l~~~L~-----~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~  236 (695)
                      |..-..|+|++..++.+..++.     ......+.|+|++|+|||+||+.+++.  ....    +.++..+.... ...+
T Consensus        21 P~~~~~~vG~~~~~~~l~~~l~~~~~~~~~~~~~ll~GppG~GKT~la~~ia~~--l~~~----~~~~~~~~~~~-~~~l   93 (328)
T PRK00080         21 PKSLDEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIANE--MGVN----IRITSGPALEK-PGDL   93 (328)
T ss_pred             cCCHHHhcCcHHHHHHHHHHHHHHHhcCCCCCcEEEECCCCccHHHHHHHHHHH--hCCC----eEEEecccccC-hHHH
Confidence            3344568999999999987776     223567899999999999999999983  3221    22332221111 1122


Q ss_pred             HHHHHhcCCCCCC-CCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCChHHHhhhccCCCC-CEEEEEcCCCCC-----
Q 042541          237 QKVLHHKGYPVPE-FQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGSESLLQKLGFQLPD-YKILVTSRSEFP-----  308 (695)
Q Consensus       237 ~~i~~~l~~~~~~-~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~~~~~~~l~~~~~g-s~iivTtR~~~~-----  308 (695)
                      ..++..+....-- .++.+.......+.+ ..+.+.+..+++|+..+...     +....++ +-|..|++....     
T Consensus        94 ~~~l~~l~~~~vl~IDEi~~l~~~~~e~l~~~~e~~~~~~~l~~~~~~~~-----~~~~l~~~~li~at~~~~~l~~~L~  168 (328)
T PRK00080         94 AAILTNLEEGDVLFIDEIHRLSPVVEEILYPAMEDFRLDIMIGKGPAARS-----IRLDLPPFTLIGATTRAGLLTSPLR  168 (328)
T ss_pred             HHHHHhcccCCEEEEecHhhcchHHHHHHHHHHHhcceeeeeccCccccc-----eeecCCCceEEeecCCcccCCHHHH
Confidence            2333332211000 000000000011111 22233344444444322211     1111233 344556664421     


Q ss_pred             -CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHHHhhCCCCHHHHHHHHHHhcCCC
Q 042541          309 -QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGGSLCGKHEVFWQRMVKECSRGE  387 (695)
Q Consensus       309 -~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~~~L~~~~~~~w~~~l~~~~~~~  387 (695)
                       ..+..+.+++++.++..+++.+.+.....   .-.++.+..|++.|+|.|..+..+...+     ..|. ...   ...
T Consensus       169 sRf~~~~~l~~~~~~e~~~il~~~~~~~~~---~~~~~~~~~ia~~~~G~pR~a~~~l~~~-----~~~a-~~~---~~~  236 (328)
T PRK00080        169 DRFGIVQRLEFYTVEELEKIVKRSARILGV---EIDEEGALEIARRSRGTPRIANRLLRRV-----RDFA-QVK---GDG  236 (328)
T ss_pred             HhcCeeeecCCCCHHHHHHHHHHHHHHcCC---CcCHHHHHHHHHHcCCCchHHHHHHHHH-----HHHH-HHc---CCC
Confidence             13457899999999999999988765332   1246789999999999997555554422     1221 110   000


Q ss_pred             Ccc-CchhhHHHHHHHHHHhccHHHHHHHh-hhcccCCCcccChHHHHHHHHHhhCCChhHHHHHHHH-HHhhccccch
Q 042541          388 SVF-QSKNDILDCLGSSLDVLNNEVKECYL-DLCSFPEDQRIPITALIDMWMELYELVDDVFAITNLH-ELSSQNLVDR  463 (695)
Q Consensus       388 ~~~-~~~~~i~~~l~~s~~~L~~~~k~cf~-~ls~fp~~~~i~~~~Li~~W~~~~~~~~~~~~~~~l~-~L~~~sLl~~  463 (695)
                      ... ..-......+...+..|++..+..+. ....|+.+ .+..+.+....    ..+.+ .+++.++ .|++.+||+.
T Consensus       237 ~I~~~~v~~~l~~~~~~~~~l~~~~~~~l~~~~~~~~~~-~~~~~~~a~~l----g~~~~-~~~~~~e~~Li~~~li~~  309 (328)
T PRK00080        237 VITKEIADKALDMLGVDELGLDEMDRKYLRTIIEKFGGG-PVGLDTLAAAL----GEERD-TIEDVYEPYLIQQGFIQR  309 (328)
T ss_pred             CCCHHHHHHHHHHhCCCcCCCCHHHHHHHHHHHHHcCCC-ceeHHHHHHHH----CCCcc-hHHHHhhHHHHHcCCccc
Confidence            000 00112334445566788888777775 66677765 45555553322    33333 6777888 9999999975

>PF05659 RPW8: Arabidopsis broad-spectrum mildew resistance protein RPW8; InterPro: IPR008808 This entry represents the RPW8 domain found in several broad-spectrum mildew resistance proteins from Arabidopsis thaliana and other dicots

Probab=99.08  E-value=6.3e-09  Score=92.73  Aligned_cols=138  Identities=48%  Similarity=0.762  Sum_probs=128.3

Q ss_pred             ChhhHHHHHHHHHHHHHHHHHHHHHHhhhhhchHHHHHHHHHHHhhhHHHHHHHHhhhccCCC-hHHHHHHHHHHHHHHH
Q 042541            1 MAAAFVGGALLGAVFGELLKAVSEEKDKAVTFKDRLEQLESTLRNSIPWIEEIEKLNQVLDRP-KQETENLVRMMEQVEQ   79 (695)
Q Consensus         1 Ma~~~v~~a~~~~v~~kl~~~l~~~~~~~~~~~~~l~~L~~~L~~i~~~l~~ae~~~~~~~~~-~~wl~~l~~~~~d~ed   79 (695)
                      |.+++++||+++.+++.+...+.+..+....++.-+++|..+++.|..++++++..+...+.. +.-+++|.+...++++
T Consensus         1 ~~~eL~~gaalG~~~~eLlk~v~~~~~k~~~fk~~l~~L~sTl~~i~P~i~eI~~~~~eld~~~~ee~e~L~~~L~~g~~   80 (147)
T PF05659_consen    1 PIAELVGGAALGAVFGELLKAVIDASKKSLSFKSILKRLESTLESIIPIIKEIDKLNVELDRPRQEEIERLKELLEKGKE   80 (147)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhhhHHHHHHHHhhhcCCchhHHHHHHHHHHHHHHH
Confidence            677889999999999999999999999999999999999999999999999999988777766 8999999999999999


Q ss_pred             HHHhccccc-hhhhcchhhHHHHHHHHHhhhhHhhccchhhhhhhhhhHHHHHHHHHHHH
Q 042541           80 LVRKCSKVK-WNCFKRYVYAKKIIKLDTSISDFFRTSLPLQHARDGKLIMVEVKEIHTMV  138 (695)
Q Consensus        80 ~ld~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~l~~~~~~~  138 (695)
                      ++..|...+ |.+.+.+.|.+++.++...+.+|+....+.+..++++++...+.++...+
T Consensus        81 LV~k~sk~~r~n~~kk~~y~~Ki~~le~~l~~f~~v~~q~~~~~D~~~l~~~~~e~~~kl  140 (147)
T PF05659_consen   81 LVEKCSKVRRWNLYKKPRYARKIEELEESLRRFIQVDLQLHQLRDIKELLAKMSEMNTKL  140 (147)
T ss_pred             HHHHhccccHHHHHhhHhHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999874 47889999999999999999999999999999999999999999887765

Plant disease resistance (R) genes control the recognition of specific pathogens and activate subsequent defence responses. The R protein-mediated defences typically involve a rapid, localized necrosis, or hypersensitive response (HR), at the site of infection, and the localised formation of antimicrobial chemicals and proteins that restrict growth of the pathogen. The A. thaliana locus Resistance to Powdery Mildew 8 (RPW8) contains two naturally polymorphic, dominant R genes: RPW8.1 and RPW8.2, which individually control resistance to a broad range of powdery mildew pathogens. They induce localised, salicylic acid-dependent defences similar to those induced by R genes that control specific resistance. Apparently, broad-spectrum resistance mediated by RPW8 uses the same mechanisms as specific resistance [, ]. RPW8.1 and RPW8.2 share similarity with an ~150 amino acid module forming the N terminus of a group of disease resistance proteins, which have a nucleotide-binding site (NBS) and leucine-rich repeats (LRRs) [, ]. The RPW8 domain sequences contain a predicted N-terminal transmembrane (TM) region or possibly a signal peptide, and a coiled-coil (CC) motif [].

>COG3903 Predicted ATPase [General function prediction only]

Probab=99.07  E-value=6.9e-10  Score=112.44  Aligned_cols=289  Identities=18%  Similarity=0.197  Sum_probs=201.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHh
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQ  266 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~  266 (695)
                      .+.+.++|.|||||||++-.+.+   +...|..++.++......+...+.-.+...++....+   .+.....+   ...
T Consensus        14 ~RlvtL~g~ggvgkttl~~~~a~---~~~~~~~~v~~vdl~pitD~~~v~~~~ag~~gl~~~~---g~~~~~~~---~~~   84 (414)
T COG3903          14 LRLVTLTGAGGVGKTTLALQAAH---AASEYADGVAFVDLAPITDPALVFPTLAGALGLHVQP---GDSAVDTL---VRR   84 (414)
T ss_pred             hheeeeeccCccceehhhhhhHh---HhhhcccceeeeeccccCchhHhHHHHHhhccccccc---chHHHHHH---HHH
Confidence            58899999999999999988875   7788988887888887777777777777778776433   12222222   244


Q ss_pred             cCCCcEEEEEeCCCCCChH---HHhhhccCCCCCEEEEEcCCCCCCCCC-eEecCCCChH-HHHHHHHHhccCCCCC--C
Q 042541          267 MRIEAILLVLDDVWPGSES---LLQKLGFQLPDYKILVTSRSEFPQFGS-VHYLKPLTYE-AARTLFLHSANLQDGN--S  339 (695)
Q Consensus       267 l~~~~~LlVlDdv~~~~~~---~~~~l~~~~~gs~iivTtR~~~~~~~~-~~~l~~L~~~-ea~~Lf~~~~~~~~~~--~  339 (695)
                      ..+++.++|+||.....+.   ....+..+.+.-.++.|+|......+. .+.+++|+.. ++.++|...+.....+  .
T Consensus        85 ~~~rr~llvldncehl~~~~a~~i~all~~~~~~~~~atsre~~l~~ge~~~~~~~L~~~d~a~~lf~~ra~~~~~~f~l  164 (414)
T COG3903          85 IGDRRALLVLDNCEHLLDACAALIVALLGACPRLAILATSREAILVAGEVHRRVPSLSLFDEAIELFVCRAVLVALSFWL  164 (414)
T ss_pred             HhhhhHHHHhcCcHHHHHHHHHHHHHHHccchhhhhHHHhHhhhcccccccccCCccccCCchhHHHHHHHHHhccceee
Confidence            4688999999997544322   344555566777899999988655554 7788888876 7999988766544332  2


Q ss_pred             CCCchHHHHHHHHhcCCchhHHHHHHHhhCCCCHHH----HHHHHHHhcCCCC-ccCchhhHHHHHHHHHHhccHHHHHH
Q 042541          340 YIPDENIVSKILRACKGCPLALKVVGGSLCGKHEVF----WQRMVKECSRGES-VFQSKNDILDCLGSSLDVLNNEVKEC  414 (695)
Q Consensus       340 ~~~~~~~~~~I~~~c~G~PLai~~~~~~L~~~~~~~----w~~~l~~~~~~~~-~~~~~~~i~~~l~~s~~~L~~~~k~c  414 (695)
                      .......+.+|.+..+|.|++|..+++..+.-...+    .......+..... ...........+.+||.-|..-.+..
T Consensus       165 ~~~~~a~v~~icr~ldg~~laielaaarv~sl~~~~i~~~L~drf~ll~~~~r~a~~~~qtl~asl~ws~~lLtgwe~~~  244 (414)
T COG3903         165 TDDNAAAVAEICRRLDGIPLAIELAAARVRSLSPDEIAAGLRDRFRLLTGGARLAVLRQQTLRASLDWSYALLTGWERAL  244 (414)
T ss_pred             cCCchHHHHHHHHHhhcchHHHHHHHHHHHhcCHHHHHHHHhhHHHHHhcccccchhHHHhccchhhhhhHhhhhHHHHH
Confidence            233567899999999999999999999888754322    2222222322211 11233467889999999999999999


Q ss_pred             HhhhcccCCCcccChHHHHHHHHHhhCCC--hhHHHHHHHHHHhhccccchhhccccCCCCCCCCCcceehhHHHHHHHH
Q 042541          415 YLDLCSFPEDQRIPITALIDMWMELYELV--DDVFAITNLHELSSQNLVDRVVTRKTAGDYGCYNDDFVMQHDLLRELTI  492 (695)
Q Consensus       415 f~~ls~fp~~~~i~~~~Li~~W~~~~~~~--~~~~~~~~l~~L~~~sLl~~~~~~~~~~~~~~~~~~~~~mHdlv~~~a~  492 (695)
                      |..++.|...+...    ...|.+.+...  +.......+..|++.+++....         ..+...|+.-+-+|.|+.
T Consensus       245 ~~rLa~~~g~f~~~----l~~~~a~g~~~~~~~y~~~~a~~ll~~kslv~a~~---------~~~~a~~Rl~eT~r~Yal  311 (414)
T COG3903         245 FGRLAVFVGGFDLG----LALAVAAGADVDVPRYLVLLALTLLVDKSLVVALD---------LLGRARYRLLETGRRYAL  311 (414)
T ss_pred             hcchhhhhhhhccc----HHHHHhcCCccccchHHHHHHHHHHhhccchhhhh---------hhhHHHHHHHHHHHHHHH
Confidence            99999999877644    34555544322  1146777888999999987633         233456777788888886


Q ss_pred             HhccC
Q 042541          493 CRSKS  497 (695)
Q Consensus       493 ~~~~~  497 (695)
                      .+..+
T Consensus       312 aeL~r  316 (414)
T COG3903         312 AELHR  316 (414)
T ss_pred             HHHHh
Confidence            65443

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=99.01  E-value=5.4e-08  Score=107.52  Aligned_cols=286  Identities=15%  Similarity=0.098  Sum_probs=156.5

Q ss_pred             CCCCCCCCcchHHHHHHHHH----cCC-ceEEEEEcCCCCcHHHHHHHHhccccc---cccCC-CcEEEEEeCCCCCHHH
Q 042541          164 PPVISPGLDVPLKELKMELF----KDG-RQFIVVSAPGGYGKTTLVQRLCKDDQV---QGKFK-DDIFYVTVSKNPNVKA  234 (695)
Q Consensus       164 ~~~~~vGr~~~~~~l~~~L~----~~~-~~vv~I~G~gGiGKTtLa~~~~~~~~~---~~~f~-~~~~wv~~~~~~~~~~  234 (695)
                      .|+.++||++|+++|...|.    ..+ ..++.|+|++|.|||+.++.|.+...-   ....+ ..+++|++....+...
T Consensus       753 VPD~LPhREeEIeeLasfL~paIkgsgpnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm~Lstp~s  832 (1164)
T PTZ00112        753 VPKYLPCREKEIKEVHGFLESGIKQSGSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGMNVVHPNA  832 (1164)
T ss_pred             CCCcCCChHHHHHHHHHHHHHHHhcCCCCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCCccCCHHH
Confidence            35678999999999998887    222 357789999999999999999873211   11222 3467888887788888


Q ss_pred             HHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhc---CCCcEEEEEeCCCCCC---hH-HHhhhcc-CCCCCEEEE--EcC
Q 042541          235 IVQKVLHHKGYPVPEFQTDEAAINDLERFFKQM---RIEAILLVLDDVWPGS---ES-LLQKLGF-QLPDYKILV--TSR  304 (695)
Q Consensus       235 ~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l---~~~~~LlVlDdv~~~~---~~-~~~~l~~-~~~gs~iiv--TtR  304 (695)
                      ++..|.+++....+..  .......+.+++..+   .+...+||||+++...   +. +..-+.+ ...+++|+|  +|.
T Consensus       833 IYqvI~qqL~g~~P~~--GlsS~evLerLF~~L~k~~r~v~IIILDEID~L~kK~QDVLYnLFR~~~~s~SKLiLIGISN  910 (1164)
T PTZ00112        833 AYQVLYKQLFNKKPPN--ALNSFKILDRLFNQNKKDNRNVSILIIDEIDYLITKTQKVLFTLFDWPTKINSKLVLIAISN  910 (1164)
T ss_pred             HHHHHHHHHcCCCCCc--cccHHHHHHHHHhhhhcccccceEEEeehHhhhCccHHHHHHHHHHHhhccCCeEEEEEecC
Confidence            9999998885443321  112223444555433   2334699999986543   22 2222322 234566554  332


Q ss_pred             CC-C---------CCCC-CeEecCCCChHHHHHHHHHhccCCCCCCC-CCchHHHHHHHHhcCCchhHHHHHHHhhCCC-
Q 042541          305 SE-F---------PQFG-SVHYLKPLTYEAARTLFLHSANLQDGNSY-IPDENIVSKILRACKGCPLALKVVGGSLCGK-  371 (695)
Q Consensus       305 ~~-~---------~~~~-~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~-~~~~~~~~~I~~~c~G~PLai~~~~~~L~~~-  371 (695)
                      .. .         ...+ ..+...|++.++-.+++..++........ ...+-+|+.++...|..-.||.++-.+.... 
T Consensus       911 dlDLperLdPRLRSRLg~eeIvF~PYTaEQL~dILk~RAe~A~gVLdDdAIELIArkVAq~SGDARKALDILRrAgEike  990 (1164)
T PTZ00112        911 TMDLPERLIPRCRSRLAFGRLVFSPYKGDEIEKIIKERLENCKEIIDHTAIQLCARKVANVSGDIRKALQICRKAFENKR  990 (1164)
T ss_pred             chhcchhhhhhhhhccccccccCCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhhcCCHHHHHHHHHHHHHhhcC
Confidence            21 0         0111 24677999999999999988764321111 1112233333444455666766665444321 


Q ss_pred             ----CHHHHHHHHHHhcCCCCccCchhhHHHHHHHHHHhccHHHHHHHhhhcccCC---CcccChHHHHHHHHH--h--h
Q 042541          372 ----HEVFWQRMVKECSRGESVFQSKNDILDCLGSSLDVLNNEVKECYLDLCSFPE---DQRIPITALIDMWME--L--Y  440 (695)
Q Consensus       372 ----~~~~w~~~l~~~~~~~~~~~~~~~i~~~l~~s~~~L~~~~k~cf~~ls~fp~---~~~i~~~~Li~~W~~--~--~  440 (695)
                          ..+.-+.++.+.            ....+.-....||.+.|-.+..+...-+   ...++...+......  +  |
T Consensus       991 gskVT~eHVrkAleei------------E~srI~e~IktLPlHqKLVLlALIlLlk~tg~~~i~TGEVYerYk~Lce~~G 1058 (1164)
T PTZ00112        991 GQKIVPRDITEATNQL------------FDSPLTNAINYLPWPFKMFLTCLIVELRMLNDFIIPYKKVLNRYKVLVETSG 1058 (1164)
T ss_pred             CCccCHHHHHHHHHHH------------HhhhHHHHHHcCCHHHHHHHHHHHHHHhhcCCCceeHHHHHHHHHHHHHhhh
Confidence                111111122111            1122344567889887765553332211   223555554443321  1  1


Q ss_pred             ---CCChh-HHHHHHHHHHhhccccch
Q 042541          441 ---ELVDD-VFAITNLHELSSQNLVDR  463 (695)
Q Consensus       441 ---~~~~~-~~~~~~l~~L~~~sLl~~  463 (695)
                         .+.+. ....+++.+|...|+|-.
T Consensus      1059 k~iGv~plTqRV~d~L~eL~~LGIIl~ 1085 (1164)
T PTZ00112       1059 KYIGMCSNNELFKIMLDKLVKMGILLI 1085 (1164)
T ss_pred             hhcCCCCcHHHHHHHHHHHHhcCeEEe
Confidence               11111 245566777777776654

>KOG0444 consensus Cytoskeletal regulator Flightless-I (contains leucine-rich and gelsolin repeats) [Cytoskeleton]

Probab=99.01  E-value=1.9e-11  Score=127.65  Aligned_cols=136  Identities=14%  Similarity=0.246  Sum_probs=87.9

Q ss_pred             CCceEEEEEEcc-CccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc-ccccccccc
Q 042541          549 GPEVKVVVLNIR-TKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL-ATVRMNHLQ  626 (695)
Q Consensus       549 ~~~l~~L~l~~~-~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp-~i~~l~~L~  626 (695)
                      +.+|.+|.+++. .....+|.++.+|.||+.+|++.|++.  .+  +..+-++.+|+.|+|++|.|+.+. .++...+|+
T Consensus       196 mtsL~vLhms~TqRTl~N~Ptsld~l~NL~dvDlS~N~Lp--~v--Pecly~l~~LrrLNLS~N~iteL~~~~~~W~~lE  271 (1255)
T KOG0444|consen  196 MTSLSVLHMSNTQRTLDNIPTSLDDLHNLRDVDLSENNLP--IV--PECLYKLRNLRRLNLSGNKITELNMTEGEWENLE  271 (1255)
T ss_pred             chhhhhhhcccccchhhcCCCchhhhhhhhhccccccCCC--cc--hHHHhhhhhhheeccCcCceeeeeccHHHHhhhh
Confidence            344555555554 334567777888888888888776551  11  223567777888888888777777 777777777


Q ss_pred             EEeeccccCCcccccchhhhcccCCCccEEeccccc-ccccCchhhcCCCCCceeecccccCCCCCCCC
Q 042541          627 KVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCN-DLIELPDGLCDIVSMEKLRITNCHRLSALPEG  694 (695)
Q Consensus       627 ~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~-~l~~lP~~i~~L~~L~~L~l~~~~~l~~lP~~  694 (695)
                      +|++|.|+++.+|.-.+     +|++|+.|.+.+|. ...-+|++||+|.+|+.+...+| ++.-+|++
T Consensus       272 tLNlSrNQLt~LP~avc-----KL~kL~kLy~n~NkL~FeGiPSGIGKL~~Levf~aanN-~LElVPEg  334 (1255)
T KOG0444|consen  272 TLNLSRNQLTVLPDAVC-----KLTKLTKLYANNNKLTFEGIPSGIGKLIQLEVFHAANN-KLELVPEG  334 (1255)
T ss_pred             hhccccchhccchHHHh-----hhHHHHHHHhccCcccccCCccchhhhhhhHHHHhhcc-ccccCchh
Confidence            77777777777665544     66667766666543 23346666666666666666663 36666654

>KOG0444 consensus Cytoskeletal regulator Flightless-I (contains leucine-rich and gelsolin repeats) [Cytoskeleton]

Probab=99.01  E-value=2e-11  Score=127.40  Aligned_cols=130  Identities=15%  Similarity=0.201  Sum_probs=77.5

Q ss_pred             CCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc-cccccccccE
Q 042541          549 GPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL-ATVRMNHLQK  627 (695)
Q Consensus       549 ~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp-~i~~l~~L~~  627 (695)
                      +.+|+.|.++.|.. ..+...++.++.||.++++.|++....++  +.+..|..|..|+|++|.+.+.| .+.+-+++-.
T Consensus        54 lqkLEHLs~~HN~L-~~vhGELs~Lp~LRsv~~R~N~LKnsGiP--~diF~l~dLt~lDLShNqL~EvP~~LE~AKn~iV  130 (1255)
T KOG0444|consen   54 LQKLEHLSMAHNQL-ISVHGELSDLPRLRSVIVRDNNLKNSGIP--TDIFRLKDLTILDLSHNQLREVPTNLEYAKNSIV  130 (1255)
T ss_pred             Hhhhhhhhhhhhhh-HhhhhhhccchhhHHHhhhccccccCCCC--chhcccccceeeecchhhhhhcchhhhhhcCcEE
Confidence            34444444433322 22233455566666666666655433332  22556666666666666666666 6666666666


Q ss_pred             EeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeeccccc
Q 042541          628 VSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCH  686 (695)
Q Consensus       628 L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~  686 (695)
                      |+||+|+|..+|.+.+.    +|+.|-.|||++ +.+..+|+.+..|.+|++|.|++|+
T Consensus       131 LNLS~N~IetIPn~lfi----nLtDLLfLDLS~-NrLe~LPPQ~RRL~~LqtL~Ls~NP  184 (1255)
T KOG0444|consen  131 LNLSYNNIETIPNSLFI----NLTDLLFLDLSN-NRLEMLPPQIRRLSMLQTLKLSNNP  184 (1255)
T ss_pred             EEcccCccccCCchHHH----hhHhHhhhcccc-chhhhcCHHHHHHhhhhhhhcCCCh
Confidence            66666666666666665    666666666666 3566666666666666666666665

>PLN03210 Resistant to P

Probab=98.99  E-value=2.3e-09  Score=129.75  Aligned_cols=59  Identities=10%  Similarity=0.084  Sum_probs=36.6

Q ss_pred             ccceEEeeecCCcccCCCCCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccC
Q 042541          527 NNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYG  585 (695)
Q Consensus       527 ~~~r~l~~~~~~~~~~~~~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~  585 (695)
                      ...+.+.+.........+....+++|+.|.+.++.....+|..+..+++|+.|++++|.
T Consensus       634 ~~Lk~L~Ls~~~~l~~ip~ls~l~~Le~L~L~~c~~L~~lp~si~~L~~L~~L~L~~c~  692 (1153)
T PLN03210        634 TGLRNIDLRGSKNLKEIPDLSMATNLETLKLSDCSSLVELPSSIQYLNKLEDLDMSRCE  692 (1153)
T ss_pred             CCCCEEECCCCCCcCcCCccccCCcccEEEecCCCCccccchhhhccCCCCEEeCCCCC
Confidence            34555555443222222222356777777777776667777777888888888887753

syringae 6; Provisional

>PF05729 NACHT: NACHT domain

Probab=98.96  E-value=6.7e-09  Score=97.00  Aligned_cols=136  Identities=20%  Similarity=0.303  Sum_probs=85.7

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhcccccccc----CCCcEEEEEeCCCCCHH---HHHHHHHHhcCCCCCCCCChHHHHHHH
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKDDQVQGK----FKDDIFYVTVSKNPNVK---AIVQKVLHHKGYPVPEFQTDEAAINDL  260 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~~~~~~~----f~~~~~wv~~~~~~~~~---~~~~~i~~~l~~~~~~~~~~~~~~~~l  260 (695)
                      +++.|+|.+|+||||+++.++..-.....    +.. ++|++.+......   .+...|..+......      .....+
T Consensus         1 r~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~------~~~~~~   73 (166)
T PF05729_consen    1 RVLWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPY-PFFFSLRDISDSNNSRSLADLLFDQLPESIA------PIEELL   73 (166)
T ss_pred             CEEEEECCCCCChHHHHHHHHHHHHhcCcccccceE-EEEEeehhhhhccccchHHHHHHHhhccchh------hhHHHH
Confidence            58999999999999999999874222222    233 6677776544332   344444444332211      111112


Q ss_pred             HHHHHhcCCCcEEEEEeCCCCCChH-----------HHhhhccC--CCCCEEEEEcCCCCC-------CCCCeEecCCCC
Q 042541          261 ERFFKQMRIEAILLVLDDVWPGSES-----------LLQKLGFQ--LPDYKILVTSRSEFP-------QFGSVHYLKPLT  320 (695)
Q Consensus       261 ~~~~~~l~~~~~LlVlDdv~~~~~~-----------~~~~l~~~--~~gs~iivTtR~~~~-------~~~~~~~l~~L~  320 (695)
                      ...+.  ..+++++|+|++++....           .+..+...  .+++++|||+|....       .....+.+.+|+
T Consensus        74 ~~~~~--~~~~~llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~~~~~~~~~~~~~~~~~~l~~~~  151 (166)
T PF05729_consen   74 QELLE--KNKRVLLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRPRAFPDLRRRLKQAQILELEPFS  151 (166)
T ss_pred             HHHHH--cCCceEEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcCChHHHHHHhcCCCcEEEECCCC
Confidence            22222  578999999998665431           23333333  568999999998732       122479999999


Q ss_pred             hHHHHHHHHHhc
Q 042541          321 YEAARTLFLHSA  332 (695)
Q Consensus       321 ~~ea~~Lf~~~~  332 (695)
                      +++..+++.++.
T Consensus       152 ~~~~~~~~~~~f  163 (166)
T PF05729_consen  152 EEDIKQYLRKYF  163 (166)
T ss_pred             HHHHHHHHHHHh
Confidence            999999998764

>PTZ00202 tuzin; Provisional

Probab=98.90  E-value=3.7e-06  Score=86.74  Aligned_cols=163  Identities=15%  Similarity=0.101  Sum_probs=106.7

Q ss_pred             CCCCCCCCCCCCCCcchHHHHHHHHHcC---CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHH
Q 042541          158 CCSAPDPPVISPGLDVPLKELKMELFKD---GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKA  234 (695)
Q Consensus       158 ~~~~~~~~~~~vGr~~~~~~l~~~L~~~---~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~  234 (695)
                      ....|..+..|+||+.++.++...|.+.   ..+++.|+|++|+|||||++.+...  ..  +.  .++++..   +..+
T Consensus       254 ~~~lPa~~~~FVGReaEla~Lr~VL~~~d~~~privvLtG~~G~GKTTLlR~~~~~--l~--~~--qL~vNpr---g~eE  324 (550)
T PTZ00202        254 LQSAPAVIRQFVSREAEESWVRQVLRRLDTAHPRIVVFTGFRGCGKSSLCRSAVRK--EG--MP--AVFVDVR---GTED  324 (550)
T ss_pred             ccCCCCCccCCCCcHHHHHHHHHHHhccCCCCceEEEEECCCCCCHHHHHHHHHhc--CC--ce--EEEECCC---CHHH
Confidence            4567778889999999999999988632   2568999999999999999999863  22  21  3344444   6799


Q ss_pred             HHHHHHHhcCCCCCCCCChHHHHHHHHHHHH--hc-CCCcEEEEEeCCCCCC-hH---HHhhhccCCCCCEEEEEcCCCC
Q 042541          235 IVQKVLHHKGYPVPEFQTDEAAINDLERFFK--QM-RIEAILLVLDDVWPGS-ES---LLQKLGFQLPDYKILVTSRSEF  307 (695)
Q Consensus       235 ~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~--~l-~~~~~LlVlDdv~~~~-~~---~~~~l~~~~~gs~iivTtR~~~  307 (695)
                      ++..++.+||.+..  ....+....+++.+.  .. ++++.+||+-==...+ ..   ..-.+.+...-|+|++---.+.
T Consensus       325 lLr~LL~ALGV~p~--~~k~dLLrqIqeaLl~~~~e~GrtPVLII~lreg~~l~rvyne~v~la~drr~ch~v~evples  402 (550)
T PTZ00202        325 TLRSVVKALGVPNV--EACGDLLDFISEACRRAKKMNGETPLLVLKLREGSSLQRVYNEVVALACDRRLCHVVIEVPLES  402 (550)
T ss_pred             HHHHHHHHcCCCCc--ccHHHHHHHHHHHHHHHHHhCCCCEEEEEEecCCCcHHHHHHHHHHHHccchhheeeeeehHhh
Confidence            99999999997432  233455566666552  22 3677777764221111 00   1222333334588887544442


Q ss_pred             CCC-------CCeEecCCCChHHHHHHHHHh
Q 042541          308 PQF-------GSVHYLKPLTYEAARTLFLHS  331 (695)
Q Consensus       308 ~~~-------~~~~~l~~L~~~ea~~Lf~~~  331 (695)
                      ..+       -..|-+++++.++|.++-.+.
T Consensus       403 lt~~~~~lprldf~~vp~fsr~qaf~y~~h~  433 (550)
T PTZ00202        403 LTIANTLLPRLDFYLVPNFSRSQAFAYTQHA  433 (550)
T ss_pred             cchhcccCccceeEecCCCCHHHHHHHHhhc
Confidence            111       127889999999998877654

>COG3899 Predicted ATPase [General function prediction only]

Probab=98.89  E-value=1.4e-07  Score=109.27  Aligned_cols=306  Identities=16%  Similarity=0.201  Sum_probs=176.3

Q ss_pred             CCCCcchHHHHHHHHH---cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEe---CCCCC---HHHHHHH
Q 042541          168 SPGLDVPLKELKMELF---KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTV---SKNPN---VKAIVQK  238 (695)
Q Consensus       168 ~vGr~~~~~~l~~~L~---~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~---~~~~~---~~~~~~~  238 (695)
                      ++||+.+++.|...+.   .+...++.+.|..|||||+|+++|..  .+.+.+.. .+-..+   ..+..   ....+++
T Consensus         2 l~GRe~ev~~Ll~~f~~v~~g~~~~~lv~G~sGIGKsalv~ev~~--~i~~~~~~-~i~~~f~q~~~~ipl~~lvq~~r~   78 (849)
T COG3899           2 LYGRETELAQLLAAFDRVSKGRGEVVLVAGESGIGKSALVNEVHK--PITQQRGY-FIKGKFDQFERNIPLSPLVQAFRD   78 (849)
T ss_pred             CCchHhHHHHHHHHHHHHhCCCeEEEEEeecCCCcHHHHHHHHHH--HHhcccee-eeHhhcccccCCCchHHHHHHHHH
Confidence            6999999999999887   45578999999999999999999987  55444221 111111   12221   1222233


Q ss_pred             HHHhc-------------------CCCCC------------------C--CCC--hHHHHH-HHHHHH--HhcCCCcEEE
Q 042541          239 VLHHK-------------------GYPVP------------------E--FQT--DEAAIN-DLERFF--KQMRIEAILL  274 (695)
Q Consensus       239 i~~~l-------------------~~~~~------------------~--~~~--~~~~~~-~l~~~~--~~l~~~~~Ll  274 (695)
                      ++.++                   +....                  .  ...  ...... .+...+  -.-+.++.++
T Consensus        79 l~~~ll~~~~~~~~~~~~~il~~~g~~~~~~~~vip~L~~i~g~~~~~~el~~~~~~~r~n~~~~~~i~~~~~~~~plVi  158 (849)
T COG3899          79 LMGQLLSESDTRILSWRARLLAALGENGQVIIDVIPELELIIGKRPPALELSPTAAQNRFNLAFLRFIQVFTAEEHPLVI  158 (849)
T ss_pred             HHHHHhhccchHHHHHHHHHHHHhcccchhHHhhhHHHHhhcCCCcchhhcccchhHHHHHHHHHHHHHHHHhccCCeEE
Confidence            33322                   11100                  0  000  000111 122222  1225779999


Q ss_pred             EEeCCCCCChH---HHhhhccCCC-----CCEEEE--EcCCCC------CCCCCeEecCCCChHHHHHHHHHhccCCCCC
Q 042541          275 VLDDVWPGSES---LLQKLGFQLP-----DYKILV--TSRSEF------PQFGSVHYLKPLTYEAARTLFLHSANLQDGN  338 (695)
Q Consensus       275 VlDdv~~~~~~---~~~~l~~~~~-----gs~iiv--TtR~~~------~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~  338 (695)
                      |+||+...+..   +++.+....+     ...|..  |.+...      ......+.|.||+..+...+.......... 
T Consensus       159 ~leDlhWaD~~SL~lL~~lm~~~~~~~~~~n~v~~~h~~~~~~~~~~~~~~~i~~I~L~PL~~~d~~~lV~~~l~~~~~-  237 (849)
T COG3899         159 VLEDLHWADSASLKLLQLLMDRIAIGAYRDNEVLLLHPLRPTLGEILKSATNITTITLAPLSRADTNQLVAATLGCTKL-  237 (849)
T ss_pred             EEecccccChhHHHHHHHHHHhcchhhhhccccccCCCccchhhHHhhcCCceeEEecCcCchhhHHHHHHHHhCCccc-
Confidence            99999655543   2333332222     112222  333321      122348999999999999999887654322 


Q ss_pred             CCCCchHHHHHHHHhcCCchhHHHHHHHhhCCC-------CHHHHHHHHHHhcCCCCccCchhhHHHHHHHHHHhccHHH
Q 042541          339 SYIPDENIVSKILRACKGCPLALKVVGGSLCGK-------HEVFWQRMVKECSRGESVFQSKNDILDCLGSSLDVLNNEV  411 (695)
Q Consensus       339 ~~~~~~~~~~~I~~~c~G~PLai~~~~~~L~~~-------~~~~w~~~l~~~~~~~~~~~~~~~i~~~l~~s~~~L~~~~  411 (695)
                         ...+....|.++..|+|+.+..+-..+...       +...|..-+.....    .+..+++...+..-.+.||...
T Consensus       238 ---~~~p~~~~i~~kt~GnPfFi~e~lk~l~~~~~i~f~~~~~~w~~~~~~i~~----~~~~~~vv~~l~~rl~kL~~~t  310 (849)
T COG3899         238 ---LPAPLLELIFEKTKGNPFFIEEFLKALYEEGLLVFNFDTGAWQCSIASLGI----LATTDAVVEFLAARLQKLPGTT  310 (849)
T ss_pred             ---ccchHHHHHHHHhcCCCccHHHHHHHHHhCCeeEecCCCcceeccHHhcCC----chhhHHHHHHHHHHHhcCCHHH
Confidence               246779999999999999999988877653       23445433332221    1222346667899999999999


Q ss_pred             HHHHhhhcccCCCcccChHHHHHHHHHhhCCChhHHHHHHHHHHhhccccchhhccccCCCCCCCCCc-ceehhHHHHHH
Q 042541          412 KECYLDLCSFPEDQRIPITALIDMWMELYELVDDVFAITNLHELSSQNLVDRVVTRKTAGDYGCYNDD-FVMQHDLLREL  490 (695)
Q Consensus       412 k~cf~~ls~fp~~~~i~~~~Li~~W~~~~~~~~~~~~~~~l~~L~~~sLl~~~~~~~~~~~~~~~~~~-~~~mHdlv~~~  490 (695)
                      ++.+...|++-..  |+...|...|-.   ... ..+...++.|....++-..+....+.   ..... |-..||.|++.
T Consensus       311 ~~Vl~~AA~iG~~--F~l~~La~l~~~---~~~-~~a~~l~~al~e~lI~~~~~~yr~~~---~~~~~~Y~F~H~~vqqa  381 (849)
T COG3899         311 REVLKAAACIGNR--FDLDTLAALAED---SPA-LEAAALLDALQEGLILPLSETYRFGS---NVDIATYKFLHDRVQQA  381 (849)
T ss_pred             HHHHHHHHHhCcc--CCHHHHHHHHhh---chH-HHHHHHHHHhHhhceecccccccccc---ccchhhHHhhHHHHHHH
Confidence            9999999998755  455666555532   222 25666666665544443211100000   11111 23479999998


Q ss_pred             HHH
Q 042541          491 TIC  493 (695)
Q Consensus       491 a~~  493 (695)
                      |-.
T Consensus       382 aY~  384 (849)
T COG3899         382 AYN  384 (849)
T ss_pred             Hhc
Confidence            844

>KOG0472 consensus Leucine-rich repeat protein [Function unknown]

Probab=98.81  E-value=1.3e-09  Score=108.75  Aligned_cols=122  Identities=19%  Similarity=0.279  Sum_probs=100.8

Q ss_pred             CccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc-cccccccccEEeeccccCCccc
Q 042541          561 TKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL-ATVRMNHLQKVSLVMCNVGQVF  639 (695)
Q Consensus       561 ~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp-~i~~l~~L~~L~l~~~~i~~~~  639 (695)
                      +....+|..++.+++|..|+|+||-..  .+  +..++.+..|+.|+++.|++..+| .+-.+.-|+.+-.++|++..++
T Consensus       422 n~isfv~~~l~~l~kLt~L~L~NN~Ln--~L--P~e~~~lv~Lq~LnlS~NrFr~lP~~~y~lq~lEtllas~nqi~~vd  497 (565)
T KOG0472|consen  422 NKISFVPLELSQLQKLTFLDLSNNLLN--DL--PEEMGSLVRLQTLNLSFNRFRMLPECLYELQTLETLLASNNQIGSVD  497 (565)
T ss_pred             CccccchHHHHhhhcceeeecccchhh--hc--chhhhhhhhhheecccccccccchHHHhhHHHHHHHHhccccccccC
Confidence            444566778899999999999987442  11  122678888999999999999999 7778888888888889999998


Q ss_pred             ccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccccCCCCCCC
Q 042541          640 RNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPE  693 (695)
Q Consensus       640 ~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~~l~~lP~  693 (695)
                      ++-..    ++.+|.+|||.+ +.+..+|+.+|++++|+||++.||+ ++ .|+
T Consensus       498 ~~~l~----nm~nL~tLDL~n-Ndlq~IPp~LgnmtnL~hLeL~gNp-fr-~Pr  544 (565)
T KOG0472|consen  498 PSGLK----NMRNLTTLDLQN-NDLQQIPPILGNMTNLRHLELDGNP-FR-QPR  544 (565)
T ss_pred             hHHhh----hhhhcceeccCC-CchhhCChhhccccceeEEEecCCc-cC-CCH
Confidence            88444    899999999998 5789999999999999999999988 54 553

>KOG4194 consensus Membrane glycoprotein LIG-1 [Signal transduction mechanisms]

Probab=98.76  E-value=1.1e-09  Score=114.04  Aligned_cols=139  Identities=17%  Similarity=0.264  Sum_probs=96.5

Q ss_pred             CCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--ccccccc
Q 042541          547 MQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNH  624 (695)
Q Consensus       547 ~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~  624 (695)
                      +++++|+.|+|++|.....-+++..-.++|+.|+|++|.+..  + ...++..|+.|+.|+|++|+++++.  .+..+.+
T Consensus       290 fgLt~L~~L~lS~NaI~rih~d~WsftqkL~~LdLs~N~i~~--l-~~~sf~~L~~Le~LnLs~Nsi~~l~e~af~~lss  366 (873)
T KOG4194|consen  290 FGLTSLEQLDLSYNAIQRIHIDSWSFTQKLKELDLSSNRITR--L-DEGSFRVLSQLEELNLSHNSIDHLAEGAFVGLSS  366 (873)
T ss_pred             cccchhhhhccchhhhheeecchhhhcccceeEecccccccc--C-ChhHHHHHHHhhhhcccccchHHHHhhHHHHhhh
Confidence            356677777777775555555566667777777777765531  1 1123666777788888888887776  6777888


Q ss_pred             ccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchh-hcCCCCCceeecccccCCCCC
Q 042541          625 LQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDG-LCDIVSMEKLRITNCHRLSAL  691 (695)
Q Consensus       625 L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~-i~~L~~L~~L~l~~~~~l~~l  691 (695)
                      |+.|||++|.+....++....+. .|++|+.|++.+| .+..+|.. |..|.+|++|||.+|. +.++
T Consensus       367 L~~LdLr~N~ls~~IEDaa~~f~-gl~~LrkL~l~gN-qlk~I~krAfsgl~~LE~LdL~~Na-iaSI  431 (873)
T KOG4194|consen  367 LHKLDLRSNELSWCIEDAAVAFN-GLPSLRKLRLTGN-QLKSIPKRAFSGLEALEHLDLGDNA-IASI  431 (873)
T ss_pred             hhhhcCcCCeEEEEEecchhhhc-cchhhhheeecCc-eeeecchhhhccCcccceecCCCCc-ceee
Confidence            88888888877766554322111 6888888888884 67888864 8889999999998866 4443

>PRK13342 recombination factor protein RarA; Reviewed

Probab=98.76  E-value=1.1e-07  Score=102.08  Aligned_cols=174  Identities=16%  Similarity=0.137  Sum_probs=105.4

Q ss_pred             CCCCCCCcchHHH---HHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHH
Q 042541          165 PVISPGLDVPLKE---LKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLH  241 (695)
Q Consensus       165 ~~~~vGr~~~~~~---l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~  241 (695)
                      -+.+||.+..+..   +..++.......+.|+|++|+||||||+.+++.  ....      |+.++.......-++.+++
T Consensus        11 l~d~vGq~~~v~~~~~L~~~i~~~~~~~ilL~GppGtGKTtLA~~ia~~--~~~~------~~~l~a~~~~~~~ir~ii~   82 (413)
T PRK13342         11 LDEVVGQEHLLGPGKPLRRMIEAGRLSSMILWGPPGTGKTTLARIIAGA--TDAP------FEALSAVTSGVKDLREVIE   82 (413)
T ss_pred             HHHhcCcHHHhCcchHHHHHHHcCCCceEEEECCCCCCHHHHHHHHHHH--hCCC------EEEEecccccHHHHHHHHH
Confidence            4467998887665   777787777778899999999999999999873  3222      3333322111111112221


Q ss_pred             hcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChHHHhhhccCC-CCCEEEE--EcCCCCC-------CCC
Q 042541          242 HKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSESLLQKLGFQL-PDYKILV--TSRSEFP-------QFG  311 (695)
Q Consensus       242 ~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~~~~~l~~~~-~gs~iiv--TtR~~~~-------~~~  311 (695)
                      ..                 ..  ....+++.+|++|+++.........+.... .|..++|  ||.+...       .-.
T Consensus        83 ~~-----------------~~--~~~~g~~~vL~IDEi~~l~~~~q~~LL~~le~~~iilI~att~n~~~~l~~aL~SR~  143 (413)
T PRK13342         83 EA-----------------RQ--RRSAGRRTILFIDEIHRFNKAQQDALLPHVEDGTITLIGATTENPSFEVNPALLSRA  143 (413)
T ss_pred             HH-----------------HH--hhhcCCceEEEEechhhhCHHHHHHHHHHhhcCcEEEEEeCCCChhhhccHHHhccc
Confidence            11                 10  111467899999999877644333332222 3444444  3333211       112


Q ss_pred             CeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHH
Q 042541          312 SVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVG  365 (695)
Q Consensus       312 ~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~  365 (695)
                      ..+.+.+++.++...++.+.+.........-..+....|++.|+|.+..+..+.
T Consensus       144 ~~~~~~~ls~e~i~~lL~~~l~~~~~~~i~i~~~al~~l~~~s~Gd~R~aln~L  197 (413)
T PRK13342        144 QVFELKPLSEEDIEQLLKRALEDKERGLVELDDEALDALARLANGDARRALNLL  197 (413)
T ss_pred             eeeEeCCCCHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHhCCCCHHHHHHHH
Confidence            378999999999999998865331111102246778899999999997665443

>PF14580 LRR_9: Leucine-rich repeat; PDB: 2JE1_D 2JE0_A 2JQD_A

Probab=98.73  E-value=9.9e-09  Score=94.88  Aligned_cols=126  Identities=17%  Similarity=0.229  Sum_probs=45.3

Q ss_pred             CCCceEEEEEEccCccccCChhhc-CCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc-cc-ccccc
Q 042541          548 QGPEVKVVVLNIRTKKYVLPDFLQ-KMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL-AT-VRMNH  624 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~~~~-~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp-~i-~~l~~  624 (695)
                      ++.+++.|.|.++.... + +.++ .+.+|+.|++++|++.     .++.+..|++|+.|++++|.|++++ .+ ..+++
T Consensus        17 n~~~~~~L~L~~n~I~~-I-e~L~~~l~~L~~L~Ls~N~I~-----~l~~l~~L~~L~~L~L~~N~I~~i~~~l~~~lp~   89 (175)
T PF14580_consen   17 NPVKLRELNLRGNQIST-I-ENLGATLDKLEVLDLSNNQIT-----KLEGLPGLPRLKTLDLSNNRISSISEGLDKNLPN   89 (175)
T ss_dssp             ---------------------S--TT-TT--EEE-TTS--S-------TT----TT--EEE--SS---S-CHHHHHH-TT
T ss_pred             ccccccccccccccccc-c-cchhhhhcCCCEEECCCCCCc-----cccCccChhhhhhcccCCCCCCccccchHHhCCc
Confidence            34456777777763321 1 2343 4677888888887663     2334667788888888888888776 55 35788


Q ss_pred             ccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCch----hhcCCCCCceeeccc
Q 042541          625 LQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPD----GLCDIVSMEKLRITN  684 (695)
Q Consensus       625 L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~----~i~~L~~L~~L~l~~  684 (695)
                      |+.|++++|.|..+-. . ..+. .+++|+.|++.+|+ +..-+.    -+..+++|+.||-..
T Consensus        90 L~~L~L~~N~I~~l~~-l-~~L~-~l~~L~~L~L~~NP-v~~~~~YR~~vi~~lP~Lk~LD~~~  149 (175)
T PF14580_consen   90 LQELYLSNNKISDLNE-L-EPLS-SLPKLRVLSLEGNP-VCEKKNYRLFVIYKLPSLKVLDGQD  149 (175)
T ss_dssp             --EEE-TTS---SCCC-C-GGGG-G-TT--EEE-TT-G-GGGSTTHHHHHHHH-TT-SEETTEE
T ss_pred             CCEEECcCCcCCChHH-h-HHHH-cCCCcceeeccCCc-ccchhhHHHHHHHHcChhheeCCEE
Confidence            8888888887766433 1 1222 67888888888764 333342    256788888887654

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=98.73  E-value=3.9e-07  Score=95.89  Aligned_cols=191  Identities=15%  Similarity=0.169  Sum_probs=111.3

Q ss_pred             CCCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccc-cCCCcEEEEEeCCCCCH--HHHHH--HH
Q 042541          165 PVISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQG-KFKDDIFYVTVSKNPNV--KAIVQ--KV  239 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~-~f~~~~~wv~~~~~~~~--~~~~~--~i  239 (695)
                      -+.++|++..++.+..++..+..+.+.++|++|+||||+|+.+.+  .+.. .+....+.+++++....  ..+..  ..
T Consensus        14 ~~~~~g~~~~~~~L~~~~~~~~~~~lll~Gp~GtGKT~la~~~~~--~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~   91 (337)
T PRK12402         14 LEDILGQDEVVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRALAR--ELYGDPWENNFTEFNVADFFDQGKKYLVEDPRF   91 (337)
T ss_pred             HHHhcCCHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHH--HhcCcccccceEEechhhhhhcchhhhhcCcch
Confidence            356799999999999988877766789999999999999999987  3322 22333445555432110  00000  00


Q ss_pred             HHhcCCCCCCCCChHHHHHHHHHHHH---h---cCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCC--
Q 042541          240 LHHKGYPVPEFQTDEAAINDLERFFK---Q---MRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEF--  307 (695)
Q Consensus       240 ~~~l~~~~~~~~~~~~~~~~l~~~~~---~---l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~--  307 (695)
                      ...++....   ........++.+++   .   ..+.+-+||+||+......    +...+....+.+++|+||....  
T Consensus        92 ~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~vlilDe~~~l~~~~~~~L~~~le~~~~~~~~Il~~~~~~~~  168 (337)
T PRK12402         92 AHFLGTDKR---IRSSKIDNFKHVLKEYASYRPLSADYKTILLDNAEALREDAQQALRRIMEQYSRTCRFIIATRQPSKL  168 (337)
T ss_pred             hhhhhhhhh---hccchHHHHHHHHHHHHhcCCCCCCCcEEEEeCcccCCHHHHHHHHHHHHhccCCCeEEEEeCChhhC
Confidence            000000000   00001122222221   1   1244568999999766533    2222333344577888775431  


Q ss_pred             ----CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHH
Q 042541          308 ----PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKV  363 (695)
Q Consensus       308 ----~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~  363 (695)
                          ...+..+.+.+++.++...++...+......   -..+.+..+++.++|.+-.+..
T Consensus       169 ~~~L~sr~~~v~~~~~~~~~~~~~l~~~~~~~~~~---~~~~al~~l~~~~~gdlr~l~~  225 (337)
T PRK12402        169 IPPIRSRCLPLFFRAPTDDELVDVLESIAEAEGVD---YDDDGLELIAYYAGGDLRKAIL  225 (337)
T ss_pred             chhhcCCceEEEecCCCHHHHHHHHHHHHHHcCCC---CCHHHHHHHHHHcCCCHHHHHH
Confidence                1223478899999999999998866433321   2367889999999998765543

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=98.71  E-value=1.4e-06  Score=96.35  Aligned_cols=189  Identities=13%  Similarity=0.109  Sum_probs=110.5

Q ss_pred             CCCCCCCcchHHHHHHHHHcCC-ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHH-HHh
Q 042541          165 PVISPGLDVPLKELKMELFKDG-RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKV-LHH  242 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~-~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i-~~~  242 (695)
                      -+.+||.+..++.|..++..+. ...+.++|..|+||||+|+.+.+...-...+.    ...+..+.+-..+...- ..-
T Consensus        15 FdEVIGQe~Vv~~L~~aL~~gRL~HAyLFtGPpGvGKTTlAriLAKaLnCe~~~~----~~PCG~C~sCr~I~~G~h~Dv   90 (830)
T PRK07003         15 FASLVGQEHVVRALTHALDGGRLHHAYLFTGTRGVGKTTLSRIFAKALNCETGVT----SQPCGVCRACREIDEGRFVDY   90 (830)
T ss_pred             HHHHcCcHHHHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCccCCC----CCCCcccHHHHHHhcCCCceE
Confidence            3467999999999999998766 45668999999999999998876311111100    00011111111110000 000


Q ss_pred             cCCCCCCCCChHHHHHHHHHHHHh-----cCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCCCC---
Q 042541          243 KGYPVPEFQTDEAAINDLERFFKQ-----MRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFPQF---  310 (695)
Q Consensus       243 l~~~~~~~~~~~~~~~~l~~~~~~-----l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~~~---  310 (695)
                      +.....    ....++.++++++.     ..++.-++|||+++.....    +++.+....++.++|+||.+.....   
T Consensus        91 iEIDAa----s~rgVDdIReLIe~a~~~P~~gr~KVIIIDEah~LT~~A~NALLKtLEEPP~~v~FILaTtd~~KIp~TI  166 (830)
T PRK07003         91 VEMDAA----SNRGVDEMAALLERAVYAPVDARFKVYMIDEVHMLTNHAFNAMLKTLEEPPPHVKFILATTDPQKIPVTV  166 (830)
T ss_pred             EEeccc----ccccHHHHHHHHHHHHhccccCCceEEEEeChhhCCHHHHHHHHHHHHhcCCCeEEEEEECChhhccchh
Confidence            000000    00112222233211     2356678999999877643    4455544556788888888763211   


Q ss_pred             ---CCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCch-hHHHHH
Q 042541          311 ---GSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCP-LALKVV  364 (695)
Q Consensus       311 ---~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~P-Lai~~~  364 (695)
                         ...+++++++.++..+.+.+.+.....   .-..+..+.|++.++|.. -++..+
T Consensus       167 rSRCq~f~Fk~Ls~eeIv~~L~~Il~~EgI---~id~eAL~lIA~~A~GsmRdALsLL  221 (830)
T PRK07003        167 LSRCLQFNLKQMPAGHIVSHLERILGEERI---AFEPQALRLLARAAQGSMRDALSLT  221 (830)
T ss_pred             hhheEEEecCCcCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHcCCCHHHHHHHH
Confidence               127999999999999999887654322   124677889999999865 455543

>KOG0472 consensus Leucine-rich repeat protein [Function unknown]

Probab=98.71  E-value=7.1e-10  Score=110.55  Aligned_cols=117  Identities=18%  Similarity=0.229  Sum_probs=102.5

Q ss_pred             CccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc-ccc-ccccccEEeeccccCCcc
Q 042541          561 TKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL-ATV-RMNHLQKVSLVMCNVGQV  638 (695)
Q Consensus       561 ~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp-~i~-~l~~L~~L~l~~~~i~~~  638 (695)
                      +..+.+|+.+++|.+|..|+|+.|.+     ..+|.|.++..|+.|.+..|.|..+| +++ +|.+|-+|||+.|+++..
T Consensus       193 N~L~tlP~~lg~l~~L~~LyL~~Nki-----~~lPef~gcs~L~Elh~g~N~i~~lpae~~~~L~~l~vLDLRdNklke~  267 (565)
T KOG0472|consen  193 NLLETLPPELGGLESLELLYLRRNKI-----RFLPEFPGCSLLKELHVGENQIEMLPAEHLKHLNSLLVLDLRDNKLKEV  267 (565)
T ss_pred             hhhhcCChhhcchhhhHHHHhhhccc-----ccCCCCCccHHHHHHHhcccHHHhhHHHHhcccccceeeeccccccccC
Confidence            45578899999999999999998765     23345788999999999999999999 666 899999999999999999


Q ss_pred             cccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccccCCCC
Q 042541          639 FRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSA  690 (695)
Q Consensus       639 ~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~~l~~  690 (695)
                      |.+++     .|++|..||+++ +.+..+|.++|+| .|+.|-+.||+ ++.
T Consensus       268 Pde~c-----lLrsL~rLDlSN-N~is~Lp~sLgnl-hL~~L~leGNP-lrT  311 (565)
T KOG0472|consen  268 PDEIC-----LLRSLERLDLSN-NDISSLPYSLGNL-HLKFLALEGNP-LRT  311 (565)
T ss_pred             chHHH-----HhhhhhhhcccC-CccccCCcccccc-eeeehhhcCCc-hHH
Confidence            98887     899999999998 5789999999999 99999999987 544

>KOG4194 consensus Membrane glycoprotein LIG-1 [Signal transduction mechanisms]

Probab=98.69  E-value=1.2e-08  Score=106.60  Aligned_cols=151  Identities=11%  Similarity=0.119  Sum_probs=74.3

Q ss_pred             ccceEEeeecCCcccCCCCC-CCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcE
Q 042541          527 NNASLLSISTDETFSSNWPD-MQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKK  605 (695)
Q Consensus       527 ~~~r~l~~~~~~~~~~~~~~-~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~  605 (695)
                      .++.+|-+.++.+....... -.+.+|.+|.|+.|....-.+..|+++++|+.|+|..|.+...   ....+..|++|+.
T Consensus       173 ~ni~~L~La~N~It~l~~~~F~~lnsL~tlkLsrNrittLp~r~Fk~L~~L~~LdLnrN~iriv---e~ltFqgL~Sl~n  249 (873)
T KOG4194|consen  173 VNIKKLNLASNRITTLETGHFDSLNSLLTLKLSRNRITTLPQRSFKRLPKLESLDLNRNRIRIV---EGLTFQGLPSLQN  249 (873)
T ss_pred             CCceEEeeccccccccccccccccchheeeecccCcccccCHHHhhhcchhhhhhccccceeee---hhhhhcCchhhhh
Confidence            35666666655433222111 2455777777776655444445788889999998887755321   1112344444555


Q ss_pred             EEeccCCCCCcc--cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecc
Q 042541          606 IRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRIT  683 (695)
Q Consensus       606 L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~  683 (695)
                      |.|..|.|..+-  .+-.|.++++|+|..|++..+......    +|++|+.|+|++|.--.--+++..-.++|+.|+|+
T Consensus       250 lklqrN~I~kL~DG~Fy~l~kme~l~L~~N~l~~vn~g~lf----gLt~L~~L~lS~NaI~rih~d~WsftqkL~~LdLs  325 (873)
T KOG4194|consen  250 LKLQRNDISKLDDGAFYGLEKMEHLNLETNRLQAVNEGWLF----GLTSLEQLDLSYNAIQRIHIDSWSFTQKLKELDLS  325 (873)
T ss_pred             hhhhhcCcccccCcceeeecccceeecccchhhhhhccccc----ccchhhhhccchhhhheeecchhhhcccceeEecc
Confidence            555555544444  333444444444444444444333322    44444444444432211122233333444444444


Q ss_pred             c
Q 042541          684 N  684 (695)
Q Consensus       684 ~  684 (695)
                      +
T Consensus       326 ~  326 (873)
T KOG4194|consen  326 S  326 (873)
T ss_pred             c
Confidence            4

>PF05496 RuvB_N: Holliday junction DNA helicase ruvB N-terminus; InterPro: IPR008824 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair

Probab=98.69  E-value=3.8e-07  Score=86.19  Aligned_cols=171  Identities=20%  Similarity=0.251  Sum_probs=94.0

Q ss_pred             CCCCCCCCCcchHHHHHHHHH-----cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHH
Q 042541          163 DPPVISPGLDVPLKELKMELF-----KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQ  237 (695)
Q Consensus       163 ~~~~~~vGr~~~~~~l~~~L~-----~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~  237 (695)
                      ..-+.|||-+.-++.+.-++.     ++...-+.+||++|+||||||.-+++  .....|    .+++.+.....     
T Consensus        21 ~~L~efiGQ~~l~~~l~i~i~aa~~r~~~l~h~lf~GPPG~GKTTLA~IIA~--e~~~~~----~~~sg~~i~k~-----   89 (233)
T PF05496_consen   21 KSLDEFIGQEHLKGNLKILIRAAKKRGEALDHMLFYGPPGLGKTTLARIIAN--ELGVNF----KITSGPAIEKA-----   89 (233)
T ss_dssp             SSCCCS-S-HHHHHHHHHHHHHHHCTTS---EEEEESSTTSSHHHHHHHHHH--HCT--E----EEEECCC--SC-----
T ss_pred             CCHHHccCcHHHHhhhHHHHHHHHhcCCCcceEEEECCCccchhHHHHHHHh--ccCCCe----EeccchhhhhH-----
Confidence            344678999988887765554     23467799999999999999999998  444443    23332111011     


Q ss_pred             HHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhcc--------CCCCC--------
Q 042541          238 KVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGF--------QLPDY--------  297 (695)
Q Consensus       238 ~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~--------~~~gs--------  297 (695)
                                          ..+..++..++ ++-+|.+|++......    ++..+..        .+++.        
T Consensus        90 --------------------~dl~~il~~l~-~~~ILFIDEIHRlnk~~qe~LlpamEd~~idiiiG~g~~ar~~~~~l~  148 (233)
T PF05496_consen   90 --------------------GDLAAILTNLK-EGDILFIDEIHRLNKAQQEILLPAMEDGKIDIIIGKGPNARSIRINLP  148 (233)
T ss_dssp             --------------------HHHHHHHHT---TT-EEEECTCCC--HHHHHHHHHHHHCSEEEEEBSSSSS-BEEEEE--
T ss_pred             --------------------HHHHHHHHhcC-CCcEEEEechhhccHHHHHHHHHHhccCeEEEEeccccccceeeccCC
Confidence                                11222333333 3557777998776532    1111111        11221        


Q ss_pred             --E-EEEEcCCCCC------CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHHHhh
Q 042541          298 --K-ILVTSRSEFP------QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGGSL  368 (695)
Q Consensus       298 --~-iivTtR~~~~------~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~~~L  368 (695)
                        . |=.|||....      ..+...+++..+.+|-.++..+.+..-..   .-.++.+.+|++.|.|-|.-..-+-...
T Consensus       149 ~FTligATTr~g~ls~pLrdRFgi~~~l~~Y~~~el~~Iv~r~a~~l~i---~i~~~~~~~Ia~rsrGtPRiAnrll~rv  225 (233)
T PF05496_consen  149 PFTLIGATTRAGLLSSPLRDRFGIVLRLEFYSEEELAKIVKRSARILNI---EIDEDAAEEIARRSRGTPRIANRLLRRV  225 (233)
T ss_dssp             --EEEEEESSGCCTSHCCCTTSSEEEE----THHHHHHHHHHCCHCTT----EE-HHHHHHHHHCTTTSHHHHHHHHHHH
T ss_pred             CceEeeeeccccccchhHHhhcceecchhcCCHHHHHHHHHHHHHHhCC---CcCHHHHHHHHHhcCCChHHHHHHHHHH
Confidence              2 3358887632      34447789999999999999987654332   1247889999999999997655544433

Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the N-terminal region of the proteins.; GO: 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1IQP_B 3PFI_B 1IXR_C 1HQC_B 1IXS_B.

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=98.68  E-value=1.7e-07  Score=94.65  Aligned_cols=207  Identities=16%  Similarity=0.165  Sum_probs=116.9

Q ss_pred             HHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHH
Q 042541          177 ELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAA  256 (695)
Q Consensus       177 ~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~  256 (695)
                      -|..++..+...-.-+||++|+||||||+.+..  .....|      ..++...+-..-++++++..             
T Consensus        38 ~lrr~v~~~~l~SmIl~GPPG~GKTTlA~liA~--~~~~~f------~~~sAv~~gvkdlr~i~e~a-------------   96 (436)
T COG2256          38 PLRRAVEAGHLHSMILWGPPGTGKTTLARLIAG--TTNAAF------EALSAVTSGVKDLREIIEEA-------------   96 (436)
T ss_pred             hHHHHHhcCCCceeEEECCCCCCHHHHHHHHHH--hhCCce------EEeccccccHHHHHHHHHHH-------------
Confidence            344555677777788999999999999999987  444443      33333322222222222221             


Q ss_pred             HHHHHHHHHhcCCCcEEEEEeCCCCCChHHHhhhccCC-CCCEEEE--EcCCCCCC-------CCCeEecCCCChHHHHH
Q 042541          257 INDLERFFKQMRIEAILLVLDDVWPGSESLLQKLGFQL-PDYKILV--TSRSEFPQ-------FGSVHYLKPLTYEAART  326 (695)
Q Consensus       257 ~~~l~~~~~~l~~~~~LlVlDdv~~~~~~~~~~l~~~~-~gs~iiv--TtR~~~~~-------~~~~~~l~~L~~~ea~~  326 (695)
                          +.  ....|++.+|++|.|..-....-+.|.+.. .|.-|+|  ||-+..-.       -..++.+++|+.++-.+
T Consensus        97 ----~~--~~~~gr~tiLflDEIHRfnK~QQD~lLp~vE~G~iilIGATTENPsF~ln~ALlSR~~vf~lk~L~~~di~~  170 (436)
T COG2256          97 ----RK--NRLLGRRTILFLDEIHRFNKAQQDALLPHVENGTIILIGATTENPSFELNPALLSRARVFELKPLSSEDIKK  170 (436)
T ss_pred             ----HH--HHhcCCceEEEEehhhhcChhhhhhhhhhhcCCeEEEEeccCCCCCeeecHHHhhhhheeeeecCCHHHHHH
Confidence                11  122489999999999776644445555544 4666666  66655321       12389999999999999


Q ss_pred             HHHHhccCCCCCCC---C-CchHHHHHHHHhcCCchhHHHH---HHHhhCCC----CHHHHHHHHHHhcCCCCc-cCchh
Q 042541          327 LFLHSANLQDGNSY---I-PDENIVSKILRACKGCPLALKV---VGGSLCGK----HEVFWQRMVKECSRGESV-FQSKN  394 (695)
Q Consensus       327 Lf~~~~~~~~~~~~---~-~~~~~~~~I~~~c~G~PLai~~---~~~~L~~~----~~~~w~~~l~~~~~~~~~-~~~~~  394 (695)
                      ++.+.+........   . -.++....+++.++|=-.++-.   ++..+...    ..+..+..+.+.....+. .+...
T Consensus       171 ~l~ra~~~~~rgl~~~~~~i~~~a~~~l~~~s~GD~R~aLN~LE~~~~~~~~~~~~~~~~l~~~l~~~~~~~Dk~gD~hY  250 (436)
T COG2256         171 LLKRALLDEERGLGGQIIVLDEEALDYLVRLSNGDARRALNLLELAALSAEPDEVLILELLEEILQRRSARFDKDGDAHY  250 (436)
T ss_pred             HHHHHHhhhhcCCCcccccCCHHHHHHHHHhcCchHHHHHHHHHHHHHhcCCCcccCHHHHHHHHhhhhhccCCCcchHH
Confidence            99984433222111   1 1356778899999886543222   22222222    123333333332211111 12233


Q ss_pred             hHHHHHHHHHHhccHH
Q 042541          395 DILDCLGSSLDVLNNE  410 (695)
Q Consensus       395 ~i~~~l~~s~~~L~~~  410 (695)
                      ++..++.-|...-+++
T Consensus       251 dliSA~hKSvRGSD~d  266 (436)
T COG2256         251 DLISALHKSVRGSDPD  266 (436)
T ss_pred             HHHHHHHHhhccCCcC
Confidence            6777777777666554

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.62  E-value=1.5e-06  Score=91.72  Aligned_cols=188  Identities=15%  Similarity=0.061  Sum_probs=106.5

Q ss_pred             CCCCCCCcchHHHHHHHHHcCC-ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhc
Q 042541          165 PVISPGLDVPLKELKMELFKDG-RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHK  243 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~-~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l  243 (695)
                      -+.++|-+..++.+...+..+. ...+.++|+.|+||||+|+.+++.-.-...+...    .+..+.+...+.....-.+
T Consensus        15 ~~~iiGq~~~~~~l~~~~~~~~~~h~~L~~Gp~G~GKTtla~~la~~l~c~~~~~~~----pc~~c~~c~~~~~~~~~d~   90 (363)
T PRK14961         15 FRDIIGQKHIVTAISNGLSLGRIHHAWLLSGTRGVGKTTIARLLAKSLNCQNGITSN----PCRKCIICKEIEKGLCLDL   90 (363)
T ss_pred             hhhccChHHHHHHHHHHHHcCCCCeEEEEecCCCCCHHHHHHHHHHHhcCCCCCCCC----CCCCCHHHHHHhcCCCCce
Confidence            3467999999999999888665 4567899999999999999998731101100000    0000000111100000000


Q ss_pred             CCCCCCCCChHHHHHHHHHHHHhc-----CCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCC------
Q 042541          244 GYPVPEFQTDEAAINDLERFFKQM-----RIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFP------  308 (695)
Q Consensus       244 ~~~~~~~~~~~~~~~~l~~~~~~l-----~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~------  308 (695)
                      ..-.+....   ..+.++++.+.+     .++.-++|+|++......    ++..+....+.+++|++|.+...      
T Consensus        91 ~~~~~~~~~---~v~~ir~i~~~~~~~p~~~~~kviIIDEa~~l~~~a~naLLk~lEe~~~~~~fIl~t~~~~~l~~tI~  167 (363)
T PRK14961         91 IEIDAASRT---KVEEMREILDNIYYSPSKSRFKVYLIDEVHMLSRHSFNALLKTLEEPPQHIKFILATTDVEKIPKTIL  167 (363)
T ss_pred             EEecccccC---CHHHHHHHHHHHhcCcccCCceEEEEEChhhcCHHHHHHHHHHHhcCCCCeEEEEEcCChHhhhHHHH
Confidence            000000000   112222222221     355679999999877643    44444444456777777754321      


Q ss_pred             CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHH
Q 042541          309 QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALK  362 (695)
Q Consensus       309 ~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~  362 (695)
                      .-...+++.+++.++..+.+...+.....   .-.++.+..|++.++|.|..+.
T Consensus       168 SRc~~~~~~~l~~~el~~~L~~~~~~~g~---~i~~~al~~ia~~s~G~~R~al  218 (363)
T PRK14961        168 SRCLQFKLKIISEEKIFNFLKYILIKESI---DTDEYALKLIAYHAHGSMRDAL  218 (363)
T ss_pred             hhceEEeCCCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHcCCCHHHHH
Confidence            11248999999999999988876644322   1235678889999999886443

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=98.62  E-value=2.7e-06  Score=88.78  Aligned_cols=198  Identities=15%  Similarity=0.135  Sum_probs=126.8

Q ss_pred             CCCCCCCcchHHHHHHHHH----cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCc-EEEEEeCCCCCHHHHHHHH
Q 042541          165 PVISPGLDVPLKELKMELF----KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDD-IFYVTVSKNPNVKAIVQKV  239 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~----~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~-~~wv~~~~~~~~~~~~~~i  239 (695)
                      |+.+.+|+++++++...|.    ++.+.-+.|+|..|.|||+.++.+.+  ++....... +++|++....+...++..|
T Consensus        16 P~~l~~Re~ei~~l~~~l~~~~~~~~p~n~~iyG~~GTGKT~~~~~v~~--~l~~~~~~~~~~yINc~~~~t~~~i~~~i   93 (366)
T COG1474          16 PEELPHREEEINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVME--ELEESSANVEVVYINCLELRTPYQVLSKI   93 (366)
T ss_pred             cccccccHHHHHHHHHHHHHHhcCCCCccEEEECCCCCCHhHHHHHHHH--HHHhhhccCceEEEeeeeCCCHHHHHHHH
Confidence            4458999999999998877    33344599999999999999999998  665554433 6799999999999999999


Q ss_pred             HHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhccCCC-CCEEEE--EcCCC------
Q 042541          240 LHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGFQLP-DYKILV--TSRSE------  306 (695)
Q Consensus       240 ~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~-gs~iiv--TtR~~------  306 (695)
                      +++++..........+..+.+.+.+.. .++.+++|||+++.....    +..-+..... +++|++  .+-+.      
T Consensus        94 ~~~~~~~p~~g~~~~~~~~~l~~~~~~-~~~~~IvvLDEid~L~~~~~~~LY~L~r~~~~~~~~v~vi~i~n~~~~~~~l  172 (366)
T COG1474          94 LNKLGKVPLTGDSSLEILKRLYDNLSK-KGKTVIVILDEVDALVDKDGEVLYSLLRAPGENKVKVSIIAVSNDDKFLDYL  172 (366)
T ss_pred             HHHcCCCCCCCCchHHHHHHHHHHHHh-cCCeEEEEEcchhhhccccchHHHHHHhhccccceeEEEEEEeccHHHHHHh
Confidence            999974444344445555555555533 578999999998654322    2222222222 344443  22221      


Q ss_pred             -----CCCCCCeEecCCCChHHHHHHHHHhccCCCCC--CCCCc-hHHHHHHHHhcCCchhHHHHHH
Q 042541          307 -----FPQFGSVHYLKPLTYEAARTLFLHSANLQDGN--SYIPD-ENIVSKILRACKGCPLALKVVG  365 (695)
Q Consensus       307 -----~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~--~~~~~-~~~~~~I~~~c~G~PLai~~~~  365 (695)
                           ..-....+..+|-+.+|-.+++..++...-..  ..... +-++...++..|-.-.||..+-
T Consensus       173 d~rv~s~l~~~~I~F~pY~a~el~~Il~~R~~~~~~~~~~~~~vl~lia~~~a~~~GDAR~aidilr  239 (366)
T COG1474         173 DPRVKSSLGPSEIVFPPYTAEELYDILRERVEEGFSAGVIDDDVLKLIAALVAAESGDARKAIDILR  239 (366)
T ss_pred             hhhhhhccCcceeeeCCCCHHHHHHHHHHHHHhhccCCCcCccHHHHHHHHHHHcCccHHHHHHHHH
Confidence                 11111257889999999999998877533221  12222 3333333444444455555543

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.61  E-value=9.5e-07  Score=99.44  Aligned_cols=188  Identities=18%  Similarity=0.100  Sum_probs=109.2

Q ss_pred             CCCCCCCcchHHHHHHHHHcCCce-EEEEEcCCCCcHHHHHHHHhcccccccc-C-CCcEEEEEeCCCCCHHHHHH---H
Q 042541          165 PVISPGLDVPLKELKMELFKDGRQ-FIVVSAPGGYGKTTLVQRLCKDDQVQGK-F-KDDIFYVTVSKNPNVKAIVQ---K  238 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~~~-vv~I~G~gGiGKTtLa~~~~~~~~~~~~-f-~~~~~wv~~~~~~~~~~~~~---~  238 (695)
                      -..+||-+..++.|..++..+... .+.++|+.|+||||+|+.+++.  +... . .. .   .+..+..-..+..   .
T Consensus        15 FddIIGQe~Iv~~LknaI~~~rl~HAyLFtGPpGtGKTTLARiLAk~--Lnce~~~~~-~---pCg~C~sC~~i~~g~~~   88 (944)
T PRK14949         15 FEQMVGQSHVLHALTNALTQQRLHHAYLFTGTRGVGKTSLARLFAKG--LNCEQGVTA-T---PCGVCSSCVEIAQGRFV   88 (944)
T ss_pred             HHHhcCcHHHHHHHHHHHHhCCCCeEEEEECCCCCCHHHHHHHHHHh--ccCccCCCC-C---CCCCchHHHHHhcCCCc
Confidence            346799999999999998877654 4589999999999999999873  3211 0 00 0   0000000000000   0


Q ss_pred             HHHhcCCCCCCCCChHHHHHHHHHHH--HhcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCCCC--
Q 042541          239 VLHHKGYPVPEFQTDEAAINDLERFF--KQMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFPQF--  310 (695)
Q Consensus       239 i~~~l~~~~~~~~~~~~~~~~l~~~~--~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~~~--  310 (695)
                      .+..+...  . ....+.+..+...+  ....++.-++|+|++......    +++.+-.....+++|++|.+...-.  
T Consensus        89 DviEidAa--s-~~kVDdIReLie~v~~~P~~gk~KViIIDEAh~LT~eAqNALLKtLEEPP~~vrFILaTTe~~kLl~T  165 (944)
T PRK14949         89 DLIEVDAA--S-RTKVDDTRELLDNVQYRPSRGRFKVYLIDEVHMLSRSSFNALLKTLEEPPEHVKFLLATTDPQKLPVT  165 (944)
T ss_pred             eEEEeccc--c-ccCHHHHHHHHHHHHhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhccCCCeEEEEECCCchhchHH
Confidence            00000000  0 00111112222211  122477889999999877643    4444444445677777766542111  


Q ss_pred             ----CCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHH
Q 042541          311 ----GSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVV  364 (695)
Q Consensus       311 ----~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~  364 (695)
                          ...|++++++.++..+.+.+.+.....   .-..+.+..|++.++|.|.-+..+
T Consensus       166 IlSRCq~f~fkpLs~eEI~~~L~~il~~EgI---~~edeAL~lIA~~S~Gd~R~ALnL  220 (944)
T PRK14949        166 VLSRCLQFNLKSLTQDEIGTQLNHILTQEQL---PFEAEALTLLAKAANGSMRDALSL  220 (944)
T ss_pred             HHHhheEEeCCCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHcCCCHHHHHHH
Confidence                238999999999999999886644221   124677899999999988644433

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=98.60  E-value=1.1e-07  Score=84.90  Aligned_cols=116  Identities=26%  Similarity=0.441  Sum_probs=75.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhcccccccc----CCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGK----FKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLER  262 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~----f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~  262 (695)
                      .+++.|+|.+|+|||++++.+.+.  ....    ....++|++++...+...+...|+.+++.............+.+.+
T Consensus         4 ~~~~~i~G~~G~GKT~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~l~~~~~~   81 (131)
T PF13401_consen    4 QRILVISGPPGSGKTTLIKRLARQ--LNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEALGLPLKSRQTSDELRSLLID   81 (131)
T ss_dssp             ---EEEEE-TTSSHHHHHHHHHHH--HHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHHHT-SSSSTS-HHHHHHHHHH
T ss_pred             CcccEEEcCCCCCHHHHHHHHHHH--hHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHHhCccccccCCHHHHHHHHHH
Confidence            478999999999999999999884  2211    0334789999888899999999999998876553334444444444


Q ss_pred             HHHhcCCCcEEEEEeCCCCC-ChHHHhhhc--cCCCCCEEEEEcCCC
Q 042541          263 FFKQMRIEAILLVLDDVWPG-SESLLQKLG--FQLPDYKILVTSRSE  306 (695)
Q Consensus       263 ~~~~l~~~~~LlVlDdv~~~-~~~~~~~l~--~~~~gs~iivTtR~~  306 (695)
                      .+..  .+..+||+||++.. ....+..+.  ....+.++|+..+..
T Consensus        82 ~l~~--~~~~~lviDe~~~l~~~~~l~~l~~l~~~~~~~vvl~G~~~  126 (131)
T PF13401_consen   82 ALDR--RRVVLLVIDEADHLFSDEFLEFLRSLLNESNIKVVLVGTPE  126 (131)
T ss_dssp             HHHH--CTEEEEEEETTHHHHTHHHHHHHHHHTCSCBEEEEEEESST
T ss_pred             HHHh--cCCeEEEEeChHhcCCHHHHHHHHHHHhCCCCeEEEEEChh
Confidence            4432  23369999999765 544333332  125667788776543

>PRK06893 DNA replication initiation factor; Validated

Probab=98.59  E-value=1.1e-06  Score=86.44  Aligned_cols=146  Identities=14%  Similarity=0.155  Sum_probs=90.0

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHH
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFK  265 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~  265 (695)
                      ..+.+.|+|++|+|||+|++.+++.  ....... +.|+++....   ...                        .+.++
T Consensus        38 ~~~~l~l~G~~G~GKThL~~ai~~~--~~~~~~~-~~y~~~~~~~---~~~------------------------~~~~~   87 (229)
T PRK06893         38 QQPFFYIWGGKSSGKSHLLKAVSNH--YLLNQRT-AIYIPLSKSQ---YFS------------------------PAVLE   87 (229)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHH--HHHcCCC-eEEeeHHHhh---hhh------------------------HHHHh
Confidence            3467899999999999999999983  3333333 5677764210   000                        01112


Q ss_pred             hcCCCcEEEEEeCCCCCC---hH---HHhhhccC-CCCCEEE-EEcCCCCC-------------CCCCeEecCCCChHHH
Q 042541          266 QMRIEAILLVLDDVWPGS---ES---LLQKLGFQ-LPDYKIL-VTSRSEFP-------------QFGSVHYLKPLTYEAA  324 (695)
Q Consensus       266 ~l~~~~~LlVlDdv~~~~---~~---~~~~l~~~-~~gs~ii-vTtR~~~~-------------~~~~~~~l~~L~~~ea  324 (695)
                      .+. +.-+|++||+|...   .+   +...+... ..|..+| +|+.....             ..+..+++++++.++.
T Consensus        88 ~~~-~~dlLilDDi~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p~~l~~~~~~L~sRl~~g~~~~l~~pd~e~~  166 (229)
T PRK06893         88 NLE-QQDLVCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSPHALSIKLPDLASRLTWGEIYQLNDLTDEQK  166 (229)
T ss_pred             hcc-cCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCChHHccccchhHHHHHhcCCeeeCCCCCHHHH
Confidence            222 33589999998642   21   11222211 2355554 45544211             2244889999999999


Q ss_pred             HHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHH
Q 042541          325 RTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVG  365 (695)
Q Consensus       325 ~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~  365 (695)
                      ++++.+.+....-   .-.+++..-|++.+.|-.-.+..+-
T Consensus       167 ~~iL~~~a~~~~l---~l~~~v~~~L~~~~~~d~r~l~~~l  204 (229)
T PRK06893        167 IIVLQRNAYQRGI---ELSDEVANFLLKRLDRDMHTLFDAL  204 (229)
T ss_pred             HHHHHHHHHHcCC---CCCHHHHHHHHHhccCCHHHHHHHH
Confidence            9999988864432   2247788999999998776655443

>PLN03025 replication factor C subunit; Provisional

Probab=98.58  E-value=1.8e-06  Score=89.53  Aligned_cols=176  Identities=11%  Similarity=0.097  Sum_probs=107.4

Q ss_pred             CCCCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccc-cccCCCcEEEEEeCCCCCHHHHHHHHHHh
Q 042541          164 PPVISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQV-QGKFKDDIFYVTVSKNPNVKAIVQKVLHH  242 (695)
Q Consensus       164 ~~~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~-~~~f~~~~~wv~~~~~~~~~~~~~~i~~~  242 (695)
                      .-+.++|.++.++.|..++..+..+.+.++|++|+||||+|+.+++  .+ ...|...++=++.++..... ..+++++.
T Consensus        11 ~l~~~~g~~~~~~~L~~~~~~~~~~~lll~Gp~G~GKTtla~~la~--~l~~~~~~~~~~eln~sd~~~~~-~vr~~i~~   87 (319)
T PLN03025         11 KLDDIVGNEDAVSRLQVIARDGNMPNLILSGPPGTGKTTSILALAH--ELLGPNYKEAVLELNASDDRGID-VVRNKIKM   87 (319)
T ss_pred             CHHHhcCcHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHH--HHhcccCccceeeecccccccHH-HHHHHHHH
Confidence            3356789888888888888777767788999999999999999987  33 22233222222223222222 12222221


Q ss_pred             cCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCC------CCCC
Q 042541          243 KGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFP------QFGS  312 (695)
Q Consensus       243 l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~------~~~~  312 (695)
                      +.....                ....++.-++|+|+++.....    ++..+......+++|+++.....      .-+.
T Consensus        88 ~~~~~~----------------~~~~~~~kviiiDE~d~lt~~aq~aL~~~lE~~~~~t~~il~~n~~~~i~~~L~SRc~  151 (319)
T PLN03025         88 FAQKKV----------------TLPPGRHKIVILDEADSMTSGAQQALRRTMEIYSNTTRFALACNTSSKIIEPIQSRCA  151 (319)
T ss_pred             HHhccc----------------cCCCCCeEEEEEechhhcCHHHHHHHHHHHhcccCCceEEEEeCCccccchhHHHhhh
Confidence            110000                000245679999999877643    22333333445777777654421      1234


Q ss_pred             eEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHH
Q 042541          313 VHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLAL  361 (695)
Q Consensus       313 ~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai  361 (695)
                      .+++++++.++....+...+...+..   -..+....|++.++|-...+
T Consensus       152 ~i~f~~l~~~~l~~~L~~i~~~egi~---i~~~~l~~i~~~~~gDlR~a  197 (319)
T PLN03025        152 IVRFSRLSDQEILGRLMKVVEAEKVP---YVPEGLEAIIFTADGDMRQA  197 (319)
T ss_pred             cccCCCCCHHHHHHHHHHHHHHcCCC---CCHHHHHHHHHHcCCCHHHH
Confidence            78999999999999998877543321   13667899999999976433

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=98.57  E-value=3e-06  Score=88.42  Aligned_cols=173  Identities=13%  Similarity=0.144  Sum_probs=106.5

Q ss_pred             CCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEe--CCCCCHHHHHHHHHHhc
Q 042541          166 VISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTV--SKNPNVKAIVQKVLHHK  243 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~--~~~~~~~~~~~~i~~~l  243 (695)
                      +.++|+++.++.+..++..+..+.+.|+|+.|+||||+|+.+++.. ....+..  .++.+  +....... ....+..+
T Consensus        17 ~~~~g~~~~~~~l~~~i~~~~~~~~ll~G~~G~GKt~~~~~l~~~l-~~~~~~~--~~i~~~~~~~~~~~~-~~~~i~~~   92 (319)
T PRK00440         17 DEIVGQEEIVERLKSYVKEKNMPHLLFAGPPGTGKTTAALALAREL-YGEDWRE--NFLELNASDERGIDV-IRNKIKEF   92 (319)
T ss_pred             HHhcCcHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHH-cCCcccc--ceEEeccccccchHH-HHHHHHHH
Confidence            4579999999999999987766778999999999999999998731 1222222  13333  22211111 11111111


Q ss_pred             CCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCC------CCCCe
Q 042541          244 GYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFP------QFGSV  313 (695)
Q Consensus       244 ~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~------~~~~~  313 (695)
                      ....+                 .....+-++++|+++.....    +...+....+.+++|+++.....      .....
T Consensus        93 ~~~~~-----------------~~~~~~~vviiDe~~~l~~~~~~~L~~~le~~~~~~~lIl~~~~~~~l~~~l~sr~~~  155 (319)
T PRK00440         93 ARTAP-----------------VGGAPFKIIFLDEADNLTSDAQQALRRTMEMYSQNTRFILSCNYSSKIIDPIQSRCAV  155 (319)
T ss_pred             HhcCC-----------------CCCCCceEEEEeCcccCCHHHHHHHHHHHhcCCCCCeEEEEeCCccccchhHHHHhhe
Confidence            00000                 00134668999998765432    33333334456778877754321      12237


Q ss_pred             EecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHH
Q 042541          314 HYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALK  362 (695)
Q Consensus       314 ~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~  362 (695)
                      +++.+++.++....+...+.....   .-.++.+..+++.++|.+.-+.
T Consensus       156 ~~~~~l~~~ei~~~l~~~~~~~~~---~i~~~al~~l~~~~~gd~r~~~  201 (319)
T PRK00440        156 FRFSPLKKEAVAERLRYIAENEGI---EITDDALEAIYYVSEGDMRKAI  201 (319)
T ss_pred             eeeCCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHcCCCHHHHH
Confidence            899999999998888877654332   1236788999999999876543

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.57  E-value=1.3e-06  Score=95.29  Aligned_cols=189  Identities=12%  Similarity=0.078  Sum_probs=108.6

Q ss_pred             CCCCCCCcchHHHHHHHHHcCCc-eEEEEEcCCCCcHHHHHHHHhccccccccC-CCcEEEEEeCCCCCHHHHHHHHHHh
Q 042541          165 PVISPGLDVPLKELKMELFKDGR-QFIVVSAPGGYGKTTLVQRLCKDDQVQGKF-KDDIFYVTVSKNPNVKAIVQKVLHH  242 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~~-~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f-~~~~~wv~~~~~~~~~~~~~~i~~~  242 (695)
                      -+.+||-+..++.|.+++..+.. ..+.++|+.|+||||+|+.+.+.-.-...- ..++-.-.++.+    .....|...
T Consensus        15 FddVIGQe~vv~~L~~al~~gRLpHA~LFtGP~GvGKTTLAriLAkaLnC~~p~~~~g~~~~PCG~C----~sC~~I~aG   90 (700)
T PRK12323         15 FTTLVGQEHVVRALTHALEQQRLHHAYLFTGTRGVGKTTLSRILAKSLNCTGADGEGGITAQPCGQC----RACTEIDAG   90 (700)
T ss_pred             HHHHcCcHHHHHHHHHHHHhCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCccccccCCCCCCccc----HHHHHHHcC
Confidence            34679999999999999987764 556899999999999999887631110000 000000000000    001111000


Q ss_pred             -----cCCCCCCCCChHHHHHHHHHHHH-----hcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCC
Q 042541          243 -----KGYPVPEFQTDEAAINDLERFFK-----QMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFP  308 (695)
Q Consensus       243 -----l~~~~~~~~~~~~~~~~l~~~~~-----~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~  308 (695)
                           +......    ...++.++++++     ...++.-++|+|+++.....    +++.+.....++++|++|.+...
T Consensus        91 ~hpDviEIdAas----~~gVDdIReLie~~~~~P~~gr~KViIIDEah~Ls~~AaNALLKTLEEPP~~v~FILaTtep~k  166 (700)
T PRK12323         91 RFVDYIEMDAAS----NRGVDEMAQLLDKAVYAPTAGRFKVYMIDEVHMLTNHAFNAMLKTLEEPPEHVKFILATTDPQK  166 (700)
T ss_pred             CCCcceEecccc----cCCHHHHHHHHHHHHhchhcCCceEEEEEChHhcCHHHHHHHHHhhccCCCCceEEEEeCChHh
Confidence                 0000000    011222222221     12467789999999877644    45555444556777776665421


Q ss_pred             CC------CCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHH
Q 042541          309 QF------GSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVV  364 (695)
Q Consensus       309 ~~------~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~  364 (695)
                      -.      ...+.++.++.++..+.+.+.+.....   ....+..+.|++.++|.|.-...+
T Consensus       167 LlpTIrSRCq~f~f~~ls~eei~~~L~~Il~~Egi---~~d~eAL~~IA~~A~Gs~RdALsL  225 (700)
T PRK12323        167 IPVTVLSRCLQFNLKQMPPGHIVSHLDAILGEEGI---AHEVNALRLLAQAAQGSMRDALSL  225 (700)
T ss_pred             hhhHHHHHHHhcccCCCChHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHcCCCHHHHHHH
Confidence            11      127899999999999998877643322   123566788999999998654443

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=98.57  E-value=1.5e-06  Score=85.74  Aligned_cols=161  Identities=19%  Similarity=0.221  Sum_probs=99.9

Q ss_pred             cchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCC
Q 042541          172 DVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQ  251 (695)
Q Consensus       172 ~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~  251 (695)
                      +..++.+..++.......|.|+|++|+|||+||+.+++.  ....... +++++++.-.+.      .            
T Consensus        23 ~~~~~~l~~~~~~~~~~~lll~G~~G~GKT~la~~~~~~--~~~~~~~-~~~i~~~~~~~~------~------------   81 (226)
T TIGR03420        23 AELLAALRQLAAGKGDRFLYLWGESGSGKSHLLQAACAA--AEERGKS-AIYLPLAELAQA------D------------   81 (226)
T ss_pred             HHHHHHHHHHHhcCCCCeEEEECCCCCCHHHHHHHHHHH--HHhcCCc-EEEEeHHHHHHh------H------------
Confidence            346777777766666788999999999999999999873  3222222 556665532210      0            


Q ss_pred             ChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCh---H---HHhhhcc-CCCCCEEEEEcCCCCC-----------C--CC
Q 042541          252 TDEAAINDLERFFKQMRIEAILLVLDDVWPGSE---S---LLQKLGF-QLPDYKILVTSRSEFP-----------Q--FG  311 (695)
Q Consensus       252 ~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~---~---~~~~l~~-~~~gs~iivTtR~~~~-----------~--~~  311 (695)
                               ...+..+.+ .-+||+||++....   +   +...+.. ...+..+|+||+....           .  .+
T Consensus        82 ---------~~~~~~~~~-~~lLvIDdi~~l~~~~~~~~~L~~~l~~~~~~~~~iIits~~~~~~~~~~~~~L~~r~~~~  151 (226)
T TIGR03420        82 ---------PEVLEGLEQ-ADLVCLDDVEAIAGQPEWQEALFHLYNRVREAGGRLLIAGRAAPAQLPLRLPDLRTRLAWG  151 (226)
T ss_pred             ---------HHHHhhccc-CCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCeEEEECCCChHHCCcccHHHHHHHhcC
Confidence                     011122222 34899999975432   1   1221111 1234588898885421           0  13


Q ss_pred             CeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHHH
Q 042541          312 SVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGG  366 (695)
Q Consensus       312 ~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~~  366 (695)
                      ..+++++++.++...++...+.....   .-.++....|++.+.|.|..+..+..
T Consensus       152 ~~i~l~~l~~~e~~~~l~~~~~~~~~---~~~~~~l~~L~~~~~gn~r~L~~~l~  203 (226)
T TIGR03420       152 LVFQLPPLSDEEKIAALQSRAARRGL---QLPDEVADYLLRHGSRDMGSLMALLD  203 (226)
T ss_pred             eeEecCCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHhccCCHHHHHHHHH
Confidence            47899999999999998875432211   12367788899999999987766543

Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.

>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold

Probab=98.54  E-value=6.3e-07  Score=81.54  Aligned_cols=121  Identities=17%  Similarity=0.197  Sum_probs=74.2

Q ss_pred             CCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCC
Q 042541          169 PGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVP  248 (695)
Q Consensus       169 vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~  248 (695)
                      +|++..++.+...+.....+.+.|+|++|+|||++++.+++.  ... ....+++++..+..........+...      
T Consensus         1 ~~~~~~~~~i~~~~~~~~~~~v~i~G~~G~GKT~l~~~i~~~--~~~-~~~~v~~~~~~~~~~~~~~~~~~~~~------   71 (151)
T cd00009           1 VGQEEAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANE--LFR-PGAPFLYLNASDLLEGLVVAELFGHF------   71 (151)
T ss_pred             CchHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHH--hhc-CCCCeEEEehhhhhhhhHHHHHhhhh------
Confidence            478888999988887766788999999999999999999983  322 22336787776544322221111100      


Q ss_pred             CCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCh----HHHhhhccC------CCCCEEEEEcCCCC
Q 042541          249 EFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSE----SLLQKLGFQ------LPDYKILVTSRSEF  307 (695)
Q Consensus       249 ~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~----~~~~~l~~~------~~gs~iivTtR~~~  307 (695)
                              .. ..........++.++|+||++....    .+...+...      ..+..+|+||....
T Consensus        72 --------~~-~~~~~~~~~~~~~~lilDe~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~ii~~~~~~~  131 (151)
T cd00009          72 --------LV-RLLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLRIDRENVRVIGATNRPL  131 (151)
T ss_pred             --------hH-hHHHHhhccCCCeEEEEeChhhhhHHHHHHHHHHHHhcCceeccCCCeEEEEecCccc
Confidence                    00 0011122346788999999986421    122222222      35778888887553

The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.52  E-value=2.2e-06  Score=93.68  Aligned_cols=169  Identities=17%  Similarity=0.176  Sum_probs=109.0

Q ss_pred             CCCCCCCcchHHHHHHHHHcCC-ceEEEEEcCCCCcHHHHHHHHhcccccc-------------------ccCCCcEEEE
Q 042541          165 PVISPGLDVPLKELKMELFKDG-RQFIVVSAPGGYGKTTLVQRLCKDDQVQ-------------------GKFKDDIFYV  224 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~-~~vv~I~G~gGiGKTtLa~~~~~~~~~~-------------------~~f~~~~~wv  224 (695)
                      -+.+||.+..++.|..++..+. ...+.++|+.|+||||+|+.+++.-.-.                   +.|.. ++.+
T Consensus        14 FddVIGQe~vv~~L~~aI~~grl~HAyLF~GPpGvGKTTlAriLAK~LnC~~~~~~~pCg~C~sC~~I~~g~hpD-viEI   92 (702)
T PRK14960         14 FNELVGQNHVSRALSSALERGRLHHAYLFTGTRGVGKTTIARILAKCLNCETGVTSTPCEVCATCKAVNEGRFID-LIEI   92 (702)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCcCCCCCCCccCHHHHHHhcCCCCc-eEEe
Confidence            3567999999999999998766 4677999999999999999887631100                   01111 1122


Q ss_pred             EeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHH-----hcCCCcEEEEEeCCCCCChH----HHhhhccCCC
Q 042541          225 TVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFK-----QMRIEAILLVLDDVWPGSES----LLQKLGFQLP  295 (695)
Q Consensus       225 ~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~-----~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~  295 (695)
                      +.+....                         .+.+++++.     ...++.-++|+|++......    ++..+....+
T Consensus        93 DAAs~~~-------------------------VddIReli~~~~y~P~~gk~KV~IIDEVh~LS~~A~NALLKtLEEPP~  147 (702)
T PRK14960         93 DAASRTK-------------------------VEDTRELLDNVPYAPTQGRFKVYLIDEVHMLSTHSFNALLKTLEEPPE  147 (702)
T ss_pred             cccccCC-------------------------HHHHHHHHHHHhhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhcCCC
Confidence            2111111                         222233221     12466779999999877643    4444444445


Q ss_pred             CCEEEEEcCCCCC------CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHH
Q 042541          296 DYKILVTSRSEFP------QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALK  362 (695)
Q Consensus       296 gs~iivTtR~~~~------~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~  362 (695)
                      +.++|++|.+...      .-...+++++++.++....+.+.+.....   .-..+....|++.++|.+..+.
T Consensus       148 ~v~FILaTtd~~kIp~TIlSRCq~feFkpLs~eEI~k~L~~Il~kEgI---~id~eAL~~IA~~S~GdLRdAL  217 (702)
T PRK14960        148 HVKFLFATTDPQKLPITVISRCLQFTLRPLAVDEITKHLGAILEKEQI---AADQDAIWQIAESAQGSLRDAL  217 (702)
T ss_pred             CcEEEEEECChHhhhHHHHHhhheeeccCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHcCCCHHHHH
Confidence            6788887765421      22238999999999999999887654332   1246678899999999875444

>PLN03150 hypothetical protein; Provisional

Probab=98.52  E-value=1.7e-07  Score=105.79  Aligned_cols=110  Identities=17%  Similarity=0.166  Sum_probs=62.8

Q ss_pred             CcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCC-Ccc-cccccccccEEeeccccCCcccccchhhhcccCCCc
Q 042541          576 LKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLP-NSL-ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNL  653 (695)
Q Consensus       576 Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~-~lp-~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L  653 (695)
                      +..|+|.+|++.+ .+  ++.++.|++|+.|+|++|.+. .+| .++.+++|++|+|++|.+.+..|..+.    .|++|
T Consensus       420 v~~L~L~~n~L~g-~i--p~~i~~L~~L~~L~Ls~N~l~g~iP~~~~~l~~L~~LdLs~N~lsg~iP~~l~----~L~~L  492 (623)
T PLN03150        420 IDGLGLDNQGLRG-FI--PNDISKLRHLQSINLSGNSIRGNIPPSLGSITSLEVLDLSYNSFNGSIPESLG----QLTSL  492 (623)
T ss_pred             EEEEECCCCCccc-cC--CHHHhCCCCCCEEECCCCcccCcCChHHhCCCCCCEEECCCCCCCCCCchHHh----cCCCC
Confidence            4555555554421 11  122556666666666666665 566 666666666666666666655554444    56666


Q ss_pred             cEEecccccccccCchhhcCC-CCCceeecccccCCCCCC
Q 042541          654 LEMDIDYCNDLIELPDGLCDI-VSMEKLRITNCHRLSALP  692 (695)
Q Consensus       654 ~~L~l~~c~~l~~lP~~i~~L-~~L~~L~l~~~~~l~~lP  692 (695)
                      +.|+|++|...+.+|..++.+ .++..+++.+|+.+...|
T Consensus       493 ~~L~Ls~N~l~g~iP~~l~~~~~~~~~l~~~~N~~lc~~p  532 (623)
T PLN03150        493 RILNLNGNSLSGRVPAALGGRLLHRASFNFTDNAGLCGIP  532 (623)
T ss_pred             CEEECcCCcccccCChHHhhccccCceEEecCCccccCCC
Confidence            666666665555666665543 355566666655444433

>PF13855 LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RFS_A 3G39_A 3VQ2_A 3VQ1_B 2Z64_A 2Z66_C 3FXI_A 2Z63_A

Probab=98.51  E-value=9.3e-08  Score=72.43  Aligned_cols=56  Identities=18%  Similarity=0.254  Sum_probs=26.7

Q ss_pred             CCcEEEeccCCCCCcc--cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccc
Q 042541          602 KLKKIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYC  661 (695)
Q Consensus       602 ~L~~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c  661 (695)
                      +|++|++++|.++.+|  .+..+++|++|++++|.++.+++..+.    .+++|++|++++|
T Consensus         2 ~L~~L~l~~n~l~~i~~~~f~~l~~L~~L~l~~N~l~~i~~~~f~----~l~~L~~L~l~~N   59 (61)
T PF13855_consen    2 NLESLDLSNNKLTEIPPDSFSNLPNLETLDLSNNNLTSIPPDAFS----NLPNLRYLDLSNN   59 (61)
T ss_dssp             TESEEEETSSTESEECTTTTTTGTTESEEEETSSSESEEETTTTT----TSTTESEEEETSS
T ss_pred             cCcEEECCCCCCCccCHHHHcCCCCCCEeEccCCccCccCHHHHc----CCCCCCEEeCcCC
Confidence            3444444444444444  444455555555555544444444443    4444444444443

...

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.50  E-value=4e-06  Score=91.40  Aligned_cols=189  Identities=15%  Similarity=0.069  Sum_probs=108.0

Q ss_pred             CCCCCCcchHHHHHHHHHcCCc-eEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcC
Q 042541          166 VISPGLDVPLKELKMELFKDGR-QFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKG  244 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~~~-~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~  244 (695)
                      +.++|-+..++.|..++..+.. ..+.++|++|+||||+|+.+++...-.+.+.. ..|.|.+.. .+......-+..+.
T Consensus        14 ~dvvGq~~v~~~L~~~i~~~~l~ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~~-~cg~C~sc~-~i~~~~h~dv~el~   91 (504)
T PRK14963         14 DEVVGQEHVKEVLLAALRQGRLGHAYLFSGPRGVGKTTTARLIAMAVNCSGEDPK-PCGECESCL-AVRRGAHPDVLEID   91 (504)
T ss_pred             HHhcChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHHhccCCCCC-CCCcChhhH-HHhcCCCCceEEec
Confidence            4579999888889888887664 45699999999999999999874221122211 112222110 00000000000000


Q ss_pred             CCCCCCCChHHHHHHHHHHHH--hcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCC-C-----CCCC
Q 042541          245 YPVPEFQTDEAAINDLERFFK--QMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEF-P-----QFGS  312 (695)
Q Consensus       245 ~~~~~~~~~~~~~~~l~~~~~--~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~-~-----~~~~  312 (695)
                      ..  . ....+.+..+.....  ...+++-++|+|+++.....    ++..+....+++.+|++|.... .     ....
T Consensus        92 ~~--~-~~~vd~iR~l~~~~~~~p~~~~~kVVIIDEad~ls~~a~naLLk~LEep~~~t~~Il~t~~~~kl~~~I~SRc~  168 (504)
T PRK14963         92 AA--S-NNSVEDVRDLREKVLLAPLRGGRKVYILDEAHMMSKSAFNALLKTLEEPPEHVIFILATTEPEKMPPTILSRTQ  168 (504)
T ss_pred             cc--c-cCCHHHHHHHHHHHhhccccCCCeEEEEECccccCHHHHHHHHHHHHhCCCCEEEEEEcCChhhCChHHhcceE
Confidence            00  0 011112222322221  12356779999999876543    3444444444566666654331 1     1223


Q ss_pred             eEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHH
Q 042541          313 VHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALK  362 (695)
Q Consensus       313 ~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~  362 (695)
                      .+++.+++.++....+.+.+...+..   -.++.+..|++.++|.+.-+.
T Consensus       169 ~~~f~~ls~~el~~~L~~i~~~egi~---i~~~Al~~ia~~s~GdlR~al  215 (504)
T PRK14963        169 HFRFRRLTEEEIAGKLRRLLEAEGRE---AEPEALQLVARLADGAMRDAE  215 (504)
T ss_pred             EEEecCCCHHHHHHHHHHHHHHcCCC---CCHHHHHHHHHHcCCCHHHHH
Confidence            89999999999999998876543321   246778999999999886543

>PF14580 LRR_9: Leucine-rich repeat; PDB: 2JE1_D 2JE0_A 2JQD_A

Probab=98.50  E-value=1.5e-07  Score=87.03  Aligned_cols=104  Identities=16%  Similarity=0.225  Sum_probs=26.4

Q ss_pred             CCCCcEEEEcccCCCCcccCcccccc-cCCCCcEEEeccCCCCCcccccccccccEEeeccccCCcccccchhhhcccCC
Q 042541          573 MDELKVLIVTNYGFSPAELNNFRVLS-ALSKLKKIRLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFP  651 (695)
Q Consensus       573 l~~Lr~L~l~~~~~~~~~~~~~~~l~-~l~~L~~L~L~~~~l~~lp~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~  651 (695)
                      ..++|.|+|++|.+.     ....++ .+.+|+.|+|++|.|..++.+..|++|++|++++|.|+.+.+....    .++
T Consensus        18 ~~~~~~L~L~~n~I~-----~Ie~L~~~l~~L~~L~Ls~N~I~~l~~l~~L~~L~~L~L~~N~I~~i~~~l~~----~lp   88 (175)
T PF14580_consen   18 PVKLRELNLRGNQIS-----TIENLGATLDKLEVLDLSNNQITKLEGLPGLPRLKTLDLSNNRISSISEGLDK----NLP   88 (175)
T ss_dssp             -----------------------S--TT-TT--EEE-TTS--S--TT----TT--EEE--SS---S-CHHHHH----H-T
T ss_pred             ccccccccccccccc-----cccchhhhhcCCCEEECCCCCCccccCccChhhhhhcccCCCCCCccccchHH----hCC
Confidence            334566666655442     111233 3555666666666665555444556666666666666554432221    355


Q ss_pred             CccEEecccccccccCc--hhhcCCCCCceeeccccc
Q 042541          652 NLLEMDIDYCNDLIELP--DGLCDIVSMEKLRITNCH  686 (695)
Q Consensus       652 ~L~~L~l~~c~~l~~lP--~~i~~L~~L~~L~l~~~~  686 (695)
                      +|++|++++| .+..+-  ..+..+++|+.|+|.+|+
T Consensus        89 ~L~~L~L~~N-~I~~l~~l~~L~~l~~L~~L~L~~NP  124 (175)
T PF14580_consen   89 NLQELYLSNN-KISDLNELEPLSSLPKLRVLSLEGNP  124 (175)
T ss_dssp             T--EEE-TTS----SCCCCGGGGG-TT--EEE-TT-G
T ss_pred             cCCEEECcCC-cCCChHHhHHHHcCCCcceeeccCCc
Confidence            6666666553 233322  224555666666666655

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.49  E-value=2.2e-06  Score=91.04  Aligned_cols=190  Identities=13%  Similarity=0.054  Sum_probs=108.3

Q ss_pred             CCCCCCCcchHHHHHHHHHcCCc-eEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhc
Q 042541          165 PVISPGLDVPLKELKMELFKDGR-QFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHK  243 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~~-~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l  243 (695)
                      -+.+||-+..+..|..++..+.. ..+.++|+.|+||||+|+.+++  .+...-...  ...+..+.+-..+...+...+
T Consensus        17 f~dvVGQe~iv~~L~~~i~~~ri~ha~Lf~GP~GtGKTTlAriLAk--~Lnce~~~~--~~pCg~C~sC~~i~~g~~~dv   92 (484)
T PRK14956         17 FRDVIHQDLAIGALQNALKSGKIGHAYIFFGPRGVGKTTIARILAK--RLNCENPIG--NEPCNECTSCLEITKGISSDV   92 (484)
T ss_pred             HHHHhChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHH--hcCcccccC--ccccCCCcHHHHHHccCCccc
Confidence            34679999999999998887765 4589999999999999999987  332111000  111122222222211110000


Q ss_pred             CCCCCCCCChHHHHHHHHHHH--HhcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCCC------CC
Q 042541          244 GYPVPEFQTDEAAINDLERFF--KQMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFPQ------FG  311 (695)
Q Consensus       244 ~~~~~~~~~~~~~~~~l~~~~--~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~~------~~  311 (695)
                      ..-........+.+..+.+.+  ....++.-++|+|+++.....    ++..+........+|++|.....-      -.
T Consensus        93 iEIdaas~~gVd~IReL~e~l~~~p~~g~~KV~IIDEah~Ls~~A~NALLKtLEEPp~~viFILaTte~~kI~~TI~SRC  172 (484)
T PRK14956         93 LEIDAASNRGIENIRELRDNVKFAPMGGKYKVYIIDEVHMLTDQSFNALLKTLEEPPAHIVFILATTEFHKIPETILSRC  172 (484)
T ss_pred             eeechhhcccHHHHHHHHHHHHhhhhcCCCEEEEEechhhcCHHHHHHHHHHhhcCCCceEEEeecCChhhccHHHHhhh
Confidence            000000001111222222222  123467779999999877654    334343333455666555543211      11


Q ss_pred             CeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHH
Q 042541          312 SVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLAL  361 (695)
Q Consensus       312 ~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai  361 (695)
                      ..|.+.+++.++..+.+.+.+...+.   .-..+....|++.++|.+.-+
T Consensus       173 q~~~f~~ls~~~i~~~L~~i~~~Egi---~~e~eAL~~Ia~~S~Gd~RdA  219 (484)
T PRK14956        173 QDFIFKKVPLSVLQDYSEKLCKIENV---QYDQEGLFWIAKKGDGSVRDM  219 (484)
T ss_pred             heeeecCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHcCChHHHH
Confidence            26999999999999988887654322   124678899999999998543

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=98.49  E-value=7.5e-06  Score=85.70  Aligned_cols=195  Identities=12%  Similarity=0.038  Sum_probs=111.4

Q ss_pred             CCCCCCCCCCCcchHHHHHHHHHcCCc-eEEEEEcCCCCcHHHHHHHHhccccccccCCCcEE---EEEeCCCCCHHHHH
Q 042541          161 APDPPVISPGLDVPLKELKMELFKDGR-QFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIF---YVTVSKNPNVKAIV  236 (695)
Q Consensus       161 ~~~~~~~~vGr~~~~~~l~~~L~~~~~-~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~---wv~~~~~~~~~~~~  236 (695)
                      .|.....++|-+...+.+.+.+..+.. ..+.++|+.|+||+|+|..+++.---.........   -.++.. ...-...
T Consensus        14 ~P~~~~~iiGq~~~~~~L~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~~A~~Llc~~~~~~~~~~~~~~~l~~-~~~c~~c   92 (365)
T PRK07471         14 HPRETTALFGHAAAEAALLDAYRSGRLHHAWLIGGPQGIGKATLAYRMARFLLATPPPGGDGAVPPPTSLAI-DPDHPVA   92 (365)
T ss_pred             CCCchhhccChHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHHhCCCCCCCCccccccccccC-CCCChHH
Confidence            444556789999999999999887764 45889999999999999887762100010000000   000000 0000111


Q ss_pred             HHHHHhcCCCC--------CCCC---ChHHHHHHHHHHHHhc-----CCCcEEEEEeCCCCCChH----HHhhhccCCCC
Q 042541          237 QKVLHHKGYPV--------PEFQ---TDEAAINDLERFFKQM-----RIEAILLVLDDVWPGSES----LLQKLGFQLPD  296 (695)
Q Consensus       237 ~~i~~~l~~~~--------~~~~---~~~~~~~~l~~~~~~l-----~~~~~LlVlDdv~~~~~~----~~~~l~~~~~g  296 (695)
                      +.+... ..+.        .+..   ...-.+++++++.+.+     .+++.++|+||++.....    +++.+....++
T Consensus        93 ~~i~~~-~HPDl~~i~~~~~~~~~~~~~~I~VdqiR~l~~~~~~~~~~~~~kVviIDead~m~~~aanaLLK~LEepp~~  171 (365)
T PRK07471         93 RRIAAG-AHGGLLTLERSWNEKGKRLRTVITVDEVRELISFFGLTAAEGGWRVVIVDTADEMNANAANALLKVLEEPPAR  171 (365)
T ss_pred             HHHHcc-CCCCeEEEecccccccccccccccHHHHHHHHHHhCcCcccCCCEEEEEechHhcCHHHHHHHHHHHhcCCCC
Confidence            111111 0000        0000   0111234444444332     367789999999877644    44555544456


Q ss_pred             CEEEEEcCCCCC------CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHH
Q 042541          297 YKILVTSRSEFP------QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVV  364 (695)
Q Consensus       297 s~iivTtR~~~~------~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~  364 (695)
                      +.+|++|.....      .-...+.+.+++.++..+++......       ...+....+++.++|.|+....+
T Consensus       172 ~~~IL~t~~~~~llpti~SRc~~i~l~~l~~~~i~~~L~~~~~~-------~~~~~~~~l~~~s~Gsp~~Al~l  238 (365)
T PRK07471        172 SLFLLVSHAPARLLPTIRSRCRKLRLRPLAPEDVIDALAAAGPD-------LPDDPRAALAALAEGSVGRALRL  238 (365)
T ss_pred             eEEEEEECCchhchHHhhccceEEECCCCCHHHHHHHHHHhccc-------CCHHHHHHHHHHcCCCHHHHHHH
Confidence            777777766521      11238999999999999999875311       12233378899999999866554

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=98.48  E-value=4e-06  Score=87.25  Aligned_cols=193  Identities=16%  Similarity=0.142  Sum_probs=113.4

Q ss_pred             CCCCCCCCCCCcchHHHHHHHHHcCC-ceEEEEEcCCCCcHHHHHHHHhcccccccc----CCCcEEEEEeCCCCCHHHH
Q 042541          161 APDPPVISPGLDVPLKELKMELFKDG-RQFIVVSAPGGYGKTTLVQRLCKDDQVQGK----FKDDIFYVTVSKNPNVKAI  235 (695)
Q Consensus       161 ~~~~~~~~vGr~~~~~~l~~~L~~~~-~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~----f~~~~~wv~~~~~~~~~~~  235 (695)
                      .|.....++|-+...+.+...+..+. ...+.|+|+.|+||||+|..+++.  +-..    +.. .   .....+..-..
T Consensus        18 ~P~~~~~l~Gh~~a~~~L~~a~~~grl~ha~L~~G~~G~GKttlA~~lA~~--Llc~~~~~~~~-~---~~~~~~~~c~~   91 (351)
T PRK09112         18 SPSENTRLFGHEEAEAFLAQAYREGKLHHALLFEGPEGIGKATLAFHLANH--ILSHPDPAEAP-E---TLADPDPASPV   91 (351)
T ss_pred             CCCchhhccCcHHHHHHHHHHHHcCCCCeeEeeECCCCCCHHHHHHHHHHH--HcCCCccccCc-c---ccCCCCCCCHH
Confidence            45566778999999999999998766 456899999999999999988873  2211    111 0   00111111112


Q ss_pred             HHHHHHh-------cCCCCCCC------CChHHHHHHHHHHHH--hcCCCcEEEEEeCCCCCChH----HHhhhccCCCC
Q 042541          236 VQKVLHH-------KGYPVPEF------QTDEAAINDLERFFK--QMRIEAILLVLDDVWPGSES----LLQKLGFQLPD  296 (695)
Q Consensus       236 ~~~i~~~-------l~~~~~~~------~~~~~~~~~l~~~~~--~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~g  296 (695)
                      .+.+...       +..+....      .-..+.+..+.+.+.  ...++.-++|+|+++.....    ++..+.....+
T Consensus        92 c~~i~~~~hPdl~~l~~~~~~~~~~~~~~I~vd~iR~l~~~l~~~~~~g~~rVviIDeAd~l~~~aanaLLk~LEEpp~~  171 (351)
T PRK09112         92 WRQIAQGAHPNLLHITRPFDEKTGKFKTAITVDEIRRVGHFLSQTSGDGNWRIVIIDPADDMNRNAANAILKTLEEPPAR  171 (351)
T ss_pred             HHHHHcCCCCCEEEeecccccccccccccCCHHHHHHHHHHhhhccccCCceEEEEEchhhcCHHHHHHHHHHHhcCCCC
Confidence            2333221       11110000      001122233333331  22467789999999877643    44555444445


Q ss_pred             CEEEEEcCCCC-C-----CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHH
Q 042541          297 YKILVTSRSEF-P-----QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVV  364 (695)
Q Consensus       297 s~iivTtR~~~-~-----~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~  364 (695)
                      +.+|++|.... .     .-...+++.+++.++..+++......  .  . -.++.+..|++.++|.|.....+
T Consensus       172 ~~fiLit~~~~~llptIrSRc~~i~l~pl~~~~~~~~L~~~~~~--~--~-~~~~~~~~i~~~s~G~pr~Al~l  240 (351)
T PRK09112        172 ALFILISHSSGRLLPTIRSRCQPISLKPLDDDELKKALSHLGSS--Q--G-SDGEITEALLQRSKGSVRKALLL  240 (351)
T ss_pred             ceEEEEECChhhccHHHHhhccEEEecCCCHHHHHHHHHHhhcc--c--C-CCHHHHHHHHHHcCCCHHHHHHH
Confidence            55555554331 1     11238999999999999999874311  1  1 22566889999999999866544

>PF13173 AAA_14: AAA domain

Probab=98.48  E-value=7.4e-07  Score=79.06  Aligned_cols=113  Identities=25%  Similarity=0.368  Sum_probs=72.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-H
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFF-K  265 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~  265 (695)
                      .+++.|.|+.|+|||||+++++.+..    -+..++++++.+.........                    + +.+.+ +
T Consensus         2 ~~~~~l~G~R~vGKTtll~~~~~~~~----~~~~~~yi~~~~~~~~~~~~~--------------------~-~~~~~~~   56 (128)
T PF13173_consen    2 RKIIILTGPRGVGKTTLLKQLAKDLL----PPENILYINFDDPRDRRLADP--------------------D-LLEYFLE   56 (128)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhc----ccccceeeccCCHHHHHHhhh--------------------h-hHHHHHH
Confidence            36899999999999999999987422    122367887765432110000                    0 11222 2


Q ss_pred             hcCCCcEEEEEeCCCCCChH--HHhhhccCCCCCEEEEEcCCCCC--------CCCC--eEecCCCChHHH
Q 042541          266 QMRIEAILLVLDDVWPGSES--LLQKLGFQLPDYKILVTSRSEFP--------QFGS--VHYLKPLTYEAA  324 (695)
Q Consensus       266 ~l~~~~~LlVlDdv~~~~~~--~~~~l~~~~~gs~iivTtR~~~~--------~~~~--~~~l~~L~~~ea  324 (695)
                      ...++..+++||++....+|  .+..+....++.+|++|+.+...        -.|.  .+++.||+..|-
T Consensus        57 ~~~~~~~~i~iDEiq~~~~~~~~lk~l~d~~~~~~ii~tgS~~~~l~~~~~~~l~gr~~~~~l~Plsf~E~  127 (128)
T PF13173_consen   57 LIKPGKKYIFIDEIQYLPDWEDALKFLVDNGPNIKIILTGSSSSLLSKDIAESLAGRVIEIELYPLSFREF  127 (128)
T ss_pred             hhccCCcEEEEehhhhhccHHHHHHHHHHhccCceEEEEccchHHHhhcccccCCCeEEEEEECCCCHHHh
Confidence            23457889999999877654  34445555567899999987621        1222  688999987763

>PRK15387 E3 ubiquitin-protein ligase SspH2; Provisional

Probab=98.48  E-value=1.7e-07  Score=105.89  Aligned_cols=145  Identities=17%  Similarity=0.117  Sum_probs=89.0

Q ss_pred             ccceEEeeecCCcccCCCCCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCccc-c---------
Q 042541          527 NNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFR-V---------  596 (695)
Q Consensus       527 ~~~r~l~~~~~~~~~~~~~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~-~---------  596 (695)
                      ...+.|.+..+.... .+.  ..++|+.|.++.|... .+|..   ..+|++|+|++|.+..  ++..+ .         
T Consensus       302 ~~L~~LdLS~N~L~~-Lp~--lp~~L~~L~Ls~N~L~-~LP~l---p~~Lq~LdLS~N~Ls~--LP~lp~~L~~L~Ls~N  372 (788)
T PRK15387        302 PGLQELSVSDNQLAS-LPA--LPSELCKLWAYNNQLT-SLPTL---PSGLQELSVSDNQLAS--LPTLPSELYKLWAYNN  372 (788)
T ss_pred             cccceeECCCCcccc-CCC--CcccccccccccCccc-ccccc---ccccceEecCCCccCC--CCCCCcccceehhhcc
Confidence            456777766543221 111  1234555555554332 23321   1357777777765532  11100 0         


Q ss_pred             -cc----cCCCCcEEEeccCCCCCcc-cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchh
Q 042541          597 -LS----ALSKLKKIRLEHVSLPNSL-ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDG  670 (695)
Q Consensus       597 -l~----~l~~L~~L~L~~~~l~~lp-~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~  670 (695)
                       +.    ...+|+.|++++|.+..+| .   ..+|+.|++++|.++.+|.        .+.+|+.|++++| .+..+|.+
T Consensus       373 ~L~~LP~l~~~L~~LdLs~N~Lt~LP~l---~s~L~~LdLS~N~LssIP~--------l~~~L~~L~Ls~N-qLt~LP~s  440 (788)
T PRK15387        373 RLTSLPALPSGLKELIVSGNRLTSLPVL---PSELKELMVSGNRLTSLPM--------LPSGLLSLSVYRN-QLTRLPES  440 (788)
T ss_pred             ccccCcccccccceEEecCCcccCCCCc---ccCCCEEEccCCcCCCCCc--------chhhhhhhhhccC-cccccChH
Confidence             00    1235777888888777777 3   2467788888888777653        2346788999985 57899999


Q ss_pred             hcCCCCCceeecccccCCCCCC
Q 042541          671 LCDIVSMEKLRITNCHRLSALP  692 (695)
Q Consensus       671 i~~L~~L~~L~l~~~~~l~~lP  692 (695)
                      ++++++|+.|+|++|+.-+..|
T Consensus       441 l~~L~~L~~LdLs~N~Ls~~~~  462 (788)
T PRK15387        441 LIHLSSETTVNLEGNPLSERTL  462 (788)
T ss_pred             HhhccCCCeEECCCCCCCchHH
Confidence            9999999999999988655544

>PLN03150 hypothetical protein; Provisional

Probab=98.47  E-value=1.7e-07  Score=105.93  Aligned_cols=89  Identities=17%  Similarity=0.222  Sum_probs=80.0

Q ss_pred             CCcEEEeccCCCC-Ccc-cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCce
Q 042541          602 KLKKIRLEHVSLP-NSL-ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEK  679 (695)
Q Consensus       602 ~L~~L~L~~~~l~-~lp-~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~  679 (695)
                      .+..|+|++|.+. .+| .+++|++|++|+|++|.+.+..|..+.    .+++|+.|+|++|...+.+|..+++|++|++
T Consensus       419 ~v~~L~L~~n~L~g~ip~~i~~L~~L~~L~Ls~N~l~g~iP~~~~----~l~~L~~LdLs~N~lsg~iP~~l~~L~~L~~  494 (623)
T PLN03150        419 FIDGLGLDNQGLRGFIPNDISKLRHLQSINLSGNSIRGNIPPSLG----SITSLEVLDLSYNSFNGSIPESLGQLTSLRI  494 (623)
T ss_pred             EEEEEECCCCCccccCCHHHhCCCCCCEEECCCCcccCcCChHHh----CCCCCCEEECCCCCCCCCCchHHhcCCCCCE
Confidence            3788999999998 888 999999999999999999876665555    8999999999999877899999999999999


Q ss_pred             eecccccCCCCCCCC
Q 042541          680 LRITNCHRLSALPEG  694 (695)
Q Consensus       680 L~l~~~~~l~~lP~~  694 (695)
                      |+|++|+..+.+|..
T Consensus       495 L~Ls~N~l~g~iP~~  509 (623)
T PLN03150        495 LNLNGNSLSGRVPAA  509 (623)
T ss_pred             EECcCCcccccCChH
Confidence            999999988899865

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=98.47  E-value=2.2e-07  Score=88.41  Aligned_cols=73  Identities=12%  Similarity=0.247  Sum_probs=41.8

Q ss_pred             CCCCcchHHHHHHHHH---cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC-----CHHHHHHHH
Q 042541          168 SPGLDVPLKELKMELF---KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP-----NVKAIVQKV  239 (695)
Q Consensus       168 ~vGr~~~~~~l~~~L~---~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~-----~~~~~~~~i  239 (695)
                      ||||+++++++...|.   ....+.+.|+|++|+|||+|+++++.  ++...... ++.+.+....     ....+++++
T Consensus         2 fvgR~~e~~~l~~~l~~~~~~~~~~~ll~G~~G~GKT~ll~~~~~--~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l   78 (185)
T PF13191_consen    2 FVGREEEIERLRDLLDAAQSGSPRNLLLTGESGSGKTSLLRALLD--RLAERGGY-VISINCDDSERNPYSPFRSALRQL   78 (185)
T ss_dssp             -TT-HHHHHHHHHTTGGTSS-----EEE-B-TTSSHHHHHHHHHH--HHHHHT---EEEEEEETTTS-HHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHcCCCcEEEEECCCCCCHHHHHHHHHH--HHHhcCCE-EEEEEEeccccchhhHHHHHHHHH
Confidence            7999999999999993   44579999999999999999999988  44444222 3344444331     124555555


Q ss_pred             HHhc
Q 042541          240 LHHK  243 (695)
Q Consensus       240 ~~~l  243 (695)
                      +.++
T Consensus        79 ~~~~   82 (185)
T PF13191_consen   79 IDQL   82 (185)
T ss_dssp             S---
T ss_pred             HHHh
Confidence            5543

>KOG0532 consensus Leucine-rich repeat (LRR) protein, contains calponin homology domain [Cytoskeleton]

Probab=98.47  E-value=1.7e-08  Score=105.33  Aligned_cols=132  Identities=20%  Similarity=0.296  Sum_probs=104.0

Q ss_pred             CCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc-cccccccccE
Q 042541          549 GPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL-ATVRMNHLQK  627 (695)
Q Consensus       549 ~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp-~i~~l~~L~~  627 (695)
                      +..|+.|+|+.|.. ..+|..+..++ |++|.++||.+..  ++  +.++.+..|..|+.+.|.+..+| .++.|.+|+.
T Consensus       120 L~~lt~l~ls~Nql-S~lp~~lC~lp-Lkvli~sNNkl~~--lp--~~ig~~~tl~~ld~s~nei~slpsql~~l~slr~  193 (722)
T KOG0532|consen  120 LEALTFLDLSSNQL-SHLPDGLCDLP-LKVLIVSNNKLTS--LP--EEIGLLPTLAHLDVSKNEIQSLPSQLGYLTSLRD  193 (722)
T ss_pred             hhHHHHhhhccchh-hcCChhhhcCc-ceeEEEecCcccc--CC--cccccchhHHHhhhhhhhhhhchHHhhhHHHHHH
Confidence            44555666655533 34566666666 8999999887632  22  22677888999999999999999 9999999999


Q ss_pred             EeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccccCCCCCCCC
Q 042541          628 VSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPEG  694 (695)
Q Consensus       628 L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~~l~~lP~~  694 (695)
                      |+++.|.+..+|+...     .| .|..||++ |+++..||-.|.+|+.|++|-|.+|+ |.+-|..
T Consensus       194 l~vrRn~l~~lp~El~-----~L-pLi~lDfS-cNkis~iPv~fr~m~~Lq~l~LenNP-LqSPPAq  252 (722)
T KOG0532|consen  194 LNVRRNHLEDLPEELC-----SL-PLIRLDFS-CNKISYLPVDFRKMRHLQVLQLENNP-LQSPPAQ  252 (722)
T ss_pred             HHHhhhhhhhCCHHHh-----CC-ceeeeecc-cCceeecchhhhhhhhheeeeeccCC-CCCChHH
Confidence            9999999999888775     23 38899999 57899999999999999999999977 8777754

>KOG1259 consensus Nischarin, modulator of integrin alpha5 subunit action [Signal transduction mechanisms; Cytoskeleton]

Probab=98.47  E-value=1.9e-08  Score=96.82  Aligned_cols=131  Identities=15%  Similarity=0.247  Sum_probs=100.4

Q ss_pred             CCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc-cccccccccE
Q 042541          549 GPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL-ATVRMNHLQK  627 (695)
Q Consensus       549 ~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp-~i~~l~~L~~  627 (695)
                      +..|+.++|++|. ...+.++++-.+.+|.|+++.|++.     ...++..|++|..|+|++|.++++- .--+|-|..+
T Consensus       283 Wq~LtelDLS~N~-I~~iDESvKL~Pkir~L~lS~N~i~-----~v~nLa~L~~L~~LDLS~N~Ls~~~Gwh~KLGNIKt  356 (490)
T KOG1259|consen  283 WQELTELDLSGNL-ITQIDESVKLAPKLRRLILSQNRIR-----TVQNLAELPQLQLLDLSGNLLAECVGWHLKLGNIKT  356 (490)
T ss_pred             Hhhhhhccccccc-hhhhhhhhhhccceeEEecccccee-----eehhhhhcccceEeecccchhHhhhhhHhhhcCEee
Confidence            3456777777663 3455667788899999999998763     2233778899999999999988776 5557888999


Q ss_pred             EeeccccCCcccccchhhhcccCCCccEEecccccccccCc--hhhcCCCCCceeecccccCCCCCCC
Q 042541          628 VSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELP--DGLCDIVSMEKLRITNCHRLSALPE  693 (695)
Q Consensus       628 L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP--~~i~~L~~L~~L~l~~~~~l~~lP~  693 (695)
                      |.|.+|.|..+ .+..     +|.+|..||+++| ++..+.  .+||+|+.|++|.|.+|+ +..+|.
T Consensus       357 L~La~N~iE~L-SGL~-----KLYSLvnLDl~~N-~Ie~ldeV~~IG~LPCLE~l~L~~NP-l~~~vd  416 (490)
T KOG1259|consen  357 LKLAQNKIETL-SGLR-----KLYSLVNLDLSSN-QIEELDEVNHIGNLPCLETLRLTGNP-LAGSVD  416 (490)
T ss_pred             eehhhhhHhhh-hhhH-----hhhhheecccccc-chhhHHHhcccccccHHHHHhhcCCC-ccccch
Confidence            99999987653 2222     7999999999985 456554  469999999999999987 666553

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=98.46  E-value=4.4e-06  Score=92.66  Aligned_cols=188  Identities=18%  Similarity=0.084  Sum_probs=109.2

Q ss_pred             CCCCCCCcchHHHHHHHHHcCCc-eEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhc
Q 042541          165 PVISPGLDVPLKELKMELFKDGR-QFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHK  243 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~~-~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l  243 (695)
                      -+.+||-+..++.|...+..+.. ..+.++|+.|+||||+|+.+++.  +.....  ...-.+..+    ...+.|...-
T Consensus        15 f~divGQe~vv~~L~~~l~~~rl~hAyLf~Gp~GvGKTTlAr~lAk~--L~c~~~--~~~~pCg~C----~~C~~i~~g~   86 (647)
T PRK07994         15 FAEVVGQEHVLTALANALDLGRLHHAYLFSGTRGVGKTTIARLLAKG--LNCETG--ITATPCGEC----DNCREIEQGR   86 (647)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHh--hhhccC--CCCCCCCCC----HHHHHHHcCC
Confidence            35679999999999988887664 44689999999999999998873  211100  000001111    1111111100


Q ss_pred             C-----CCCCCCCChHHHHHHHHHHH--HhcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCCCC--
Q 042541          244 G-----YPVPEFQTDEAAINDLERFF--KQMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFPQF--  310 (695)
Q Consensus       244 ~-----~~~~~~~~~~~~~~~l~~~~--~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~~~--  310 (695)
                      .     .........++ +..+...+  ....++.-++|+|+++.....    +++.+....+.+++|++|.+...-.  
T Consensus        87 ~~D~ieidaas~~~Vdd-iR~li~~~~~~p~~g~~KV~IIDEah~Ls~~a~NALLKtLEEPp~~v~FIL~Tt~~~kLl~T  165 (647)
T PRK07994         87 FVDLIEIDAASRTKVED-TRELLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVT  165 (647)
T ss_pred             CCCceeecccccCCHHH-HHHHHHHHHhhhhcCCCEEEEEechHhCCHHHHHHHHHHHHcCCCCeEEEEecCCccccchH
Confidence            0     00000001111 12222211  223577789999999877643    4555555555677777666552111  


Q ss_pred             ----CCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHH
Q 042541          311 ----GSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVV  364 (695)
Q Consensus       311 ----~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~  364 (695)
                          ...|.+++++.++....+.+.+.....   ....+....|++.++|.+.-+..+
T Consensus       166 I~SRC~~~~f~~Ls~~ei~~~L~~il~~e~i---~~e~~aL~~Ia~~s~Gs~R~Al~l  220 (647)
T PRK07994        166 ILSRCLQFHLKALDVEQIRQQLEHILQAEQI---PFEPRALQLLARAADGSMRDALSL  220 (647)
T ss_pred             HHhhheEeeCCCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHcCCCHHHHHHH
Confidence                238999999999999998876533221   123566788999999988644443

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=98.45  E-value=4.4e-06  Score=92.30  Aligned_cols=170  Identities=16%  Similarity=0.180  Sum_probs=108.0

Q ss_pred             CCCCCCCcchHHHHHHHHHcCC-ceEEEEEcCCCCcHHHHHHHHhccccccc-------------------cCCCcEEEE
Q 042541          165 PVISPGLDVPLKELKMELFKDG-RQFIVVSAPGGYGKTTLVQRLCKDDQVQG-------------------KFKDDIFYV  224 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~-~~vv~I~G~gGiGKTtLa~~~~~~~~~~~-------------------~f~~~~~wv  224 (695)
                      -+.+||.+..++.|..++..+. ...+.++|+.|+||||+|+.+.+.---..                   .|.. ++.+
T Consensus        15 FddIIGQe~vv~~L~~ai~~~rl~Ha~Lf~GP~GvGKTTlAriLAk~LnC~~~~~~~pCg~C~sCr~i~~g~~~D-vlEi   93 (709)
T PRK08691         15 FADLVGQEHVVKALQNALDEGRLHHAYLLTGTRGVGKTTIARILAKSLNCENAQHGEPCGVCQSCTQIDAGRYVD-LLEI   93 (709)
T ss_pred             HHHHcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCcHHHHHHHHHHHhcccCCCCCCCCcccHHHHHHhccCccc-eEEE
Confidence            3567999999999999998766 45689999999999999998876211010                   0111 1122


Q ss_pred             EeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHh-----cCCCcEEEEEeCCCCCChH----HHhhhccCCC
Q 042541          225 TVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQ-----MRIEAILLVLDDVWPGSES----LLQKLGFQLP  295 (695)
Q Consensus       225 ~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~-----l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~  295 (695)
                      +......                         .+.++++++.     ..+++-++|+|++......    +++.+.....
T Consensus        94 daAs~~g-------------------------Vd~IRelle~a~~~P~~gk~KVIIIDEad~Ls~~A~NALLKtLEEPp~  148 (709)
T PRK08691         94 DAASNTG-------------------------IDNIREVLENAQYAPTAGKYKVYIIDEVHMLSKSAFNAMLKTLEEPPE  148 (709)
T ss_pred             eccccCC-------------------------HHHHHHHHHHHHhhhhhCCcEEEEEECccccCHHHHHHHHHHHHhCCC
Confidence            1111111                         1222222211     2356779999999876643    4444544445


Q ss_pred             CCEEEEEcCCCCCCC------CCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHH
Q 042541          296 DYKILVTSRSEFPQF------GSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKV  363 (695)
Q Consensus       296 gs~iivTtR~~~~~~------~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~  363 (695)
                      .+++|++|.+.....      ...+.+.+++.++....+.+.+...+.   .-..+....|++.++|.+.-+..
T Consensus       149 ~v~fILaTtd~~kL~~TIrSRC~~f~f~~Ls~eeI~~~L~~Il~kEgi---~id~eAL~~Ia~~A~GslRdAln  219 (709)
T PRK08691        149 HVKFILATTDPHKVPVTVLSRCLQFVLRNMTAQQVADHLAHVLDSEKI---AYEPPALQLLGRAAAGSMRDALS  219 (709)
T ss_pred             CcEEEEEeCCccccchHHHHHHhhhhcCCCCHHHHHHHHHHHHHHcCC---CcCHHHHHHHHHHhCCCHHHHHH
Confidence            677887776542211      126788899999999999877654332   12466789999999998854443

>PRK04195 replication factor C large subunit; Provisional

Probab=98.45  E-value=2.2e-05  Score=86.29  Aligned_cols=175  Identities=14%  Similarity=0.156  Sum_probs=110.2

Q ss_pred             CCCCCCCCcchHHHHHHHHHc---C-CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHH
Q 042541          164 PPVISPGLDVPLKELKMELFK---D-GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKV  239 (695)
Q Consensus       164 ~~~~~vGr~~~~~~l~~~L~~---~-~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i  239 (695)
                      .-+.++|.+..++++..|+..   + ..+.+.|+|++|+||||+|+.+++.  .  .|+  ++-++.++..+... +..+
T Consensus        12 ~l~dlvg~~~~~~~l~~~l~~~~~g~~~~~lLL~GppG~GKTtla~ala~e--l--~~~--~ielnasd~r~~~~-i~~~   84 (482)
T PRK04195         12 TLSDVVGNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALAND--Y--GWE--VIELNASDQRTADV-IERV   84 (482)
T ss_pred             CHHHhcCCHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHH--c--CCC--EEEEcccccccHHH-HHHH
Confidence            345689999999999999873   2 2688999999999999999999983  2  122  44555554433322 2233


Q ss_pred             HHhcCCCCCCCCChHHHHHHHHHHHHhcC-CCcEEEEEeCCCCCCh----H----HHhhhccCCCCCEEEEEcCCCC---
Q 042541          240 LHHKGYPVPEFQTDEAAINDLERFFKQMR-IEAILLVLDDVWPGSE----S----LLQKLGFQLPDYKILVTSRSEF---  307 (695)
Q Consensus       240 ~~~l~~~~~~~~~~~~~~~~l~~~~~~l~-~~~~LlVlDdv~~~~~----~----~~~~l~~~~~gs~iivTtR~~~---  307 (695)
                      +......                  ..+. .++.+||+|+++....    .    +...+.  ..+..||+|+.+..   
T Consensus        85 i~~~~~~------------------~sl~~~~~kvIiIDEaD~L~~~~d~~~~~aL~~~l~--~~~~~iIli~n~~~~~~  144 (482)
T PRK04195         85 AGEAATS------------------GSLFGARRKLILLDEVDGIHGNEDRGGARAILELIK--KAKQPIILTANDPYDPS  144 (482)
T ss_pred             HHHhhcc------------------CcccCCCCeEEEEecCcccccccchhHHHHHHHHHH--cCCCCEEEeccCccccc
Confidence            2222110                  0111 3678999999976532    1    222222  23455676665431   


Q ss_pred             ----CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHHHhh
Q 042541          308 ----PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGGSL  368 (695)
Q Consensus       308 ----~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~~~L  368 (695)
                          ......+.+.+++.++....+...+......   -..+....|++.++|-...+......+
T Consensus       145 ~k~Lrsr~~~I~f~~~~~~~i~~~L~~i~~~egi~---i~~eaL~~Ia~~s~GDlR~ain~Lq~~  206 (482)
T PRK04195        145 LRELRNACLMIEFKRLSTRSIVPVLKRICRKEGIE---CDDEALKEIAERSGGDLRSAINDLQAI  206 (482)
T ss_pred             hhhHhccceEEEecCCCHHHHHHHHHHHHHHcCCC---CCHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence                1123478999999999999888776543322   236789999999999776555433333

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=98.42  E-value=9e-06  Score=84.21  Aligned_cols=169  Identities=12%  Similarity=0.116  Sum_probs=106.7

Q ss_pred             CCCCCcchHHHHHHHHHcCC-ceEEEEEcCCCCcHHHHHHHHhccc----cccccCCCcEEEEEe-CCCCCHHHHHHHHH
Q 042541          167 ISPGLDVPLKELKMELFKDG-RQFIVVSAPGGYGKTTLVQRLCKDD----QVQGKFKDDIFYVTV-SKNPNVKAIVQKVL  240 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~~~~-~~vv~I~G~gGiGKTtLa~~~~~~~----~~~~~f~~~~~wv~~-~~~~~~~~~~~~i~  240 (695)
                      .++|-+..++.+...+..+. .....++|+.|+||||+|+.++..-    ....|.+. ..|... +.....++ .+++.
T Consensus         5 ~i~g~~~~~~~l~~~~~~~~~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~-~~~~~~~~~~i~v~~-ir~~~   82 (313)
T PRK05564          5 TIIGHENIKNRIKNSIIKNRFSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDI-IEFKPINKKSIGVDD-IRNII   82 (313)
T ss_pred             hccCcHHHHHHHHHHHHcCCCCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCe-EEeccccCCCCCHHH-HHHHH
Confidence            46898888899999988665 4567899999999999999988721    11233332 223221 12222222 22222


Q ss_pred             HhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCC------CC
Q 042541          241 HHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFP------QF  310 (695)
Q Consensus       241 ~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~------~~  310 (695)
                      +.+...                   ...+++-++|+|+++.....    ++..+....+++.+|++|.+...      .-
T Consensus        83 ~~~~~~-------------------p~~~~~kv~iI~~ad~m~~~a~naLLK~LEepp~~t~~il~~~~~~~ll~TI~SR  143 (313)
T PRK05564         83 EEVNKK-------------------PYEGDKKVIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENLEQILDTIKSR  143 (313)
T ss_pred             HHHhcC-------------------cccCCceEEEEechhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCcHHHHhh
Confidence            222111                   11356678888887655532    55666666678888888865521      12


Q ss_pred             CCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHH
Q 042541          311 GSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKV  363 (695)
Q Consensus       311 ~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~  363 (695)
                      +..+.+.++++++....+.+...       ....+.+..++..++|.|.-+..
T Consensus       144 c~~~~~~~~~~~~~~~~l~~~~~-------~~~~~~~~~l~~~~~g~~~~a~~  189 (313)
T PRK05564        144 CQIYKLNRLSKEEIEKFISYKYN-------DIKEEEKKSAIAFSDGIPGKVEK  189 (313)
T ss_pred             ceeeeCCCcCHHHHHHHHHHHhc-------CCCHHHHHHHHHHcCCCHHHHHH
Confidence            23889999999999888866532       11245577899999999875543

>PRK08727 hypothetical protein; Validated

Probab=98.42  E-value=8.5e-06  Score=80.29  Aligned_cols=161  Identities=19%  Similarity=0.153  Sum_probs=96.6

Q ss_pred             CCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCC
Q 042541          167 ISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYP  246 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~  246 (695)
                      +++|-...+..+...........+.|+|..|+|||.|++.+++  ....... .+.|+++.+      ....        
T Consensus        21 f~~~~~n~~~~~~~~~~~~~~~~l~l~G~~G~GKThL~~a~~~--~~~~~~~-~~~y~~~~~------~~~~--------   83 (233)
T PRK08727         21 YIAAPDGLLAQLQALAAGQSSDWLYLSGPAGTGKTHLALALCA--AAEQAGR-SSAYLPLQA------AAGR--------   83 (233)
T ss_pred             ccCCcHHHHHHHHHHHhccCCCeEEEECCCCCCHHHHHHHHHH--HHHHcCC-cEEEEeHHH------hhhh--------
Confidence            3344434444444433333446799999999999999999988  3333322 256776432      1111        


Q ss_pred             CCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCC---hH---HHhhhcc-CCCCCEEEEEcCCCCCC----------
Q 042541          247 VPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGS---ES---LLQKLGF-QLPDYKILVTSRSEFPQ----------  309 (695)
Q Consensus       247 ~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~---~~---~~~~l~~-~~~gs~iivTtR~~~~~----------  309 (695)
                                   +...++.+ .+.-+||+||+....   .+   +...+.. ...|..||+||+.....          
T Consensus        84 -------------~~~~~~~l-~~~dlLiIDDi~~l~~~~~~~~~lf~l~n~~~~~~~~vI~ts~~~p~~l~~~~~dL~S  149 (233)
T PRK08727         84 -------------LRDALEAL-EGRSLVALDGLESIAGQREDEVALFDFHNRARAAGITLLYTARQMPDGLALVLPDLRS  149 (233)
T ss_pred             -------------HHHHHHHH-hcCCEEEEeCcccccCChHHHHHHHHHHHHHHHcCCeEEEECCCChhhhhhhhHHHHH
Confidence                         11111222 234589999986432   11   2221111 12367799999976221          


Q ss_pred             ---CCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHH
Q 042541          310 ---FGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLAL  361 (695)
Q Consensus       310 ---~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai  361 (695)
                         .+..+++++++.++-.+++.+++....-   .-.++....|++.++|-.-.+
T Consensus       150 Rl~~~~~~~l~~~~~e~~~~iL~~~a~~~~l---~l~~e~~~~La~~~~rd~r~~  201 (233)
T PRK08727        150 RLAQCIRIGLPVLDDVARAAVLRERAQRRGL---ALDEAAIDWLLTHGERELAGL  201 (233)
T ss_pred             HHhcCceEEecCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHhCCCCHHHH
Confidence               1348899999999999999987654322   224678889999998765544

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.41  E-value=6.9e-06  Score=89.76  Aligned_cols=172  Identities=18%  Similarity=0.148  Sum_probs=105.8

Q ss_pred             CCCCCCcchHHHHHHHHHcCCc-eEEEEEcCCCCcHHHHHHHHhccccccc---------------------cCCCcEEE
Q 042541          166 VISPGLDVPLKELKMELFKDGR-QFIVVSAPGGYGKTTLVQRLCKDDQVQG---------------------KFKDDIFY  223 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~~~-~vv~I~G~gGiGKTtLa~~~~~~~~~~~---------------------~f~~~~~w  223 (695)
                      +.++|-+..++.|...+..+.. ..+.++|+.|+||||+|+.+++.  +..                     .|.. +++
T Consensus        16 ~diiGq~~~v~~L~~~i~~~rl~ha~Lf~Gp~GvGKTTlAr~lAk~--L~c~~~~~~~pCg~C~sC~~i~~~~~~d-lie   92 (546)
T PRK14957         16 AEVAGQQHALNSLVHALETQKVHHAYLFTGTRGVGKTTLGRLLAKC--LNCKTGVTAEPCNKCENCVAINNNSFID-LIE   92 (546)
T ss_pred             HHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHH--hCCCCCCCCCCCcccHHHHHHhcCCCCc-eEE
Confidence            4579999999999998886654 55789999999999999998862  211                     1222 223


Q ss_pred             EEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHH--hcCCCcEEEEEeCCCCCChH----HHhhhccCCCCC
Q 042541          224 VTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFK--QMRIEAILLVLDDVWPGSES----LLQKLGFQLPDY  297 (695)
Q Consensus       224 v~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~--~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs  297 (695)
                      ++......+.+                      ...+...+.  ...+++-++|+|++......    ++..+......+
T Consensus        93 idaas~~gvd~----------------------ir~ii~~~~~~p~~g~~kViIIDEa~~ls~~a~naLLK~LEepp~~v  150 (546)
T PRK14957         93 IDAASRTGVEE----------------------TKEILDNIQYMPSQGRYKVYLIDEVHMLSKQSFNALLKTLEEPPEYV  150 (546)
T ss_pred             eecccccCHHH----------------------HHHHHHHHHhhhhcCCcEEEEEechhhccHHHHHHHHHHHhcCCCCc
Confidence            32221111111                      111111111  12467779999999776543    444444444566


Q ss_pred             EEEEEcCCCC-C-----CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchh-HHHHHH
Q 042541          298 KILVTSRSEF-P-----QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPL-ALKVVG  365 (695)
Q Consensus       298 ~iivTtR~~~-~-----~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PL-ai~~~~  365 (695)
                      .+|++|.+.. .     .-+..+++.+++.++....+.+.+...+.   ...++....|++.++|-+. |+..+-
T Consensus       151 ~fIL~Ttd~~kil~tI~SRc~~~~f~~Ls~~eI~~~L~~il~~egi---~~e~~Al~~Ia~~s~GdlR~alnlLe  222 (546)
T PRK14957        151 KFILATTDYHKIPVTILSRCIQLHLKHISQADIKDQLKIILAKENI---NSDEQSLEYIAYHAKGSLRDALSLLD  222 (546)
T ss_pred             eEEEEECChhhhhhhHHHheeeEEeCCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            6665554431 1     11348999999999988888875543221   1246677899999999664 444443

>PRK15370 E3 ubiquitin-protein ligase SlrP; Provisional

Probab=98.41  E-value=8.1e-07  Score=101.11  Aligned_cols=150  Identities=17%  Similarity=0.194  Sum_probs=81.4

Q ss_pred             cceEEeeecCCcccCCCCCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEE
Q 042541          528 NASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIR  607 (695)
Q Consensus       528 ~~r~l~~~~~~~~~~~~~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~  607 (695)
                      +.+.|.+..+.. ...+ ..-.++|+.|.++.|... .+|..+.  .+|+.|++++|.+.  .++.  .+  ..+|++|+
T Consensus       221 nL~~L~Ls~N~L-tsLP-~~l~~~L~~L~Ls~N~L~-~LP~~l~--s~L~~L~Ls~N~L~--~LP~--~l--~~sL~~L~  289 (754)
T PRK15370        221 NIKTLYANSNQL-TSIP-ATLPDTIQEMELSINRIT-ELPERLP--SALQSLDLFHNKIS--CLPE--NL--PEELRYLS  289 (754)
T ss_pred             CCCEEECCCCcc-ccCC-hhhhccccEEECcCCccC-cCChhHh--CCCCEEECcCCccC--cccc--cc--CCCCcEEE
Confidence            456666554321 1111 112345667777666433 5565543  46777777776553  1211  12  24688888


Q ss_pred             eccCCCCCcc-cccccccccEEeeccccCCcccccchh-------------hhcc-cCCCccEEecccccccccCchhhc
Q 042541          608 LEHVSLPNSL-ATVRMNHLQKVSLVMCNVGQVFRNSTF-------------RISD-AFPNLLEMDIDYCNDLIELPDGLC  672 (695)
Q Consensus       608 L~~~~l~~lp-~i~~l~~L~~L~l~~~~i~~~~~~~~~-------------~l~~-~l~~L~~L~l~~c~~l~~lP~~i~  672 (695)
                      +++|+++.+| .+.  .+|++|++++|.++.+|+....             .+|. ..++|+.|++++| .+..+|..+.
T Consensus       290 Ls~N~Lt~LP~~lp--~sL~~L~Ls~N~Lt~LP~~l~~sL~~L~Ls~N~Lt~LP~~l~~sL~~L~Ls~N-~L~~LP~~lp  366 (754)
T PRK15370        290 VYDNSIRTLPAHLP--SGITHLNVQSNSLTALPETLPPGLKTLEAGENALTSLPASLPPELQVLDVSKN-QITVLPETLP  366 (754)
T ss_pred             CCCCccccCcccch--hhHHHHHhcCCccccCCccccccceeccccCCccccCChhhcCcccEEECCCC-CCCcCChhhc
Confidence            8888777766 432  2444445555444443322110             0010 1246777778775 4567776553


Q ss_pred             CCCCCceeecccccCCCCCCCC
Q 042541          673 DIVSMEKLRITNCHRLSALPEG  694 (695)
Q Consensus       673 ~L~~L~~L~l~~~~~l~~lP~~  694 (695)
                        ++|+.|+|++|+ +..+|+.
T Consensus       367 --~~L~~LdLs~N~-Lt~LP~~  385 (754)
T PRK15370        367 --PTITTLDVSRNA-LTNLPEN  385 (754)
T ss_pred             --CCcCEEECCCCc-CCCCCHh
Confidence              578888888865 7777754

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.41  E-value=5.5e-06  Score=90.56  Aligned_cols=175  Identities=18%  Similarity=0.154  Sum_probs=107.6

Q ss_pred             CCCCCCCcchHHHHHHHHHcCCc-eEEEEEcCCCCcHHHHHHHHhcccccc-------------------ccCCCcEEEE
Q 042541          165 PVISPGLDVPLKELKMELFKDGR-QFIVVSAPGGYGKTTLVQRLCKDDQVQ-------------------GKFKDDIFYV  224 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~~-~vv~I~G~gGiGKTtLa~~~~~~~~~~-------------------~~f~~~~~wv  224 (695)
                      -+.+||-+..++.|..++..+.. ..+.++|+.|+||||+|+.+++.---.                   +.|.. ++.+
T Consensus        15 f~divGq~~v~~~L~~~~~~~~l~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~g~~~d-~~ei   93 (509)
T PRK14958         15 FQEVIGQAPVVRALSNALDQQYLHHAYLFTGTRGVGKTTISRILAKCLNCEKGVSANPCNDCENCREIDEGRFPD-LFEV   93 (509)
T ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCeeEEEECCCCCCHHHHHHHHHHHhcCCCCCCcccCCCCHHHHHHhcCCCce-EEEE
Confidence            34679999999999999987664 457899999999999999887631111                   11222 2233


Q ss_pred             EeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEE
Q 042541          225 TVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKIL  300 (695)
Q Consensus       225 ~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~ii  300 (695)
                      +.+....++++ +++++.+..                   ....++.-++|+|+++.....    +++.+....+.+++|
T Consensus        94 daas~~~v~~i-R~l~~~~~~-------------------~p~~~~~kV~iIDE~~~ls~~a~naLLk~LEepp~~~~fI  153 (509)
T PRK14958         94 DAASRTKVEDT-RELLDNIPY-------------------APTKGRFKVYLIDEVHMLSGHSFNALLKTLEEPPSHVKFI  153 (509)
T ss_pred             cccccCCHHHH-HHHHHHHhh-------------------ccccCCcEEEEEEChHhcCHHHHHHHHHHHhccCCCeEEE
Confidence            32222222221 122222111                   112466779999999876643    445555555577777


Q ss_pred             EEcCCCCC------CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHH
Q 042541          301 VTSRSEFP------QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKV  363 (695)
Q Consensus       301 vTtR~~~~------~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~  363 (695)
                      ++|.+...      .-...+++++++.++....+...+...+.   .-..+....|++.++|.+.-+..
T Consensus       154 lattd~~kl~~tI~SRc~~~~f~~l~~~~i~~~l~~il~~egi---~~~~~al~~ia~~s~GslR~al~  219 (509)
T PRK14958        154 LATTDHHKLPVTVLSRCLQFHLAQLPPLQIAAHCQHLLKEENV---EFENAALDLLARAANGSVRDALS  219 (509)
T ss_pred             EEECChHhchHHHHHHhhhhhcCCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHcCCcHHHHHH
Confidence            76654421      11237889999999988877766543322   11356678899999998864443

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=98.41  E-value=7.8e-06  Score=86.28  Aligned_cols=165  Identities=15%  Similarity=0.143  Sum_probs=102.6

Q ss_pred             CCCCCcchHHHHHHHHHcCC----------ceEEEEEcCCCCcHHHHHHHHhcccccc------------------ccCC
Q 042541          167 ISPGLDVPLKELKMELFKDG----------RQFIVVSAPGGYGKTTLVQRLCKDDQVQ------------------GKFK  218 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~~~~----------~~vv~I~G~gGiGKTtLa~~~~~~~~~~------------------~~f~  218 (695)
                      .++|-+..++.|..++..+.          ..-+.++|+.|+|||++|+.++..---.                  ..++
T Consensus         6 ~IiGq~~~~~~L~~~i~~~~~~~~~~~~~l~ha~Lf~Gp~G~GKt~lA~~lA~~l~c~~~~~~~Cg~C~~C~~~~~~~hp   85 (394)
T PRK07940          6 DLVGQEAVVAELRAAARAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFAAALQCTDPDEPGCGECRACRTVLAGTHP   85 (394)
T ss_pred             hccChHHHHHHHHHHHHhccccccccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCC
Confidence            46898888999999888653          4568899999999999999887621000                  0111


Q ss_pred             CcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHh-----cCCCcEEEEEeCCCCCChH----HHhh
Q 042541          219 DDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQ-----MRIEAILLVLDDVWPGSES----LLQK  289 (695)
Q Consensus       219 ~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~-----l~~~~~LlVlDdv~~~~~~----~~~~  289 (695)
                      . +.++.....                        ...+++++.+.+.     ..+++-++|+|+++.....    +++.
T Consensus        86 D-~~~i~~~~~------------------------~i~i~~iR~l~~~~~~~p~~~~~kViiIDead~m~~~aanaLLk~  140 (394)
T PRK07940         86 D-VRVVAPEGL------------------------SIGVDEVRELVTIAARRPSTGRWRIVVIEDADRLTERAANALLKA  140 (394)
T ss_pred             C-EEEeccccc------------------------cCCHHHHHHHHHHHHhCcccCCcEEEEEechhhcCHHHHHHHHHH
Confidence            1 212211100                        0011222222211     2356668899999877643    4555


Q ss_pred             hccCCCCCEEEEEcCCCCC------CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHH
Q 042541          290 LGFQLPDYKILVTSRSEFP------QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKV  363 (695)
Q Consensus       290 l~~~~~gs~iivTtR~~~~------~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~  363 (695)
                      +....+++.+|++|.+...      .-...+.+++++.++..+.+.+...        ...+.+..++..++|.|.....
T Consensus       141 LEep~~~~~fIL~a~~~~~llpTIrSRc~~i~f~~~~~~~i~~~L~~~~~--------~~~~~a~~la~~s~G~~~~A~~  212 (394)
T PRK07940        141 VEEPPPRTVWLLCAPSPEDVLPTIRSRCRHVALRTPSVEAVAEVLVRRDG--------VDPETARRAARASQGHIGRARR  212 (394)
T ss_pred             hhcCCCCCeEEEEECChHHChHHHHhhCeEEECCCCCHHHHHHHHHHhcC--------CCHHHHHHHHHHcCCCHHHHHH
Confidence            5555567777777666521      1123889999999999988874321        1245688899999999975544


Q ss_pred             H
Q 042541          364 V  364 (695)
Q Consensus       364 ~  364 (695)
                      +
T Consensus       213 l  213 (394)
T PRK07940        213 L  213 (394)
T ss_pred             H
Confidence            3

>PF14516 AAA_35: AAA-like domain

Probab=98.40  E-value=0.0002  Score=74.53  Aligned_cols=202  Identities=16%  Similarity=0.195  Sum_probs=123.8

Q ss_pred             CCCCCCCCCCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCC-----CCH
Q 042541          158 CCSAPDPPVISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKN-----PNV  232 (695)
Q Consensus       158 ~~~~~~~~~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~-----~~~  232 (695)
                      .+++|......|.|...-+++.+.|.+++ ..+.|.|+-.+|||+|...+.+..+- ..|.  ++++++...     .+.
T Consensus         3 ~g~~~~~~~~Yi~R~~~e~~~~~~i~~~G-~~~~I~apRq~GKTSll~~l~~~l~~-~~~~--~v~id~~~~~~~~~~~~   78 (331)
T PF14516_consen    3 GGPLPLDSPFYIERPPAEQECYQEIVQPG-SYIRIKAPRQMGKTSLLLRLLERLQQ-QGYR--CVYIDLQQLGSAIFSDL   78 (331)
T ss_pred             CCCCCCCCCcccCchHHHHHHHHHHhcCC-CEEEEECcccCCHHHHHHHHHHHHHH-CCCE--EEEEEeecCCCcccCCH
Confidence            34566666777999966677777777643 68999999999999999998873222 3343  568988752     245


Q ss_pred             HHHHHHH----HHhcCCCCCC-------CCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCCh------HHHhhhcc--
Q 042541          233 KAIVQKV----LHHKGYPVPE-------FQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGSE------SLLQKLGF--  292 (695)
Q Consensus       233 ~~~~~~i----~~~l~~~~~~-------~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~~------~~~~~l~~--  292 (695)
                      ..+++.+    .++++....-       ..........+.+.+ .. .+++.+|++|+++....      .++..+..  
T Consensus        79 ~~f~~~~~~~i~~~L~l~~~l~~~w~~~~~~~~~~~~~~~~~ll~~-~~~~lVL~iDEiD~l~~~~~~~~dF~~~LR~~~  157 (331)
T PF14516_consen   79 EQFLRWFCEEISRQLKLDEKLDEYWDEEIGSKISCTEYFEEYLLKQ-IDKPLVLFIDEIDRLFEYPQIADDFFGLLRSWY  157 (331)
T ss_pred             HHHHHHHHHHHHHHcCCChhHHHHHHHhcCChhhHHHHHHHHHHhc-CCCCEEEEEechhhhccCcchHHHHHHHHHHHH
Confidence            5555444    4455443210       011112222333333 22 37899999999965432      12222111  


Q ss_pred             -C---CC--C-CEEEEEcCCC--C--------CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcC
Q 042541          293 -Q---LP--D-YKILVTSRSE--F--------PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACK  355 (695)
Q Consensus       293 -~---~~--g-s~iivTtR~~--~--------~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~  355 (695)
                       .   .+  . -++++....+  .        -..+..++|++++.+|...|+.+.-..       -..+..++|...+|
T Consensus       158 ~~~~~~~~~~~L~li~~~~t~~~~~~~~~~SPFNIg~~i~L~~Ft~~ev~~L~~~~~~~-------~~~~~~~~l~~~tg  230 (331)
T PF14516_consen  158 EQRKNNPIWQKLRLILAGSTEDYIILDINQSPFNIGQPIELPDFTPEEVQELAQRYGLE-------FSQEQLEQLMDWTG  230 (331)
T ss_pred             HhcccCcccceEEEEEecCcccccccCCCCCCcccccceeCCCCCHHHHHHHHHhhhcc-------CCHHHHHHHHHHHC
Confidence             1   11  1 1222221111  0        022348899999999999998876321       12344999999999


Q ss_pred             CchhHHHHHHHhhCCC
Q 042541          356 GCPLALKVVGGSLCGK  371 (695)
Q Consensus       356 G~PLai~~~~~~L~~~  371 (695)
                      |+|.-+..++..+...
T Consensus       231 GhP~Lv~~~~~~l~~~  246 (331)
T PF14516_consen  231 GHPYLVQKACYLLVEE  246 (331)
T ss_pred             CCHHHHHHHHHHHHHc
Confidence            9999999999988654

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=98.39  E-value=1.2e-05  Score=76.58  Aligned_cols=152  Identities=20%  Similarity=0.212  Sum_probs=91.5

Q ss_pred             HHHHHHHcCCc-eEEEEEcCCCCcHHHHHHHHhccccccc---------------------cCCCcEEEEEeCCC-CCHH
Q 042541          177 ELKMELFKDGR-QFIVVSAPGGYGKTTLVQRLCKDDQVQG---------------------KFKDDIFYVTVSKN-PNVK  233 (695)
Q Consensus       177 ~l~~~L~~~~~-~vv~I~G~gGiGKTtLa~~~~~~~~~~~---------------------~f~~~~~wv~~~~~-~~~~  233 (695)
                      .+.+.+..+.. ..+.++|+.|+||||+|+.+..  .+..                     .++. ..++..... ... 
T Consensus         3 ~l~~~i~~~~~~~~~L~~G~~G~gkt~~a~~~~~--~l~~~~~~~~~~c~~~~~c~~~~~~~~~d-~~~~~~~~~~~~~-   78 (188)
T TIGR00678         3 QLKRALEKGRLAHAYLFAGPEGVGKELLALALAK--ALLCEQPGGGEPCGECPSCRLIEAGNHPD-LHRLEPEGQSIKV-   78 (188)
T ss_pred             HHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHH--HHcCCCCCCCCCCCCCHHHHHHHcCCCCc-EEEeccccCcCCH-
Confidence            45566666654 6789999999999999998876  3221                     1111 122222111 111 


Q ss_pred             HHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCC--
Q 042541          234 AIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEF--  307 (695)
Q Consensus       234 ~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~--  307 (695)
                      +..+++++.+..                   ....+.+-++|+||+......    ++..+....+.+.+|++|++..  
T Consensus        79 ~~i~~i~~~~~~-------------------~~~~~~~kviiide~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l  139 (188)
T TIGR00678        79 DQVRELVEFLSR-------------------TPQESGRRVVIIEDAERMNEAAANALLKTLEEPPPNTLFILITPSPEKL  139 (188)
T ss_pred             HHHHHHHHHHcc-------------------CcccCCeEEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhC
Confidence            111111221111                   011356778999999776543    4444544445677777776541  


Q ss_pred             ----CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhH
Q 042541          308 ----PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLA  360 (695)
Q Consensus       308 ----~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLa  360 (695)
                          ......+.+.+++.++..+.+.+.  +       -.++.+..|++.++|.|..
T Consensus       140 ~~~i~sr~~~~~~~~~~~~~~~~~l~~~--g-------i~~~~~~~i~~~~~g~~r~  187 (188)
T TIGR00678       140 LPTIRSRCQVLPFPPLSEEALLQWLIRQ--G-------ISEEAAELLLALAGGSPGA  187 (188)
T ss_pred             hHHHHhhcEEeeCCCCCHHHHHHHHHHc--C-------CCHHHHHHHHHHcCCCccc
Confidence                112238999999999999988876  1       1256799999999998853

At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=98.39  E-value=3.6e-06  Score=95.33  Aligned_cols=170  Identities=16%  Similarity=0.174  Sum_probs=98.4

Q ss_pred             CCCCCCCCcchHH---HHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHH
Q 042541          164 PPVISPGLDVPLK---ELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVL  240 (695)
Q Consensus       164 ~~~~~vGr~~~~~---~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~  240 (695)
                      .-+.++|.+..+.   .+...+..+....+.|+|++|+||||||+.+++  .....|.    .++... ....++ +   
T Consensus        26 tldd~vGQe~ii~~~~~L~~~i~~~~~~slLL~GPpGtGKTTLA~aIA~--~~~~~f~----~lna~~-~~i~di-r---   94 (725)
T PRK13341         26 TLEEFVGQDHILGEGRLLRRAIKADRVGSLILYGPPGVGKTTLARIIAN--HTRAHFS----SLNAVL-AGVKDL-R---   94 (725)
T ss_pred             cHHHhcCcHHHhhhhHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHH--HhcCcce----eehhhh-hhhHHH-H---
Confidence            3356799888774   566667777777889999999999999999997  3433331    111110 001000 0   


Q ss_pred             HhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChHHHhhhccCC-CCCEEEEE--cCCCCC-------CC
Q 042541          241 HHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSESLLQKLGFQL-PDYKILVT--SRSEFP-------QF  310 (695)
Q Consensus       241 ~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~~~~~l~~~~-~gs~iivT--tR~~~~-------~~  310 (695)
                                    .........+. ..+++.+|++||++.........+.... .|+.++|+  |.+...       .-
T Consensus        95 --------------~~i~~a~~~l~-~~~~~~IL~IDEIh~Ln~~qQdaLL~~lE~g~IiLI~aTTenp~~~l~~aL~SR  159 (725)
T PRK13341         95 --------------AEVDRAKERLE-RHGKRTILFIDEVHRFNKAQQDALLPWVENGTITLIGATTENPYFEVNKALVSR  159 (725)
T ss_pred             --------------HHHHHHHHHhh-hcCCceEEEEeChhhCCHHHHHHHHHHhcCceEEEEEecCCChHhhhhhHhhcc
Confidence                          11111111111 1256789999999766543333333222 34445543  333211       11


Q ss_pred             CCeEecCCCChHHHHHHHHHhccCCC----CCCCCCchHHHHHHHHhcCCchh
Q 042541          311 GSVHYLKPLTYEAARTLFLHSANLQD----GNSYIPDENIVSKILRACKGCPL  359 (695)
Q Consensus       311 ~~~~~l~~L~~~ea~~Lf~~~~~~~~----~~~~~~~~~~~~~I~~~c~G~PL  359 (695)
                      ...+.+++++.++...++.+.+....    .....-.++....|++.+.|.-.
T Consensus       160 ~~v~~l~pLs~edi~~IL~~~l~~~~~~~g~~~v~I~deaL~~La~~s~GD~R  212 (725)
T PRK13341        160 SRLFRLKSLSDEDLHQLLKRALQDKERGYGDRKVDLEPEAEKHLVDVANGDAR  212 (725)
T ss_pred             ccceecCCCCHHHHHHHHHHHHHHHHhhcCCcccCCCHHHHHHHHHhCCCCHH
Confidence            34799999999999999987664110    00111236678889999998754

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.37  E-value=9.7e-06  Score=87.29  Aligned_cols=174  Identities=18%  Similarity=0.178  Sum_probs=110.2

Q ss_pred             CCCCCCCcchHHHHHHHHHcCCc-eEEEEEcCCCCcHHHHHHHHhccc------c------------cc-ccCCCcEEEE
Q 042541          165 PVISPGLDVPLKELKMELFKDGR-QFIVVSAPGGYGKTTLVQRLCKDD------Q------------VQ-GKFKDDIFYV  224 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~~-~vv~I~G~gGiGKTtLa~~~~~~~------~------------~~-~~f~~~~~wv  224 (695)
                      -+.+||-+..++.+...+..+.. ..+.++|+.|+||||+|+.++..-      .            +. +.+.. ++.+
T Consensus        12 f~dliGQe~vv~~L~~a~~~~ri~ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~~~~~pCg~C~~C~~i~~~~~~D-v~ei   90 (491)
T PRK14964         12 FKDLVGQDVLVRILRNAFTLNKIPQSILLVGASGVGKTTCARIISLCLNCSNGPTSDPCGTCHNCISIKNSNHPD-VIEI   90 (491)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCccHHHHHHHHHHHHcCcCCCCCCCccccHHHHHHhccCCCC-EEEE
Confidence            34679999888888888887665 478999999999999999887510      0            00 11122 4444


Q ss_pred             EeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEE
Q 042541          225 TVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKIL  300 (695)
Q Consensus       225 ~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~ii  300 (695)
                      +.+....+.++ +++++....                   .-..++.-++|+|++......    +++.+....+.+++|
T Consensus        91 daas~~~vddI-R~Iie~~~~-------------------~P~~~~~KVvIIDEah~Ls~~A~NaLLK~LEePp~~v~fI  150 (491)
T PRK14964         91 DAASNTSVDDI-KVILENSCY-------------------LPISSKFKVYIIDEVHMLSNSAFNALLKTLEEPAPHVKFI  150 (491)
T ss_pred             ecccCCCHHHH-HHHHHHHHh-------------------ccccCCceEEEEeChHhCCHHHHHHHHHHHhCCCCCeEEE
Confidence            44433333221 222222110                   011356779999999776543    455555555677777


Q ss_pred             EEcCCCC------CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHH
Q 042541          301 VTSRSEF------PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALK  362 (695)
Q Consensus       301 vTtR~~~------~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~  362 (695)
                      ++|....      ..-...+.+.+++.++....+.+.+.....   .-.++.+..|++.++|.+..+.
T Consensus       151 latte~~Kl~~tI~SRc~~~~f~~l~~~el~~~L~~ia~~Egi---~i~~eAL~lIa~~s~GslR~al  215 (491)
T PRK14964        151 LATTEVKKIPVTIISRCQRFDLQKIPTDKLVEHLVDIAKKENI---EHDEESLKLIAENSSGSMRNAL  215 (491)
T ss_pred             EEeCChHHHHHHHHHhheeeecccccHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHcCCCHHHHH
Confidence            7664331      112337899999999999999887754332   1236678899999999876443

>KOG2028 consensus ATPase related to the helicase subunit of the Holliday junction resolvase [Replication, recombination and repair]

Probab=98.37  E-value=4.4e-06  Score=82.96  Aligned_cols=170  Identities=15%  Similarity=0.125  Sum_probs=104.9

Q ss_pred             CCCCCcchH---HHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhc
Q 042541          167 ISPGLDVPL---KELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHK  243 (695)
Q Consensus       167 ~~vGr~~~~---~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l  243 (695)
                      ..||.+..+   --|...+.++..+-+.+||++|+||||||+.+...  .+.+-   ..+|.+|....-..-.+.|+++.
T Consensus       139 dyvGQ~hlv~q~gllrs~ieq~~ipSmIlWGppG~GKTtlArlia~t--sk~~S---yrfvelSAt~a~t~dvR~ife~a  213 (554)
T KOG2028|consen  139 DYVGQSHLVGQDGLLRSLIEQNRIPSMILWGPPGTGKTTLARLIAST--SKKHS---YRFVELSATNAKTNDVRDIFEQA  213 (554)
T ss_pred             HhcchhhhcCcchHHHHHHHcCCCCceEEecCCCCchHHHHHHHHhh--cCCCc---eEEEEEeccccchHHHHHHHHHH
Confidence            345544322   33445566778888999999999999999999873  33331   55888876654444444554442


Q ss_pred             CCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChHHHhhhccC-CCCCEEEE--EcCCCCCC-------CCCe
Q 042541          244 GYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSESLLQKLGFQ-LPDYKILV--TSRSEFPQ-------FGSV  313 (695)
Q Consensus       244 ~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~~~~~l~~~-~~gs~iiv--TtR~~~~~-------~~~~  313 (695)
                      .                 . ...+.+++.+|.+|.|..-....-+.|.+. ..|.-++|  ||.+..-.       -..+
T Consensus       214 q-----------------~-~~~l~krkTilFiDEiHRFNksQQD~fLP~VE~G~I~lIGATTENPSFqln~aLlSRC~V  275 (554)
T KOG2028|consen  214 Q-----------------N-EKSLTKRKTILFIDEIHRFNKSQQDTFLPHVENGDITLIGATTENPSFQLNAALLSRCRV  275 (554)
T ss_pred             H-----------------H-HHhhhcceeEEEeHHhhhhhhhhhhcccceeccCceEEEecccCCCccchhHHHHhccce
Confidence            1                 1 123468899999999965543333444443 34666666  66665321       1238


Q ss_pred             EecCCCChHHHHHHHHHhcc--CC----CCCCCCC----chHHHHHHHHhcCCchh
Q 042541          314 HYLKPLTYEAARTLFLHSAN--LQ----DGNSYIP----DENIVSKILRACKGCPL  359 (695)
Q Consensus       314 ~~l~~L~~~ea~~Lf~~~~~--~~----~~~~~~~----~~~~~~~I~~~c~G~PL  359 (695)
                      +.|++|..++-..++.+...  +.    ....+..    ...+.+-++..|.|-..
T Consensus       276 fvLekL~~n~v~~iL~raia~l~dser~~~~l~n~s~~ve~siidyla~lsdGDaR  331 (554)
T KOG2028|consen  276 FVLEKLPVNAVVTILMRAIASLGDSERPTDPLPNSSMFVEDSIIDYLAYLSDGDAR  331 (554)
T ss_pred             eEeccCCHHHHHHHHHHHHHhhccccccCCCCCCcchhhhHHHHHHHHHhcCchHH
Confidence            99999999999999887332  11    1111221    23466667777888643

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.36  E-value=1.2e-05  Score=86.89  Aligned_cols=178  Identities=17%  Similarity=0.143  Sum_probs=104.2

Q ss_pred             CCCCCCCcchHHHHHHHHHcCCc-eEEEEEcCCCCcHHHHHHHHhcccccccc--C-CC---------------cEEEEE
Q 042541          165 PVISPGLDVPLKELKMELFKDGR-QFIVVSAPGGYGKTTLVQRLCKDDQVQGK--F-KD---------------DIFYVT  225 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~~-~vv~I~G~gGiGKTtLa~~~~~~~~~~~~--f-~~---------------~~~wv~  225 (695)
                      -+.+||.+...+.|...+..+.. ..+.++|++|+||||+|+.+++.-.-...  + ++               .++.++
T Consensus        13 ~~divGq~~i~~~L~~~i~~~~l~~~~Lf~GPpGtGKTTlA~~lA~~l~~~~~~~~~pc~~c~~c~~i~~g~~~dv~el~   92 (472)
T PRK14962         13 FSEVVGQDHVKKLIINALKKNSISHAYIFAGPRGTGKTTVARILAKSLNCENRKGVEPCNECRACRSIDEGTFMDVIELD   92 (472)
T ss_pred             HHHccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCCCcccHHHHHHhcCCCCccEEEe
Confidence            35679998888888888877665 56899999999999999999773111000  0 00               022222


Q ss_pred             eCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHH--hcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEE
Q 042541          226 VSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFK--QMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKI  299 (695)
Q Consensus       226 ~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~--~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~i  299 (695)
                      .+.......                      ...+.....  ...+++-++|+|+++.....    ++..+....+.+.+
T Consensus        93 aa~~~gid~----------------------iR~i~~~~~~~p~~~~~kVvIIDE~h~Lt~~a~~~LLk~LE~p~~~vv~  150 (472)
T PRK14962         93 AASNRGIDE----------------------IRKIRDAVGYRPMEGKYKVYIIDEVHMLTKEAFNALLKTLEEPPSHVVF  150 (472)
T ss_pred             CcccCCHHH----------------------HHHHHHHHhhChhcCCeEEEEEEChHHhHHHHHHHHHHHHHhCCCcEEE
Confidence            221111111                      112222111  12356779999999765432    33334333334455


Q ss_pred             EEEcCCCC------CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCC-chhHHHHHHHh
Q 042541          300 LVTSRSEF------PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKG-CPLALKVVGGS  367 (695)
Q Consensus       300 ivTtR~~~------~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G-~PLai~~~~~~  367 (695)
                      |++|....      ......+.+.+++.++....+.+.+.....   .-.++....|++.++| .+.++..+-.+
T Consensus       151 Ilattn~~kl~~~L~SR~~vv~f~~l~~~el~~~L~~i~~~egi---~i~~eal~~Ia~~s~GdlR~aln~Le~l  222 (472)
T PRK14962        151 VLATTNLEKVPPTIISRCQVIEFRNISDELIIKRLQEVAEAEGI---EIDREALSFIAKRASGGLRDALTMLEQV  222 (472)
T ss_pred             EEEeCChHhhhHHHhcCcEEEEECCccHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence            44444321      112248899999999999988887643322   1236678889998865 56777766553

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=98.35  E-value=6e-06  Score=89.65  Aligned_cols=188  Identities=15%  Similarity=0.157  Sum_probs=105.8

Q ss_pred             CCCCCCCcchHHHHHHHHHcCC-ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHH---HH
Q 042541          165 PVISPGLDVPLKELKMELFKDG-RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQK---VL  240 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~-~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~---i~  240 (695)
                      -..+||-+..++.|...+..+. ...+.++|+.|+||||+|+.+++.-.-......+--+..+..+.+-..+...   -+
T Consensus        20 f~dliGq~~vv~~L~~ai~~~ri~~a~Lf~Gp~G~GKTT~ArilAk~Lnc~~~~~~~~~~~~C~~C~~C~~i~~~~h~Dv   99 (507)
T PRK06645         20 FAELQGQEVLVKVLSYTILNDRLAGGYLLTGIRGVGKTTSARIIAKAVNCSALITENTTIKTCEQCTNCISFNNHNHPDI   99 (507)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHhcCccccccCcCcCCCCCChHHHHHhcCCCCcE
Confidence            3457999998998888777665 4678899999999999999998731111100000000111111110110000   00


Q ss_pred             HhcCCCCCCCCChHHHHHHHHHHHH-----hcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCC-CC--
Q 042541          241 HHKGYPVPEFQTDEAAINDLERFFK-----QMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSE-FP--  308 (695)
Q Consensus       241 ~~l~~~~~~~~~~~~~~~~l~~~~~-----~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~-~~--  308 (695)
                      ..+....      ....+.++.+++     -..+++-++|+|+++.....    ++..+....+.+.+|++|... ..  
T Consensus       100 ~eidaas------~~~vd~Ir~iie~a~~~P~~~~~KVvIIDEa~~Ls~~a~naLLk~LEepp~~~vfI~aTte~~kI~~  173 (507)
T PRK06645        100 IEIDAAS------KTSVDDIRRIIESAEYKPLQGKHKIFIIDEVHMLSKGAFNALLKTLEEPPPHIIFIFATTEVQKIPA  173 (507)
T ss_pred             EEeeccC------CCCHHHHHHHHHHHHhccccCCcEEEEEEChhhcCHHHHHHHHHHHhhcCCCEEEEEEeCChHHhhH
Confidence            0000000      001222233221     12467789999999876543    344444444566766554332 11  


Q ss_pred             ---CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHH
Q 042541          309 ---QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLAL  361 (695)
Q Consensus       309 ---~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai  361 (695)
                         .-...+++.+++.++....+.+.+.....   .-..+....|++.++|.+.-+
T Consensus       174 tI~SRc~~~ef~~ls~~el~~~L~~i~~~egi---~ie~eAL~~Ia~~s~GslR~a  226 (507)
T PRK06645        174 TIISRCQRYDLRRLSFEEIFKLLEYITKQENL---KTDIEALRIIAYKSEGSARDA  226 (507)
T ss_pred             HHHhcceEEEccCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHcCCCHHHH
Confidence               12237899999999999999988754332   123567888999999987544

>KOG0618 consensus Serine/threonine phosphatase 2C containing leucine-rich repeats, similar to SCN circadian oscillatory protein (SCOP) [Signal transduction mechanisms]

Probab=98.35  E-value=4e-08  Score=108.16  Aligned_cols=128  Identities=18%  Similarity=0.233  Sum_probs=96.3

Q ss_pred             CCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc-cccccccccE
Q 042541          549 GPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL-ATVRMNHLQK  627 (695)
Q Consensus       549 ~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp-~i~~l~~L~~  627 (695)
                      .+.|+.|++-+|......-+-+.++++||+|+|++|.+.  .++. ..+.++..|+.|.|+||.++.+| ++.++..|++
T Consensus       358 ~~~Lq~LylanN~Ltd~c~p~l~~~~hLKVLhLsyNrL~--~fpa-s~~~kle~LeeL~LSGNkL~~Lp~tva~~~~L~t  434 (1081)
T KOG0618|consen  358 HAALQELYLANNHLTDSCFPVLVNFKHLKVLHLSYNRLN--SFPA-SKLRKLEELEELNLSGNKLTTLPDTVANLGRLHT  434 (1081)
T ss_pred             hHHHHHHHHhcCcccccchhhhccccceeeeeecccccc--cCCH-HHHhchHHhHHHhcccchhhhhhHHHHhhhhhHH
Confidence            445666666667666666667888999999999998542  1111 22678888999999999999999 9999999999


Q ss_pred             EeeccccCCcccccchhhhcccCCCccEEeccccccccc--CchhhcCCCCCceeecccccC
Q 042541          628 VSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIE--LPDGLCDIVSMEKLRITNCHR  687 (695)
Q Consensus       628 L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~--lP~~i~~L~~L~~L~l~~~~~  687 (695)
                      |...+|.+...| ...     .++.|+++|++. +++..  +|..... ++|++||++||..
T Consensus       435 L~ahsN~l~~fP-e~~-----~l~qL~~lDlS~-N~L~~~~l~~~~p~-p~LkyLdlSGN~~  488 (1081)
T KOG0618|consen  435 LRAHSNQLLSFP-ELA-----QLPQLKVLDLSC-NNLSEVTLPEALPS-PNLKYLDLSGNTR  488 (1081)
T ss_pred             HhhcCCceeech-hhh-----hcCcceEEeccc-chhhhhhhhhhCCC-cccceeeccCCcc
Confidence            999999888877 444     799999999995 55654  3332222 7999999999874

>PF13855 LRR_8: Leucine rich repeat; PDB: 2O6S_A 3A79_B 3RFS_A 3G39_A 3VQ2_A 3VQ1_B 2Z64_A 2Z66_C 3FXI_A 2Z63_A

Probab=98.32  E-value=4.4e-07  Score=68.72  Aligned_cols=59  Identities=19%  Similarity=0.367  Sum_probs=52.9

Q ss_pred             ccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCch-hhcCCCCCceeeccccc
Q 042541          623 NHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPD-GLCDIVSMEKLRITNCH  686 (695)
Q Consensus       623 ~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~-~i~~L~~L~~L~l~~~~  686 (695)
                      ++|++|++++|+++.+++..+.    .+++|++|++++| .+..+|. .|..+++|++|++++|+
T Consensus         1 p~L~~L~l~~n~l~~i~~~~f~----~l~~L~~L~l~~N-~l~~i~~~~f~~l~~L~~L~l~~N~   60 (61)
T PF13855_consen    1 PNLESLDLSNNKLTEIPPDSFS----NLPNLETLDLSNN-NLTSIPPDAFSNLPNLRYLDLSNNN   60 (61)
T ss_dssp             TTESEEEETSSTESEECTTTTT----TGTTESEEEETSS-SESEEETTTTTTSTTESEEEETSSS
T ss_pred             CcCcEEECCCCCCCccCHHHHc----CCCCCCEeEccCC-ccCccCHHHHcCCCCCCEEeCcCCc
Confidence            4799999999999999998887    8999999999975 5677775 58999999999999986

...

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.32  E-value=2.1e-05  Score=86.66  Aligned_cols=167  Identities=18%  Similarity=0.182  Sum_probs=104.7

Q ss_pred             CCCCCCcchHHHHHHHHHcCCc-eEEEEEcCCCCcHHHHHHHHhccccccc-------------------cCCCcEEEEE
Q 042541          166 VISPGLDVPLKELKMELFKDGR-QFIVVSAPGGYGKTTLVQRLCKDDQVQG-------------------KFKDDIFYVT  225 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~~~-~vv~I~G~gGiGKTtLa~~~~~~~~~~~-------------------~f~~~~~wv~  225 (695)
                      +.+||-+..++.+..++..+.. ..+.++|+.|+||||+|+.++..---..                   .|.. +++++
T Consensus        16 ~divGq~~v~~~L~~~i~~~~~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pcg~C~~C~~i~~~~~~d-~~ei~   94 (527)
T PRK14969         16 SELVGQEHVVRALTNALEQQRLHHAYLFTGTRGVGKTTLARILAKSLNCETGVTATPCGVCSACLEIDSGRFVD-LIEVD   94 (527)
T ss_pred             HHhcCcHHHHHHHHHHHHcCCCCEEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCc-eeEee
Confidence            4579999999999999887664 4568999999999999999876311000                   1111 22222


Q ss_pred             eCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHH-----hcCCCcEEEEEeCCCCCChH----HHhhhccCCCC
Q 042541          226 VSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFK-----QMRIEAILLVLDDVWPGSES----LLQKLGFQLPD  296 (695)
Q Consensus       226 ~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~-----~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~g  296 (695)
                      .+....                         .+.++++++     -..+++-++|+|+++.....    +++.+......
T Consensus        95 ~~~~~~-------------------------vd~ir~l~~~~~~~p~~~~~kVvIIDEad~ls~~a~naLLK~LEepp~~  149 (527)
T PRK14969         95 AASNTQ-------------------------VDAMRELLDNAQYAPTRGRFKVYIIDEVHMLSKSAFNAMLKTLEEPPEH  149 (527)
T ss_pred             ccccCC-------------------------HHHHHHHHHHHhhCcccCCceEEEEcCcccCCHHHHHHHHHHHhCCCCC
Confidence            111111                         122222221     12466779999999877643    45555554456


Q ss_pred             CEEEEEcCCCCCCC------CCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHH
Q 042541          297 YKILVTSRSEFPQF------GSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLAL  361 (695)
Q Consensus       297 s~iivTtR~~~~~~------~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai  361 (695)
                      +.+|++|.+.....      ...+++++++.++....+.+.+...+.   ...++.+..|++.++|.+.-+
T Consensus       150 ~~fIL~t~d~~kil~tI~SRc~~~~f~~l~~~~i~~~L~~il~~egi---~~~~~al~~la~~s~Gslr~a  217 (527)
T PRK14969        150 VKFILATTDPQKIPVTVLSRCLQFNLKQMPPPLIVSHLQHILEQENI---PFDATALQLLARAAAGSMRDA  217 (527)
T ss_pred             EEEEEEeCChhhCchhHHHHHHHHhcCCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHcCCCHHHH
Confidence            77776665442111      227899999999999888776643322   123566788999999987533

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.32  E-value=1.7e-05  Score=87.97  Aligned_cols=193  Identities=13%  Similarity=0.138  Sum_probs=107.3

Q ss_pred             CCCCCCCcchHHHHHHHHHcCCc-eEEEEEcCCCCcHHHHHHHHhccccccccCC-CcEEEEEeCCCCCHHHHHHHHHHh
Q 042541          165 PVISPGLDVPLKELKMELFKDGR-QFIVVSAPGGYGKTTLVQRLCKDDQVQGKFK-DDIFYVTVSKNPNVKAIVQKVLHH  242 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~~-~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~-~~~~wv~~~~~~~~~~~~~~i~~~  242 (695)
                      -+.+||-+..++.|..++..+.. ..+.++|+.|+||||+|+.+.+.---..... .+.-.-.++.+    ...+.|...
T Consensus        15 f~dviGQe~vv~~L~~~l~~~rl~ha~Lf~Gp~GvGKTtlAr~lAk~LnC~~~~~~~~~~~~pCg~C----~~C~~i~~g   90 (618)
T PRK14951         15 FSEMVGQEHVVQALTNALTQQRLHHAYLFTGTRGVGKTTVSRILAKSLNCQGPDGQGGITATPCGVC----QACRDIDSG   90 (618)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCcccccCCCCCCCCcc----HHHHHHHcC
Confidence            34679988888889898887664 5678999999999999999865211000000 00000001111    111111000


Q ss_pred             cCCCCCCCC-ChHHHHHHHHHHHHh-----cCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCC-----
Q 042541          243 KGYPVPEFQ-TDEAAINDLERFFKQ-----MRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEF-----  307 (695)
Q Consensus       243 l~~~~~~~~-~~~~~~~~l~~~~~~-----l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~-----  307 (695)
                      -........ ......+.++++++.     ..++.-++|+|+++.....    ++..+......+++|++|.+..     
T Consensus        91 ~h~D~~eldaas~~~Vd~iReli~~~~~~p~~g~~KV~IIDEvh~Ls~~a~NaLLKtLEEPP~~~~fIL~Ttd~~kil~T  170 (618)
T PRK14951         91 RFVDYTELDAASNRGVDEVQQLLEQAVYKPVQGRFKVFMIDEVHMLTNTAFNAMLKTLEEPPEYLKFVLATTDPQKVPVT  170 (618)
T ss_pred             CCCceeecCcccccCHHHHHHHHHHHHhCcccCCceEEEEEChhhCCHHHHHHHHHhcccCCCCeEEEEEECCchhhhHH
Confidence            000000000 000112223333322     2355679999999887654    3444444444567776665431     


Q ss_pred             -CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHH
Q 042541          308 -PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVV  364 (695)
Q Consensus       308 -~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~  364 (695)
                       ..-+..+++++++.++....+.+.+...+.   .-..+....|++.++|.+.-+..+
T Consensus       171 IlSRc~~~~f~~Ls~eei~~~L~~i~~~egi---~ie~~AL~~La~~s~GslR~al~l  225 (618)
T PRK14951        171 VLSRCLQFNLRPMAPETVLEHLTQVLAAENV---PAEPQALRLLARAARGSMRDALSL  225 (618)
T ss_pred             HHHhceeeecCCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHcCCCHHHHHHH
Confidence             112348999999999999999877644332   123567899999999987554443

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=98.30  E-value=1.6e-06  Score=85.50  Aligned_cols=95  Identities=16%  Similarity=0.099  Sum_probs=61.9

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCC--CCHHHHHHHHHHhcCCCCCCCCChH--HHHHHH
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKN--PNVKAIVQKVLHHKGYPVPEFQTDE--AAINDL  260 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~--~~~~~~~~~i~~~l~~~~~~~~~~~--~~~~~l  260 (695)
                      .....++|+|++|+|||||++.++++.... +|+. +.|+.+.+.  .++.++++.+...+-....+.+...  .....+
T Consensus        14 ~~Gqr~~I~G~~G~GKTTLlr~I~n~l~~~-~fdv-~~~v~vI~er~~ev~el~~~I~~~~v~~~~~~~~~~~~~~~~~~   91 (249)
T cd01128          14 GKGQRGLIVAPPKAGKTTLLQSIANAITKN-HPEV-YLIVLLIDERPEEVTDMQRSVKGEVIASTFDEPPERHVQVAEMV   91 (249)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHhccccc-cCCe-EEEEEEccCCCccHHHHHHHhccEEEEecCCCCHHHHHHHHHHH
Confidence            345789999999999999999999964333 7887 669997766  7899999999443322211111111  111111


Q ss_pred             HHHHHh--cCCCcEEEEEeCCCC
Q 042541          261 ERFFKQ--MRIEAILLVLDDVWP  281 (695)
Q Consensus       261 ~~~~~~--l~~~~~LlVlDdv~~  281 (695)
                      ....+.  -.+++.++++|++..
T Consensus        92 ~~~a~~~~~~G~~vll~iDei~r  114 (249)
T cd01128          92 LEKAKRLVEHGKDVVILLDSITR  114 (249)
T ss_pred             HHHHHHHHHCCCCEEEEEECHHH
Confidence            122211  258999999999854

It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the C-terminal ATP binding domain.

>PRK08084 DNA replication initiation factor; Provisional

Probab=98.29  E-value=2.5e-05  Score=77.12  Aligned_cols=166  Identities=17%  Similarity=0.207  Sum_probs=98.8

Q ss_pred             CCCCCCCcc-hHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhc
Q 042541          165 PVISPGLDV-PLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHK  243 (695)
Q Consensus       165 ~~~~vGr~~-~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l  243 (695)
                      .++++|-.. .+..+..+......+.+.|+|+.|+|||+|++.+++.  .... ...+.++++.....            
T Consensus        22 d~f~~~~n~~a~~~l~~~~~~~~~~~l~l~Gp~G~GKThLl~a~~~~--~~~~-~~~v~y~~~~~~~~------------   86 (235)
T PRK08084         22 ASFYPGDNDSLLAALQNALRQEHSGYIYLWSREGAGRSHLLHAACAE--LSQR-GRAVGYVPLDKRAW------------   86 (235)
T ss_pred             cccccCccHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHH--HHhC-CCeEEEEEHHHHhh------------
Confidence            345567333 3344444444455578999999999999999999883  3322 22366777643100            


Q ss_pred             CCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCC---hH---HHhhhccC-CCC-CEEEEEcCCCCC-------
Q 042541          244 GYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGS---ES---LLQKLGFQ-LPD-YKILVTSRSEFP-------  308 (695)
Q Consensus       244 ~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~---~~---~~~~l~~~-~~g-s~iivTtR~~~~-------  308 (695)
                              .    ...+.   +.+.. --+|++||+....   .+   +...+... ..| .++|+||+....       
T Consensus        87 --------~----~~~~~---~~~~~-~dlliiDdi~~~~~~~~~~~~lf~l~n~~~e~g~~~li~ts~~~p~~l~~~~~  150 (235)
T PRK08084         87 --------F----VPEVL---EGMEQ-LSLVCIDNIECIAGDELWEMAIFDLYNRILESGRTRLLITGDRPPRQLNLGLP  150 (235)
T ss_pred             --------h----hHHHH---HHhhh-CCEEEEeChhhhcCCHHHHHHHHHHHHHHHHcCCCeEEEeCCCChHHcCcccH
Confidence                    0    00111   11111 2478999995432   11   12222221 133 479999986621       


Q ss_pred             ------CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHH
Q 042541          309 ------QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVV  364 (695)
Q Consensus       309 ------~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~  364 (695)
                            ..+.++++++++.++-.+++.+++....-   .-.+++..-|++.+.|..-.+..+
T Consensus       151 ~L~SRl~~g~~~~l~~~~~~~~~~~l~~~a~~~~~---~l~~~v~~~L~~~~~~d~r~l~~~  209 (235)
T PRK08084        151 DLASRLDWGQIYKLQPLSDEEKLQALQLRARLRGF---ELPEDVGRFLLKRLDREMRTLFMT  209 (235)
T ss_pred             HHHHHHhCCceeeecCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHhhcCCHHHHHHH
Confidence                  22358999999999999999876643321   224788899999999876555444

>PRK15370 E3 ubiquitin-protein ligase SlrP; Provisional

Probab=98.29  E-value=1.1e-06  Score=100.01  Aligned_cols=144  Identities=17%  Similarity=0.197  Sum_probs=91.5

Q ss_pred             ccceEEeeecCCcccCCCCCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEE
Q 042541          527 NNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKI  606 (695)
Q Consensus       527 ~~~r~l~~~~~~~~~~~~~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L  606 (695)
                      ...+.|.+.++... ..+. ..+++|+.|.++.|... .+|..+.  .+|+.|++++|.+.  .++.  .+  ..+|++|
T Consensus       199 ~~L~~L~Ls~N~Lt-sLP~-~l~~nL~~L~Ls~N~Lt-sLP~~l~--~~L~~L~Ls~N~L~--~LP~--~l--~s~L~~L  267 (754)
T PRK15370        199 EQITTLILDNNELK-SLPE-NLQGNIKTLYANSNQLT-SIPATLP--DTIQEMELSINRIT--ELPE--RL--PSALQSL  267 (754)
T ss_pred             cCCcEEEecCCCCC-cCCh-hhccCCCEEECCCCccc-cCChhhh--ccccEEECcCCccC--cCCh--hH--hCCCCEE
Confidence            35666666555332 2222 22357777777766433 4565443  36778888777653  2211  12  2468888


Q ss_pred             EeccCCCCCcc-cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccc
Q 042541          607 RLEHVSLPNSL-ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNC  685 (695)
Q Consensus       607 ~L~~~~l~~lp-~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~  685 (695)
                      ++++|++..+| .+.  .+|++|++++|.++.+|+..       .++|+.|++++| .+..+|..+.  ++|+.|++++|
T Consensus       268 ~Ls~N~L~~LP~~l~--~sL~~L~Ls~N~Lt~LP~~l-------p~sL~~L~Ls~N-~Lt~LP~~l~--~sL~~L~Ls~N  335 (754)
T PRK15370        268 DLFHNKISCLPENLP--EELRYLSVYDNSIRTLPAHL-------PSGITHLNVQSN-SLTALPETLP--PGLKTLEAGEN  335 (754)
T ss_pred             ECcCCccCccccccC--CCCcEEECCCCccccCcccc-------hhhHHHHHhcCC-ccccCCcccc--ccceeccccCC
Confidence            88888888777 553  47888888888887766432       246778888875 5667776543  68999999987


Q ss_pred             cCCCCCCCC
Q 042541          686 HRLSALPEG  694 (695)
Q Consensus       686 ~~l~~lP~~  694 (695)
                      . +..+|..
T Consensus       336 ~-Lt~LP~~  343 (754)
T PRK15370        336 A-LTSLPAS  343 (754)
T ss_pred             c-cccCChh
Confidence            6 7778754

>cd00116 LRR_RI Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily

Probab=98.29  E-value=3.8e-07  Score=95.13  Aligned_cols=161  Identities=13%  Similarity=0.050  Sum_probs=99.6

Q ss_pred             CccceEEeeecCCcccCCCCC-CCC---CceEEEEEEccCcc----ccCChhhcCC-CCCcEEEEcccCCCCcccCc-cc
Q 042541          526 PNNASLLSISTDETFSSNWPD-MQG---PEVKVVVLNIRTKK----YVLPDFLQKM-DELKVLIVTNYGFSPAELNN-FR  595 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~~~~~~-~~~---~~l~~L~l~~~~~~----~~~p~~~~~l-~~Lr~L~l~~~~~~~~~~~~-~~  595 (695)
                      ....+++.+.+.......... ..+   ++|+.|.++.+...    ..+...+..+ ++|+.|++++|.+....... ..
T Consensus        80 ~~~L~~L~l~~~~~~~~~~~~~~~l~~~~~L~~L~ls~~~~~~~~~~~l~~~l~~~~~~L~~L~L~~n~l~~~~~~~~~~  159 (319)
T cd00116          80 GCGLQELDLSDNALGPDGCGVLESLLRSSSLQELKLNNNGLGDRGLRLLAKGLKDLPPALEKLVLGRNRLEGASCEALAK  159 (319)
T ss_pred             cCceeEEEccCCCCChhHHHHHHHHhccCcccEEEeeCCccchHHHHHHHHHHHhCCCCceEEEcCCCcCCchHHHHHHH
Confidence            446777777654332111000 012   45899999887543    2334456677 88999999998775332211 12


Q ss_pred             ccccCCCCcEEEeccCCCC-----Ccc-cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCch
Q 042541          596 VLSALSKLKKIRLEHVSLP-----NSL-ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPD  669 (695)
Q Consensus       596 ~l~~l~~L~~L~L~~~~l~-----~lp-~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~  669 (695)
                      .+..+.+|++|++++|.+.     .++ .+..+++|++|++++|.++......+......+++|++|++++|..-..-+.
T Consensus       160 ~~~~~~~L~~L~l~~n~l~~~~~~~l~~~l~~~~~L~~L~L~~n~i~~~~~~~l~~~~~~~~~L~~L~ls~n~l~~~~~~  239 (319)
T cd00116         160 ALRANRDLKELNLANNGIGDAGIRALAEGLKANCNLEVLDLNNNGLTDEGASALAETLASLKSLEVLNLGDNNLTDAGAA  239 (319)
T ss_pred             HHHhCCCcCEEECcCCCCchHHHHHHHHHHHhCCCCCEEeccCCccChHHHHHHHHHhcccCCCCEEecCCCcCchHHHH
Confidence            3566778999999999887     234 4556679999999999876443222111111678899999998753221111


Q ss_pred             hhc-----CCCCCceeeccccc
Q 042541          670 GLC-----DIVSMEKLRITNCH  686 (695)
Q Consensus       670 ~i~-----~L~~L~~L~l~~~~  686 (695)
                      .+.     ..++|++|++++|.
T Consensus       240 ~l~~~~~~~~~~L~~L~l~~n~  261 (319)
T cd00116         240 ALASALLSPNISLLTLSLSCND  261 (319)
T ss_pred             HHHHHHhccCCCceEEEccCCC
Confidence            221     24799999999976

LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).

>PRK15387 E3 ubiquitin-protein ligase SspH2; Provisional

Probab=98.28  E-value=1.7e-06  Score=98.01  Aligned_cols=33  Identities=15%  Similarity=0.028  Sum_probs=16.9

Q ss_pred             ceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCC
Q 042541          551 EVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFS  587 (695)
Q Consensus       551 ~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~  587 (695)
                      +|+.|.++.|.. ..+|.   .+++|+.|++++|.+.
T Consensus       283 ~L~~L~Ls~N~L-t~LP~---~p~~L~~LdLS~N~L~  315 (788)
T PRK15387        283 GLCKLWIFGNQL-TSLPV---LPPGLQELSVSDNQLA  315 (788)
T ss_pred             hcCEEECcCCcc-ccccc---cccccceeECCCCccc
Confidence            344455544422 22333   1356777777777553

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=98.28  E-value=1.7e-05  Score=86.81  Aligned_cols=191  Identities=14%  Similarity=0.120  Sum_probs=105.4

Q ss_pred             CCCCCCCcchHHHHHHHHHcCC-ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhc
Q 042541          165 PVISPGLDVPLKELKMELFKDG-RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHK  243 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~-~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l  243 (695)
                      -..++|.+..++.+...+..+. ...+.++|+.|+||||+|+.+++.  +...     -|.... .++.-...+.+....
T Consensus        15 F~dIIGQe~iv~~L~~aI~~~rl~hA~Lf~GP~GvGKTTlA~~lAk~--L~C~-----~~~~~~-~Cg~C~sCr~i~~~~   86 (605)
T PRK05896         15 FKQIIGQELIKKILVNAILNNKLTHAYIFSGPRGIGKTSIAKIFAKA--INCL-----NPKDGD-CCNSCSVCESINTNQ   86 (605)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHH--hcCC-----CCCCCC-CCcccHHHHHHHcCC
Confidence            3567999999999999887655 456889999999999999998873  2110     011110 001111111111110


Q ss_pred             CCCC---C-CCCChHHHHHHHHHHHHh--cCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCC-----
Q 042541          244 GYPV---P-EFQTDEAAINDLERFFKQ--MRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFP-----  308 (695)
Q Consensus       244 ~~~~---~-~~~~~~~~~~~l~~~~~~--l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~-----  308 (695)
                      ....   . .....-+.+..+......  ..+++-++|+|+++.....    ++..+....+.+.+|++|.....     
T Consensus        87 h~DiieIdaas~igVd~IReIi~~~~~~P~~~~~KVIIIDEad~Lt~~A~NaLLKtLEEPp~~tvfIL~Tt~~~KLl~TI  166 (605)
T PRK05896         87 SVDIVELDAASNNGVDEIRNIIDNINYLPTTFKYKVYIIDEAHMLSTSAWNALLKTLEEPPKHVVFIFATTEFQKIPLTI  166 (605)
T ss_pred             CCceEEeccccccCHHHHHHHHHHHHhchhhCCcEEEEEechHhCCHHHHHHHHHHHHhCCCcEEEEEECCChHhhhHHH
Confidence            0000   0 000011111222221111  1244557999999776533    33444434445666665543311     


Q ss_pred             -CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchh-HHHHHHH
Q 042541          309 -QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPL-ALKVVGG  366 (695)
Q Consensus       309 -~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PL-ai~~~~~  366 (695)
                       .-+..+++.+++.++....+...+...+..   -..+.+..+++.++|.+. |+..+-.
T Consensus       167 ~SRcq~ieF~~Ls~~eL~~~L~~il~kegi~---Is~eal~~La~lS~GdlR~AlnlLek  223 (605)
T PRK05896        167 ISRCQRYNFKKLNNSELQELLKSIAKKEKIK---IEDNAIDKIADLADGSLRDGLSILDQ  223 (605)
T ss_pred             HhhhhhcccCCCCHHHHHHHHHHHHHHcCCC---CCHHHHHHHHHHcCCcHHHHHHHHHH
Confidence             113378999999999998888766433221   135678899999999664 4444433

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=98.28  E-value=4.1e-05  Score=81.17  Aligned_cols=175  Identities=16%  Similarity=0.157  Sum_probs=105.7

Q ss_pred             CCCCCCCcchHHHHHHHHHcCC-ceEEEEEcCCCCcHHHHHHHHhcccccc--c------------------cCCCcEEE
Q 042541          165 PVISPGLDVPLKELKMELFKDG-RQFIVVSAPGGYGKTTLVQRLCKDDQVQ--G------------------KFKDDIFY  223 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~-~~vv~I~G~gGiGKTtLa~~~~~~~~~~--~------------------~f~~~~~w  223 (695)
                      -..++|.+..++.+.+++..+. ...+.++|+.|+||||+|+.+...-.-.  .                  +++  +.+
T Consensus        13 ~~~iig~~~~~~~l~~~~~~~~~~~~~Ll~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~~--~~~   90 (355)
T TIGR02397        13 FEDVIGQEHIVQTLKNAIKNGRIAHAYLFSGPRGTGKTSIARIFAKALNCQNGPDGEPCNECESCKEINSGSSLD--VIE   90 (355)
T ss_pred             HhhccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCC--EEE
Confidence            3457999999999999998665 4567899999999999998887631100  0                  111  222


Q ss_pred             EEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEE
Q 042541          224 VTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKI  299 (695)
Q Consensus       224 v~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~i  299 (695)
                      ++-+....... .++++..+..                   ....+++-++|+|++......    ++..+....+.+.+
T Consensus        91 ~~~~~~~~~~~-~~~l~~~~~~-------------------~p~~~~~~vviidea~~l~~~~~~~Ll~~le~~~~~~~l  150 (355)
T TIGR02397        91 IDAASNNGVDD-IREILDNVKY-------------------APSSGKYKVYIIDEVHMLSKSAFNALLKTLEEPPEHVVF  150 (355)
T ss_pred             eeccccCCHHH-HHHHHHHHhc-------------------CcccCCceEEEEeChhhcCHHHHHHHHHHHhCCccceeE
Confidence            22211111111 1111111110                   112355668999998765432    44445444455677


Q ss_pred             EEEcCCCC------CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHH
Q 042541          300 LVTSRSEF------PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVV  364 (695)
Q Consensus       300 ivTtR~~~------~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~  364 (695)
                      |++|.+..      ......+++.++++++....+...+...+.   .-.++.+..+++.++|.|..+...
T Consensus       151 Il~~~~~~~l~~~l~sr~~~~~~~~~~~~~l~~~l~~~~~~~g~---~i~~~a~~~l~~~~~g~~~~a~~~  218 (355)
T TIGR02397       151 ILATTEPHKIPATILSRCQRFDFKRIPLEDIVERLKKILDKEGI---KIEDEALELIARAADGSLRDALSL  218 (355)
T ss_pred             EEEeCCHHHHHHHHHhheeEEEcCCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHcCCChHHHHHH
Confidence            77764431      112347888999999999988876643322   113577889999999988765544

This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=98.27  E-value=4.7e-07  Score=104.67  Aligned_cols=129  Identities=16%  Similarity=0.175  Sum_probs=97.7

Q ss_pred             CCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCC-CCCcc-cccccccc
Q 042541          548 QGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVS-LPNSL-ATVRMNHL  625 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~-l~~lp-~i~~l~~L  625 (695)
                      .....+...+..+.. ..++... ..++|++|-+..|......+ ....+..++.|++|||++|. +..+| +|++|-||
T Consensus       521 ~~~~~rr~s~~~~~~-~~~~~~~-~~~~L~tLll~~n~~~l~~i-s~~ff~~m~~LrVLDLs~~~~l~~LP~~I~~Li~L  597 (889)
T KOG4658|consen  521 SWNSVRRMSLMNNKI-EHIAGSS-ENPKLRTLLLQRNSDWLLEI-SGEFFRSLPLLRVLDLSGNSSLSKLPSSIGELVHL  597 (889)
T ss_pred             chhheeEEEEeccch-hhccCCC-CCCccceEEEeecchhhhhc-CHHHHhhCcceEEEECCCCCccCcCChHHhhhhhh
Confidence            445566666655422 2223222 33479999998875210111 11227789999999999875 56999 99999999


Q ss_pred             cEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeeccc
Q 042541          626 QKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITN  684 (695)
Q Consensus       626 ~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~  684 (695)
                      |||+++++.+..+|.++.     +|.+|.+|++.++..+..+|..+..|++|++|.+..
T Consensus       598 ryL~L~~t~I~~LP~~l~-----~Lk~L~~Lnl~~~~~l~~~~~i~~~L~~Lr~L~l~~  651 (889)
T KOG4658|consen  598 RYLDLSDTGISHLPSGLG-----NLKKLIYLNLEVTGRLESIPGILLELQSLRVLRLPR  651 (889)
T ss_pred             hcccccCCCccccchHHH-----HHHhhheeccccccccccccchhhhcccccEEEeec
Confidence            999999999999998887     899999999999888888877777799999999976

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.25  E-value=5.3e-05  Score=80.51  Aligned_cols=173  Identities=14%  Similarity=0.149  Sum_probs=101.9

Q ss_pred             CCCCCCcchHHHHHHHHHcCC-ceEEEEEcCCCCcHHHHHHHHhccccc------cccCCCcEEEEEeCCCCCHHHHHHH
Q 042541          166 VISPGLDVPLKELKMELFKDG-RQFIVVSAPGGYGKTTLVQRLCKDDQV------QGKFKDDIFYVTVSKNPNVKAIVQK  238 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~~-~~vv~I~G~gGiGKTtLa~~~~~~~~~------~~~f~~~~~wv~~~~~~~~~~~~~~  238 (695)
                      +.++|.+..++.+...+..+. .+.+.++|+.|+||||+|+.+.+.-.-      ...|...++-++.....+..+ ..+
T Consensus        17 ~~iig~~~~~~~l~~~i~~~~~~~~~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-i~~   95 (367)
T PRK14970         17 DDVVGQSHITNTLLNAIENNHLAQALLFCGPRGVGKTTCARILARKINQPGYDDPNEDFSFNIFELDAASNNSVDD-IRN   95 (367)
T ss_pred             HhcCCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCcceEEeccccCCCHHH-HHH
Confidence            456999999999999998665 458889999999999999998773111      012222122221111111111 112


Q ss_pred             HHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCC--C----
Q 042541          239 VLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEF--P----  308 (695)
Q Consensus       239 i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~--~----  308 (695)
                      +++.+..                   ....+++-++++|++......    ++..+....+.+.+|++|....  .    
T Consensus        96 l~~~~~~-------------------~p~~~~~kiviIDE~~~l~~~~~~~ll~~le~~~~~~~~Il~~~~~~kl~~~l~  156 (367)
T PRK14970         96 LIDQVRI-------------------PPQTGKYKIYIIDEVHMLSSAAFNAFLKTLEEPPAHAIFILATTEKHKIIPTIL  156 (367)
T ss_pred             HHHHHhh-------------------ccccCCcEEEEEeChhhcCHHHHHHHHHHHhCCCCceEEEEEeCCcccCCHHHH
Confidence            2221110                   011245668999998765543    2232333333456666554331  1    


Q ss_pred             CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHH
Q 042541          309 QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLAL  361 (695)
Q Consensus       309 ~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai  361 (695)
                      ..+..++.++++.++....+...+...+..   -..+.+..|++.++|.+-.+
T Consensus       157 sr~~~v~~~~~~~~~l~~~l~~~~~~~g~~---i~~~al~~l~~~~~gdlr~~  206 (367)
T PRK14970        157 SRCQIFDFKRITIKDIKEHLAGIAVKEGIK---FEDDALHIIAQKADGALRDA  206 (367)
T ss_pred             hcceeEecCCccHHHHHHHHHHHHHHcCCC---CCHHHHHHHHHhCCCCHHHH
Confidence            123378999999999998888766443321   13678899999999966533

>KOG0618 consensus Serine/threonine phosphatase 2C containing leucine-rich repeats, similar to SCN circadian oscillatory protein (SCOP) [Signal transduction mechanisms]

Probab=98.24  E-value=1.1e-07  Score=104.67  Aligned_cols=106  Identities=19%  Similarity=0.270  Sum_probs=88.8

Q ss_pred             CCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--cccccccccEEeeccccCCcccccchhhhcccC
Q 042541          573 MDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAF  650 (695)
Q Consensus       573 l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l  650 (695)
                      ++.|..|.+.+|.+....   ++.+.+..+||.|+|++|.+..+|  .+.+|..|+.|+|+||.++.+|..+.     .+
T Consensus       358 ~~~Lq~LylanN~Ltd~c---~p~l~~~~hLKVLhLsyNrL~~fpas~~~kle~LeeL~LSGNkL~~Lp~tva-----~~  429 (1081)
T KOG0618|consen  358 HAALQELYLANNHLTDSC---FPVLVNFKHLKVLHLSYNRLNSFPASKLRKLEELEELNLSGNKLTTLPDTVA-----NL  429 (1081)
T ss_pred             hHHHHHHHHhcCcccccc---hhhhccccceeeeeecccccccCCHHHHhchHHhHHHhcccchhhhhhHHHH-----hh
Confidence            445666777777664433   344778999999999999999999  88899999999999999999986665     89


Q ss_pred             CCccEEecccccccccCchhhcCCCCCceeecccccCCC
Q 042541          651 PNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLS  689 (695)
Q Consensus       651 ~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~~l~  689 (695)
                      ..|++|...+ +.+..+| .+.+++.|+++|++.|+ |.
T Consensus       430 ~~L~tL~ahs-N~l~~fP-e~~~l~qL~~lDlS~N~-L~  465 (1081)
T KOG0618|consen  430 GRLHTLRAHS-NQLLSFP-ELAQLPQLKVLDLSCNN-LS  465 (1081)
T ss_pred             hhhHHHhhcC-Cceeech-hhhhcCcceEEecccch-hh
Confidence            9999999987 4688999 69999999999999765 54

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=98.24  E-value=2.9e-05  Score=76.47  Aligned_cols=164  Identities=19%  Similarity=0.164  Sum_probs=94.6

Q ss_pred             CCCCCcchH-HHHHHHHH-cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcC
Q 042541          167 ISPGLDVPL-KELKMELF-KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKG  244 (695)
Q Consensus       167 ~~vGr~~~~-~~l~~~L~-~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~  244 (695)
                      ++.|..... ..+.++.. ....+.+.|+|..|+|||+||+.+++.. .....  .+.+++......      .    + 
T Consensus        20 f~~~~~~~~~~~l~~~~~~~~~~~~~~l~G~~G~GKT~La~ai~~~~-~~~~~--~~~~i~~~~~~~------~----~-   85 (227)
T PRK08903         20 FVAGENAELVARLRELAAGPVADRFFYLWGEAGSGRSHLLQALVADA-SYGGR--NARYLDAASPLL------A----F-   85 (227)
T ss_pred             cccCCcHHHHHHHHHHHhccCCCCeEEEECCCCCCHHHHHHHHHHHH-HhCCC--cEEEEehHHhHH------H----H-
Confidence            334655443 33333333 2335678999999999999999998832 12222  244665543210      0    0 


Q ss_pred             CCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhccC-CCCC-EEEEEcCCCCC----------
Q 042541          245 YPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGFQ-LPDY-KILVTSRSEFP----------  308 (695)
Q Consensus       245 ~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~-~~gs-~iivTtR~~~~----------  308 (695)
                                          .. ....-+||+||+.....+    +...+... ..+. .+|+|++....          
T Consensus        86 --------------------~~-~~~~~~liiDdi~~l~~~~~~~L~~~~~~~~~~~~~~vl~~~~~~~~~~~l~~~L~s  144 (227)
T PRK08903         86 --------------------DF-DPEAELYAVDDVERLDDAQQIALFNLFNRVRAHGQGALLVAGPAAPLALPLREDLRT  144 (227)
T ss_pred             --------------------hh-cccCCEEEEeChhhcCchHHHHHHHHHHHHHHcCCcEEEEeCCCCHHhCCCCHHHHH
Confidence                                01 123447899999654432    12222111 1233 46677664311          


Q ss_pred             C--CCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHHHhh
Q 042541          309 Q--FGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGGSL  368 (695)
Q Consensus       309 ~--~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~~~L  368 (695)
                      .  .+..++++++++++-..++.+.+.....   .-.++....+++.+.|.+..+..+...+
T Consensus       145 r~~~~~~i~l~pl~~~~~~~~l~~~~~~~~v---~l~~~al~~L~~~~~gn~~~l~~~l~~l  203 (227)
T PRK08903        145 RLGWGLVYELKPLSDADKIAALKAAAAERGL---QLADEVPDYLLTHFRRDMPSLMALLDAL  203 (227)
T ss_pred             HHhcCeEEEecCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHhccCCHHHHHHHHHHH
Confidence            1  1348899999998877777664422211   1246788899999999998887765543

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.23  E-value=1.9e-05  Score=84.43  Aligned_cols=191  Identities=14%  Similarity=0.107  Sum_probs=105.8

Q ss_pred             CCCCCCCcchHHHHHHHHHcCCce-EEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEE-----EeCCCCCHHHHHHH
Q 042541          165 PVISPGLDVPLKELKMELFKDGRQ-FIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYV-----TVSKNPNVKAIVQK  238 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~~~-vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv-----~~~~~~~~~~~~~~  238 (695)
                      -+.++|-+..++.|..++.++..+ .+.++|+.|+||||+|+.+++.-.-...+.. .-|.     .++.+.    ..+.
T Consensus        15 ~~eiiGq~~~~~~L~~~~~~~~~~ha~lf~Gp~G~GKtt~A~~~a~~l~c~~~~~~-~~~~~~~~~~c~~c~----~c~~   89 (397)
T PRK14955         15 FADITAQEHITRTIQNSLRMGRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDD-ADYLQEVTEPCGECE----SCRD   89 (397)
T ss_pred             HhhccChHHHHHHHHHHHHhCCcceeEEEECCCCCCHHHHHHHHHHHhcCCCCcCc-ccccccCCCCCCCCH----HHHH
Confidence            456799998889998888876654 4889999999999999998873111111100 0010     111111    1111


Q ss_pred             HHHhcCCCCCCCCC-hHHHHHHHHHHHHhc-----CCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCC-
Q 042541          239 VLHHKGYPVPEFQT-DEAAINDLERFFKQM-----RIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEF-  307 (695)
Q Consensus       239 i~~~l~~~~~~~~~-~~~~~~~l~~~~~~l-----~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~-  307 (695)
                      +............. .....+.++.+.+.+     .+.+-++|+|++......    ++..+....+.+.+|++|.... 
T Consensus        90 ~~~~~~~n~~~~~~~~~~~id~Ir~l~~~~~~~p~~~~~kvvIIdea~~l~~~~~~~LLk~LEep~~~t~~Il~t~~~~k  169 (397)
T PRK14955         90 FDAGTSLNISEFDAASNNSVDDIRLLRENVRYGPQKGRYRVYIIDEVHMLSIAAFNAFLKTLEEPPPHAIFIFATTELHK  169 (397)
T ss_pred             HhcCCCCCeEeecccccCCHHHHHHHHHHHhhchhcCCeEEEEEeChhhCCHHHHHHHHHHHhcCCCCeEEEEEeCChHH
Confidence            11100000000000 000122233222222     356678999999766532    4445554555677766653321 


Q ss_pred             CC-----CCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHH
Q 042541          308 PQ-----FGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKV  363 (695)
Q Consensus       308 ~~-----~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~  363 (695)
                      ..     .+..+++.+++.++....+...+.....   .-..+.+..|++.++|.+--+..
T Consensus       170 l~~tl~sR~~~v~f~~l~~~ei~~~l~~~~~~~g~---~i~~~al~~l~~~s~g~lr~a~~  227 (397)
T PRK14955        170 IPATIASRCQRFNFKRIPLEEIQQQLQGICEAEGI---SVDADALQLIGRKAQGSMRDAQS  227 (397)
T ss_pred             hHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHcCCCHHHHHH
Confidence            11     1237889999999998888876543221   12467899999999998754433

>PRK05642 DNA replication initiation factor; Validated

Probab=98.19  E-value=5.1e-05  Score=74.83  Aligned_cols=145  Identities=14%  Similarity=0.179  Sum_probs=89.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQM  267 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l  267 (695)
                      ..+.|+|..|+|||.|++.+++  ..... ...++|++..+      +...                  ..   ...+.+
T Consensus        46 ~~l~l~G~~G~GKTHLl~a~~~--~~~~~-~~~v~y~~~~~------~~~~------------------~~---~~~~~~   95 (234)
T PRK05642         46 SLIYLWGKDGVGRSHLLQAACL--RFEQR-GEPAVYLPLAE------LLDR------------------GP---ELLDNL   95 (234)
T ss_pred             CeEEEECCCCCCHHHHHHHHHH--HHHhC-CCcEEEeeHHH------HHhh------------------hH---HHHHhh
Confidence            6789999999999999999987  33322 23366777543      1110                  01   111222


Q ss_pred             CCCcEEEEEeCCCCCC---hH---HHhhhcc-CCCCCEEEEEcCCCCC-------------CCCCeEecCCCChHHHHHH
Q 042541          268 RIEAILLVLDDVWPGS---ES---LLQKLGF-QLPDYKILVTSRSEFP-------------QFGSVHYLKPLTYEAARTL  327 (695)
Q Consensus       268 ~~~~~LlVlDdv~~~~---~~---~~~~l~~-~~~gs~iivTtR~~~~-------------~~~~~~~l~~L~~~ea~~L  327 (695)
                      .+-. +||+||+....   .+   +..-+.. ...|..+|+|++....             ..+..+++++++.++-.++
T Consensus        96 ~~~d-~LiiDDi~~~~~~~~~~~~Lf~l~n~~~~~g~~ilits~~~p~~l~~~~~~L~SRl~~gl~~~l~~~~~e~~~~i  174 (234)
T PRK05642         96 EQYE-LVCLDDLDVIAGKADWEEALFHLFNRLRDSGRRLLLAASKSPRELPIKLPDLKSRLTLALVFQMRGLSDEDKLRA  174 (234)
T ss_pred             hhCC-EEEEechhhhcCChHHHHHHHHHHHHHHhcCCEEEEeCCCCHHHcCccCccHHHHHhcCeeeecCCCCHHHHHHH
Confidence            2222 68899996331   21   2222221 2346789999887521             1134789999999999999


Q ss_pred             HHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHHH
Q 042541          328 FLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGG  366 (695)
Q Consensus       328 f~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~~  366 (695)
                      +..++....-   .-.+++..-|++.+.|-.-.+..+-.
T Consensus       175 l~~ka~~~~~---~l~~ev~~~L~~~~~~d~r~l~~~l~  210 (234)
T PRK05642        175 LQLRASRRGL---HLTDEVGHFILTRGTRSMSALFDLLE  210 (234)
T ss_pred             HHHHHHHcCC---CCCHHHHHHHHHhcCCCHHHHHHHHH
Confidence            9866543321   12367888999999987665554433

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=98.18  E-value=3.5e-05  Score=86.56  Aligned_cols=200  Identities=17%  Similarity=0.162  Sum_probs=104.4

Q ss_pred             CCCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccC--CCcEEEEEeCCC---CCHHHHHHHH
Q 042541          165 PVISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKF--KDDIFYVTVSKN---PNVKAIVQKV  239 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f--~~~~~wv~~~~~---~~~~~~~~~i  239 (695)
                      -+.++|++..++.+...+.......+.|+|++|+||||||+.+++.......+  ....-|+.+...   .+...+...+
T Consensus       153 ~~~iiGqs~~~~~l~~~ia~~~~~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv~i~~~~l~~d~~~i~~~l  232 (615)
T TIGR02903       153 FSEIVGQERAIKALLAKVASPFPQHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEVDGTTLRWDPREVTNPL  232 (615)
T ss_pred             HHhceeCcHHHHHHHHHHhcCCCCeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeEEEechhccCCHHHHhHHh
Confidence            34579999999999888876667789999999999999999998753332222  111235555421   1222221111


Q ss_pred             ---------------HHhcCCCCCCC-------------CChHHHHHHHH-HHHHhcCCCcEEEEEeCCCCCChHHHhh-
Q 042541          240 ---------------LHHKGYPVPEF-------------QTDEAAINDLE-RFFKQMRIEAILLVLDDVWPGSESLLQK-  289 (695)
Q Consensus       240 ---------------~~~l~~~~~~~-------------~~~~~~~~~l~-~~~~~l~~~~~LlVlDdv~~~~~~~~~~-  289 (695)
                                     +...+......             ++....-...+ .+++.+.++++.++-|+.|..++..+.. 
T Consensus       233 lg~~~~~~~~~a~~~l~~~gl~~~~~g~v~~asgGvL~LDEi~~Ld~~~Q~~Ll~~Le~~~v~~~~~~~~~~~~~~~~~i  312 (615)
T TIGR02903       233 LGSVHDPIYQGARRDLAETGVPEPKTGLVTDAHGGVLFIDEIGELDPLLQNKLLKVLEDKRVEFSSSYYDPDDPNVPKYI  312 (615)
T ss_pred             cCCccHHHHHHHHHHHHHcCCCchhcCchhhcCCCeEEEeccccCCHHHHHHHHHHHhhCeEEeecceeccCCcccchhh
Confidence                           11111100000             00000000111 2224445566666655555443221211 


Q ss_pred             ---hccCCCCCEEEE--EcCCCCC------CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCch
Q 042541          290 ---LGFQLPDYKILV--TSRSEFP------QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCP  358 (695)
Q Consensus       290 ---l~~~~~gs~iiv--TtR~~~~------~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~P  358 (695)
                         +....+...++|  ||++...      .....+.+.+++.++.+.++.+.+.....   .-.+++.+.|.+.+..-+
T Consensus       313 k~~~~~~~~~~~VLI~aTt~~~~~l~~aLrSR~~~i~~~pls~edi~~Il~~~a~~~~v---~ls~eal~~L~~ys~~gR  389 (615)
T TIGR02903       313 KKLFEEGAPADFVLIGATTRDPEEINPALRSRCAEVFFEPLTPEDIALIVLNAAEKINV---HLAAGVEELIARYTIEGR  389 (615)
T ss_pred             hhhcccCccceEEEEEeccccccccCHHHHhceeEEEeCCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHCCCcHH
Confidence               122223333444  5554421      11126788999999999999987653221   112455666666665556


Q ss_pred             hHHHHHHHh
Q 042541          359 LALKVVGGS  367 (695)
Q Consensus       359 Lai~~~~~~  367 (695)
                      .++..++..
T Consensus       390 raln~L~~~  398 (615)
T TIGR02903       390 KAVNILADV  398 (615)
T ss_pred             HHHHHHHHH
Confidence            666655443

Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC.

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.17  E-value=4.9e-05  Score=84.00  Aligned_cols=190  Identities=13%  Similarity=0.087  Sum_probs=107.6

Q ss_pred             CCCCCCCcchHHHHHHHHHcCCce-EEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhc
Q 042541          165 PVISPGLDVPLKELKMELFKDGRQ-FIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHK  243 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~~~-vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l  243 (695)
                      -+.+||.+..++.|..++..+... .+.++|+.|+||||+|+.++..  +.-....  -+..++.+.+    .+.+...-
T Consensus        12 f~eivGq~~i~~~L~~~i~~~r~~ha~Lf~Gp~G~GKTt~A~~lAk~--l~c~~~~--~~~pCg~C~~----C~~i~~~~   83 (584)
T PRK14952         12 FAEVVGQEHVTEPLSSALDAGRINHAYLFSGPRGCGKTSSARILARS--LNCAQGP--TATPCGVCES----CVALAPNG   83 (584)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHH--hccccCC--CCCcccccHH----HHHhhccc
Confidence            346799999999999999877654 4789999999999999998862  2110000  0001111110    11111000


Q ss_pred             C-------CCCCCCCChHHHHHHHHHHHHh--cCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCC---
Q 042541          244 G-------YPVPEFQTDEAAINDLERFFKQ--MRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEF---  307 (695)
Q Consensus       244 ~-------~~~~~~~~~~~~~~~l~~~~~~--l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~---  307 (695)
                      +       .... .....+.+..+......  ..++.-++|+|++......    ++..+......+.+|++|....   
T Consensus        84 ~~~~dvieidaa-s~~gvd~iRel~~~~~~~P~~~~~KVvIIDEah~Lt~~A~NALLK~LEEpp~~~~fIL~tte~~kll  162 (584)
T PRK14952         84 PGSIDVVELDAA-SHGGVDDTRELRDRAFYAPAQSRYRIFIVDEAHMVTTAGFNALLKIVEEPPEHLIFIFATTEPEKVL  162 (584)
T ss_pred             CCCceEEEeccc-cccCHHHHHHHHHHHHhhhhcCCceEEEEECCCcCCHHHHHHHHHHHhcCCCCeEEEEEeCChHhhH
Confidence            0       0000 00111222222222211  2356679999999876643    4444544445666666654331   


Q ss_pred             ---CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchh-HHHHHHH
Q 042541          308 ---PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPL-ALKVVGG  366 (695)
Q Consensus       308 ---~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PL-ai~~~~~  366 (695)
                         ..-+..+++.+++.++..+.+.+.+.....   .-..+.+..|++.++|-+. ++..+-.
T Consensus       163 ~TI~SRc~~~~F~~l~~~~i~~~L~~i~~~egi---~i~~~al~~Ia~~s~GdlR~aln~Ldq  222 (584)
T PRK14952        163 PTIRSRTHHYPFRLLPPRTMRALIARICEQEGV---VVDDAVYPLVIRAGGGSPRDTLSVLDQ  222 (584)
T ss_pred             HHHHHhceEEEeeCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence               112348999999999998888876643322   1235677889999999774 4444433

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=98.16  E-value=9.8e-05  Score=80.43  Aligned_cols=172  Identities=14%  Similarity=0.112  Sum_probs=108.0

Q ss_pred             CCCCCCCcchHHHHHHHHHcCCc-eEEEEEcCCCCcHHHHHHHHhcccc---ccc---------------cCCCcEEEEE
Q 042541          165 PVISPGLDVPLKELKMELFKDGR-QFIVVSAPGGYGKTTLVQRLCKDDQ---VQG---------------KFKDDIFYVT  225 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~~-~vv~I~G~gGiGKTtLa~~~~~~~~---~~~---------------~f~~~~~wv~  225 (695)
                      -+.+||-+...+.+...+..+.. .+..++|+.|+||||+|+.+++.--   -.+               .+...++.++
T Consensus        13 fdeiiGqe~v~~~L~~~I~~grl~hayLf~Gp~G~GKTt~Ar~LAk~L~c~~~~~~~pC~~C~~C~~~~~~~h~dv~eld   92 (535)
T PRK08451         13 FDELIGQESVSKTLSLALDNNRLAHAYLFSGLRGSGKTSSARIFARALVCEQGPSSTPCDTCIQCQSALENRHIDIIEMD   92 (535)
T ss_pred             HHHccCcHHHHHHHHHHHHcCCCCeeEEEECCCCCcHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHhhcCCCeEEEec
Confidence            34579988889999998887665 4668999999999999998776210   001               0111122222


Q ss_pred             eCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHh-----cCCCcEEEEEeCCCCCChH----HHhhhccCCCC
Q 042541          226 VSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQ-----MRIEAILLVLDDVWPGSES----LLQKLGFQLPD  296 (695)
Q Consensus       226 ~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~-----l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~g  296 (695)
                      .+....                         .+.++..++.     ..+++-++|+|++......    ++..+....+.
T Consensus        93 aas~~g-------------------------Id~IRelie~~~~~P~~~~~KVvIIDEad~Lt~~A~NALLK~LEEpp~~  147 (535)
T PRK08451         93 AASNRG-------------------------IDDIRELIEQTKYKPSMARFKIFIIDEVHMLTKEAFNALLKTLEEPPSY  147 (535)
T ss_pred             cccccC-------------------------HHHHHHHHHHHhhCcccCCeEEEEEECcccCCHHHHHHHHHHHhhcCCc
Confidence            111111                         1222222211     1256679999999777643    44455555556


Q ss_pred             CEEEEEcCCCCC------CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHH
Q 042541          297 YKILVTSRSEFP------QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVV  364 (695)
Q Consensus       297 s~iivTtR~~~~------~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~  364 (695)
                      +++|++|.+...      .-...+++.+++.++....+...+...+.   .-.++.+..|++.++|.+.-+..+
T Consensus       148 t~FIL~ttd~~kL~~tI~SRc~~~~F~~Ls~~ei~~~L~~Il~~EGi---~i~~~Al~~Ia~~s~GdlR~alnl  218 (535)
T PRK08451        148 VKFILATTDPLKLPATILSRTQHFRFKQIPQNSIISHLKTILEKEGV---SYEPEALEILARSGNGSLRDTLTL  218 (535)
T ss_pred             eEEEEEECChhhCchHHHhhceeEEcCCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHcCCcHHHHHHH
Confidence            777777765421      12338999999999999988876644322   123678899999999998655444

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=98.15  E-value=4.7e-05  Score=75.70  Aligned_cols=185  Identities=17%  Similarity=0.203  Sum_probs=112.0

Q ss_pred             hHHHHHHHHHcC---CceEEEEEcCCCCcHHHHHHHHhcccccccc---CCCcEEEEEeCCCCCHHHHHHHHHHhcCCCC
Q 042541          174 PLKELKMELFKD---GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGK---FKDDIFYVTVSKNPNVKAIVQKVLHHKGYPV  247 (695)
Q Consensus       174 ~~~~l~~~L~~~---~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~---f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~  247 (695)
                      .++++.+.+..+   ..+-+.|||.+|.|||++++.+.........   -..-|+.|.....++...+...|+.+++.+.
T Consensus        45 ~L~~L~~Ll~~P~~~Rmp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~~~~Y~~IL~~lgaP~  124 (302)
T PF05621_consen   45 ALDRLEELLEYPKRHRMPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEPDERRFYSAILEALGAPY  124 (302)
T ss_pred             HHHHHHHHHhCCcccCCCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCCChHHHHHHHHHHhCccc
Confidence            355665656533   3567999999999999999999864221110   0123778889999999999999999999887


Q ss_pred             CCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCC-------hH---HHhhhccCCCCCEEEEEcCCCCC------CCC
Q 042541          248 PEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGS-------ES---LLQKLGFQLPDYKILVTSRSEFP------QFG  311 (695)
Q Consensus       248 ~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~-------~~---~~~~l~~~~~gs~iivTtR~~~~------~~~  311 (695)
                      ..............++++.+  +--+||+|++.+.-       ..   .++.+.....=+-|.|-|+....      ...
T Consensus       125 ~~~~~~~~~~~~~~~llr~~--~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~L~NeL~ipiV~vGt~~A~~al~~D~QLa  202 (302)
T PF05621_consen  125 RPRDRVAKLEQQVLRLLRRL--GVRMLIIDEFHNLLAGSYRKQREFLNALKFLGNELQIPIVGVGTREAYRALRTDPQLA  202 (302)
T ss_pred             CCCCCHHHHHHHHHHHHHHc--CCcEEEeechHHHhcccHHHHHHHHHHHHHHhhccCCCeEEeccHHHHHHhccCHHHH
Confidence            66555544444445555543  35689999996632       11   22333222233556666665411      111


Q ss_pred             ---CeEecCCCCh-HHHHHHHHHhccC--CCCCCCCCchHHHHHHHHhcCCchhH
Q 042541          312 ---SVHYLKPLTY-EAARTLFLHSANL--QDGNSYIPDENIVSKILRACKGCPLA  360 (695)
Q Consensus       312 ---~~~~l~~L~~-~ea~~Lf~~~~~~--~~~~~~~~~~~~~~~I~~~c~G~PLa  360 (695)
                         .++.++.... ++...|+......  -.........+.++.|...++|+.=-
T Consensus       203 ~RF~~~~Lp~W~~d~ef~~LL~s~e~~LPLr~~S~l~~~~la~~i~~~s~G~iG~  257 (302)
T PF05621_consen  203 SRFEPFELPRWELDEEFRRLLASFERALPLRKPSNLASPELARRIHERSEGLIGE  257 (302)
T ss_pred             hccCCccCCCCCCCcHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHcCCchHH
Confidence               1455555443 3444555432211  11122334578999999999997643

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.15  E-value=7.7e-05  Score=83.72  Aligned_cols=190  Identities=13%  Similarity=0.087  Sum_probs=108.6

Q ss_pred             CCCCCCCcchHHHHHHHHHcCCc-eEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhc
Q 042541          165 PVISPGLDVPLKELKMELFKDGR-QFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHK  243 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~~-~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l  243 (695)
                      -+.+||-+..++.|..++..+.. ..+.++|+.|+||||+|+.+++.-.-......   +    ..++.-...+.+....
T Consensus        15 ~~eiiGq~~~~~~L~~~i~~~~i~~a~Lf~Gp~G~GKTtlA~~lA~~l~c~~~~~~---~----~~c~~c~~c~~i~~~~   87 (585)
T PRK14950         15 FAELVGQEHVVQTLRNAIAEGRVAHAYLFTGPRGVGKTSTARILAKAVNCTTNDPK---G----RPCGTCEMCRAIAEGS   87 (585)
T ss_pred             HHHhcCCHHHHHHHHHHHHhCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCCCCC---C----CCCccCHHHHHHhcCC
Confidence            34679999999999888886654 55789999999999999999863111010000   0    0111112223332221


Q ss_pred             CCCC----CCCCChHHHHHHHHHHHH--hcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCC-----
Q 042541          244 GYPV----PEFQTDEAAINDLERFFK--QMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFP-----  308 (695)
Q Consensus       244 ~~~~----~~~~~~~~~~~~l~~~~~--~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~-----  308 (695)
                      ....    .......+.+..+.+.+.  ...+++-++|+|++......    ++..+....+.+.+|++|.....     
T Consensus        88 ~~d~~~i~~~~~~~vd~ir~ii~~~~~~p~~~~~kVvIIDEa~~L~~~a~naLLk~LEepp~~tv~Il~t~~~~kll~tI  167 (585)
T PRK14950         88 AVDVIEMDAASHTSVDDAREIIERVQFRPALARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHAIFILATTEVHKVPATI  167 (585)
T ss_pred             CCeEEEEeccccCCHHHHHHHHHHHhhCcccCCeEEEEEeChHhCCHHHHHHHHHHHhcCCCCeEEEEEeCChhhhhHHH
Confidence            1100    000011111222222221  12356779999999766543    44444444456677766644311     


Q ss_pred             -CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHH
Q 042541          309 -QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVV  364 (695)
Q Consensus       309 -~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~  364 (695)
                       .....+.+.+++.++....+...+...+..   -..+.+..|++.++|.+..+...
T Consensus       168 ~SR~~~i~f~~l~~~el~~~L~~~a~~egl~---i~~eal~~La~~s~Gdlr~al~~  221 (585)
T PRK14950        168 LSRCQRFDFHRHSVADMAAHLRKIAAAEGIN---LEPGALEAIARAATGSMRDAENL  221 (585)
T ss_pred             HhccceeeCCCCCHHHHHHHHHHHHHHcCCC---CCHHHHHHHHHHcCCCHHHHHHH
Confidence             122478899999999988888776543321   23577889999999988655443

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=98.15  E-value=5.9e-06  Score=84.93  Aligned_cols=101  Identities=15%  Similarity=0.127  Sum_probs=65.5

Q ss_pred             HHHHHHH-cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC--CHHHHHHHHHHhcCCCCCCCCCh
Q 042541          177 ELKMELF-KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP--NVKAIVQKVLHHKGYPVPEFQTD  253 (695)
Q Consensus       177 ~l~~~L~-~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~--~~~~~~~~i~~~l~~~~~~~~~~  253 (695)
                      ++++.+. -+..+..+|+|++|+||||||+.+|++.... +|+. ..||.+.+..  .+.++++.+...+-....+....
T Consensus       158 rvID~l~PIGkGQR~lIvgppGvGKTTLaK~Ian~I~~n-hFDv-~~~VvLIgER~~EVtdiqrsIlg~vv~st~d~~~~  235 (416)
T PRK09376        158 RIIDLIAPIGKGQRGLIVAPPKAGKTVLLQNIANSITTN-HPEV-HLIVLLIDERPEEVTDMQRSVKGEVVASTFDEPAE  235 (416)
T ss_pred             eeeeeecccccCceEEEeCCCCCChhHHHHHHHHHHHhh-cCCe-EEEEEEeCCchhHHHHHHHHhcCcEEEECCCCCHH
Confidence            4445554 2345778999999999999999999964443 8887 6799998887  77888888864332222221111


Q ss_pred             H------HHHHHHHHHHHhcCCCcEEEEEeCCCC
Q 042541          254 E------AAINDLERFFKQMRIEAILLVLDDVWP  281 (695)
Q Consensus       254 ~------~~~~~l~~~~~~l~~~~~LlVlDdv~~  281 (695)
                      .      ...+....+.  -.+++++|++|++..
T Consensus       236 ~~~~~a~~~ie~Ae~~~--e~G~dVlL~iDsItR  267 (416)
T PRK09376        236 RHVQVAEMVIEKAKRLV--EHGKDVVILLDSITR  267 (416)
T ss_pred             HHHHHHHHHHHHHHHHH--HcCCCEEEEEEChHH
Confidence            1      1111111111  268999999999854

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=98.15  E-value=0.00017  Score=77.96  Aligned_cols=182  Identities=14%  Similarity=0.118  Sum_probs=109.2

Q ss_pred             CCCCCCCcch--HHHHHHHHHcCC--ceEEEEEcCCCCcHHHHHHHHhccccccc-cCCCcEEEEEeCCCCCHHHHHHHH
Q 042541          165 PVISPGLDVP--LKELKMELFKDG--RQFIVVSAPGGYGKTTLVQRLCKDDQVQG-KFKDDIFYVTVSKNPNVKAIVQKV  239 (695)
Q Consensus       165 ~~~~vGr~~~--~~~l~~~L~~~~--~~vv~I~G~gGiGKTtLa~~~~~~~~~~~-~f~~~~~wv~~~~~~~~~~~~~~i  239 (695)
                      ..+++|....  ......+...++  ..-+.|+|..|+|||.|++++.+  .+.. +-...+++++.      .++...+
T Consensus       115 dnFv~g~~n~~A~~aa~~~a~~~~~~~npl~i~G~~G~GKTHLl~Ai~~--~l~~~~~~~~v~yv~~------~~f~~~~  186 (450)
T PRK14087        115 ENFVIGSSNEQAFIAVQTVSKNPGISYNPLFIYGESGMGKTHLLKAAKN--YIESNFSDLKVSYMSG------DEFARKA  186 (450)
T ss_pred             hcccCCCcHHHHHHHHHHHHhCcCcccCceEEECCCCCcHHHHHHHHHH--HHHHhCCCCeEEEEEH------HHHHHHH
Confidence            4456776543  222222222222  34589999999999999999988  3332 22333555543      4566666


Q ss_pred             HHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCC--hH----HHhhhcc-CCCCCEEEEEcCCCCC----
Q 042541          240 LHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGS--ES----LLQKLGF-QLPDYKILVTSRSEFP----  308 (695)
Q Consensus       240 ~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~--~~----~~~~l~~-~~~gs~iivTtR~~~~----  308 (695)
                      ...++...          ..+....+.++ ..-+||+||+....  +.    +..-+.. ...|..||+|+.....    
T Consensus       187 ~~~l~~~~----------~~~~~~~~~~~-~~dvLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iIltsd~~P~~l~~  255 (450)
T PRK14087        187 VDILQKTH----------KEIEQFKNEIC-QNDVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLFFSSDKSPELLNG  255 (450)
T ss_pred             HHHHHHhh----------hHHHHHHHHhc-cCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCcEEEECCCCHHHHhh
Confidence            66654210          12222333333 34588999996543  21    2222211 1235578888775521    


Q ss_pred             ---------CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHHH
Q 042541          309 ---------QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGG  366 (695)
Q Consensus       309 ---------~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~~  366 (695)
                               ..|..+.+++++.++-.+++.+++...... ..-.+++..-|++.++|.|..+.-+..
T Consensus       256 l~~rL~SR~~~Gl~~~L~~pd~e~r~~iL~~~~~~~gl~-~~l~~evl~~Ia~~~~gd~R~L~gaL~  321 (450)
T PRK14087        256 FDNRLITRFNMGLSIAIQKLDNKTATAIIKKEIKNQNIK-QEVTEEAINFISNYYSDDVRKIKGSVS  321 (450)
T ss_pred             ccHHHHHHHhCCceeccCCcCHHHHHHHHHHHHHhcCCC-CCCCHHHHHHHHHccCCCHHHHHHHHH
Confidence                     224478899999999999999887543211 123478899999999999987776553

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=98.15  E-value=5.2e-05  Score=87.19  Aligned_cols=171  Identities=12%  Similarity=0.066  Sum_probs=104.9

Q ss_pred             CCCCCCcchHHHHHHHHHcCCc-eEEEEEcCCCCcHHHHHHHHhccccccccC---CCc-----------------EEEE
Q 042541          166 VISPGLDVPLKELKMELFKDGR-QFIVVSAPGGYGKTTLVQRLCKDDQVQGKF---KDD-----------------IFYV  224 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~~~-~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f---~~~-----------------~~wv  224 (695)
                      ..+||.+..++.|..++..+.. ..+.++|+.|+||||+|+.+.+...-....   .|+                 ++++
T Consensus        15 ~eiiGqe~v~~~L~~~i~~~ri~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~~~~~~~pCg~C~sC~~~~~g~~~~~dv~ei   94 (824)
T PRK07764         15 AEVIGQEHVTEPLSTALDSGRINHAYLFSGPRGCGKTSSARILARSLNCVEGPTSTPCGECDSCVALAPGGPGSLDVTEI   94 (824)
T ss_pred             HHhcCcHHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhCcccCCCCCCCcccHHHHHHHcCCCCCCcEEEe
Confidence            4579999999999999987665 457899999999999999987631110110   110                 1122


Q ss_pred             EeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHH--HhcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCE
Q 042541          225 TVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFF--KQMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYK  298 (695)
Q Consensus       225 ~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~--~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~  298 (695)
                      +-....                      ..+.+..+.+..  .-..++.-++|||+++.....    +++.+......+.
T Consensus        95 daas~~----------------------~Vd~iR~l~~~~~~~p~~~~~KV~IIDEad~lt~~a~NaLLK~LEEpP~~~~  152 (824)
T PRK07764         95 DAASHG----------------------GVDDARELRERAFFAPAESRYKIFIIDEAHMVTPQGFNALLKIVEEPPEHLK  152 (824)
T ss_pred             cccccC----------------------CHHHHHHHHHHHHhchhcCCceEEEEechhhcCHHHHHHHHHHHhCCCCCeE
Confidence            111111                      111112222211  223466778999999877644    4555555555677


Q ss_pred             EEEEcCCCCC------CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHH
Q 042541          299 ILVTSRSEFP------QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLAL  361 (695)
Q Consensus       299 iivTtR~~~~------~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai  361 (695)
                      +|++|.+...      .-+..|++..++.++..+++.+.+.....   .-..+....|++.++|.+..+
T Consensus       153 fIl~tt~~~kLl~TIrSRc~~v~F~~l~~~~l~~~L~~il~~EGv---~id~eal~lLa~~sgGdlR~A  218 (824)
T PRK07764        153 FIFATTEPDKVIGTIRSRTHHYPFRLVPPEVMRGYLERICAQEGV---PVEPGVLPLVIRAGGGSVRDS  218 (824)
T ss_pred             EEEEeCChhhhhHHHHhheeEEEeeCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHcCCCHHHH
Confidence            7766643311      12347899999999998888876533222   123566788999999988443

>PRK09087 hypothetical protein; Validated

Probab=98.14  E-value=4.7e-05  Score=74.39  Aligned_cols=135  Identities=14%  Similarity=0.145  Sum_probs=86.4

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHh
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQ  266 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~  266 (695)
                      .+.+.|+|+.|+|||+|++.++..  .    .  +.|++..      .+...++.                        .
T Consensus        44 ~~~l~l~G~~GsGKThLl~~~~~~--~----~--~~~i~~~------~~~~~~~~------------------------~   85 (226)
T PRK09087         44 SPVVVLAGPVGSGKTHLASIWREK--S----D--ALLIHPN------EIGSDAAN------------------------A   85 (226)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHh--c----C--CEEecHH------HcchHHHH------------------------h
Confidence            467999999999999999988863  1    1  2244332      11111111                        1


Q ss_pred             cCCCcEEEEEeCCCCCC---hHHHhhhcc-CCCCCEEEEEcCCCCC-------------CCCCeEecCCCChHHHHHHHH
Q 042541          267 MRIEAILLVLDDVWPGS---ESLLQKLGF-QLPDYKILVTSRSEFP-------------QFGSVHYLKPLTYEAARTLFL  329 (695)
Q Consensus       267 l~~~~~LlVlDdv~~~~---~~~~~~l~~-~~~gs~iivTtR~~~~-------------~~~~~~~l~~L~~~ea~~Lf~  329 (695)
                      +.+  -+|++||+....   +.+...+.. ...|..+|+|++....             ..+..+++++++.++-.+++.
T Consensus        86 ~~~--~~l~iDDi~~~~~~~~~lf~l~n~~~~~g~~ilits~~~p~~~~~~~~dL~SRl~~gl~~~l~~pd~e~~~~iL~  163 (226)
T PRK09087         86 AAE--GPVLIEDIDAGGFDETGLFHLINSVRQAGTSLLMTSRLWPSSWNVKLPDLKSRLKAATVVEIGEPDDALLSQVIF  163 (226)
T ss_pred             hhc--CeEEEECCCCCCCCHHHHHHHHHHHHhCCCeEEEECCCChHHhccccccHHHHHhCCceeecCCCCHHHHHHHHH
Confidence            111  378889995432   223333322 2237789999986411             234589999999999999999


Q ss_pred             HhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHH
Q 042541          330 HSANLQDGNSYIPDENIVSKILRACKGCPLALKVV  364 (695)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~  364 (695)
                      +.+....-   .-.+++..-|++.+.|..-++..+
T Consensus       164 ~~~~~~~~---~l~~ev~~~La~~~~r~~~~l~~~  195 (226)
T PRK09087        164 KLFADRQL---YVDPHVVYYLVSRMERSLFAAQTI  195 (226)
T ss_pred             HHHHHcCC---CCCHHHHHHHHHHhhhhHHHHHHH
Confidence            88754322   224788999999999887766643

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=98.13  E-value=3e-05  Score=86.10  Aligned_cols=192  Identities=15%  Similarity=0.121  Sum_probs=110.5

Q ss_pred             CCCCCCCCcchHHHHHHHHHcCCc-eEEEEEcCCCCcHHHHHHHHhccccccccCC--C-cEEEEEeCCCCCHHHHHHHH
Q 042541          164 PPVISPGLDVPLKELKMELFKDGR-QFIVVSAPGGYGKTTLVQRLCKDDQVQGKFK--D-DIFYVTVSKNPNVKAIVQKV  239 (695)
Q Consensus       164 ~~~~~vGr~~~~~~l~~~L~~~~~-~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~--~-~~~wv~~~~~~~~~~~~~~i  239 (695)
                      .-+.++|.+..++.|...+..+.. .-+.++|+.|+||||+|+.+++.  +.-...  . +.-+-.+..+    .-.+.|
T Consensus        22 ~f~dliGq~~~v~~L~~~~~~gri~ha~L~~Gp~GvGKTt~Ar~lAk~--L~c~~~~~~~~~~~~~cg~c----~~C~~i   95 (598)
T PRK09111         22 TFDDLIGQEAMVRTLTNAFETGRIAQAFMLTGVRGVGKTTTARILARA--LNYEGPDGDGGPTIDLCGVG----EHCQAI   95 (598)
T ss_pred             CHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHh--hCcCCccccCCCccccCccc----HHHHHH
Confidence            345679999999999999987764 46889999999999999999873  211110  0 0000001111    111112


Q ss_pred             HHhcCCCCCCCC-ChHHHHHHHHHHHHh-----cCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCC-C-
Q 042541          240 LHHKGYPVPEFQ-TDEAAINDLERFFKQ-----MRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSE-F-  307 (695)
Q Consensus       240 ~~~l~~~~~~~~-~~~~~~~~l~~~~~~-----l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~-~-  307 (695)
                      ...-........ .....++.++++++.     ..+++-++|+|++......    +++.+....+++++|++|... . 
T Consensus        96 ~~g~h~Dv~e~~a~s~~gvd~IReIie~~~~~P~~a~~KVvIIDEad~Ls~~a~naLLKtLEePp~~~~fIl~tte~~kl  175 (598)
T PRK09111         96 MEGRHVDVLEMDAASHTGVDDIREIIESVRYRPVSARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHVKFIFATTEIRKV  175 (598)
T ss_pred             hcCCCCceEEecccccCCHHHHHHHHHHHHhchhcCCcEEEEEEChHhCCHHHHHHHHHHHHhCCCCeEEEEEeCChhhh
Confidence            111100000000 000112233333322     2355678999999776643    444554555667777666332 1 


Q ss_pred             ----CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHH
Q 042541          308 ----PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVV  364 (695)
Q Consensus       308 ----~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~  364 (695)
                          ..-...+.+.+++.++....+.+.+.....   .-..+.+..|++.++|.+.-+...
T Consensus       176 l~tI~SRcq~~~f~~l~~~el~~~L~~i~~kegi---~i~~eAl~lIa~~a~Gdlr~al~~  233 (598)
T PRK09111        176 PVTVLSRCQRFDLRRIEADVLAAHLSRIAAKEGV---EVEDEALALIARAAEGSVRDGLSL  233 (598)
T ss_pred             hHHHHhheeEEEecCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHcCCCHHHHHHH
Confidence                112237899999999999999887643322   123577899999999998655443

>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication

Probab=98.12  E-value=0.00016  Score=70.43  Aligned_cols=175  Identities=18%  Similarity=0.238  Sum_probs=99.0

Q ss_pred             CCCCCCcch-HHHHHHHHH-cCC--ceEEEEEcCCCCcHHHHHHHHhcccccccc-CCCcEEEEEeCCCCCHHHHHHHHH
Q 042541          166 VISPGLDVP-LKELKMELF-KDG--RQFIVVSAPGGYGKTTLVQRLCKDDQVQGK-FKDDIFYVTVSKNPNVKAIVQKVL  240 (695)
Q Consensus       166 ~~~vGr~~~-~~~l~~~L~-~~~--~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~-f~~~~~wv~~~~~~~~~~~~~~i~  240 (695)
                      .+++|-..+ .-.....+. .++  ...+.|+|..|+|||.|.+++++  .+... -...++|++.      .++...+.
T Consensus         9 nfv~g~~N~~a~~~~~~ia~~~~~~~~~l~l~G~~G~GKTHLL~Ai~~--~~~~~~~~~~v~y~~~------~~f~~~~~   80 (219)
T PF00308_consen    9 NFVVGESNELAYAAAKAIAENPGERYNPLFLYGPSGLGKTHLLQAIAN--EAQKQHPGKRVVYLSA------EEFIREFA   80 (219)
T ss_dssp             CS--TTTTHHHHHHHHHHHHSTTTSSSEEEEEESTTSSHHHHHHHHHH--HHHHHCTTS-EEEEEH------HHHHHHHH
T ss_pred             cCCcCCcHHHHHHHHHHHHhcCCCCCCceEEECCCCCCHHHHHHHHHH--HHHhccccccceeecH------HHHHHHHH
Confidence            445674333 233333343 322  35689999999999999999998  44433 2344667644      34555555


Q ss_pred             HhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH------HHhhhcc-CCCCCEEEEEcCCCCCC----
Q 042541          241 HHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES------LLQKLGF-QLPDYKILVTSRSEFPQ----  309 (695)
Q Consensus       241 ~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~------~~~~l~~-~~~gs~iivTtR~~~~~----  309 (695)
                      ..+...     .       +..+.+.++ .-=+|++||++.....      +..-+.. ...|.++|+|+......    
T Consensus        81 ~~~~~~-----~-------~~~~~~~~~-~~DlL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~~l~~~  147 (219)
T PF00308_consen   81 DALRDG-----E-------IEEFKDRLR-SADLLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSDRPPSELSGL  147 (219)
T ss_dssp             HHHHTT-----S-------HHHHHHHHC-TSSEEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-TTTTTTS
T ss_pred             HHHHcc-----c-------chhhhhhhh-cCCEEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCCCcccccc
Confidence            554321     1       122223333 3558899999654421      1111111 12477999999776322    


Q ss_pred             ---------CCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHH
Q 042541          310 ---------FGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVV  364 (695)
Q Consensus       310 ---------~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~  364 (695)
                               .|..+++++.+.++...++.+.+....-.   -.++++.-|++.+.+..-.+..+
T Consensus       148 ~~~L~SRl~~Gl~~~l~~pd~~~r~~il~~~a~~~~~~---l~~~v~~~l~~~~~~~~r~L~~~  208 (219)
T PF00308_consen  148 LPDLRSRLSWGLVVELQPPDDEDRRRILQKKAKERGIE---LPEEVIEYLARRFRRDVRELEGA  208 (219)
T ss_dssp             -HHHHHHHHCSEEEEE----HHHHHHHHHHHHHHTT-----S-HHHHHHHHHHTTSSHHHHHHH
T ss_pred             ChhhhhhHhhcchhhcCCCCHHHHHHHHHHHHHHhCCC---CcHHHHHHHHHhhcCCHHHHHHH
Confidence                     23389999999999999999887644332   23678888888888766555443

DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; PDB: 2KJQ_A 2Z4S_A 2Z4R_C 2HCB_B 3R8F_C 1L8Q_A 3SC3_B 3BOS_A.

>KOG2543 consensus Origin recognition complex, subunit 5 [Replication, recombination and repair]

Probab=98.11  E-value=7.3e-05  Score=75.30  Aligned_cols=159  Identities=17%  Similarity=0.226  Sum_probs=101.7

Q ss_pred             CCCCCCCcchHHHHHHHHHcCC---ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHH
Q 042541          165 PVISPGLDVPLKELKMELFKDG---RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLH  241 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~---~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~  241 (695)
                      .+.+.+|+.++..+...+-+..   +..|.|+|..|.|||.+.+.+++..  ..    .-+|+++-++++...++..|+.
T Consensus         5 ~~~v~~Re~qi~~L~~Llg~~~~~~PS~~~iyG~sgTGKT~~~r~~l~~~--n~----~~vw~n~~ecft~~~lle~IL~   78 (438)
T KOG2543|consen    5 EPNVPCRESQIRRLKSLLGNNSCTIPSIVHIYGHSGTGKTYLVRQLLRKL--NL----ENVWLNCVECFTYAILLEKILN   78 (438)
T ss_pred             ccCccchHHHHHHHHHHhCCCCcccceeEEEeccCCCchhHHHHHHHhhc--CC----cceeeehHHhccHHHHHHHHHH
Confidence            4567899999999988887443   4567899999999999999999843  11    2349999999999999999999


Q ss_pred             hcC-CCCCCCCChH--HHHHHHHHHHH---hc--CCCcEEEEEeCCCCCChH---HHhhhc-----cCCCCCEEEEEcCC
Q 042541          242 HKG-YPVPEFQTDE--AAINDLERFFK---QM--RIEAILLVLDDVWPGSES---LLQKLG-----FQLPDYKILVTSRS  305 (695)
Q Consensus       242 ~l~-~~~~~~~~~~--~~~~~l~~~~~---~l--~~~~~LlVlDdv~~~~~~---~~~~l~-----~~~~gs~iivTtR~  305 (695)
                      ..+ .+.++.....  +........++   ..  +++.++||||+++...+.   ++..+.     ...+.. +|+++-.
T Consensus        79 ~~~~~d~dg~~~~~~~en~~d~i~~l~q~~~~t~~d~~~~liLDnad~lrD~~a~ll~~l~~L~el~~~~~i-~iils~~  157 (438)
T KOG2543|consen   79 KSQLADKDGDKVEGDAENFSDFIYLLVQWPAATNRDQKVFLILDNADALRDMDAILLQCLFRLYELLNEPTI-VIILSAP  157 (438)
T ss_pred             HhccCCCchhhhhhHHHHHHHHHHHHHhhHHhhccCceEEEEEcCHHhhhccchHHHHHHHHHHHHhCCCce-EEEEecc
Confidence            986 2222211111  22222233331   12  356899999998654321   222111     122333 3444433


Q ss_pred             C-----CCCCCC----eEecCCCChHHHHHHHHH
Q 042541          306 E-----FPQFGS----VHYLKPLTYEAARTLFLH  330 (695)
Q Consensus       306 ~-----~~~~~~----~~~l~~L~~~ea~~Lf~~  330 (695)
                      .     ....|+    ++..+.-+.+|...++.+
T Consensus       158 ~~e~~y~~n~g~~~i~~l~fP~Ys~~e~~~Il~~  191 (438)
T KOG2543|consen  158 SCEKQYLINTGTLEIVVLHFPQYSVEETQVILSR  191 (438)
T ss_pred             ccHHHhhcccCCCCceEEecCCCCHHHHHHHHhc
Confidence            2     111232    677888899999888865

>cd00116 LRR_RI Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily

Probab=98.11  E-value=1.6e-06  Score=90.47  Aligned_cols=162  Identities=16%  Similarity=0.152  Sum_probs=109.5

Q ss_pred             ccceEEeeecCCcccCCC-----CCCCC-CceEEEEEEccCcc----ccCChhhcCCCCCcEEEEcccCCCCcccCcc-c
Q 042541          527 NNASLLSISTDETFSSNW-----PDMQG-PEVKVVVLNIRTKK----YVLPDFLQKMDELKVLIVTNYGFSPAELNNF-R  595 (695)
Q Consensus       527 ~~~r~l~~~~~~~~~~~~-----~~~~~-~~l~~L~l~~~~~~----~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~-~  595 (695)
                      ...+++.+..........     .-..+ ++|+.|.+..+...    ..++..+..+.+|+.|++++|++....+..+ .
T Consensus       108 ~~L~~L~ls~~~~~~~~~~~l~~~l~~~~~~L~~L~L~~n~l~~~~~~~~~~~~~~~~~L~~L~l~~n~l~~~~~~~l~~  187 (319)
T cd00116         108 SSLQELKLNNNGLGDRGLRLLAKGLKDLPPALEKLVLGRNRLEGASCEALAKALRANRDLKELNLANNGIGDAGIRALAE  187 (319)
T ss_pred             CcccEEEeeCCccchHHHHHHHHHHHhCCCCceEEEcCCCcCCchHHHHHHHHHHhCCCcCEEECcCCCCchHHHHHHHH
Confidence            357777776553321000     01134 78999999988654    2345567788899999999988754332221 2


Q ss_pred             ccccCCCCcEEEeccCCCC-----Ccc-cccccccccEEeeccccCCcccc-cchhhhcccCCCccEEeccccccc----
Q 042541          596 VLSALSKLKKIRLEHVSLP-----NSL-ATVRMNHLQKVSLVMCNVGQVFR-NSTFRISDAFPNLLEMDIDYCNDL----  664 (695)
Q Consensus       596 ~l~~l~~L~~L~L~~~~l~-----~lp-~i~~l~~L~~L~l~~~~i~~~~~-~~~~~l~~~l~~L~~L~l~~c~~l----  664 (695)
                      .+..+++|++|++++|.+.     .++ .+..+++|++|++++|.++.... .+...++...++|+.|++++|...    
T Consensus       188 ~l~~~~~L~~L~L~~n~i~~~~~~~l~~~~~~~~~L~~L~ls~n~l~~~~~~~l~~~~~~~~~~L~~L~l~~n~i~~~~~  267 (319)
T cd00116         188 GLKANCNLEVLDLNNNGLTDEGASALAETLASLKSLEVLNLGDNNLTDAGAAALASALLSPNISLLTLSLSCNDITDDGA  267 (319)
T ss_pred             HHHhCCCCCEEeccCCccChHHHHHHHHHhcccCCCCEEecCCCcCchHHHHHHHHHHhccCCCceEEEccCCCCCcHHH
Confidence            3456679999999999886     234 56678999999999998875222 122111112489999999998532    


Q ss_pred             ccCchhhcCCCCCceeecccccCCC
Q 042541          665 IELPDGLCDIVSMEKLRITNCHRLS  689 (695)
Q Consensus       665 ~~lP~~i~~L~~L~~L~l~~~~~l~  689 (695)
                      ..++..+..+++|++|++++|. ++
T Consensus       268 ~~l~~~~~~~~~L~~l~l~~N~-l~  291 (319)
T cd00116         268 KDLAEVLAEKESLLELDLRGNK-FG  291 (319)
T ss_pred             HHHHHHHhcCCCccEEECCCCC-Cc
Confidence            3456667788999999999976 44

LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1).

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.11  E-value=6.3e-05  Score=82.90  Aligned_cols=192  Identities=14%  Similarity=0.081  Sum_probs=108.5

Q ss_pred             CCCCCCcchHHHHHHHHHcCC-ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcC
Q 042541          166 VISPGLDVPLKELKMELFKDG-RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKG  244 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~~-~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~  244 (695)
                      +.++|-+..++.|...+..+. ...+.++|+.|+||||+|+.+++..--......    ..+..+    ...+.+.....
T Consensus        16 ~dIiGQe~v~~~L~~ai~~~ri~ha~Lf~GPpG~GKTtiArilAk~L~C~~~~~~----~pCg~C----~sC~~i~~g~h   87 (624)
T PRK14959         16 AEVAGQETVKAILSRAAQENRVAPAYLFSGTRGVGKTTIARIFAKALNCETAPTG----EPCNTC----EQCRKVTQGMH   87 (624)
T ss_pred             HHhcCCHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHhccccCCCCC----CCCccc----HHHHHHhcCCC
Confidence            456898888888888887665 567889999999999999998873211000000    000111    11111111100


Q ss_pred             CCC----CCCCChHHHHHHHHHHHH--hcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCC------
Q 042541          245 YPV----PEFQTDEAAINDLERFFK--QMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFP------  308 (695)
Q Consensus       245 ~~~----~~~~~~~~~~~~l~~~~~--~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~------  308 (695)
                      ...    .......+....+.+.+.  ...+++-++|+|++......    ++..+....+...+|++|.....      
T Consensus        88 pDv~eId~a~~~~Id~iR~L~~~~~~~p~~g~~kVIIIDEad~Lt~~a~naLLk~LEEP~~~~ifILaTt~~~kll~TI~  167 (624)
T PRK14959         88 VDVVEIDGASNRGIDDAKRLKEAIGYAPMEGRYKVFIIDEAHMLTREAFNALLKTLEEPPARVTFVLATTEPHKFPVTIV  167 (624)
T ss_pred             CceEEEecccccCHHHHHHHHHHHHhhhhcCCceEEEEEChHhCCHHHHHHHHHHhhccCCCEEEEEecCChhhhhHHHH
Confidence            000    000001112222332221  22466779999999777543    44444333345666666654311      


Q ss_pred             CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCch-hHHHHHHHhh
Q 042541          309 QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCP-LALKVVGGSL  368 (695)
Q Consensus       309 ~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~P-Lai~~~~~~L  368 (695)
                      .-...+++++++.++....+...+.....   .-..+.+..|++.++|.+ .|+..+..++
T Consensus       168 SRcq~i~F~pLs~~eL~~~L~~il~~egi---~id~eal~lIA~~s~GdlR~Al~lLeqll  225 (624)
T PRK14959        168 SRCQHFTFTRLSEAGLEAHLTKVLGREGV---DYDPAAVRLIARRAAGSVRDSMSLLGQVL  225 (624)
T ss_pred             hhhhccccCCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence            11237899999999999888876643322   124677899999999965 6777765444

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=98.10  E-value=9.4e-05  Score=82.80  Aligned_cols=183  Identities=14%  Similarity=0.114  Sum_probs=103.5

Q ss_pred             CCCCCCCcchHHHHHHHHHcCC-ceEEEEEcCCCCcHHHHHHHHhccccccc-cCCCcEEEEEeCCCCCHHHHHHHHHHh
Q 042541          165 PVISPGLDVPLKELKMELFKDG-RQFIVVSAPGGYGKTTLVQRLCKDDQVQG-KFKDDIFYVTVSKNPNVKAIVQKVLHH  242 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~-~~vv~I~G~gGiGKTtLa~~~~~~~~~~~-~f~~~~~wv~~~~~~~~~~~~~~i~~~  242 (695)
                      -..++|-+..++.|...+..+. ...+.++|+.|+||||+|+.++..  +-. +...  .+-.+..+       ...   
T Consensus        17 f~dIiGQe~~v~~L~~aI~~~rl~HAYLF~GP~GtGKTt~AriLAk~--LnC~~~~~--~~~pC~~C-------~~~---   82 (725)
T PRK07133         17 FDDIVGQDHIVQTLKNIIKSNKISHAYLFSGPRGTGKTSVAKIFANA--LNCSHKTD--LLEPCQEC-------IEN---   82 (725)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCcHHHHHHHHHHH--hcccccCC--CCCchhHH-------HHh---
Confidence            3457999999999999998766 456789999999999999998762  211 1000  00000000       000   


Q ss_pred             cCCCC------CCCCChHHHHHHHHHHHHh--cCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCC-C-
Q 042541          243 KGYPV------PEFQTDEAAINDLERFFKQ--MRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEF-P-  308 (695)
Q Consensus       243 l~~~~------~~~~~~~~~~~~l~~~~~~--l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~-~-  308 (695)
                      .+...      .......+.+..+.+....  ..+++-++|+|++......    ++..+....+.+.+|++|.... . 
T Consensus        83 ~~~~~Dvieidaasn~~vd~IReLie~~~~~P~~g~~KV~IIDEa~~LT~~A~NALLKtLEEPP~~tifILaTte~~KLl  162 (725)
T PRK07133         83 VNNSLDIIEMDAASNNGVDEIRELIENVKNLPTQSKYKIYIIDEVHMLSKSAFNALLKTLEEPPKHVIFILATTEVHKIP  162 (725)
T ss_pred             hcCCCcEEEEeccccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhCCHHHHHHHHHHhhcCCCceEEEEEcCChhhhh
Confidence            00000      0000111122233332222  2367779999999766533    3444444444556555554331 1 


Q ss_pred             ----CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchh-HHHHH
Q 042541          309 ----QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPL-ALKVV  364 (695)
Q Consensus       309 ----~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PL-ai~~~  364 (695)
                          .-+..+++.+++.++....+...+...+.   .-..+.+..|++.++|.+. |+..+
T Consensus       163 ~TI~SRcq~ieF~~L~~eeI~~~L~~il~kegI---~id~eAl~~LA~lS~GslR~AlslL  220 (725)
T PRK07133        163 LTILSRVQRFNFRRISEDEIVSRLEFILEKENI---SYEKNALKLIAKLSSGSLRDALSIA  220 (725)
T ss_pred             HHHHhhceeEEccCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHcCCCHHHHHHHH
Confidence                11238999999999999888876543222   1135668899999999765 44433

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.09  E-value=0.00013  Score=79.49  Aligned_cols=173  Identities=14%  Similarity=0.109  Sum_probs=104.5

Q ss_pred             CCCCCCcchHHHHHHHHHcCCc-eEEEEEcCCCCcHHHHHHHHhccccccc----c-CCCc---------------EEEE
Q 042541          166 VISPGLDVPLKELKMELFKDGR-QFIVVSAPGGYGKTTLVQRLCKDDQVQG----K-FKDD---------------IFYV  224 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~~~-~vv~I~G~gGiGKTtLa~~~~~~~~~~~----~-f~~~---------------~~wv  224 (695)
                      ..++|-+..++.+..++..+.. ..+.++|+.|+||||+|+.++..  +..    . .+++               ++++
T Consensus        16 ~diiGq~~i~~~L~~~i~~~~i~hayLf~Gp~G~GKTtlAr~lAk~--L~c~~~~~~~pc~~c~nc~~i~~g~~~d~~ei   93 (486)
T PRK14953         16 KEVIGQEIVVRILKNAVKLQRVSHAYIFAGPRGTGKTTIARILAKV--LNCLNPQEGEPCGKCENCVEIDKGSFPDLIEI   93 (486)
T ss_pred             HHccChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHH--hcCcCCCCCCCCCccHHHHHHhcCCCCcEEEE
Confidence            4578999999999999987654 45678999999999999988762  210    0 1110               2222


Q ss_pred             EeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHh--cCCCcEEEEEeCCCCCChH----HHhhhccCCCCCE
Q 042541          225 TVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQ--MRIEAILLVLDDVWPGSES----LLQKLGFQLPDYK  298 (695)
Q Consensus       225 ~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~--l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~  298 (695)
                      +.+..                      ...+....+......  ..+++-++|+|+++.....    ++..+....+.+.
T Consensus        94 daas~----------------------~gvd~ir~I~~~~~~~P~~~~~KVvIIDEad~Lt~~a~naLLk~LEepp~~~v  151 (486)
T PRK14953         94 DAASN----------------------RGIDDIRALRDAVSYTPIKGKYKVYIIDEAHMLTKEAFNALLKTLEEPPPRTI  151 (486)
T ss_pred             eCccC----------------------CCHHHHHHHHHHHHhCcccCCeeEEEEEChhhcCHHHHHHHHHHHhcCCCCeE
Confidence            11111                      111112223322222  2466789999999766532    3444444444556


Q ss_pred             EEEEcCCC-C-----CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHH
Q 042541          299 ILVTSRSE-F-----PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVG  365 (695)
Q Consensus       299 iivTtR~~-~-----~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~  365 (695)
                      +|++|... .     ...+..+.+.+++.++....+...+...+.   .-..+.+..|++.++|.+..+....
T Consensus       152 ~Il~tt~~~kl~~tI~SRc~~i~f~~ls~~el~~~L~~i~k~egi---~id~~al~~La~~s~G~lr~al~~L  221 (486)
T PRK14953        152 FILCTTEYDKIPPTILSRCQRFIFSKPTKEQIKEYLKRICNEEKI---EYEEKALDLLAQASEGGMRDAASLL  221 (486)
T ss_pred             EEEEECCHHHHHHHHHHhceEEEcCCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            55554322 1     112347899999999998888876643322   1235678889999999876554443

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=98.05  E-value=0.00017  Score=78.04  Aligned_cols=175  Identities=18%  Similarity=0.122  Sum_probs=104.5

Q ss_pred             CCCCCCCcchHHHHHHHHHcCCc-eEEEEEcCCCCcHHHHHHHHhccccccc----cCCC---------------cEEEE
Q 042541          165 PVISPGLDVPLKELKMELFKDGR-QFIVVSAPGGYGKTTLVQRLCKDDQVQG----KFKD---------------DIFYV  224 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~~-~vv~I~G~gGiGKTtLa~~~~~~~~~~~----~f~~---------------~~~wv  224 (695)
                      -+.++|.+..++.+..++..+.. ..+.++|+.|+||||+|+.+++.---..    .-.+               .++++
T Consensus        16 ~~diiGq~~~v~~L~~~i~~~~i~ha~Lf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~c~~c~~C~~i~~~~~~d~~~i   95 (451)
T PRK06305         16 FSEILGQDAVVAVLKNALRFNRAAHAYLFSGIRGTGKTTLARIFAKALNCQNPTEDQEPCNQCASCKEISSGTSLDVLEI   95 (451)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCCCceEEEEEcCCCCCHHHHHHHHHHHhcCCCcccCCCCCcccHHHHHHhcCCCCceEEe
Confidence            34679999999999999987664 5688999999999999998876211000    0000               01111


Q ss_pred             EeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHH--HhcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCE
Q 042541          225 TVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFF--KQMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYK  298 (695)
Q Consensus       225 ~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~--~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~  298 (695)
                      .-......                      +.+..+.+.+  ....+++-++|+|++......    ++..+....+++.
T Consensus        96 ~g~~~~gi----------------------d~ir~i~~~l~~~~~~~~~kvvIIdead~lt~~~~n~LLk~lEep~~~~~  153 (451)
T PRK06305         96 DGASHRGI----------------------EDIRQINETVLFTPSKSRYKIYIIDEVHMLTKEAFNSLLKTLEEPPQHVK  153 (451)
T ss_pred             eccccCCH----------------------HHHHHHHHHHHhhhhcCCCEEEEEecHHhhCHHHHHHHHHHhhcCCCCce
Confidence            11011111                      1112222222  112366778999998765432    3444444445667


Q ss_pred             EEEEcCCCC------CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchh-HHHHH
Q 042541          299 ILVTSRSEF------PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPL-ALKVV  364 (695)
Q Consensus       299 iivTtR~~~------~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PL-ai~~~  364 (695)
                      +|++|....      ..-...+++.++++++....+...+...+.   .-..+.+..|++.++|.+. |+..+
T Consensus       154 ~Il~t~~~~kl~~tI~sRc~~v~f~~l~~~el~~~L~~~~~~eg~---~i~~~al~~L~~~s~gdlr~a~~~L  223 (451)
T PRK06305        154 FFLATTEIHKIPGTILSRCQKMHLKRIPEETIIDKLALIAKQEGI---ETSREALLPIARAAQGSLRDAESLY  223 (451)
T ss_pred             EEEEeCChHhcchHHHHhceEEeCCCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            776664331      112337899999999998888876543221   1246778999999999764 44443

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.04  E-value=0.0001  Score=82.16  Aligned_cols=191  Identities=14%  Similarity=0.135  Sum_probs=103.5

Q ss_pred             CCCCCCCcchHHHHHHHHHcCCc-eEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEE-eCCCCCHHHHHHHHHHh
Q 042541          165 PVISPGLDVPLKELKMELFKDGR-QFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVT-VSKNPNVKAIVQKVLHH  242 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~~-~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~-~~~~~~~~~~~~~i~~~  242 (695)
                      -..+||-+..++.|...+..+.. ..+.++|+.|+||||+|+.+++.---....+. ..|.. +...+..-...+.+...
T Consensus        15 f~eivGQe~i~~~L~~~i~~~ri~ha~Lf~Gp~GvGKttlA~~lAk~L~c~~~~~~-~~~~~~~~~~Cg~C~sC~~~~~g   93 (620)
T PRK14954         15 FADITAQEHITHTIQNSLRMDRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDD-PVYLQEVTEPCGECESCRDFDAG   93 (620)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCCCCeeEEEECCCCCCHHHHHHHHHHHhCCCCcCCc-cccccccCCCCccCHHHHHHhcc
Confidence            35679999999999888887665 45889999999999999988763111111110 00110 00000000111111110


Q ss_pred             cCCCCCCCCC-hHHHHHHHHHHHHh-----cCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCC-----
Q 042541          243 KGYPVPEFQT-DEAAINDLERFFKQ-----MRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEF-----  307 (695)
Q Consensus       243 l~~~~~~~~~-~~~~~~~l~~~~~~-----l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~-----  307 (695)
                      -......... .....+.++.+.+.     ..+.+-++|+|+++.....    ++..+....+.+.+|++|....     
T Consensus        94 ~~~n~~~~d~~s~~~vd~Ir~l~e~~~~~P~~~~~KVvIIdEad~Lt~~a~naLLK~LEePp~~tv~IL~t~~~~kLl~T  173 (620)
T PRK14954         94 TSLNISEFDAASNNSVDDIRQLRENVRYGPQKGRYRVYIIDEVHMLSTAAFNAFLKTLEEPPPHAIFIFATTELHKIPAT  173 (620)
T ss_pred             CCCCeEEecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEeChhhcCHHHHHHHHHHHhCCCCCeEEEEEeCChhhhhHH
Confidence            0000000000 00012222222222     2356668999999776542    4444444444566665554331     


Q ss_pred             -CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchh
Q 042541          308 -PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPL  359 (695)
Q Consensus       308 -~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PL  359 (695)
                       ...+..+++.+++.++....+.+.+.....   .-..+.+..|++.++|..-
T Consensus       174 I~SRc~~vef~~l~~~ei~~~L~~i~~~egi---~I~~eal~~La~~s~Gdlr  223 (620)
T PRK14954        174 IASRCQRFNFKRIPLDEIQSQLQMICRAEGI---QIDADALQLIARKAQGSMR  223 (620)
T ss_pred             HHhhceEEecCCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHhCCCHH
Confidence             122348999999999988888776543221   1246778999999999654

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.04  E-value=0.00021  Score=80.15  Aligned_cols=171  Identities=14%  Similarity=0.144  Sum_probs=104.4

Q ss_pred             CCCCCCcchHHHHHHHHHcCCc-eEEEEEcCCCCcHHHHHHHHhccccc---------------------cccCCCcEEE
Q 042541          166 VISPGLDVPLKELKMELFKDGR-QFIVVSAPGGYGKTTLVQRLCKDDQV---------------------QGKFKDDIFY  223 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~~~-~vv~I~G~gGiGKTtLa~~~~~~~~~---------------------~~~f~~~~~w  223 (695)
                      +.++|-+..++.|..++..+.. ..+.++|+.|+||||+|+.+....--                     ..+|+  +..
T Consensus        17 ~~viGq~~~~~~L~~~i~~~~l~hayLf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~Cg~C~sC~~~~~~~~~n--~~~   94 (614)
T PRK14971         17 ESVVGQEALTTTLKNAIATNKLAHAYLFCGPRGVGKTTCARIFAKTINCQNLTADGEACNECESCVAFNEQRSYN--IHE   94 (614)
T ss_pred             HHhcCcHHHHHHHHHHHHcCCCCeeEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCCCcchHHHHHhcCCCCc--eEE
Confidence            4679999999999999987664 55889999999999999887763110                     01222  223


Q ss_pred             EEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEE
Q 042541          224 VTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKI  299 (695)
Q Consensus       224 v~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~i  299 (695)
                      ++.+......++ +.++.++...                   -..+++-++|+|++......    ++..+.....++.+
T Consensus        95 ld~~~~~~vd~I-r~li~~~~~~-------------------P~~~~~KVvIIdea~~Ls~~a~naLLK~LEepp~~tif  154 (614)
T PRK14971         95 LDAASNNSVDDI-RNLIEQVRIP-------------------PQIGKYKIYIIDEVHMLSQAAFNAFLKTLEEPPSYAIF  154 (614)
T ss_pred             ecccccCCHHHH-HHHHHHHhhC-------------------cccCCcEEEEEECcccCCHHHHHHHHHHHhCCCCCeEE
Confidence            332222222211 1111211110                   11245668899999776643    34444444455666


Q ss_pred             EEEcCCCC------CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHH
Q 042541          300 LVTSRSEF------PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLAL  361 (695)
Q Consensus       300 ivTtR~~~------~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai  361 (695)
                      |++|....      ..-+..+++.+++.++....+.+.+...+.   .-..+.+..|++.++|-..-+
T Consensus       155 IL~tt~~~kIl~tI~SRc~iv~f~~ls~~ei~~~L~~ia~~egi---~i~~~al~~La~~s~gdlr~a  219 (614)
T PRK14971        155 ILATTEKHKILPTILSRCQIFDFNRIQVADIVNHLQYVASKEGI---TAEPEALNVIAQKADGGMRDA  219 (614)
T ss_pred             EEEeCCchhchHHHHhhhheeecCCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHcCCCHHHH
Confidence            66554331      122348999999999999988876644322   123567899999999976543

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=98.03  E-value=5.7e-05  Score=80.00  Aligned_cols=165  Identities=15%  Similarity=0.201  Sum_probs=97.5

Q ss_pred             CCCCCCCcchHHHHHHHHHc-------------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCC
Q 042541          165 PVISPGLDVPLKELKMELFK-------------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPN  231 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~-------------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~  231 (695)
                      .+.+.|++..+++|.+.+..             ..++-+.|+|++|+|||++|+.+++  .....|      +.+..   
T Consensus       121 ~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~lakaia~--~l~~~~------~~v~~---  189 (364)
T TIGR01242       121 YEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAH--ETNATF------IRVVG---  189 (364)
T ss_pred             HHHhCChHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHH--hCCCCE------Eecch---
Confidence            34679999999999887751             1245689999999999999999998  343332      22221   


Q ss_pred             HHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHh-cCCCcEEEEEeCCCCCC-----------hH-------HHhhhcc
Q 042541          232 VKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQ-MRIEAILLVLDDVWPGS-----------ES-------LLQKLGF  292 (695)
Q Consensus       232 ~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~-l~~~~~LlVlDdv~~~~-----------~~-------~~~~l~~  292 (695)
                       ..+....   ++          .....+...++. -...+.+|++||++...           ..       ++..+..
T Consensus       190 -~~l~~~~---~g----------~~~~~i~~~f~~a~~~~p~il~iDEiD~l~~~~~~~~~~~~~~~~~~l~~ll~~ld~  255 (364)
T TIGR01242       190 -SELVRKY---IG----------EGARLVREIFELAKEKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAELDG  255 (364)
T ss_pred             -HHHHHHh---hh----------HHHHHHHHHHHHHHhcCCcEEEhhhhhhhccccccCCCCccHHHHHHHHHHHHHhhC
Confidence             1111111   11          111223333322 23567899999986431           00       1111111


Q ss_pred             --CCCCCEEEEEcCCCC------C---CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCch
Q 042541          293 --QLPDYKILVTSRSEF------P---QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCP  358 (695)
Q Consensus       293 --~~~gs~iivTtR~~~------~---~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~P  358 (695)
                        ...+..||.||....      .   .....+.++..+.++..++|...+........    .....+++.+.|..
T Consensus       256 ~~~~~~v~vI~ttn~~~~ld~al~r~grfd~~i~v~~P~~~~r~~Il~~~~~~~~l~~~----~~~~~la~~t~g~s  328 (364)
T TIGR01242       256 FDPRGNVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMKLAED----VDLEAIAKMTEGAS  328 (364)
T ss_pred             CCCCCCEEEEEecCChhhCChhhcCcccCceEEEeCCcCHHHHHHHHHHHHhcCCCCcc----CCHHHHHHHcCCCC
Confidence              123567888887541      1   22347889999999999999987644332111    12567888887764

Many proteins may score above the trusted cutoff because an internal

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=98.03  E-value=6.6e-05  Score=78.14  Aligned_cols=139  Identities=17%  Similarity=0.175  Sum_probs=83.5

Q ss_pred             CCCCCCCCCcchHHHHHHHHHcCC-ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHH
Q 042541          163 DPPVISPGLDVPLKELKMELFKDG-RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLH  241 (695)
Q Consensus       163 ~~~~~~vGr~~~~~~l~~~L~~~~-~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~  241 (695)
                      ..-+.++|.+...+.+..++..+. ..++.++|++|+||||+|+.+++.  ...    .+..++.+. .... ..+..  
T Consensus        18 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~lll~G~~G~GKT~la~~l~~~--~~~----~~~~i~~~~-~~~~-~i~~~--   87 (316)
T PHA02544         18 STIDECILPAADKETFKSIVKKGRIPNMLLHSPSPGTGKTTVAKALCNE--VGA----EVLFVNGSD-CRID-FVRNR--   87 (316)
T ss_pred             CcHHHhcCcHHHHHHHHHHHhcCCCCeEEEeeCcCCCCHHHHHHHHHHH--hCc----cceEeccCc-ccHH-HHHHH--
Confidence            334567999999999999988665 467777999999999999999873  221    234555544 2211 11111  


Q ss_pred             hcCCCCCCCCChHHHHHHHHHHHHh--cCCCcEEEEEeCCCCC-ChH---HHhh-hccCCCCCEEEEEcCCCCC------
Q 042541          242 HKGYPVPEFQTDEAAINDLERFFKQ--MRIEAILLVLDDVWPG-SES---LLQK-LGFQLPDYKILVTSRSEFP------  308 (695)
Q Consensus       242 ~l~~~~~~~~~~~~~~~~l~~~~~~--l~~~~~LlVlDdv~~~-~~~---~~~~-l~~~~~gs~iivTtR~~~~------  308 (695)
                                        +......  ..+.+-++|+||+... ...   .+.. +.....++.+|+||.....      
T Consensus        88 ------------------l~~~~~~~~~~~~~~vliiDe~d~l~~~~~~~~L~~~le~~~~~~~~Ilt~n~~~~l~~~l~  149 (316)
T PHA02544         88 ------------------LTRFASTVSLTGGGKVIIIDEFDRLGLADAQRHLRSFMEAYSKNCSFIITANNKNGIIEPLR  149 (316)
T ss_pred             ------------------HHHHHHhhcccCCCeEEEEECcccccCHHHHHHHHHHHHhcCCCceEEEEcCChhhchHHHH
Confidence                              1111111  1245668999999765 221   2222 3333456788888865421      


Q ss_pred             CCCCeEecCCCChHHHHHHHH
Q 042541          309 QFGSVHYLKPLTYEAARTLFL  329 (695)
Q Consensus       309 ~~~~~~~l~~L~~~ea~~Lf~  329 (695)
                      .....+.++..+.++..+++.
T Consensus       150 sR~~~i~~~~p~~~~~~~il~  170 (316)
T PHA02544        150 SRCRVIDFGVPTKEEQIEMMK  170 (316)
T ss_pred             hhceEEEeCCCCHHHHHHHHH
Confidence            112256777777777766554

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=98.00  E-value=0.00092  Score=72.01  Aligned_cols=175  Identities=14%  Similarity=0.179  Sum_probs=101.8

Q ss_pred             CCCCCCCcchH--HHHHHHHHcCC--ceEEEEEcCCCCcHHHHHHHHhccccccccC-CCcEEEEEeCCCCCHHHHHHHH
Q 042541          165 PVISPGLDVPL--KELKMELFKDG--RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKF-KDDIFYVTVSKNPNVKAIVQKV  239 (695)
Q Consensus       165 ~~~~vGr~~~~--~~l~~~L~~~~--~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f-~~~~~wv~~~~~~~~~~~~~~i  239 (695)
                      ..+++|.....  ..+..+...++  ...+.|+|+.|+|||.|++++++  .+.... ...++|++.      .++...+
T Consensus       110 d~fi~g~~n~~a~~~~~~~~~~~~~~~n~l~l~G~~G~GKThL~~ai~~--~l~~~~~~~~v~yi~~------~~~~~~~  181 (405)
T TIGR00362       110 DNFVVGKSNRLAHAAALAVAENPGKAYNPLFIYGGVGLGKTHLLHAIGN--EILENNPNAKVVYVSS------EKFTNDF  181 (405)
T ss_pred             cccccCCcHHHHHHHHHHHHhCcCccCCeEEEECCCCCcHHHHHHHHHH--HHHHhCCCCcEEEEEH------HHHHHHH
Confidence            34566755542  22222222222  34689999999999999999998  443333 344667653      3344455


Q ss_pred             HHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCh------HHHhhhcc-CCCCCEEEEEcCCCCC----
Q 042541          240 LHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSE------SLLQKLGF-QLPDYKILVTSRSEFP----  308 (695)
Q Consensus       240 ~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~------~~~~~l~~-~~~gs~iivTtR~~~~----  308 (695)
                      ...+...     .    ...+...+   ++ .-+|+|||+.....      .+...+.. ...|..+|+||.....    
T Consensus       182 ~~~~~~~-----~----~~~~~~~~---~~-~dlLiiDDi~~l~~~~~~~~~l~~~~n~~~~~~~~iiits~~~p~~l~~  248 (405)
T TIGR00362       182 VNALRNN-----K----MEEFKEKY---RS-VDLLLIDDIQFLAGKERTQEEFFHTFNALHENGKQIVLTSDRPPKELPG  248 (405)
T ss_pred             HHHHHcC-----C----HHHHHHHH---Hh-CCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCCEEEecCCCHHHHhh
Confidence            5554321     1    11222222   22 34899999964321      12222211 1235678888865310    


Q ss_pred             ---------CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHH
Q 042541          309 ---------QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKV  363 (695)
Q Consensus       309 ---------~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~  363 (695)
                               ..+..+.+++.+.++-..++.+.+.....   .-.+++...|++.+.|..-.+.-
T Consensus       249 l~~~l~SRl~~g~~v~i~~pd~~~r~~il~~~~~~~~~---~l~~e~l~~ia~~~~~~~r~l~~  309 (405)
T TIGR00362       249 LEERLRSRFEWGLVVDIEPPDLETRLAILQKKAEEEGL---ELPDEVLEFIAKNIRSNVRELEG  309 (405)
T ss_pred             hhhhhhhhccCCeEEEeCCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHhcCCCHHHHHH
Confidence                     11347899999999999999988754322   12367889999999987765443

DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).

>KOG1259 consensus Nischarin, modulator of integrin alpha5 subunit action [Signal transduction mechanisms; Cytoskeleton]

Probab=98.00  E-value=1.4e-06  Score=84.19  Aligned_cols=107  Identities=14%  Similarity=0.188  Sum_probs=83.8

Q ss_pred             hhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcccccccccccEEeeccccCCcccccchhhhcc
Q 042541          569 FLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISD  648 (695)
Q Consensus       569 ~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~  648 (695)
                      .+.-.+.|..+||++|.+..-.    .+..-++.++.|++++|++..+..+..|++|+.|||++|.++.+.. .-.    
T Consensus       279 ~~dTWq~LtelDLS~N~I~~iD----ESvKL~Pkir~L~lS~N~i~~v~nLa~L~~L~~LDLS~N~Ls~~~G-wh~----  349 (490)
T KOG1259|consen  279 SADTWQELTELDLSGNLITQID----ESVKLAPKLRRLILSQNRIRTVQNLAELPQLQLLDLSGNLLAECVG-WHL----  349 (490)
T ss_pred             ecchHhhhhhccccccchhhhh----hhhhhccceeEEeccccceeeehhhhhcccceEeecccchhHhhhh-hHh----
Confidence            3445678999999998664211    2245678899999999999876667789999999999998776433 222    


Q ss_pred             cCCCccEEecccccccccCchhhcCCCCCceeeccccc
Q 042541          649 AFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCH  686 (695)
Q Consensus       649 ~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~  686 (695)
                      +|-|.++|.|+.| .+..+ +++++|-+|..||+++|+
T Consensus       350 KLGNIKtL~La~N-~iE~L-SGL~KLYSLvnLDl~~N~  385 (490)
T KOG1259|consen  350 KLGNIKTLKLAQN-KIETL-SGLRKLYSLVNLDLSSNQ  385 (490)
T ss_pred             hhcCEeeeehhhh-hHhhh-hhhHhhhhheeccccccc
Confidence            7999999999984 56666 579999999999999975

>PF12799 LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_A 1XEU_A 2OMX_A 2OMU_A 2UZY_A 2WQU_D 1D0B_A 2WQW_A 1OTO_A 2WQV_B

Probab=97.99  E-value=7.5e-06  Score=56.79  Aligned_cols=39  Identities=10%  Similarity=0.227  Sum_probs=27.7

Q ss_pred             CCCcEEEeccCCCCCcc-cccccccccEEeeccccCCccc
Q 042541          601 SKLKKIRLEHVSLPNSL-ATVRMNHLQKVSLVMCNVGQVF  639 (695)
Q Consensus       601 ~~L~~L~L~~~~l~~lp-~i~~l~~L~~L~l~~~~i~~~~  639 (695)
                      ++|++|++++|.|+.+| .+++|++|++|++++|+++.++
T Consensus         1 ~~L~~L~l~~N~i~~l~~~l~~l~~L~~L~l~~N~i~~i~   40 (44)
T PF12799_consen    1 KNLEELDLSNNQITDLPPELSNLPNLETLNLSNNPISDIS   40 (44)
T ss_dssp             TT-SEEEETSSS-SSHGGHGTTCTTSSEEEETSSCCSBEG
T ss_pred             CcceEEEccCCCCcccCchHhCCCCCCEEEecCCCCCCCc
Confidence            35777888888887777 5778888888888888776543

...

>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]

Probab=97.99  E-value=1.3e-06  Score=88.77  Aligned_cols=131  Identities=18%  Similarity=0.230  Sum_probs=70.4

Q ss_pred             CCCceEEEEEEccCccccCCh-hhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCC-CCCcc-ccccccc
Q 042541          548 QGPEVKVVVLNIRTKKYVLPD-FLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVS-LPNSL-ATVRMNH  624 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~-~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~-l~~lp-~i~~l~~  624 (695)
                      .+|+|+.|.++.|........ .-..+++|+.|.|+.|+++...+...  +-.+++|..|.|.+|. +..-- +...++.
T Consensus       170 qLp~Le~LNls~Nrl~~~~~s~~~~~l~~lK~L~l~~CGls~k~V~~~--~~~fPsl~~L~L~~N~~~~~~~~~~~i~~~  247 (505)
T KOG3207|consen  170 QLPSLENLNLSSNRLSNFISSNTTLLLSHLKQLVLNSCGLSWKDVQWI--LLTFPSLEVLYLEANEIILIKATSTKILQT  247 (505)
T ss_pred             hcccchhcccccccccCCccccchhhhhhhheEEeccCCCCHHHHHHH--HHhCCcHHHhhhhcccccceecchhhhhhH
Confidence            456666666655532211111 11235566666666666643322211  4456666677776663 22111 3445667


Q ss_pred             ccEEeeccccCCcccc--cchhhhcccCCCccEEeccccccccc--Cchh-----hcCCCCCceeeccccc
Q 042541          625 LQKVSLVMCNVGQVFR--NSTFRISDAFPNLLEMDIDYCNDLIE--LPDG-----LCDIVSMEKLRITNCH  686 (695)
Q Consensus       625 L~~L~l~~~~i~~~~~--~~~~~l~~~l~~L~~L~l~~c~~l~~--lP~~-----i~~L~~L~~L~l~~~~  686 (695)
                      |+.|||++|.+...+.  ...     .|+.|..|+++.|. +.+  +|+.     .-.+++|+.|++..|+
T Consensus       248 L~~LdLs~N~li~~~~~~~~~-----~l~~L~~Lnls~tg-i~si~~~d~~s~~kt~~f~kL~~L~i~~N~  312 (505)
T KOG3207|consen  248 LQELDLSNNNLIDFDQGYKVG-----TLPGLNQLNLSSTG-IASIAEPDVESLDKTHTFPKLEYLNISENN  312 (505)
T ss_pred             HhhccccCCcccccccccccc-----cccchhhhhccccC-cchhcCCCccchhhhcccccceeeecccCc
Confidence            7777777776655542  222     57777777777653 332  2332     3456778888887765

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=97.98  E-value=7.1e-05  Score=87.15  Aligned_cols=175  Identities=11%  Similarity=0.083  Sum_probs=100.9

Q ss_pred             CCCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhcccccccc------CCCcEEEEEeCCCCCHHHHHHH
Q 042541          165 PVISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGK------FKDDIFYVTVSKNPNVKAIVQK  238 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~------f~~~~~wv~~~~~~~~~~~~~~  238 (695)
                      -+.+|||+.++.++++.|......-+.++|++|+||||+|+.+++  ++...      ....++.++++.-.        
T Consensus       186 ld~~iGr~~ei~~~i~~l~r~~~~n~lLvG~pGvGKTal~~~La~--~i~~~~v~~~l~~~~i~~l~l~~l~--------  255 (852)
T TIGR03345       186 IDPVLGRDDEIRQMIDILLRRRQNNPILTGEAGVGKTAVVEGLAL--RIAAGDVPPALRNVRLLSLDLGLLQ--------  255 (852)
T ss_pred             CCcccCCHHHHHHHHHHHhcCCcCceeEECCCCCCHHHHHHHHHH--HHhhCCCCccccCCeEEEeehhhhh--------
Confidence            356799999999999999866656677999999999999999987  33221      12223333333210        


Q ss_pred             HHHhcCCCCCCCCChHHHHHHHHHHHHhc--CCCcEEEEEeCCCCCC--------hHHHhhhccC-CCC-CEEEEEcCCC
Q 042541          239 VLHHKGYPVPEFQTDEAAINDLERFFKQM--RIEAILLVLDDVWPGS--------ESLLQKLGFQ-LPD-YKILVTSRSE  306 (695)
Q Consensus       239 i~~~l~~~~~~~~~~~~~~~~l~~~~~~l--~~~~~LlVlDdv~~~~--------~~~~~~l~~~-~~g-s~iivTtR~~  306 (695)
                           .    ......+...+++.+++.+  .+++.+|++|++....        ......+.+. ..| -++|-||...
T Consensus       256 -----a----g~~~~ge~e~~lk~ii~e~~~~~~~~ILfIDEih~l~~~g~~~~~~d~~n~Lkp~l~~G~l~~IgaTT~~  326 (852)
T TIGR03345       256 -----A----GASVKGEFENRLKSVIDEVKASPQPIILFIDEAHTLIGAGGQAGQGDAANLLKPALARGELRTIAATTWA  326 (852)
T ss_pred             -----c----ccccchHHHHHHHHHHHHHHhcCCCeEEEEeChHHhccCCCccccccHHHHhhHHhhCCCeEEEEecCHH
Confidence                 0    0011223335555666433  2578999999985432        1111112221 123 4555555431


Q ss_pred             ----CCC-------CCCeEecCCCChHHHHHHHHHhccCCCCCCC-CCchHHHHHHHHhcCCch
Q 042541          307 ----FPQ-------FGSVHYLKPLTYEAARTLFLHSANLQDGNSY-IPDENIVSKILRACKGCP  358 (695)
Q Consensus       307 ----~~~-------~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~-~~~~~~~~~I~~~c~G~P  358 (695)
                          ...       --..+.+++++.+++.+++......-..... .-..+....+++.+.++.
T Consensus       327 e~~~~~~~d~AL~rRf~~i~v~eps~~~~~~iL~~~~~~~e~~~~v~i~d~al~~~~~ls~ryi  390 (852)
T TIGR03345       327 EYKKYFEKDPALTRRFQVVKVEEPDEETAIRMLRGLAPVLEKHHGVLILDEAVVAAVELSHRYI  390 (852)
T ss_pred             HHhhhhhccHHHHHhCeEEEeCCCCHHHHHHHHHHHHHhhhhcCCCeeCHHHHHHHHHHccccc
Confidence                110       1128999999999999997544321111111 113566777888776654

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>KOG0532 consensus Leucine-rich repeat (LRR) protein, contains calponin homology domain [Cytoskeleton]

Probab=97.98  E-value=7.7e-07  Score=93.24  Aligned_cols=130  Identities=18%  Similarity=0.305  Sum_probs=103.1

Q ss_pred             eEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc-cccccccccEEee
Q 042541          552 VKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL-ATVRMNHLQKVSL  630 (695)
Q Consensus       552 l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp-~i~~l~~L~~L~l  630 (695)
                      |+.+.|..+ ....+|+.+.++..|.+|+|+.|.++.  ++  ..++.|+ |+.|-+++|+++.+| .++.+.+|..||.
T Consensus       100 Le~liLy~n-~~r~ip~~i~~L~~lt~l~ls~NqlS~--lp--~~lC~lp-Lkvli~sNNkl~~lp~~ig~~~tl~~ld~  173 (722)
T KOG0532|consen  100 LESLILYHN-CIRTIPEAICNLEALTFLDLSSNQLSH--LP--DGLCDLP-LKVLIVSNNKLTSLPEEIGLLPTLAHLDV  173 (722)
T ss_pred             HHHHHHHhc-cceecchhhhhhhHHHHhhhccchhhc--CC--hhhhcCc-ceeEEEecCccccCCcccccchhHHHhhh
Confidence            344444333 345678889999999999999886631  11  1245555 999999999999999 9999999999999


Q ss_pred             ccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccccCCCCCCCCC
Q 042541          631 VMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPEGI  695 (695)
Q Consensus       631 ~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~~l~~lP~~i  695 (695)
                      +.|.+..+|+...     +|.+|+.|.++. +++..+|..++.| .|..||++. |++..||-.|
T Consensus       174 s~nei~slpsql~-----~l~slr~l~vrR-n~l~~lp~El~~L-pLi~lDfSc-Nkis~iPv~f  230 (722)
T KOG0532|consen  174 SKNEIQSLPSQLG-----YLTSLRDLNVRR-NHLEDLPEELCSL-PLIRLDFSC-NKISYLPVDF  230 (722)
T ss_pred             hhhhhhhchHHhh-----hHHHHHHHHHhh-hhhhhCCHHHhCC-ceeeeeccc-Cceeecchhh
Confidence            9999999888777     899999999998 4688999999854 688999986 6699998653

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=97.96  E-value=0.00041  Score=77.13  Aligned_cols=187  Identities=16%  Similarity=0.101  Sum_probs=103.8

Q ss_pred             CCCCCCCCcchHHHHHHHHHcCC-ceEEEEEcCCCCcHHHHHHHHhccccccc-cCCCcEEEEEeCCCCCHHHHHHHHHH
Q 042541          164 PPVISPGLDVPLKELKMELFKDG-RQFIVVSAPGGYGKTTLVQRLCKDDQVQG-KFKDDIFYVTVSKNPNVKAIVQKVLH  241 (695)
Q Consensus       164 ~~~~~vGr~~~~~~l~~~L~~~~-~~vv~I~G~gGiGKTtLa~~~~~~~~~~~-~f~~~~~wv~~~~~~~~~~~~~~i~~  241 (695)
                      .-+.++|.+..++.+..++..+. ...+.++|+.|+||||+|+.+...  +.. +-..+.   .++.+    .....+..
T Consensus        14 ~f~~viGq~~v~~~L~~~i~~~~~~hayLf~Gp~GtGKTt~Ak~lAka--l~c~~~~~~~---pC~~C----~~C~~i~~   84 (559)
T PRK05563         14 TFEDVVGQEHITKTLKNAIKQGKISHAYLFSGPRGTGKTSAAKIFAKA--VNCLNPPDGE---PCNEC----EICKAITN   84 (559)
T ss_pred             cHHhccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHH--hcCCCCCCCC---CCCcc----HHHHHHhc
Confidence            34567999999999999998665 455778999999999999988762  210 000000   00111    11111111


Q ss_pred             hcCCCC----CCCCChHHHHHHHHHHHHh--cCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCC---
Q 042541          242 HKGYPV----PEFQTDEAAINDLERFFKQ--MRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFP---  308 (695)
Q Consensus       242 ~l~~~~----~~~~~~~~~~~~l~~~~~~--l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~---  308 (695)
                      ......    .......+.+..+......  ..++.-++|+|++......    ++..+....+.+.+|++|.....   
T Consensus        85 g~~~dv~eidaas~~~vd~ir~i~~~v~~~p~~~~~kViIIDE~~~Lt~~a~naLLKtLEepp~~~ifIlatt~~~ki~~  164 (559)
T PRK05563         85 GSLMDVIEIDAASNNGVDEIRDIRDKVKYAPSEAKYKVYIIDEVHMLSTGAFNALLKTLEEPPAHVIFILATTEPHKIPA  164 (559)
T ss_pred             CCCCCeEEeeccccCCHHHHHHHHHHHhhCcccCCeEEEEEECcccCCHHHHHHHHHHhcCCCCCeEEEEEeCChhhCcH
Confidence            100000    0000111112222222211  2466779999999876543    44444444345566655543311   


Q ss_pred             ---CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHH
Q 042541          309 ---QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALK  362 (695)
Q Consensus       309 ---~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~  362 (695)
                         .-...+...+++.++....+...+...+.   .-..+.+..|++.++|.+.-+.
T Consensus       165 tI~SRc~~~~f~~~~~~ei~~~L~~i~~~egi---~i~~~al~~ia~~s~G~~R~al  218 (559)
T PRK05563        165 TILSRCQRFDFKRISVEDIVERLKYILDKEGI---EYEDEALRLIARAAEGGMRDAL  218 (559)
T ss_pred             HHHhHheEEecCCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHcCCCHHHHH
Confidence               11226888999999998888876643322   1135678889999999875443

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=97.96  E-value=0.0011  Score=68.23  Aligned_cols=189  Identities=15%  Similarity=0.175  Sum_probs=108.9

Q ss_pred             CCCCCcchHHHHHHHHHcCC-ceEEEEEcCCCCcHHHHHHHHhccc---c---------c-cccCCCcEEEEEeCCCCCH
Q 042541          167 ISPGLDVPLKELKMELFKDG-RQFIVVSAPGGYGKTTLVQRLCKDD---Q---------V-QGKFKDDIFYVTVSKNPNV  232 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~~~~-~~vv~I~G~gGiGKTtLa~~~~~~~---~---------~-~~~f~~~~~wv~~~~~~~~  232 (695)
                      .++|-+..++.+...+..+. .....++|+.|+||+++|..+++.-   .         + ...++. +.|+.-.....-
T Consensus         5 ~iiGq~~~~~~L~~~i~~~rl~ha~Lf~G~~G~Gk~~~A~~~a~~llc~~~c~~c~~~~~~~~~hPD-l~~i~p~~~~~g   83 (314)
T PRK07399          5 NLIGQPLAIELLTAAIKQNRIAPAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRRRLEEGNHPD-LLWVEPTYQHQG   83 (314)
T ss_pred             HhCCHHHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCCcHhcccccCCCCC-EEEEeccccccc
Confidence            46899999999999998776 4789999999999999998876521   0         0 122333 445542110000


Q ss_pred             HHHHHHHHHhcCC--CCCCCCChHHHHHHHHHHH--HhcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcC
Q 042541          233 KAIVQKVLHHKGY--PVPEFQTDEAAINDLERFF--KQMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSR  304 (695)
Q Consensus       233 ~~~~~~i~~~l~~--~~~~~~~~~~~~~~l~~~~--~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR  304 (695)
                      ..+-..-+...+.  ..... -..+.+..+.+.+  ....+++-++|+|++......    +++.+.... .+.+|++|.
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~-I~id~ir~i~~~l~~~p~~~~~kVvII~~ae~m~~~aaNaLLK~LEEPp-~~~fILi~~  161 (314)
T PRK07399         84 KLITASEAEEAGLKRKAPPQ-IRLEQIREIKRFLSRPPLEAPRKVVVIEDAETMNEAAANALLKTLEEPG-NGTLILIAP  161 (314)
T ss_pred             cccchhhhhhcccccccccc-CcHHHHHHHHHHHccCcccCCceEEEEEchhhcCHHHHHHHHHHHhCCC-CCeEEEEEC
Confidence            0000011111110  00000 0111223333333  123477889999999776643    455554444 556666665


Q ss_pred             CCCC------CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHH
Q 042541          305 SEFP------QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVV  364 (695)
Q Consensus       305 ~~~~------~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~  364 (695)
                      +...      .-...+++.+++.++..+.+.+......      .......++..++|.|..+..+
T Consensus       162 ~~~~Ll~TI~SRcq~i~f~~l~~~~~~~~L~~~~~~~~------~~~~~~~l~~~a~Gs~~~al~~  221 (314)
T PRK07399        162 SPESLLPTIVSRCQIIPFYRLSDEQLEQVLKRLGDEEI------LNINFPELLALAQGSPGAAIAN  221 (314)
T ss_pred             ChHhCcHHHHhhceEEecCCCCHHHHHHHHHHhhcccc------chhHHHHHHHHcCCCHHHHHHH
Confidence            4421      1223899999999999999987642111      1112468899999999765543

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=97.94  E-value=0.00022  Score=77.07  Aligned_cols=176  Identities=17%  Similarity=0.185  Sum_probs=105.1

Q ss_pred             CCCCCCCcchH--HHHHHHHHcCC-ceEEEEEcCCCCcHHHHHHHHhcccccccc-CCCcEEEEEeCCCCCHHHHHHHHH
Q 042541          165 PVISPGLDVPL--KELKMELFKDG-RQFIVVSAPGGYGKTTLVQRLCKDDQVQGK-FKDDIFYVTVSKNPNVKAIVQKVL  240 (695)
Q Consensus       165 ~~~~vGr~~~~--~~l~~~L~~~~-~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~-f~~~~~wv~~~~~~~~~~~~~~i~  240 (695)
                      +.+++|-....  ....++..+++ ..-+.|+|++|+|||+|++.+++  .+... ....++|++.      .++...+.
T Consensus       105 dnFv~g~~n~~a~~~~~~~~~~~~~~n~l~lyG~~G~GKTHLl~ai~~--~l~~~~~~~~v~yi~~------~~f~~~~~  176 (440)
T PRK14088        105 ENFVVGPGNSFAYHAALEVAKNPGRYNPLFIYGGVGLGKTHLLQSIGN--YVVQNEPDLRVMYITS------EKFLNDLV  176 (440)
T ss_pred             cccccCCchHHHHHHHHHHHhCcCCCCeEEEEcCCCCcHHHHHHHHHH--HHHHhCCCCeEEEEEH------HHHHHHHH
Confidence            34556744432  23333333332 34599999999999999999998  44433 3445677754      34566666


Q ss_pred             HhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCC------hHHHhhhcc-CCCCCEEEEEcCCCC------
Q 042541          241 HHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGS------ESLLQKLGF-QLPDYKILVTSRSEF------  307 (695)
Q Consensus       241 ~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~------~~~~~~l~~-~~~gs~iivTtR~~~------  307 (695)
                      ..+...     .    ...+.   +.++.+.-+|++||+....      ..+...+.. ...|..||+||....      
T Consensus       177 ~~~~~~-----~----~~~f~---~~~~~~~dvLlIDDi~~l~~~~~~q~elf~~~n~l~~~~k~iIitsd~~p~~l~~l  244 (440)
T PRK14088        177 DSMKEG-----K----LNEFR---EKYRKKVDVLLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEF  244 (440)
T ss_pred             HHHhcc-----c----HHHHH---HHHHhcCCEEEEechhhhcCcHHHHHHHHHHHHHHHHcCCeEEEECCCCHHHHHHH
Confidence            655321     1    11122   2223345689999997432      112222211 123567888886431      


Q ss_pred             -------CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHH
Q 042541          308 -------PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKV  363 (695)
Q Consensus       308 -------~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~  363 (695)
                             ...|..+.+++.+.+.-.+++.+.+.....   .-.+++...|++.+.|.-..+.-
T Consensus       245 ~~rL~SR~~~gl~v~i~~pd~e~r~~IL~~~~~~~~~---~l~~ev~~~Ia~~~~~~~R~L~g  304 (440)
T PRK14088        245 QDRLVSRFQMGLVAKLEPPDEETRKKIARKMLEIEHG---ELPEEVLNFVAENVDDNLRRLRG  304 (440)
T ss_pred             HHHHhhHHhcCceEeeCCCCHHHHHHHHHHHHHhcCC---CCCHHHHHHHHhccccCHHHHHH
Confidence                   123448899999999999999888754322   12367899999999887554443

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=97.93  E-value=0.00029  Score=78.07  Aligned_cols=185  Identities=12%  Similarity=0.099  Sum_probs=106.1

Q ss_pred             CCCCCCCcchHHHHHHHHHcCCc-eEEEEEcCCCCcHHHHHHHHhccccccc---cCCCcEEEEEeCCCCCHHHHHHHHH
Q 042541          165 PVISPGLDVPLKELKMELFKDGR-QFIVVSAPGGYGKTTLVQRLCKDDQVQG---KFKDDIFYVTVSKNPNVKAIVQKVL  240 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~~-~vv~I~G~gGiGKTtLa~~~~~~~~~~~---~f~~~~~wv~~~~~~~~~~~~~~i~  240 (695)
                      -..++|-+..++.|..++..+.. ..+.++|+.|+||||+|+.+++.---..   .++|       ..+.+-..    +.
T Consensus        15 f~diiGqe~iv~~L~~~i~~~~i~hayLf~Gp~G~GKTt~Ar~lAk~L~c~~~~~~~pC-------~~C~~C~~----i~   83 (563)
T PRK06647         15 FNSLEGQDFVVETLKHSIESNKIANAYIFSGPRGVGKTSSARAFARCLNCVNGPTPMPC-------GECSSCKS----ID   83 (563)
T ss_pred             HHHccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhccccCCCCCCC-------ccchHHHH----HH
Confidence            34679999999999999987654 5688999999999999999987311110   1111       11111111    11


Q ss_pred             HhcCCC---CCCC-CChHHHHHHHHHHH--HhcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCC---
Q 042541          241 HHKGYP---VPEF-QTDEAAINDLERFF--KQMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEF---  307 (695)
Q Consensus       241 ~~l~~~---~~~~-~~~~~~~~~l~~~~--~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~---  307 (695)
                      ..-...   ..+. ...-+.+..+.+..  .-..+++-++|+|++......    ++..+....+.+.+|++|....   
T Consensus        84 ~~~~~dv~~idgas~~~vddIr~l~e~~~~~p~~~~~KVvIIDEa~~Ls~~a~naLLK~LEepp~~~vfI~~tte~~kL~  163 (563)
T PRK06647         84 NDNSLDVIEIDGASNTSVQDVRQIKEEIMFPPASSRYRVYIIDEVHMLSNSAFNALLKTIEEPPPYIVFIFATTEVHKLP  163 (563)
T ss_pred             cCCCCCeEEecCcccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhcCHHHHHHHHHhhccCCCCEEEEEecCChHHhH
Confidence            000000   0000 01111112222111  112466778999999776643    3444444445567766664331   


Q ss_pred             ---CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHH
Q 042541          308 ---PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKV  363 (695)
Q Consensus       308 ---~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~  363 (695)
                         ..-...++..+++.++-...+...+.....   .-.++.+..|++.++|.+..+..
T Consensus       164 ~tI~SRc~~~~f~~l~~~el~~~L~~i~~~egi---~id~eAl~lLa~~s~GdlR~als  219 (563)
T PRK06647        164 ATIKSRCQHFNFRLLSLEKIYNMLKKVCLEDQI---KYEDEALKWIAYKSTGSVRDAYT  219 (563)
T ss_pred             HHHHHhceEEEecCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHcCCCHHHHHH
Confidence               111236899999999998888876643322   12467788899999998854443

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=97.93  E-value=8.3e-05  Score=79.15  Aligned_cols=164  Identities=12%  Similarity=0.123  Sum_probs=95.1

Q ss_pred             CCCCCCCcchHHHHHHHHHc-------------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCC
Q 042541          165 PVISPGLDVPLKELKMELFK-------------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPN  231 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~-------------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~  231 (695)
                      .+.+.|+++.++++.+.+..             ..++-|.++|++|+|||++|+++++  .....      |+.++.   
T Consensus       130 ~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAkaia~--~~~~~------~i~v~~---  198 (389)
T PRK03992        130 YEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAH--ETNAT------FIRVVG---  198 (389)
T ss_pred             HHHhCCcHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHHHHHH--HhCCC------EEEeeh---
Confidence            34678999999999887641             2356699999999999999999987  33222      333321   


Q ss_pred             HHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHH-hcCCCcEEEEEeCCCCCC-----------hH---HHhhhc----c
Q 042541          232 VKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFK-QMRIEAILLVLDDVWPGS-----------ES---LLQKLG----F  292 (695)
Q Consensus       232 ~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~-~l~~~~~LlVlDdv~~~~-----------~~---~~~~l~----~  292 (695)
                       .++.    ....+      .   ....+..+++ .-...+.+|++||++...           ..   .+..+.    .
T Consensus       199 -~~l~----~~~~g------~---~~~~i~~~f~~a~~~~p~IlfiDEiD~l~~~r~~~~~~~~~~~~~~l~~lL~~ld~  264 (389)
T PRK03992        199 -SELV----QKFIG------E---GARLVRELFELAREKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAEMDG  264 (389)
T ss_pred             -HHHh----Hhhcc------c---hHHHHHHHHHHHHhcCCeEEEEechhhhhcccccCCCCccHHHHHHHHHHHHhccc
Confidence             1111    11100      0   1122333332 223567899999986431           11   111111    1


Q ss_pred             --CCCCCEEEEEcCCCC------C---CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCc
Q 042541          293 --QLPDYKILVTSRSEF------P---QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGC  357 (695)
Q Consensus       293 --~~~gs~iivTtR~~~------~---~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~  357 (695)
                        ...+..||.||....      .   .....+.+++.+.++-.++|+.+.........    .....+++.+.|.
T Consensus       265 ~~~~~~v~VI~aTn~~~~ld~allRpgRfd~~I~v~~P~~~~R~~Il~~~~~~~~~~~~----~~~~~la~~t~g~  336 (389)
T PRK03992        265 FDPRGNVKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLADD----VDLEELAELTEGA  336 (389)
T ss_pred             cCCCCCEEEEEecCChhhCCHHHcCCccCceEEEECCCCHHHHHHHHHHHhccCCCCCc----CCHHHHHHHcCCC
Confidence              112456777776541      1   23347899999999999999877643322111    1256677777775

>TIGR00767 rho transcription termination factor Rho

Probab=97.93  E-value=2.6e-05  Score=80.70  Aligned_cols=96  Identities=15%  Similarity=0.097  Sum_probs=63.0

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCC--CCHHHHHHHHHHhcCCCCCCCCChH--HHHHHH
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKN--PNVKAIVQKVLHHKGYPVPEFQTDE--AAINDL  260 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~--~~~~~~~~~i~~~l~~~~~~~~~~~--~~~~~l  260 (695)
                      +....++|+|++|+|||||++.+++... .++|+. ..|+.+.+.  .++.++++.+...+-....+.+...  .....+
T Consensus       166 g~Gq~~~IvG~~g~GKTtL~~~i~~~I~-~nhfdv-~v~VlLIgER~~EVtDLqrsIlg~Vvast~d~p~~~~~~va~~v  243 (415)
T TIGR00767       166 GKGQRGLIVAPPKAGKTVLLQKIAQAIT-RNHPEV-ELIVLLIDERPEEVTDMQRSVKGEVVASTFDEPASRHVQVAEMV  243 (415)
T ss_pred             CCCCEEEEECCCCCChhHHHHHHHHhhc-ccCCce-EEEEEEcCCCCccHHHHHHHhhceEEEecCCCChHHHHHHHHHH
Confidence            3457899999999999999999998432 236887 559998866  6899999999654433222211111  111112


Q ss_pred             HHHHHh--cCCCcEEEEEeCCCCC
Q 042541          261 ERFFKQ--MRIEAILLVLDDVWPG  282 (695)
Q Consensus       261 ~~~~~~--l~~~~~LlVlDdv~~~  282 (695)
                      .+..+.  -.|++++|++|++...
T Consensus       244 ~e~Ae~~~~~GkdVVLlIDEitR~  267 (415)
T TIGR00767       244 IEKAKRLVEHKKDVVILLDSITRL  267 (415)
T ss_pred             HHHHHHHHHcCCCeEEEEEChhHH
Confidence            222211  2589999999998543

Members of this family differ in the specificity of RNA binding.

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.92  E-value=0.00025  Score=79.22  Aligned_cols=189  Identities=14%  Similarity=0.108  Sum_probs=104.9

Q ss_pred             CCCCCCCcchHHHHHHHHHcCCc-eEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhc
Q 042541          165 PVISPGLDVPLKELKMELFKDGR-QFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHK  243 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~~-~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l  243 (695)
                      -+.+||.+..++.|...+..+.. ..+.++|+.|+||||+|+.+++.---......    -.+..+    .....|...-
T Consensus        15 f~~iiGq~~v~~~L~~~i~~~~~~hayLf~Gp~G~GKtt~A~~lak~l~c~~~~~~----~~c~~c----~~c~~i~~g~   86 (576)
T PRK14965         15 FSDLTGQEHVSRTLQNAIDTGRVAHAFLFTGARGVGKTSTARILAKALNCEQGLTA----EPCNVC----PPCVEITEGR   86 (576)
T ss_pred             HHHccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhcCCCCCCC----CCCCcc----HHHHHHhcCC
Confidence            35679999999999999887664 55689999999999999988763110010000    000000    0111111000


Q ss_pred             CCCC---C-CCCChHHHHHHHHHHHHh--cCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCC-----
Q 042541          244 GYPV---P-EFQTDEAAINDLERFFKQ--MRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFP-----  308 (695)
Q Consensus       244 ~~~~---~-~~~~~~~~~~~l~~~~~~--l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~-----  308 (695)
                      ....   . ......+.+..+......  ..++.-++|+|+++.....    ++..+....+.+.+|++|.+...     
T Consensus        87 ~~d~~eid~~s~~~v~~ir~l~~~~~~~p~~~~~KVvIIdev~~Lt~~a~naLLk~LEepp~~~~fIl~t~~~~kl~~tI  166 (576)
T PRK14965         87 SVDVFEIDGASNTGVDDIRELRENVKYLPSRSRYKIFIIDEVHMLSTNAFNALLKTLEEPPPHVKFIFATTEPHKVPITI  166 (576)
T ss_pred             CCCeeeeeccCccCHHHHHHHHHHHHhccccCCceEEEEEChhhCCHHHHHHHHHHHHcCCCCeEEEEEeCChhhhhHHH
Confidence            0000   0 000111112222222211  1355678999999776543    44555555556777766644311     


Q ss_pred             -CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCch-hHHHHH
Q 042541          309 -QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCP-LALKVV  364 (695)
Q Consensus       309 -~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~P-Lai~~~  364 (695)
                       .-...+++.+++.++....+...+...+.   .-..+.+..|++.++|.. .|+..+
T Consensus       167 ~SRc~~~~f~~l~~~~i~~~L~~i~~~egi---~i~~~al~~la~~a~G~lr~al~~L  221 (576)
T PRK14965        167 LSRCQRFDFRRIPLQKIVDRLRYIADQEGI---SISDAALALVARKGDGSMRDSLSTL  221 (576)
T ss_pred             HHhhhhhhcCCCCHHHHHHHHHHHHHHhCC---CCCHHHHHHHHHHcCCCHHHHHHHH
Confidence             11237889999999988888766543322   123667888999999965 444444

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=97.90  E-value=6.2e-05  Score=73.69  Aligned_cols=176  Identities=14%  Similarity=0.126  Sum_probs=110.6

Q ss_pred             CCCCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhc
Q 042541          164 PPVISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHK  243 (695)
Q Consensus       164 ~~~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l  243 (695)
                      .-+.++|-+..++-|...+.....++...+|++|.|||+-|..++...--.+.|++++.=.++|....+.-+-..+ .  
T Consensus        34 t~de~~gQe~vV~~L~~a~~~~~lp~~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~lnaSderGisvvr~Ki-k--  110 (346)
T KOG0989|consen   34 TFDELAGQEHVVQVLKNALLRRILPHYLFYGPPGTGKTSTALAFARALNCEQLFPCRVLELNASDERGISVVREKI-K--  110 (346)
T ss_pred             cHHhhcchHHHHHHHHHHHhhcCCceEEeeCCCCCcHhHHHHHHHHHhcCccccccchhhhcccccccccchhhhh-c--
Confidence            3456799999999999988887789999999999999999998876322246788877655666544332110000 0  


Q ss_pred             CCCCCCCCChHHHHHHHHHHHHhc---CCCc-EEEEEeCCCCCChHHHhhh----ccCCCCCEEEEEcCCCCCCC-----
Q 042541          244 GYPVPEFQTDEAAINDLERFFKQM---RIEA-ILLVLDDVWPGSESLLQKL----GFQLPDYKILVTSRSEFPQF-----  310 (695)
Q Consensus       244 ~~~~~~~~~~~~~~~~l~~~~~~l---~~~~-~LlVlDdv~~~~~~~~~~l----~~~~~gs~iivTtR~~~~~~-----  310 (695)
                                  ..+.+.......   .-++ -.+|||+++.....-+..+    ......++.|+.+-.-..-.     
T Consensus       111 ------------~fakl~~~~~~~~~~~~~~fKiiIlDEcdsmtsdaq~aLrr~mE~~s~~trFiLIcnylsrii~pi~S  178 (346)
T KOG0989|consen  111 ------------NFAKLTVLLKRSDGYPCPPFKIIILDECDSMTSDAQAALRRTMEDFSRTTRFILICNYLSRIIRPLVS  178 (346)
T ss_pred             ------------CHHHHhhccccccCCCCCcceEEEEechhhhhHHHHHHHHHHHhccccceEEEEEcCChhhCChHHHh
Confidence                        000011000000   1122 5889999987765433333    23334566655544432111     


Q ss_pred             -CCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCc
Q 042541          311 -GSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGC  357 (695)
Q Consensus       311 -~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~  357 (695)
                       ...|+.++|.+++...-+...+...+..   -..+..+.|++.++|-
T Consensus       179 RC~KfrFk~L~d~~iv~rL~~Ia~~E~v~---~d~~al~~I~~~S~Gd  223 (346)
T KOG0989|consen  179 RCQKFRFKKLKDEDIVDRLEKIASKEGVD---IDDDALKLIAKISDGD  223 (346)
T ss_pred             hHHHhcCCCcchHHHHHHHHHHHHHhCCC---CCHHHHHHHHHHcCCc
Confidence             1278899999999999888887554442   2467789999999994

>PRK06620 hypothetical protein; Validated

Probab=97.88  E-value=0.00035  Score=67.71  Aligned_cols=155  Identities=14%  Similarity=0.078  Sum_probs=90.2

Q ss_pred             CCCCCCCCCcc--hHHHHHHHHHcCC--c--eEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHH
Q 042541          163 DPPVISPGLDV--PLKELKMELFKDG--R--QFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIV  236 (695)
Q Consensus       163 ~~~~~~vGr~~--~~~~l~~~L~~~~--~--~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~  236 (695)
                      ...+++||-..  ....+.++-...+  .  +.+.|+|++|+|||+|++.+++..  .      ..++.  ..+.     
T Consensus        14 tfd~Fvvg~~N~~a~~~~~~~~~~~~~~~~~~~l~l~Gp~G~GKThLl~a~~~~~--~------~~~~~--~~~~-----   78 (214)
T PRK06620         14 HPDEFIVSSSNDQAYNIIKNWQCGFGVNPYKFTLLIKGPSSSGKTYLTKIWQNLS--N------AYIIK--DIFF-----   78 (214)
T ss_pred             CchhhEecccHHHHHHHHHHHHHccccCCCcceEEEECCCCCCHHHHHHHHHhcc--C------CEEcc--hhhh-----
Confidence            34556677633  2333333332211  2  568999999999999999987632  1      11221  0000     


Q ss_pred             HHHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH-HHhhhcc-CCCCCEEEEEcCCCCCC-----
Q 042541          237 QKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES-LLQKLGF-QLPDYKILVTSRSEFPQ-----  309 (695)
Q Consensus       237 ~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~-~~~~l~~-~~~gs~iivTtR~~~~~-----  309 (695)
                                     . .       ...    ...-+|++||+....+. +..-+.. ...|..+|+|++.....     
T Consensus        79 ---------------~-~-------~~~----~~~d~lliDdi~~~~~~~lf~l~N~~~e~g~~ilits~~~p~~l~l~~  131 (214)
T PRK06620         79 ---------------N-E-------EIL----EKYNAFIIEDIENWQEPALLHIFNIINEKQKYLLLTSSDKSRNFTLPD  131 (214)
T ss_pred             ---------------c-h-------hHH----hcCCEEEEeccccchHHHHHHHHHHHHhcCCEEEEEcCCCccccchHH
Confidence                           0 0       001    12357889999754322 2211111 13467899999876332     


Q ss_pred             ------CCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHH
Q 042541          310 ------FGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALK  362 (695)
Q Consensus       310 ------~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~  362 (695)
                            .+..+++++++.++-..++.+.+....-   .-.+++..-|++.+.|---.+.
T Consensus       132 L~SRl~~gl~~~l~~pd~~~~~~~l~k~~~~~~l---~l~~ev~~~L~~~~~~d~r~l~  187 (214)
T PRK06620        132 LSSRIKSVLSILLNSPDDELIKILIFKHFSISSV---TISRQIIDFLLVNLPREYSKII  187 (214)
T ss_pred             HHHHHhCCceEeeCCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHccCCHHHHH
Confidence                  2337999999999988888877643211   1237788889998888654443

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=97.88  E-value=0.00089  Score=73.07  Aligned_cols=173  Identities=14%  Similarity=0.164  Sum_probs=101.7

Q ss_pred             CCCCCCcch--HHHHHHHHHcC--CceEEEEEcCCCCcHHHHHHHHhccccccccC-CCcEEEEEeCCCCCHHHHHHHHH
Q 042541          166 VISPGLDVP--LKELKMELFKD--GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKF-KDDIFYVTVSKNPNVKAIVQKVL  240 (695)
Q Consensus       166 ~~~vGr~~~--~~~l~~~L~~~--~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f-~~~~~wv~~~~~~~~~~~~~~i~  240 (695)
                      .+++|....  ...+..+...+  ...-+.|+|+.|+|||+|++.+++  .+...+ ...+++++..      ++...+.
T Consensus       123 ~fv~g~~n~~a~~~~~~~~~~~~~~~~~l~l~G~~G~GKThL~~ai~~--~~~~~~~~~~v~yi~~~------~~~~~~~  194 (450)
T PRK00149        123 NFVVGKSNRLAHAAALAVAENPGKAYNPLFIYGGVGLGKTHLLHAIGN--YILEKNPNAKVVYVTSE------KFTNDFV  194 (450)
T ss_pred             ccccCCCcHHHHHHHHHHHhCcCccCCeEEEECCCCCCHHHHHHHHHH--HHHHhCCCCeEEEEEHH------HHHHHHH
Confidence            455675543  22333333322  235689999999999999999998  454443 3335566543      3334444


Q ss_pred             HhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCC--h----HHHhhhcc-CCCCCEEEEEcCCCCC-----
Q 042541          241 HHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGS--E----SLLQKLGF-QLPDYKILVTSRSEFP-----  308 (695)
Q Consensus       241 ~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~--~----~~~~~l~~-~~~gs~iivTtR~~~~-----  308 (695)
                      ..+...     .    ...+.   +.++ +.-+||+||+....  +    .+...+.. ...|..+|+||.....     
T Consensus       195 ~~~~~~-----~----~~~~~---~~~~-~~dlLiiDDi~~l~~~~~~~~~l~~~~n~l~~~~~~iiits~~~p~~l~~l  261 (450)
T PRK00149        195 NALRNN-----T----MEEFK---EKYR-SVDVLLIDDIQFLAGKERTQEEFFHTFNALHEAGKQIVLTSDRPPKELPGL  261 (450)
T ss_pred             HHHHcC-----c----HHHHH---HHHh-cCCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCcEEEECCCCHHHHHHH
Confidence            444211     1    11222   2223 34589999996432  1    12222211 1235568888875411     


Q ss_pred             --------CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHH
Q 042541          309 --------QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALK  362 (695)
Q Consensus       309 --------~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~  362 (695)
                              ..+..+.+++.+.++-..++.+.+.....   .-.+++...|++.+.|....+.
T Consensus       262 ~~~l~SRl~~gl~v~i~~pd~~~r~~il~~~~~~~~~---~l~~e~l~~ia~~~~~~~R~l~  320 (450)
T PRK00149        262 EERLRSRFEWGLTVDIEPPDLETRIAILKKKAEEEGI---DLPDEVLEFIAKNITSNVRELE  320 (450)
T ss_pred             HHHHHhHhcCCeeEEecCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHcCcCCCHHHHH
Confidence                    12347899999999999999988754221   1246789999999999876544

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=97.86  E-value=9.4e-05  Score=77.96  Aligned_cols=110  Identities=13%  Similarity=0.143  Sum_probs=70.7

Q ss_pred             CCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHh-cC
Q 042541          166 VISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHH-KG  244 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~-l~  244 (695)
                      ..+++.+..++.+...|...  +.|.++|++|+|||++|+.+++.......|.. +.||.+++..+..+++..+.-. .+
T Consensus       175 ~d~~i~e~~le~l~~~L~~~--~~iil~GppGtGKT~lA~~la~~l~~~~~~~~-v~~VtFHpsySYeDFI~G~rP~~vg  251 (459)
T PRK11331        175 NDLFIPETTIETILKRLTIK--KNIILQGPPGVGKTFVARRLAYLLTGEKAPQR-VNMVQFHQSYSYEDFIQGYRPNGVG  251 (459)
T ss_pred             hcccCCHHHHHHHHHHHhcC--CCEEEECCCCCCHHHHHHHHHHHhcCCcccce-eeEEeecccccHHHHhcccCCCCCC
Confidence            45688899999999988753  56788999999999999999884333344554 7899999988877765433110 11


Q ss_pred             CCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCC
Q 042541          245 YPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGS  283 (695)
Q Consensus       245 ~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~  283 (695)
                      ..     ........+......-.+++++||+|++....
T Consensus       252 y~-----~~~G~f~~~~~~A~~~p~~~~vliIDEINRan  285 (459)
T PRK11331        252 FR-----RKDGIFYNFCQQAKEQPEKKYVFIIDEINRAN  285 (459)
T ss_pred             eE-----ecCchHHHHHHHHHhcccCCcEEEEehhhccC
Confidence            00     00001111111111113578999999997765

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=97.86  E-value=0.0014  Score=62.91  Aligned_cols=176  Identities=16%  Similarity=0.208  Sum_probs=110.7

Q ss_pred             cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeC-CCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHH
Q 042541          184 KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVS-KNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLER  262 (695)
Q Consensus       184 ~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~-~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~  262 (695)
                      .++.+++.++|.-|.|||.++++....  ..   +..+.-+.+. ...+...+...|+..+..+.  ..........+.+
T Consensus        48 ~d~qg~~~vtGevGsGKTv~~Ral~~s--~~---~d~~~~v~i~~~~~s~~~~~~ai~~~l~~~p--~~~~~~~~e~~~~  120 (269)
T COG3267          48 ADGQGILAVTGEVGSGKTVLRRALLAS--LN---EDQVAVVVIDKPTLSDATLLEAIVADLESQP--KVNVNAVLEQIDR  120 (269)
T ss_pred             hcCCceEEEEecCCCchhHHHHHHHHh--cC---CCceEEEEecCcchhHHHHHHHHHHHhccCc--cchhHHHHHHHHH
Confidence            455679999999999999999955431  21   1112223443 44577888888988887632  1223333333444


Q ss_pred             HH--HhcCCCc-EEEEEeCCCCCChHHHhhhc---cCCC-C---CEEEEEcCCCC----C-----CCC----CeEecCCC
Q 042541          263 FF--KQMRIEA-ILLVLDDVWPGSESLLQKLG---FQLP-D---YKILVTSRSEF----P-----QFG----SVHYLKPL  319 (695)
Q Consensus       263 ~~--~~l~~~~-~LlVlDdv~~~~~~~~~~l~---~~~~-g---s~iivTtR~~~----~-----~~~----~~~~l~~L  319 (695)
                      .+  ..-++++ ..+++||+.+.....++.+.   .... +   -+|+..-..+.    .     ...    ..|.+.|+
T Consensus       121 ~L~al~~~g~r~v~l~vdEah~L~~~~le~Lrll~nl~~~~~~~l~ivL~Gqp~L~~~lr~~~l~e~~~R~~ir~~l~P~  200 (269)
T COG3267         121 ELAALVKKGKRPVVLMVDEAHDLNDSALEALRLLTNLEEDSSKLLSIVLIGQPKLRPRLRLPVLRELEQRIDIRIELPPL  200 (269)
T ss_pred             HHHHHHHhCCCCeEEeehhHhhhChhHHHHHHHHHhhcccccCceeeeecCCcccchhhchHHHHhhhheEEEEEecCCc
Confidence            33  2225677 99999998766544333322   1111 1   22333322221    0     111    13899999


Q ss_pred             ChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHHH
Q 042541          320 TYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGG  366 (695)
Q Consensus       320 ~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~~  366 (695)
                      +.++...++..+..+...+.+....+....|.....|.|.+|..++.
T Consensus       201 ~~~~t~~yl~~~Le~a~~~~~l~~~~a~~~i~~~sqg~P~lin~~~~  247 (269)
T COG3267         201 TEAETGLYLRHRLEGAGLPEPLFSDDALLLIHEASQGIPRLINNLAT  247 (269)
T ss_pred             ChHHHHHHHHHHHhccCCCcccCChhHHHHHHHHhccchHHHHHHHH
Confidence            99999999998887765544444578889999999999999998765

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=97.84  E-value=9.2e-05  Score=85.56  Aligned_cols=149  Identities=13%  Similarity=0.129  Sum_probs=86.8

Q ss_pred             CCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccc---cccccC-CCcEEEEEeCCCCCHHHHHHHHHH
Q 042541          166 VISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDD---QVQGKF-KDDIFYVTVSKNPNVKAIVQKVLH  241 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~---~~~~~f-~~~~~wv~~~~~~~~~~~~~~i~~  241 (695)
                      +.++||+.+++++++.|......-+.++|++|+|||++|+.+++..   .+...+ ...++.++++          .++.
T Consensus       182 ~~~igr~~ei~~~~~~L~~~~~~n~lL~G~pG~GKT~l~~~la~~~~~~~~p~~l~~~~~~~~~~~----------~l~a  251 (731)
T TIGR02639       182 DPLIGREDELERTIQVLCRRKKNNPLLVGEPGVGKTAIAEGLALRIAEGKVPENLKNAKIYSLDMG----------SLLA  251 (731)
T ss_pred             CcccCcHHHHHHHHHHHhcCCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCeEEEecHH----------HHhh
Confidence            4679999999999999986655667899999999999999998731   111112 2223333221          1111


Q ss_pred             hcCCCCCCCCChHHHHHHHHHHHHhc-CCCcEEEEEeCCCCCC---------hHHHhhhccCC-CC-CEEEE-EcCCC--
Q 042541          242 HKGYPVPEFQTDEAAINDLERFFKQM-RIEAILLVLDDVWPGS---------ESLLQKLGFQL-PD-YKILV-TSRSE--  306 (695)
Q Consensus       242 ~l~~~~~~~~~~~~~~~~l~~~~~~l-~~~~~LlVlDdv~~~~---------~~~~~~l~~~~-~g-s~iiv-TtR~~--  306 (695)
                      ...       ...+....+..+++.+ ..++.+|++|++....         ......+.+.. .| -++|- ||..+  
T Consensus       252 ~~~-------~~g~~e~~l~~i~~~~~~~~~~ILfiDEih~l~~~g~~~~~~~~~~~~L~~~l~~g~i~~IgaTt~~e~~  324 (731)
T TIGR02639       252 GTK-------YRGDFEERLKAVVSEIEKEPNAILFIDEIHTIVGAGATSGGSMDASNLLKPALSSGKLRCIGSTTYEEYK  324 (731)
T ss_pred             hcc-------ccchHHHHHHHHHHHHhccCCeEEEEecHHHHhccCCCCCccHHHHHHHHHHHhCCCeEEEEecCHHHHH
Confidence            000       0112334566666444 3468999999985321         11111122211 23 34444 44421  


Q ss_pred             -C--------CCCCCeEecCCCChHHHHHHHHHhc
Q 042541          307 -F--------PQFGSVHYLKPLTYEAARTLFLHSA  332 (695)
Q Consensus       307 -~--------~~~~~~~~l~~L~~~ea~~Lf~~~~  332 (695)
                       .        ... ..+.+++++.++..+++....
T Consensus       325 ~~~~~d~al~rRf-~~i~v~~p~~~~~~~il~~~~  358 (731)
T TIGR02639       325 NHFEKDRALSRRF-QKIDVGEPSIEETVKILKGLK  358 (731)
T ss_pred             HHhhhhHHHHHhC-ceEEeCCCCHHHHHHHHHHHH
Confidence             0        112 278999999999999998654

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.84  E-value=0.00073  Score=75.79  Aligned_cols=189  Identities=13%  Similarity=0.140  Sum_probs=106.5

Q ss_pred             CCCCCCcchHHHHHHHHHcCC-ceEEEEEcCCCCcHHHHHHHHhccccccc-cCCCcEEEEEeCCCCCHHHHHHHHHHhc
Q 042541          166 VISPGLDVPLKELKMELFKDG-RQFIVVSAPGGYGKTTLVQRLCKDDQVQG-KFKDDIFYVTVSKNPNVKAIVQKVLHHK  243 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~~-~~vv~I~G~gGiGKTtLa~~~~~~~~~~~-~f~~~~~wv~~~~~~~~~~~~~~i~~~l  243 (695)
                      ..++|.+..++.|..++..+. ...+.++|+.|+||||+|+.+++.  +.. .... .    ....+..-...+.+....
T Consensus        16 ~~liGq~~i~~~L~~~l~~~rl~~a~Lf~Gp~G~GKttlA~~lAk~--L~c~~~~~-~----~~~~Cg~C~~C~~i~~g~   88 (620)
T PRK14948         16 DELVGQEAIATTLKNALISNRIAPAYLFTGPRGTGKTSSARILAKS--LNCLNSDK-P----TPEPCGKCELCRAIAAGN   88 (620)
T ss_pred             hhccChHHHHHHHHHHHHcCCCCceEEEECCCCCChHHHHHHHHHH--hcCCCcCC-C----CCCCCcccHHHHHHhcCC
Confidence            457999999999988888665 367889999999999999999873  211 1100 0    000111112222222211


Q ss_pred             CCCCCCC-CChHHHHHHHHHHHHhc-----CCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCC-----
Q 042541          244 GYPVPEF-QTDEAAINDLERFFKQM-----RIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFP-----  308 (695)
Q Consensus       244 ~~~~~~~-~~~~~~~~~l~~~~~~l-----~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~-----  308 (695)
                      ....... .......+.++++++..     .+++-++|+|+++.....    ++..+......+.+|++|.+...     
T Consensus        89 h~D~~ei~~~~~~~vd~IReii~~a~~~p~~~~~KViIIDEad~Lt~~a~naLLK~LEePp~~tvfIL~t~~~~~llpTI  168 (620)
T PRK14948         89 ALDVIEIDAASNTGVDNIRELIERAQFAPVQARWKVYVIDECHMLSTAAFNALLKTLEEPPPRVVFVLATTDPQRVLPTI  168 (620)
T ss_pred             CccEEEEeccccCCHHHHHHHHHHHhhChhcCCceEEEEECccccCHHHHHHHHHHHhcCCcCeEEEEEeCChhhhhHHH
Confidence            1100000 00011123333333221     356679999999876643    44444443345666655544311     


Q ss_pred             -CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHH
Q 042541          309 -QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVV  364 (695)
Q Consensus       309 -~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~  364 (695)
                       .-...+.+.+++.++....+...+......   -..+.+..|++.++|.+..+..+
T Consensus       169 rSRc~~~~f~~l~~~ei~~~L~~ia~kegi~---is~~al~~La~~s~G~lr~A~~l  222 (620)
T PRK14948        169 ISRCQRFDFRRIPLEAMVQHLSEIAEKESIE---IEPEALTLVAQRSQGGLRDAESL  222 (620)
T ss_pred             HhheeEEEecCCCHHHHHHHHHHHHHHhCCC---CCHHHHHHHHHHcCCCHHHHHHH
Confidence             112378888999998888877665432221   13567889999999987655443

>KOG4237 consensus Extracellular matrix protein slit, contains leucine-rich and EGF-like repeats [Extracellular structures; Signal transduction mechanisms]

Probab=97.83  E-value=1.7e-06  Score=86.88  Aligned_cols=128  Identities=13%  Similarity=0.170  Sum_probs=102.3

Q ss_pred             ceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEecc-CCCCCcc--cccccccccE
Q 042541          551 EVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEH-VSLPNSL--ATVRMNHLQK  627 (695)
Q Consensus       551 ~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~-~~l~~lp--~i~~l~~L~~  627 (695)
                      ....+.|+.|......|..|+.+++||.|||++|+++--   .+..+..|.+|-.|-+.+ |.|+.+|  .+++|..|+-
T Consensus        68 ~tveirLdqN~I~~iP~~aF~~l~~LRrLdLS~N~Is~I---~p~AF~GL~~l~~Lvlyg~NkI~~l~k~~F~gL~slqr  144 (498)
T KOG4237|consen   68 ETVEIRLDQNQISSIPPGAFKTLHRLRRLDLSKNNISFI---APDAFKGLASLLSLVLYGNNKITDLPKGAFGGLSSLQR  144 (498)
T ss_pred             cceEEEeccCCcccCChhhccchhhhceecccccchhhc---ChHhhhhhHhhhHHHhhcCCchhhhhhhHhhhHHHHHH
Confidence            345566766655555556999999999999999987421   223366777776666655 8999999  9999999999


Q ss_pred             EeeccccCCcccccchhhhcccCCCccEEecccccccccCch-hhcCCCCCceeeccccc
Q 042541          628 VSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPD-GLCDIVSMEKLRITNCH  686 (695)
Q Consensus       628 L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~-~i~~L~~L~~L~l~~~~  686 (695)
                      |.+.-|.+..+++..+-    .|++|..|.+-+ +.+..++. .+..+.+++++++.-|+
T Consensus       145 LllNan~i~Cir~~al~----dL~~l~lLslyD-n~~q~i~~~tf~~l~~i~tlhlA~np  199 (498)
T KOG4237|consen  145 LLLNANHINCIRQDALR----DLPSLSLLSLYD-NKIQSICKGTFQGLAAIKTLHLAQNP  199 (498)
T ss_pred             HhcChhhhcchhHHHHH----Hhhhcchhcccc-hhhhhhccccccchhccchHhhhcCc
Confidence            99999999999888886    899999999988 46788888 58899999999987765

>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

Probab=97.82  E-value=0.00026  Score=68.69  Aligned_cols=170  Identities=20%  Similarity=0.242  Sum_probs=103.9

Q ss_pred             CCCCCCCCCCcchHHHHHHHHH-----cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHH
Q 042541          162 PDPPVISPGLDVPLKELKMELF-----KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIV  236 (695)
Q Consensus       162 ~~~~~~~vGr~~~~~~l~~~L~-----~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~  236 (695)
                      |..-..|||-++-++++.-++.     ++..-.|.++|++|.||||||.-+++  .....+..     .-+..       
T Consensus        22 P~~l~efiGQ~~vk~~L~ifI~AAk~r~e~lDHvLl~GPPGlGKTTLA~IIA~--Emgvn~k~-----tsGp~-------   87 (332)
T COG2255          22 PKTLDEFIGQEKVKEQLQIFIKAAKKRGEALDHVLLFGPPGLGKTTLAHIIAN--ELGVNLKI-----TSGPA-------   87 (332)
T ss_pred             cccHHHhcChHHHHHHHHHHHHHHHhcCCCcCeEEeeCCCCCcHHHHHHHHHH--HhcCCeEe-----ccccc-------
Confidence            3334568999988888877776     33467899999999999999999998  44443321     00100       


Q ss_pred             HHHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChHH-------Hhhh-----ccCCCCCE------
Q 042541          237 QKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSESL-------LQKL-----GFQLPDYK------  298 (695)
Q Consensus       237 ~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~~-------~~~l-----~~~~~gs~------  298 (695)
                                       -+.-..+..++..++.+. +|.+|.+.......       .+.|     .-.++++|      
T Consensus        88 -----------------leK~gDlaaiLt~Le~~D-VLFIDEIHrl~~~vEE~LYpaMEDf~lDI~IG~gp~Arsv~ldL  149 (332)
T COG2255          88 -----------------LEKPGDLAAILTNLEEGD-VLFIDEIHRLSPAVEEVLYPAMEDFRLDIIIGKGPAARSIRLDL  149 (332)
T ss_pred             -----------------ccChhhHHHHHhcCCcCC-eEEEehhhhcChhHHHHhhhhhhheeEEEEEccCCccceEeccC
Confidence                             001122333443344333 44557765443211       1111     11223333      


Q ss_pred             -----EEEEcCCCC------CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHHH
Q 042541          299 -----ILVTSRSEF------PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGG  366 (695)
Q Consensus       299 -----iivTtR~~~------~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~~  366 (695)
                           |=.|||.-.      ...|.+.+++..+.+|-.++..+.+..-..   .-.++.+.+|+++..|-|.-..-+-+
T Consensus       150 ppFTLIGATTr~G~lt~PLrdRFGi~~rlefY~~~eL~~Iv~r~a~~l~i---~i~~~~a~eIA~rSRGTPRIAnRLLr  225 (332)
T COG2255         150 PPFTLIGATTRAGMLTNPLRDRFGIIQRLEFYTVEELEEIVKRSAKILGI---EIDEEAALEIARRSRGTPRIANRLLR  225 (332)
T ss_pred             CCeeEeeeccccccccchhHHhcCCeeeeecCCHHHHHHHHHHHHHHhCC---CCChHHHHHHHHhccCCcHHHHHHHH
Confidence                 224888762      245668999999999999999987743322   12467899999999999975544433

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=97.80  E-value=0.001  Score=68.11  Aligned_cols=165  Identities=16%  Similarity=0.134  Sum_probs=98.9

Q ss_pred             hHHHHHHHHHcCCc-eEEEEEcCCCCcHHHHHHHHhcccccc----------------ccCCCcEEEEEeCCCCCHHHHH
Q 042541          174 PLKELKMELFKDGR-QFIVVSAPGGYGKTTLVQRLCKDDQVQ----------------GKFKDDIFYVTVSKNPNVKAIV  236 (695)
Q Consensus       174 ~~~~l~~~L~~~~~-~vv~I~G~gGiGKTtLa~~~~~~~~~~----------------~~f~~~~~wv~~~~~~~~~~~~  236 (695)
                      ..+.+...+..+.. ..+.++|+.|+||+++|..++..---.                +..+. +.|+......      
T Consensus        12 ~~~~l~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~lA~~LlC~~~~~~~~c~~c~~~~~g~HPD-~~~i~~~p~~------   84 (319)
T PRK08769         12 AYDQTVAALDAGRLGHGLLICGPEGLGKRAVALALAEHVLASGPDPAAAQRTRQLIAAGTHPD-LQLVSFIPNR------   84 (319)
T ss_pred             HHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHHHHHHHhCCCCCCCCcchHHHHHhcCCCCC-EEEEecCCCc------
Confidence            45666666666654 468899999999999998877621001                11111 2233210000      


Q ss_pred             HHHHHhcCCCCCCCCChHHHHHHHHHHHHhc-----CCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCC
Q 042541          237 QKVLHHKGYPVPEFQTDEAAINDLERFFKQM-----RIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEF  307 (695)
Q Consensus       237 ~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l-----~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~  307 (695)
                               . .......-.+++++++.+.+     .+++-++|+|+++.....    +++.+....+++.+|++|....
T Consensus        85 ---------~-~~k~~~~I~idqIR~l~~~~~~~p~~g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~~~fiL~~~~~~  154 (319)
T PRK08769         85 ---------T-GDKLRTEIVIEQVREISQKLALTPQYGIAQVVIVDPADAINRAACNALLKTLEEPSPGRYLWLISAQPA  154 (319)
T ss_pred             ---------c-cccccccccHHHHHHHHHHHhhCcccCCcEEEEeccHhhhCHHHHHHHHHHhhCCCCCCeEEEEECChh
Confidence                     0 00000112234444444322     466789999999877643    6666666667888888877652


Q ss_pred             CCC------CCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHH
Q 042541          308 PQF------GSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVV  364 (695)
Q Consensus       308 ~~~------~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~  364 (695)
                      .-.      ...+.+.+++.+++.+.+....         .....+..++..++|.|+.+..+
T Consensus       155 ~lLpTIrSRCq~i~~~~~~~~~~~~~L~~~~---------~~~~~a~~~~~l~~G~p~~A~~~  208 (319)
T PRK08769        155 RLPATIRSRCQRLEFKLPPAHEALAWLLAQG---------VSERAAQEALDAARGHPGLAAQW  208 (319)
T ss_pred             hCchHHHhhheEeeCCCcCHHHHHHHHHHcC---------CChHHHHHHHHHcCCCHHHHHHH
Confidence            211      2278899999999988886531         12334778899999999866544

>KOG3665 consensus ZYG-1-like serine/threonine protein kinases [General function prediction only]

Probab=97.79  E-value=9.5e-06  Score=91.60  Aligned_cols=129  Identities=17%  Similarity=0.248  Sum_probs=85.3

Q ss_pred             CccceEEeeecCCcccCCCC---CCCCCceEEEEEEccCc-cccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCC
Q 042541          526 PNNASLLSISTDETFSSNWP---DMQGPEVKVVVLNIRTK-KYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALS  601 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~~~~~---~~~~~~l~~L~l~~~~~-~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~  601 (695)
                      ..+.|||.+.+...+...|+   ...+|.|++|.+.+... ...+.....++++|+.||+++++.     .++..++.|.
T Consensus       121 r~nL~~LdI~G~~~~s~~W~~kig~~LPsL~sL~i~~~~~~~~dF~~lc~sFpNL~sLDIS~TnI-----~nl~GIS~Lk  195 (699)
T KOG3665|consen  121 RQNLQHLDISGSELFSNGWPKKIGTMLPSLRSLVISGRQFDNDDFSQLCASFPNLRSLDISGTNI-----SNLSGISRLK  195 (699)
T ss_pred             HHhhhhcCccccchhhccHHHHHhhhCcccceEEecCceecchhHHHHhhccCccceeecCCCCc-----cCcHHHhccc
Confidence            35789999988877776664   34688888888877533 223344456778888888887554     3445578888


Q ss_pred             CCcEEEeccCCCCCcc---cccccccccEEeeccccCCcccccchh---hhcccCCCccEEeccc
Q 042541          602 KLKKIRLEHVSLPNSL---ATVRMNHLQKVSLVMCNVGQVFRNSTF---RISDAFPNLLEMDIDY  660 (695)
Q Consensus       602 ~L~~L~L~~~~l~~lp---~i~~l~~L~~L~l~~~~i~~~~~~~~~---~l~~~l~~L~~L~l~~  660 (695)
                      ||+.|.+.+-.+..-+   .+.+|++|+.||+|..+....+ .+..   .-...||+|+.||.++
T Consensus       196 nLq~L~mrnLe~e~~~~l~~LF~L~~L~vLDIS~~~~~~~~-~ii~qYlec~~~LpeLrfLDcSg  259 (699)
T KOG3665|consen  196 NLQVLSMRNLEFESYQDLIDLFNLKKLRVLDISRDKNNDDT-KIIEQYLECGMVLPELRFLDCSG  259 (699)
T ss_pred             cHHHHhccCCCCCchhhHHHHhcccCCCeeeccccccccch-HHHHHHHHhcccCccccEEecCC
Confidence            8888888877766433   6667888888888877544433 1110   0011577777777776

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=97.79  E-value=0.0007  Score=69.96  Aligned_cols=89  Identities=15%  Similarity=0.085  Sum_probs=61.2

Q ss_pred             CCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCCCC------CCeEecCCCChHHHHHHHHHhccCCCCC
Q 042541          269 IEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFPQF------GSVHYLKPLTYEAARTLFLHSANLQDGN  338 (695)
Q Consensus       269 ~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~~~------~~~~~l~~L~~~ea~~Lf~~~~~~~~~~  338 (695)
                      +++-++|+|+++.....    +++.+....+++.+|+||.+...-.      ...+.+.+++.+++.+.+......    
T Consensus       105 ~~~kv~iI~~a~~m~~~aaNaLLK~LEEPp~~~~fiL~t~~~~~ll~TI~SRc~~~~~~~~~~~~~~~~L~~~~~~----  180 (328)
T PRK05707        105 GGRKVVLIEPAEAMNRNAANALLKSLEEPSGDTVLLLISHQPSRLLPTIKSRCQQQACPLPSNEESLQWLQQALPE----  180 (328)
T ss_pred             CCCeEEEECChhhCCHHHHHHHHHHHhCCCCCeEEEEEECChhhCcHHHHhhceeeeCCCcCHHHHHHHHHHhccc----
Confidence            55556678999877643    5565655556788888887763211      227899999999999988765310    


Q ss_pred             CCCCchHHHHHHHHhcCCchhHHHHH
Q 042541          339 SYIPDENIVSKILRACKGCPLALKVV  364 (695)
Q Consensus       339 ~~~~~~~~~~~I~~~c~G~PLai~~~  364 (695)
                         ...+.+..++..++|.|+.+..+
T Consensus       181 ---~~~~~~~~~l~la~Gsp~~A~~l  203 (328)
T PRK05707        181 ---SDERERIELLTLAGGSPLRALQL  203 (328)
T ss_pred             ---CChHHHHHHHHHcCCCHHHHHHH
Confidence               12345678899999999765544

>KOG2227 consensus Pre-initiation complex, subunit CDC6, AAA+ superfamily ATPase [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=97.78  E-value=0.00073  Score=70.12  Aligned_cols=167  Identities=20%  Similarity=0.264  Sum_probs=105.7

Q ss_pred             CCCCCCCCCcchHHHHHHHHH----cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHH
Q 042541          163 DPPVISPGLDVPLKELKMELF----KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQK  238 (695)
Q Consensus       163 ~~~~~~vGr~~~~~~l~~~L~----~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~  238 (695)
                      ..+..++||+.|+..+.+++.    ....+-+-|.|-+|.|||.+...++.+..-...-. .++++++..-....+++..
T Consensus       147 ~~p~~l~gRe~e~~~v~~F~~~hle~~t~gSlYVsG~PGtgkt~~l~rvl~~~~~~~~~~-~~v~inc~sl~~~~aiF~k  225 (529)
T KOG2227|consen  147 APPGTLKGRELEMDIVREFFSLHLELNTSGSLYVSGQPGTGKTALLSRVLDSLSKSSKSP-VTVYINCTSLTEASAIFKK  225 (529)
T ss_pred             CCCCCccchHHHHHHHHHHHHhhhhcccCcceEeeCCCCcchHHHHHHHHHhhhhhcccc-eeEEEeeccccchHHHHHH
Confidence            346678999999999999887    33467788999999999999999988532211111 2468887776777778887


Q ss_pred             HHHhcC--CCCCCCCChHHHHHHHHHHHHhcC--CCcEEEEEeCCCCCCh----HHHhhhcc-CCCCCEEEEEcCCC---
Q 042541          239 VLHHKG--YPVPEFQTDEAAINDLERFFKQMR--IEAILLVLDDVWPGSE----SLLQKLGF-QLPDYKILVTSRSE---  306 (695)
Q Consensus       239 i~~~l~--~~~~~~~~~~~~~~~l~~~~~~l~--~~~~LlVlDdv~~~~~----~~~~~l~~-~~~gs~iivTtR~~---  306 (695)
                      |...+.  ...+.  ..   .+.+..+-++..  ...+|+|+|.++....    .+...|.+ ..+++++|+.--..   
T Consensus       226 I~~~~~q~~~s~~--~~---~~~~~~~~~h~~q~k~~~llVlDEmD~L~tr~~~vLy~lFewp~lp~sr~iLiGiANslD  300 (529)
T KOG2227|consen  226 IFSSLLQDLVSPG--TG---MQHLEKFEKHTKQSKFMLLLVLDEMDHLITRSQTVLYTLFEWPKLPNSRIILIGIANSLD  300 (529)
T ss_pred             HHHHHHHHhcCCc--hh---HHHHHHHHHHHhcccceEEEEechhhHHhhcccceeeeehhcccCCcceeeeeeehhhhh
Confidence            777762  11111  11   222222223332  2468999999854321    12233333 34677766532221   


Q ss_pred             ------------CCCCCCeEecCCCChHHHHHHHHHhccCC
Q 042541          307 ------------FPQFGSVHYLKPLTYEAARTLFLHSANLQ  335 (695)
Q Consensus       307 ------------~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~  335 (695)
                                  ....+..+..+|.+.++-.++|..+....
T Consensus       301 lTdR~LprL~~~~~~~P~~l~F~PYTk~qI~~Il~~rl~~~  341 (529)
T KOG2227|consen  301 LTDRFLPRLNLDLTIKPKLLVFPPYTKDQIVEILQQRLSEE  341 (529)
T ss_pred             HHHHHhhhhhhccCCCCceeeecCCCHHHHHHHHHHHHhcc
Confidence                        11223378889999999999999887443

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=97.77  E-value=0.00033  Score=70.47  Aligned_cols=148  Identities=15%  Similarity=0.145  Sum_probs=77.2

Q ss_pred             CCCCCcchHHHHHHHHH---------------cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCC
Q 042541          167 ISPGLDVPLKELKMELF---------------KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPN  231 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~---------------~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~  231 (695)
                      .++|.+..+++|.+...               .+...-+.++|++|+||||+|+.+++...-.+....+ .++.++..  
T Consensus         7 ~~~Gl~~vk~~i~~~~~~~~~~~~~~~~g~~~~~~~~~vll~GppGtGKTtlA~~ia~~l~~~~~~~~~-~~v~~~~~--   83 (261)
T TIGR02881         7 RMVGLDEVKALIKEIYAWIQINEKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGKLFKEMNVLSKG-HLIEVERA--   83 (261)
T ss_pred             HhcChHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCcceEEEEcCCCCCHHHHHHHHHHHHHhcCcccCC-ceEEecHH--
Confidence            46888887766654322               1124568899999999999999998631101111111 13333221  


Q ss_pred             HHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCC--------hH----HHhhhccCCCCCEE
Q 042541          232 VKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGS--------ES----LLQKLGFQLPDYKI  299 (695)
Q Consensus       232 ~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~--------~~----~~~~l~~~~~gs~i  299 (695)
                        ++...   ..+          +....+..+++...  ..+|++|++....        ..    ++..+........+
T Consensus        84 --~l~~~---~~g----------~~~~~~~~~~~~a~--~~VL~IDE~~~L~~~~~~~~~~~~i~~Ll~~~e~~~~~~~v  146 (261)
T TIGR02881        84 --DLVGE---YIG----------HTAQKTREVIKKAL--GGVLFIDEAYSLARGGEKDFGKEAIDTLVKGMEDNRNEFVL  146 (261)
T ss_pred             --Hhhhh---hcc----------chHHHHHHHHHhcc--CCEEEEechhhhccCCccchHHHHHHHHHHHHhccCCCEEE
Confidence              11111   011          01123344443322  3588999996522        11    22222222223355


Q ss_pred             EEEcCCCC------------CCCCCeEecCCCChHHHHHHHHHhccC
Q 042541          300 LVTSRSEF------------PQFGSVHYLKPLTYEAARTLFLHSANL  334 (695)
Q Consensus       300 ivTtR~~~------------~~~~~~~~l~~L~~~ea~~Lf~~~~~~  334 (695)
                      |+++....            ......+.+++++.++-.+++.+.+..
T Consensus       147 ila~~~~~~~~~~~~~p~L~sRf~~~i~f~~~~~~el~~Il~~~~~~  193 (261)
T TIGR02881       147 ILAGYSDEMDYFLSLNPGLRSRFPISIDFPDYTVEELMEIAERMVKE  193 (261)
T ss_pred             EecCCcchhHHHHhcChHHHhccceEEEECCCCHHHHHHHHHHHHHH
Confidence            55543321            112336889999999999999877643

Members of this protein family are the stage V sporulation protein K (SpoVK), a close homolog of the Rubisco expression protein CbbX (TIGR02880) and a members of the ATPase family associated with various cellular activities (pfam00004). Members are strictly limited to bacterial endospore-forming species, but are not universal in this group and are missing from the Clostridium group.

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=97.74  E-value=0.0009  Score=75.13  Aligned_cols=112  Identities=15%  Similarity=0.207  Sum_probs=66.7

Q ss_pred             CCCCCCcchHHHHHHHHH-------cC--CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHH
Q 042541          166 VISPGLDVPLKELKMELF-------KD--GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIV  236 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~-------~~--~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~  236 (695)
                      ..++|-+..++.+.+.+.       ++  ........|+.|||||.||+.++.  .+-+.=+. .+-++.|+....    
T Consensus       491 ~rViGQd~AV~avs~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~--~Lfg~e~a-liR~DMSEy~Ek----  563 (786)
T COG0542         491 KRVIGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAE--ALFGDEQA-LIRIDMSEYMEK----  563 (786)
T ss_pred             cceeChHHHHHHHHHHHHHHhcCCCCCCCCceEEEeeCCCcccHHHHHHHHHH--HhcCCCcc-ceeechHHHHHH----
Confidence            346999999999988887       11  246777899999999999999887  23221122 334444443221    


Q ss_pred             HHHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcE-EEEEeCCCCCChHHHhh
Q 042541          237 QKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAI-LLVLDDVWPGSESLLQK  289 (695)
Q Consensus       237 ~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~-LlVlDdv~~~~~~~~~~  289 (695)
                       .-+..|-+.+|+-...++. ..|-   +..+.++| ++.||++...+..+..-
T Consensus       564 -HsVSrLIGaPPGYVGyeeG-G~LT---EaVRr~PySViLlDEIEKAHpdV~ni  612 (786)
T COG0542         564 -HSVSRLIGAPPGYVGYEEG-GQLT---EAVRRKPYSVILLDEIEKAHPDVFNL  612 (786)
T ss_pred             -HHHHHHhCCCCCCceeccc-cchh---HhhhcCCCeEEEechhhhcCHHHHHH
Confidence             2223333333332222221 1122   45567777 88899998887664433

>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]

Probab=97.72  E-value=9.7e-06  Score=82.65  Aligned_cols=135  Identities=17%  Similarity=0.190  Sum_probs=96.6

Q ss_pred             CCCCceEEEEEEccCccc-cCChhhcCCCCCcEEEEcccC-CCCcccCcccccccCCCCcEEEeccCCCCCcc---cccc
Q 042541          547 MQGPEVKVVVLNIRTKKY-VLPDFLQKMDELKVLIVTNYG-FSPAELNNFRVLSALSKLKKIRLEHVSLPNSL---ATVR  621 (695)
Q Consensus       547 ~~~~~l~~L~l~~~~~~~-~~p~~~~~l~~Lr~L~l~~~~-~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp---~i~~  621 (695)
                      ..+++++.|.|+.|.... .+...+..+++|..|.|..|. ....   .. ...-+..|+.|+|++|++-.++   ..+.
T Consensus       194 ~~l~~lK~L~l~~CGls~k~V~~~~~~fPsl~~L~L~~N~~~~~~---~~-~~~i~~~L~~LdLs~N~li~~~~~~~~~~  269 (505)
T KOG3207|consen  194 LLLSHLKQLVLNSCGLSWKDVQWILLTFPSLEVLYLEANEIILIK---AT-STKILQTLQELDLSNNNLIDFDQGYKVGT  269 (505)
T ss_pred             hhhhhhheEEeccCCCCHHHHHHHHHhCCcHHHhhhhccccccee---cc-hhhhhhHHhhccccCCccccccccccccc
Confidence            368899999999985443 344456778999999999873 2111   11 1334667999999999987555   7889


Q ss_pred             cccccEEeeccccCCccc--ccchhhhcccCCCccEEecccccccccCch--hhcCCCCCceeeccccc
Q 042541          622 MNHLQKVSLVMCNVGQVF--RNSTFRISDAFPNLLEMDIDYCNDLIELPD--GLCDIVSMEKLRITNCH  686 (695)
Q Consensus       622 l~~L~~L~l~~~~i~~~~--~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~--~i~~L~~L~~L~l~~~~  686 (695)
                      |+.|+.|+++.|.+..+-  +.-.....+.+++|+.|++..| ++..+|+  .+..+.+|++|.+..|.
T Consensus       270 l~~L~~Lnls~tgi~si~~~d~~s~~kt~~f~kL~~L~i~~N-~I~~w~sl~~l~~l~nlk~l~~~~n~  337 (505)
T KOG3207|consen  270 LPGLNQLNLSSTGIASIAEPDVESLDKTHTFPKLEYLNISEN-NIRDWRSLNHLRTLENLKHLRITLNY  337 (505)
T ss_pred             ccchhhhhccccCcchhcCCCccchhhhcccccceeeecccC-ccccccccchhhccchhhhhhccccc
Confidence            999999999999877653  3211122237999999999985 4555553  36677888999887755

>PF10443 RNA12: RNA12 protein; InterPro: IPR018850 Mitochondrial escape protein 2 (also known as RNA12) plays a role in maintaining the mitochondrial genome and in controlling mtDNA escape [, ]

Probab=97.72  E-value=0.0048  Score=64.41  Aligned_cols=192  Identities=17%  Similarity=0.191  Sum_probs=123.5

Q ss_pred             CcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHH-HHHhccccccccCCCcEEEEEeCCC---CCHHHHHHHHHHhcCCC
Q 042541          171 LDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLV-QRLCKDDQVQGKFKDDIFYVTVSKN---PNVKAIVQKVLHHKGYP  246 (695)
Q Consensus       171 r~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa-~~~~~~~~~~~~f~~~~~wv~~~~~---~~~~~~~~~i~~~l~~~  246 (695)
                      |.+.+++|..||....-..|.|.||-|+||+.|+ .++.++      .+. ++.+++.+-   .+-..++..+..++|+.
T Consensus         1 R~e~~~~L~~wL~e~~~TFIvV~GPrGSGK~elV~d~~L~~------r~~-vL~IDC~~i~~ar~D~~~I~~lA~qvGY~   73 (431)
T PF10443_consen    1 RKEAIEQLKSWLNENPNTFIVVQGPRGSGKRELVMDHVLKD------RKN-VLVIDCDQIVKARGDAAFIKNLASQVGYF   73 (431)
T ss_pred             CchHHHHHHHHHhcCCCeEEEEECCCCCCccHHHHHHHHhC------CCC-EEEEEChHhhhccChHHHHHHHHHhcCCC
Confidence            6678899999999777789999999999999999 777663      222 778887643   35667777777777652


Q ss_pred             C-----------------------CCCCChHHHHHHHHHHH----Hhc--------------------------CCCcEE
Q 042541          247 V-----------------------PEFQTDEAAINDLERFF----KQM--------------------------RIEAIL  273 (695)
Q Consensus       247 ~-----------------------~~~~~~~~~~~~l~~~~----~~l--------------------------~~~~~L  273 (695)
                      +                       .+..  +....+++.++    ..|                          ..++=+
T Consensus        74 PvFsw~nSiss~IDLa~qGltGqKaGfS--es~e~Ql~~IL~~t~~ALr~ial~~~~~~~~~~~l~e~~yl~~hPe~~PV  151 (431)
T PF10443_consen   74 PVFSWMNSISSFIDLAVQGLTGQKAGFS--ESLETQLKKILQTTATALRDIALSNRKKDDKDANLKEEDYLEAHPERRPV  151 (431)
T ss_pred             cchHHHHHHHHHHHHHHhhccccccCCC--CChHHHHHHHHHHHHHHHHHHHHHhhhccccccccCchhhhhhCCccCCE
Confidence            2                       1111  11112222222    111                          123568


Q ss_pred             EEEeCCCCCChH---------HHhhhccCCCCCEEEEEcCCCCC----------CCCCeEecCCCChHHHHHHHHHhccC
Q 042541          274 LVLDDVWPGSES---------LLQKLGFQLPDYKILVTSRSEFP----------QFGSVHYLKPLTYEAARTLFLHSANL  334 (695)
Q Consensus       274 lVlDdv~~~~~~---------~~~~l~~~~~gs~iivTtR~~~~----------~~~~~~~l~~L~~~ea~~Lf~~~~~~  334 (695)
                      ||+||.-...+.         .|.......+=.+||++|-+...          ..-..+.|.-.+++.|..+...+...
T Consensus       152 VVIdnF~~k~~~~~~iy~~laeWAa~Lv~~nIAHVIFlT~dv~~~k~LskaLPn~vf~tI~L~Das~~~Ak~yV~~~L~~  231 (431)
T PF10443_consen  152 VVIDNFLHKAEENDFIYDKLAEWAASLVQNNIAHVIFLTDDVSYSKPLSKALPNRVFKTISLSDASPESAKQYVLSQLDE  231 (431)
T ss_pred             EEEcchhccCcccchHHHHHHHHHHHHHhcCccEEEEECCCCchhhhHHHhCCCCceeEEeecCCCHHHHHHHHHHHhcc
Confidence            999998443311         23333333344789998877621          11237889999999999999988754


Q ss_pred             CCCC------------CC-----CCchHHHHHHHHhcCCchhHHHHHHHhhCCC
Q 042541          335 QDGN------------SY-----IPDENIVSKILRACKGCPLALKVVGGSLCGK  371 (695)
Q Consensus       335 ~~~~------------~~-----~~~~~~~~~I~~~c~G~PLai~~~~~~L~~~  371 (695)
                      ....            ..     ..........++.+||=-.-+..+++.++..
T Consensus       232 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~eld~~i~~LGGRltDLe~lvrRiksG  285 (431)
T PF10443_consen  232 DTEDSSDSKESNEQNKNDKSAENEKDLAELDECIEPLGGRLTDLEFLVRRIKSG  285 (431)
T ss_pred             cccccccccccccccccccccccccchHHHHHHHHHcCCcHHHHHHHHHHHHcC
Confidence            3210            00     1234556778888999888888888888753

It is also involved in the regulation of mtDNA nucleotide structure and number []. Additionally, this protein have a dispensable role in the early maturation of pre-rRNA [].

>CHL00095 clpC Clp protease ATP binding subunit

Probab=97.71  E-value=0.00015  Score=84.94  Aligned_cols=174  Identities=14%  Similarity=0.163  Sum_probs=94.3

Q ss_pred             CCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhcccc---ccccCCCcEEEEEeCCCCCHHHHHHHHHHh
Q 042541          166 VISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQ---VQGKFKDDIFYVTVSKNPNVKAIVQKVLHH  242 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~---~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~  242 (695)
                      +.++||+++++++++.|......-+.++|++|+|||++|..++....   +........+|. +    +...+    +. 
T Consensus       179 ~~~igr~~ei~~~~~~L~r~~~~n~lL~G~pGvGKTal~~~la~~i~~~~vp~~l~~~~i~~-l----~~~~l----~a-  248 (821)
T CHL00095        179 DPVIGREKEIERVIQILGRRTKNNPILIGEPGVGKTAIAEGLAQRIVNRDVPDILEDKLVIT-L----DIGLL----LA-  248 (821)
T ss_pred             CCCCCcHHHHHHHHHHHcccccCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEE-e----eHHHH----hc-
Confidence            35799999999999999865555667999999999999999987311   111121213332 1    11111    11 


Q ss_pred             cCCCCCCCCChHHHHHHHHHHHHhc-CCCcEEEEEeCCCCCC--------hHHHhhhccCC-CC-CEEEEEcC-CCC---
Q 042541          243 KGYPVPEFQTDEAAINDLERFFKQM-RIEAILLVLDDVWPGS--------ESLLQKLGFQL-PD-YKILVTSR-SEF---  307 (695)
Q Consensus       243 l~~~~~~~~~~~~~~~~l~~~~~~l-~~~~~LlVlDdv~~~~--------~~~~~~l~~~~-~g-s~iivTtR-~~~---  307 (695)
                        +..    ...+..+.+..+++.+ ..++.+|++|++....        ......+.+.. .| -++|.+|. .+.   
T Consensus       249 --g~~----~~ge~e~rl~~i~~~~~~~~~~ILfiDEih~l~~~g~~~g~~~~a~lLkp~l~rg~l~~IgaTt~~ey~~~  322 (821)
T CHL00095        249 --GTK----YRGEFEERLKRIFDEIQENNNIILVIDEVHTLIGAGAAEGAIDAANILKPALARGELQCIGATTLDEYRKH  322 (821)
T ss_pred             --cCC----CccHHHHHHHHHHHHHHhcCCeEEEEecHHHHhcCCCCCCcccHHHHhHHHHhCCCcEEEEeCCHHHHHHH
Confidence              110    1123344566666433 3568999999984211        01111121111 22 45555444 321   


Q ss_pred             ----C---CCCCeEecCCCChHHHHHHHHHhccC--CCCCCCCCchHHHHHHHHhcCC
Q 042541          308 ----P---QFGSVHYLKPLTYEAARTLFLHSANL--QDGNSYIPDENIVSKILRACKG  356 (695)
Q Consensus       308 ----~---~~~~~~~l~~L~~~ea~~Lf~~~~~~--~~~~~~~~~~~~~~~I~~~c~G  356 (695)
                          .   ..-..+.+...+.++...++......  ...... -..+....+++.++|
T Consensus       323 ie~D~aL~rRf~~I~v~ep~~~e~~aILr~l~~~~e~~~~v~-i~deal~~i~~ls~~  379 (821)
T CHL00095        323 IEKDPALERRFQPVYVGEPSVEETIEILFGLRSRYEKHHNLS-ISDKALEAAAKLSDQ  379 (821)
T ss_pred             HhcCHHHHhcceEEecCCCCHHHHHHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHhhc
Confidence                1   11126788889999988887653211  001111 134556666666654

>PRK10865 protein disaggregation chaperone; Provisional

Probab=97.70  E-value=0.00034  Score=81.83  Aligned_cols=147  Identities=13%  Similarity=0.137  Sum_probs=84.6

Q ss_pred             CCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhcccccccc------CCCcEEEEEeCCCCCHHHHHHHH
Q 042541          166 VISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGK------FKDDIFYVTVSKNPNVKAIVQKV  239 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~------f~~~~~wv~~~~~~~~~~~~~~i  239 (695)
                      +.++||+.++.++++.|......-+.++|++|+|||++|+.++.  ++...      ....++.++++.-.         
T Consensus       178 ~~vigr~~ei~~~i~iL~r~~~~n~lL~G~pGvGKT~l~~~la~--~i~~~~vp~~l~~~~~~~l~l~~l~---------  246 (857)
T PRK10865        178 DPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQ--RIINGEVPEGLKGRRVLALDMGALV---------  246 (857)
T ss_pred             CcCCCCHHHHHHHHHHHhcCCcCceEEECCCCCCHHHHHHHHHH--HhhcCCCchhhCCCEEEEEehhhhh---------
Confidence            45799999999999999866666777999999999999999987  33221      12334444443210         


Q ss_pred             HHhcCCCCCCCCChHHHHHHHHHHHHhc--CCCcEEEEEeCCCCCCh--------HHHhhhccCC-CC-CEEEE-EcCCC
Q 042541          240 LHHKGYPVPEFQTDEAAINDLERFFKQM--RIEAILLVLDDVWPGSE--------SLLQKLGFQL-PD-YKILV-TSRSE  306 (695)
Q Consensus       240 ~~~l~~~~~~~~~~~~~~~~l~~~~~~l--~~~~~LlVlDdv~~~~~--------~~~~~l~~~~-~g-s~iiv-TtR~~  306 (695)
                       ...       ....+....+..+++.+  .+++.+|++|++.....        ..-..+.+.. .| -++|- ||..+
T Consensus       247 -ag~-------~~~g~~e~~lk~~~~~~~~~~~~~ILfIDEih~l~~~~~~~~~~d~~~~lkp~l~~g~l~~IgaTt~~e  318 (857)
T PRK10865        247 -AGA-------KYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALARGELHCVGATTLDE  318 (857)
T ss_pred             -hcc-------chhhhhHHHHHHHHHHHHHcCCCeEEEEecHHHhccCCCCccchhHHHHhcchhhcCCCeEEEcCCCHH
Confidence             000       01112233455555332  35789999999854321        0111122221 23 45554 44443


Q ss_pred             CC-----------CCCCeEecCCCChHHHHHHHHHhc
Q 042541          307 FP-----------QFGSVHYLKPLTYEAARTLFLHSA  332 (695)
Q Consensus       307 ~~-----------~~~~~~~l~~L~~~ea~~Lf~~~~  332 (695)
                      ..           .. ..+.+..-+.++...++....
T Consensus       319 ~r~~~~~d~al~rRf-~~i~v~eP~~~~~~~iL~~l~  354 (857)
T PRK10865        319 YRQYIEKDAALERRF-QKVFVAEPSVEDTIAILRGLK  354 (857)
T ss_pred             HHHHhhhcHHHHhhC-CEEEeCCCCHHHHHHHHHHHh
Confidence            10           11 155666668888888886543

>CHL00181 cbbX CbbX; Provisional

Probab=97.67  E-value=0.0013  Score=66.70  Aligned_cols=148  Identities=16%  Similarity=0.138  Sum_probs=78.9

Q ss_pred             CCCCCcchHHHHHHHH---H-----c-------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCC
Q 042541          167 ISPGLDVPLKELKMEL---F-----K-------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPN  231 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L---~-----~-------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~  231 (695)
                      .++|.+..+++|.++.   .     .       .....+.++|++|+||||+|+.+++...-.+.-.. .-|+.++.   
T Consensus        24 ~l~Gl~~vK~~i~e~~~~~~~~~~~~~~g~~~~~~~~~ill~G~pGtGKT~lAr~la~~~~~~g~~~~-~~~~~v~~---   99 (287)
T CHL00181         24 ELVGLAPVKTRIREIAALLLIDRLRKNLGLTSSNPGLHMSFTGSPGTGKTTVALKMADILYKLGYIKK-GHLLTVTR---   99 (287)
T ss_pred             hcCCcHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHHcCCCCC-CceEEecH---
Confidence            3578777666554442   1     0       11335889999999999999999763111111111 11444442   


Q ss_pred             HHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCC---------ChH----HHhhhccCCCCCE
Q 042541          232 VKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPG---------SES----LLQKLGFQLPDYK  298 (695)
Q Consensus       232 ~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~---------~~~----~~~~l~~~~~gs~  298 (695)
                       .++....   .+..      .    ......++...  .-+|++|++...         ...    +...+.....+..
T Consensus       100 -~~l~~~~---~g~~------~----~~~~~~l~~a~--ggVLfIDE~~~l~~~~~~~~~~~e~~~~L~~~me~~~~~~~  163 (287)
T CHL00181        100 -DDLVGQY---IGHT------A----PKTKEVLKKAM--GGVLFIDEAYYLYKPDNERDYGSEAIEILLQVMENQRDDLV  163 (287)
T ss_pred             -HHHHHHH---hccc------h----HHHHHHHHHcc--CCEEEEEccchhccCCCccchHHHHHHHHHHHHhcCCCCEE
Confidence             1222221   1110      0    11233443222  359999999642         111    2222323334566


Q ss_pred             EEEEcCCCC------------CCCCCeEecCCCChHHHHHHHHHhccC
Q 042541          299 ILVTSRSEF------------PQFGSVHYLKPLTYEAARTLFLHSANL  334 (695)
Q Consensus       299 iivTtR~~~------------~~~~~~~~l~~L~~~ea~~Lf~~~~~~  334 (695)
                      ||+++....            ......+.+++++.+|..+++...+..
T Consensus       164 vI~ag~~~~~~~~~~~np~L~sR~~~~i~F~~~t~~el~~I~~~~l~~  211 (287)
T CHL00181        164 VIFAGYKDRMDKFYESNPGLSSRIANHVDFPDYTPEELLQIAKIMLEE  211 (287)
T ss_pred             EEEeCCcHHHHHHHhcCHHHHHhCCceEEcCCcCHHHHHHHHHHHHHH
Confidence            767664321            123347899999999999988877643

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=97.67  E-value=0.007  Score=65.40  Aligned_cols=146  Identities=18%  Similarity=0.208  Sum_probs=87.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQM  267 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l  267 (695)
                      .-+.|+|+.|+|||+|++.+++  .+... ...+++++.      ..+...+...+...         ..+.+.   ..+
T Consensus       142 npl~L~G~~G~GKTHLl~Ai~~--~l~~~-~~~v~yi~~------~~f~~~~~~~l~~~---------~~~~f~---~~~  200 (445)
T PRK12422        142 NPIYLFGPEGSGKTHLMQAAVH--ALRES-GGKILYVRS------ELFTEHLVSAIRSG---------EMQRFR---QFY  200 (445)
T ss_pred             ceEEEEcCCCCCHHHHHHHHHH--HHHHc-CCCEEEeeH------HHHHHHHHHHHhcc---------hHHHHH---HHc
Confidence            5688999999999999999998  34322 233666653      34445555554321         011122   222


Q ss_pred             CCCcEEEEEeCCCCCCh------HHHhhhcc-CCCCCEEEEEcCCCC-------------CCCCCeEecCCCChHHHHHH
Q 042541          268 RIEAILLVLDDVWPGSE------SLLQKLGF-QLPDYKILVTSRSEF-------------PQFGSVHYLKPLTYEAARTL  327 (695)
Q Consensus       268 ~~~~~LlVlDdv~~~~~------~~~~~l~~-~~~gs~iivTtR~~~-------------~~~~~~~~l~~L~~~ea~~L  327 (695)
                       ...-+|++||+.....      .+...+.. ...|..||+||....             ...|..+.+.+++.++-..+
T Consensus       201 -~~~dvLiIDDiq~l~~k~~~qeelf~l~N~l~~~~k~IIlts~~~p~~l~~l~~rL~SR~~~Gl~~~l~~pd~e~r~~i  279 (445)
T PRK12422        201 -RNVDALFIEDIEVFSGKGATQEEFFHTFNSLHTEGKLIVISSTCAPQDLKAMEERLISRFEWGIAIPLHPLTKEGLRSF  279 (445)
T ss_pred             -ccCCEEEEcchhhhcCChhhHHHHHHHHHHHHHCCCcEEEecCCCHHHHhhhHHHHHhhhcCCeEEecCCCCHHHHHHH
Confidence             2345888999854321      12222211 124667888886531             12245889999999999999


Q ss_pred             HHHhccCCCCCCCCCchHHHHHHHHhcCCch
Q 042541          328 FLHSANLQDGNSYIPDENIVSKILRACKGCP  358 (695)
Q Consensus       328 f~~~~~~~~~~~~~~~~~~~~~I~~~c~G~P  358 (695)
                      +.+.+.....   .-.+++..-|++.+.|.-
T Consensus       280 L~~k~~~~~~---~l~~evl~~la~~~~~di  307 (445)
T PRK12422        280 LERKAEALSI---RIEETALDFLIEALSSNV  307 (445)
T ss_pred             HHHHHHHcCC---CCCHHHHHHHHHhcCCCH
Confidence            9887754322   123667777888777543

>KOG2004 consensus Mitochondrial ATP-dependent protease PIM1/LON [Posttranslational modification, protein turnover, chaperones]

Probab=97.67  E-value=0.0021  Score=70.04  Aligned_cols=150  Identities=17%  Similarity=0.157  Sum_probs=93.2

Q ss_pred             CCCCCcchHHHHHHHHH------cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHH
Q 042541          167 ISPGLDVPLKELKMELF------KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVL  240 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~------~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~  240 (695)
                      .-+|.++-.++|.+++.      +-+.++++.+|++|||||++|+.++.  .+...|    +-++++.-.+..+|-..=-
T Consensus       412 DHYgm~dVKeRILEfiAV~kLrgs~qGkIlCf~GPPGVGKTSI~kSIA~--ALnRkF----fRfSvGG~tDvAeIkGHRR  485 (906)
T KOG2004|consen  412 DHYGMEDVKERILEFIAVGKLRGSVQGKILCFVGPPGVGKTSIAKSIAR--ALNRKF----FRFSVGGMTDVAEIKGHRR  485 (906)
T ss_pred             cccchHHHHHHHHHHHHHHhhcccCCCcEEEEeCCCCCCcccHHHHHHH--HhCCce----EEEeccccccHHhhcccce
Confidence            34999999999999987      23468999999999999999999987  454444    3567777766665532111


Q ss_pred             HhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCC--------hHHHhhhccCC-------------CCCEE
Q 042541          241 HHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGS--------ESLLQKLGFQL-------------PDYKI  299 (695)
Q Consensus       241 ~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~--------~~~~~~l~~~~-------------~gs~i  299 (695)
                      ..+|..      .    .++-+-++..+..+=|+.+|.|+...        ..+++-+.+-.             .=|+|
T Consensus       486 TYVGAM------P----GkiIq~LK~v~t~NPliLiDEvDKlG~g~qGDPasALLElLDPEQNanFlDHYLdVp~DLSkV  555 (906)
T KOG2004|consen  486 TYVGAM------P----GKIIQCLKKVKTENPLILIDEVDKLGSGHQGDPASALLELLDPEQNANFLDHYLDVPVDLSKV  555 (906)
T ss_pred             eeeccC------C----hHHHHHHHhhCCCCceEEeehhhhhCCCCCCChHHHHHHhcChhhccchhhhccccccchhhe
Confidence            112111      1    12333344556777899999986432        11333332211             12677


Q ss_pred             EEE-cCCC-CCC------CCCeEecCCCChHHHHHHHHHhc
Q 042541          300 LVT-SRSE-FPQ------FGSVHYLKPLTYEAARTLFLHSA  332 (695)
Q Consensus       300 ivT-tR~~-~~~------~~~~~~l~~L~~~ea~~Lf~~~~  332 (695)
                      ++. |-+. ...      --..+++.+...+|-.++-.++.
T Consensus       556 LFicTAN~idtIP~pLlDRMEvIelsGYv~eEKv~IA~~yL  596 (906)
T KOG2004|consen  556 LFICTANVIDTIPPPLLDRMEVIELSGYVAEEKVKIAERYL  596 (906)
T ss_pred             EEEEeccccccCChhhhhhhheeeccCccHHHHHHHHHHhh
Confidence            653 3332 111      12388999999999888777654

>KOG3665 consensus ZYG-1-like serine/threonine protein kinases [General function prediction only]

Probab=97.64  E-value=1.9e-05  Score=89.28  Aligned_cols=61  Identities=15%  Similarity=0.360  Sum_probs=28.3

Q ss_pred             CCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcccccccccccEEeeccccC
Q 042541          573 MDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSLATVRMNHLQKVSLVMCNV  635 (695)
Q Consensus       573 l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp~i~~l~~L~~L~l~~~~i  635 (695)
                      +|+|++|.+.+-.+.......  ...+++||..||+++++++.+.++++|++|+.|.+++=.+
T Consensus       147 LPsL~sL~i~~~~~~~~dF~~--lc~sFpNL~sLDIS~TnI~nl~GIS~LknLq~L~mrnLe~  207 (699)
T KOG3665|consen  147 LPSLRSLVISGRQFDNDDFSQ--LCASFPNLRSLDISGTNISNLSGISRLKNLQVLSMRNLEF  207 (699)
T ss_pred             CcccceEEecCceecchhHHH--HhhccCccceeecCCCCccCcHHHhccccHHHHhccCCCC
Confidence            455555555543332221111  1334555555555555555444455555555555544433

>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]

Probab=97.63  E-value=0.00056  Score=74.69  Aligned_cols=151  Identities=17%  Similarity=0.140  Sum_probs=93.7

Q ss_pred             CCCCCCcchHHHHHHHHH------cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHH
Q 042541          166 VISPGLDVPLKELKMELF------KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKV  239 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~------~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i  239 (695)
                      .+-+|.++..++|+++|.      .-..+++++||++|+|||+|++.++.  .+...|    +-++++...+..++-..=
T Consensus       323 ~dHYGLekVKeRIlEyLAV~~l~~~~kGpILcLVGPPGVGKTSLgkSIA~--al~Rkf----vR~sLGGvrDEAEIRGHR  396 (782)
T COG0466         323 KDHYGLEKVKERILEYLAVQKLTKKLKGPILCLVGPPGVGKTSLGKSIAK--ALGRKF----VRISLGGVRDEAEIRGHR  396 (782)
T ss_pred             ccccCchhHHHHHHHHHHHHHHhccCCCcEEEEECCCCCCchhHHHHHHH--HhCCCE----EEEecCccccHHHhcccc
Confidence            344999999999999987      22358999999999999999999997  555554    255666666655542111


Q ss_pred             HHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCh--------HHHhhhccCCC-------------CCE
Q 042541          240 LHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSE--------SLLQKLGFQLP-------------DYK  298 (695)
Q Consensus       240 ~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~--------~~~~~l~~~~~-------------gs~  298 (695)
                      -..+|.-      .    .++-+-+...+.++=+++||.++....        .+++-+.+-.+             =|+
T Consensus       397 RTYIGam------P----GrIiQ~mkka~~~NPv~LLDEIDKm~ss~rGDPaSALLEVLDPEQN~~F~DhYLev~yDLS~  466 (782)
T COG0466         397 RTYIGAM------P----GKIIQGMKKAGVKNPVFLLDEIDKMGSSFRGDPASALLEVLDPEQNNTFSDHYLEVPYDLSK  466 (782)
T ss_pred             ccccccC------C----hHHHHHHHHhCCcCCeEEeechhhccCCCCCChHHHHHhhcCHhhcCchhhccccCccchhh
Confidence            1111111      1    112222233467788999999865431        13343333111             144


Q ss_pred             EE-EEcCCCCC-CC------CCeEecCCCChHHHHHHHHHhc
Q 042541          299 IL-VTSRSEFP-QF------GSVHYLKPLTYEAARTLFLHSA  332 (695)
Q Consensus       299 ii-vTtR~~~~-~~------~~~~~l~~L~~~ea~~Lf~~~~  332 (695)
                      |+ |||-+... ..      -.++++.+.+++|-.++-+++.
T Consensus       467 VmFiaTANsl~tIP~PLlDRMEiI~lsgYt~~EKl~IAk~~L  508 (782)
T COG0466         467 VMFIATANSLDTIPAPLLDRMEVIRLSGYTEDEKLEIAKRHL  508 (782)
T ss_pred             eEEEeecCccccCChHHhcceeeeeecCCChHHHHHHHHHhc
Confidence            54 45544422 11      2389999999999998887765

>PF12799 LRR_4: Leucine Rich repeats (2 copies); PDB: 2OMT_A 1XEU_A 2OMX_A 2OMU_A 2UZY_A 2WQU_D 1D0B_A 2WQW_A 1OTO_A 2WQV_B

Probab=97.63  E-value=3.9e-05  Score=53.18  Aligned_cols=33  Identities=15%  Similarity=0.302  Sum_probs=17.5

Q ss_pred             cccEEeeccccCCcccccchhhhcccCCCccEEecccc
Q 042541          624 HLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYC  661 (695)
Q Consensus       624 ~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c  661 (695)
                      +|++|++++|.|+.+|+.+.     .|++|++|++++|
T Consensus         2 ~L~~L~l~~N~i~~l~~~l~-----~l~~L~~L~l~~N   34 (44)
T PF12799_consen    2 NLEELDLSNNQITDLPPELS-----NLPNLETLNLSNN   34 (44)
T ss_dssp             T-SEEEETSSS-SSHGGHGT-----TCTTSSEEEETSS
T ss_pred             cceEEEccCCCCcccCchHh-----CCCCCCEEEecCC
Confidence            45666666666665554333     5556666666554

...

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=97.62  E-value=0.0013  Score=66.84  Aligned_cols=147  Identities=14%  Similarity=0.106  Sum_probs=78.5

Q ss_pred             CCCCCcchHHHHHHHHH---------c-----C-CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCC
Q 042541          167 ISPGLDVPLKELKMELF---------K-----D-GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPN  231 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~---------~-----~-~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~  231 (695)
                      .++|.+..+++|.++..         .     . ...-+.++|++|+|||++|+.++....-......+ -++.++.   
T Consensus        23 ~l~Gl~~vk~~i~e~~~~~~~~~~r~~~g~~~~~~~~~vll~G~pGTGKT~lA~~ia~~l~~~g~~~~~-~~v~v~~---   98 (284)
T TIGR02880        23 ELIGLKPVKTRIREIAALLLVERLRQRLGLASAAPTLHMSFTGNPGTGKTTVALRMAQILHRLGYVRKG-HLVSVTR---   98 (284)
T ss_pred             hccCHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCCCceEEEEcCCCCCHHHHHHHHHHHHHHcCCcccc-eEEEecH---
Confidence            45887776666654322         0     0 12258899999999999998776521111111111 1444442   


Q ss_pred             HHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCC---------Ch----HHHhhhccCCCCCE
Q 042541          232 VKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPG---------SE----SLLQKLGFQLPDYK  298 (695)
Q Consensus       232 ~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~---------~~----~~~~~l~~~~~gs~  298 (695)
                       .++    +..+.+.     ..    ......++...  .-+|++|++...         ..    .++..+.....+.+
T Consensus        99 -~~l----~~~~~g~-----~~----~~~~~~~~~a~--~gvL~iDEi~~L~~~~~~~~~~~~~~~~Ll~~le~~~~~~~  162 (284)
T TIGR02880        99 -DDL----VGQYIGH-----TA----PKTKEILKRAM--GGVLFIDEAYYLYRPDNERDYGQEAIEILLQVMENQRDDLV  162 (284)
T ss_pred             -HHH----hHhhccc-----ch----HHHHHHHHHcc--CcEEEEechhhhccCCCccchHHHHHHHHHHHHhcCCCCEE
Confidence             122    2222111     11    12334443332  368999998632         01    12233333334566


Q ss_pred             EEEEcCCCC------------CCCCCeEecCCCChHHHHHHHHHhcc
Q 042541          299 ILVTSRSEF------------PQFGSVHYLKPLTYEAARTLFLHSAN  333 (695)
Q Consensus       299 iivTtR~~~------------~~~~~~~~l~~L~~~ea~~Lf~~~~~  333 (695)
                      ||+++....            ......+.+++++.+|-.+++...+.
T Consensus       163 vI~a~~~~~~~~~~~~np~L~sR~~~~i~fp~l~~edl~~I~~~~l~  209 (284)
T TIGR02880       163 VILAGYKDRMDSFFESNPGFSSRVAHHVDFPDYSEAELLVIAGLMLK  209 (284)
T ss_pred             EEEeCCcHHHHHHHhhCHHHHhhCCcEEEeCCcCHHHHHHHHHHHHH
Confidence            777664321            11234789999999999999887653

Proteins in this family are now designated CbbX. Some previously were CfxQ (carbon fixation Q). Its gene is often found immmediately downstream of the Rubisco large and small chain genes, and it is suggested to be necessary for Rubisco expression. CbbX has been shown to be necessary for photoautotrophic growth. This protein belongs to the larger family of pfam00004, ATPase family Associated with various cellular Activities. Within that larger family, members of this family are most closely related to the stage V sporulation protein K, or SpoVK, in endospore-forming bacteria such as Bacillus subtilis.

>TIGR03689 pup_AAA proteasome ATPase

Probab=97.62  E-value=0.00072  Score=73.38  Aligned_cols=151  Identities=14%  Similarity=0.179  Sum_probs=84.7

Q ss_pred             CCCCCCcchHHHHHHHHHc-------------CCceEEEEEcCCCCcHHHHHHHHhccccccccC----CCcEEEEEeCC
Q 042541          166 VISPGLDVPLKELKMELFK-------------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKF----KDDIFYVTVSK  228 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~-------------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f----~~~~~wv~~~~  228 (695)
                      ..+.|.+..++++.+.+..             ..++-+.++|++|+|||++|+.+++.  +...+    .....++++..
T Consensus       182 ~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAlA~e--L~~~i~~~~~~~~~fl~v~~  259 (512)
T TIGR03689       182 ADIGGLDSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAVANS--LAQRIGAETGDKSYFLNIKG  259 (512)
T ss_pred             HHcCChHHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHHHHh--hccccccccCCceeEEeccc
Confidence            4567899999998887641             12456899999999999999999983  33221    11234555543


Q ss_pred             CCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHH--hcCCCcEEEEEeCCCCCC---------h---HHHhhhcc--
Q 042541          229 NPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFK--QMRIEAILLVLDDVWPGS---------E---SLLQKLGF--  292 (695)
Q Consensus       229 ~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~--~l~~~~~LlVlDdv~~~~---------~---~~~~~l~~--  292 (695)
                      .    ++    +....+      ..+.....+.....  ...+++++++||+++...         +   ..+..+..  
T Consensus       260 ~----eL----l~kyvG------ete~~ir~iF~~Ar~~a~~g~p~IIfIDEiD~L~~~R~~~~s~d~e~~il~~LL~~L  325 (512)
T TIGR03689       260 P----EL----LNKYVG------ETERQIRLIFQRAREKASDGRPVIVFFDEMDSIFRTRGSGVSSDVETTVVPQLLSEL  325 (512)
T ss_pred             h----hh----cccccc------hHHHHHHHHHHHHHHHhhcCCCceEEEehhhhhhcccCCCccchHHHHHHHHHHHHh
Confidence            2    11    111100      11111112211111  113578999999996421         0   01122211  


Q ss_pred             -C---CCCCEEEEEcCCCC------C---CCCCeEecCCCChHHHHHHHHHhc
Q 042541          293 -Q---LPDYKILVTSRSEF------P---QFGSVHYLKPLTYEAARTLFLHSA  332 (695)
Q Consensus       293 -~---~~gs~iivTtR~~~------~---~~~~~~~l~~L~~~ea~~Lf~~~~  332 (695)
                       +   ..+..||.||....      .   .....++++..+.++..++|..+.
T Consensus       326 Dgl~~~~~ViVI~ATN~~d~LDpALlRpGRfD~~I~~~~Pd~e~r~~Il~~~l  378 (512)
T TIGR03689       326 DGVESLDNVIVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAAADIFSKYL  378 (512)
T ss_pred             cccccCCceEEEeccCChhhCCHhhcCccccceEEEeCCCCHHHHHHHHHHHh
Confidence             1   12334555554431      1   223368999999999999998876

In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=97.60  E-value=0.00033  Score=82.31  Aligned_cols=148  Identities=14%  Similarity=0.125  Sum_probs=86.3

Q ss_pred             CCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhcccccccc------CCCcEEEEEeCCCCCHHHHHHHH
Q 042541          166 VISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGK------FKDDIFYVTVSKNPNVKAIVQKV  239 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~------f~~~~~wv~~~~~~~~~~~~~~i  239 (695)
                      +.++||+.++.++++.|......-+.++|++|+|||++|..+++  ++...      ....++.++++.          +
T Consensus       173 ~~~igr~~ei~~~~~~l~r~~~~n~lL~G~pGvGKT~l~~~la~--~i~~~~~p~~l~~~~~~~l~~~~----------l  240 (852)
T TIGR03346       173 DPVIGRDEEIRRTIQVLSRRTKNNPVLIGEPGVGKTAIVEGLAQ--RIVNGDVPESLKNKRLLALDMGA----------L  240 (852)
T ss_pred             CcCCCcHHHHHHHHHHHhcCCCCceEEEcCCCCCHHHHHHHHHH--HHhccCCchhhcCCeEEEeeHHH----------H
Confidence            45799999999999999866656677999999999999999887  33221      122233333211          1


Q ss_pred             HHhcCCCCCCCCChHHHHHHHHHHHHhc--CCCcEEEEEeCCCCCCh--------HHHhhhccCC-CC-CEEEE-EcCCC
Q 042541          240 LHHKGYPVPEFQTDEAAINDLERFFKQM--RIEAILLVLDDVWPGSE--------SLLQKLGFQL-PD-YKILV-TSRSE  306 (695)
Q Consensus       240 ~~~l~~~~~~~~~~~~~~~~l~~~~~~l--~~~~~LlVlDdv~~~~~--------~~~~~l~~~~-~g-s~iiv-TtR~~  306 (695)
                      +...  .     ...+....+..+++.+  .+++.+|++|++.....        .....+.+.. .| -++|- ||...
T Consensus       241 ~a~~--~-----~~g~~e~~l~~~l~~~~~~~~~~ILfIDEih~l~~~g~~~~~~d~~~~Lk~~l~~g~i~~IgaTt~~e  313 (852)
T TIGR03346       241 IAGA--K-----YRGEFEERLKAVLNEVTKSEGQIILFIDELHTLVGAGKAEGAMDAGNMLKPALARGELHCIGATTLDE  313 (852)
T ss_pred             hhcc--h-----hhhhHHHHHHHHHHHHHhcCCCeEEEeccHHHhhcCCCCcchhHHHHHhchhhhcCceEEEEeCcHHH
Confidence            1000  0     1112234455555443  25689999999863320        1112222222 23 34444 44433


Q ss_pred             C---C-------CCCCeEecCCCChHHHHHHHHHhc
Q 042541          307 F---P-------QFGSVHYLKPLTYEAARTLFLHSA  332 (695)
Q Consensus       307 ~---~-------~~~~~~~l~~L~~~ea~~Lf~~~~  332 (695)
                      .   .       .--..+.++..+.++...++....
T Consensus       314 ~r~~~~~d~al~rRf~~i~v~~p~~~~~~~iL~~~~  349 (852)
T TIGR03346       314 YRKYIEKDAALERRFQPVFVDEPTVEDTISILRGLK  349 (852)
T ss_pred             HHHHhhcCHHHHhcCCEEEeCCCCHHHHHHHHHHHH
Confidence            1   1       001267888889999999887653

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>COG4886 Leucine-rich repeat (LRR) protein [Function unknown]

Probab=97.59  E-value=4.3e-05  Score=82.27  Aligned_cols=126  Identities=18%  Similarity=0.247  Sum_probs=61.7

Q ss_pred             ceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc-cccccccccEEe
Q 042541          551 EVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL-ATVRMNHLQKVS  629 (695)
Q Consensus       551 ~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp-~i~~l~~L~~L~  629 (695)
                      +|+.|.+..+.. ..+|..+..+++|+.|++.+|....  ++  +..+.+++|+.|++++|.+..+| .++.+.+|++|.
T Consensus       141 nL~~L~l~~N~i-~~l~~~~~~l~~L~~L~l~~N~l~~--l~--~~~~~~~~L~~L~ls~N~i~~l~~~~~~~~~L~~l~  215 (394)
T COG4886         141 NLKELDLSDNKI-ESLPSPLRNLPNLKNLDLSFNDLSD--LP--KLLSNLSNLNNLDLSGNKISDLPPEIELLSALEELD  215 (394)
T ss_pred             hcccccccccch-hhhhhhhhccccccccccCCchhhh--hh--hhhhhhhhhhheeccCCccccCchhhhhhhhhhhhh
Confidence            455555444322 2233344555555555555554321  00  00124445555555555555555 434444455555


Q ss_pred             eccc-----------------------cCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeeccccc
Q 042541          630 LVMC-----------------------NVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCH  686 (695)
Q Consensus       630 l~~~-----------------------~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~  686 (695)
                      +++|                       .+..++....     .+++|+.|++++| .+..++. ++.+.+|++|+++++.
T Consensus       216 ~~~N~~~~~~~~~~~~~~l~~l~l~~n~~~~~~~~~~-----~l~~l~~L~~s~n-~i~~i~~-~~~~~~l~~L~~s~n~  288 (394)
T COG4886         216 LSNNSIIELLSSLSNLKNLSGLELSNNKLEDLPESIG-----NLSNLETLDLSNN-QISSISS-LGSLTNLRELDLSGNS  288 (394)
T ss_pred             hcCCcceecchhhhhcccccccccCCceeeeccchhc-----cccccceeccccc-ccccccc-ccccCccCEEeccCcc
Confidence            5444                       3222211111     5666777777763 4556665 7777777777777755


Q ss_pred             CC
Q 042541          687 RL  688 (695)
Q Consensus       687 ~l  688 (695)
                      ..
T Consensus       289 ~~  290 (394)
T COG4886         289 LS  290 (394)
T ss_pred             cc
Confidence            33

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=97.59  E-value=0.00083  Score=71.27  Aligned_cols=164  Identities=16%  Similarity=0.185  Sum_probs=93.0

Q ss_pred             CCCCCCcchHHHHHHHHH----c---------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCH
Q 042541          166 VISPGLDVPLKELKMELF----K---------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNV  232 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~----~---------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~  232 (695)
                      ..+.|.+..+++|.+.+.    .         ..++-|.++|++|+|||+||+.+++.  ....      ++.+..    
T Consensus       145 ~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~LAkalA~~--l~~~------fi~i~~----  212 (398)
T PTZ00454        145 SDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHH--TTAT------FIRVVG----  212 (398)
T ss_pred             HHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHh--cCCC------EEEEeh----
Confidence            356888888888887664    1         12577999999999999999999983  3222      222211    


Q ss_pred             HHHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCC-----------hH-------HHhhhcc-
Q 042541          233 KAIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGS-----------ES-------LLQKLGF-  292 (695)
Q Consensus       233 ~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~-----------~~-------~~~~l~~-  292 (695)
                      ..+...   .++          +....+..++ ......+.+|++|+++...           ..       ++..+.. 
T Consensus       213 s~l~~k---~~g----------e~~~~lr~lf~~A~~~~P~ILfIDEID~i~~~r~~~~~~~d~~~~r~l~~LL~~ld~~  279 (398)
T PTZ00454        213 SEFVQK---YLG----------EGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGADREVQRILLELLNQMDGF  279 (398)
T ss_pred             HHHHHH---hcc----------hhHHHHHHHHHHHHhcCCeEEEEECHhhhccccccccCCccHHHHHHHHHHHHHhhcc
Confidence            111111   111          0112233444 2234678999999975321           00       1111111 


Q ss_pred             -CCCCCEEEEEcCCCC------C---CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCch
Q 042541          293 -QLPDYKILVTSRSEF------P---QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCP  358 (695)
Q Consensus       293 -~~~gs~iivTtR~~~------~---~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~P  358 (695)
                       ...+..||+||....      .   .....+.++..+.++..++|...........    .-...++++.+.|+-
T Consensus       280 ~~~~~v~VI~aTN~~d~LDpAllR~GRfd~~I~~~~P~~~~R~~Il~~~~~~~~l~~----dvd~~~la~~t~g~s  351 (398)
T PTZ00454        280 DQTTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITSKMNLSE----EVDLEDFVSRPEKIS  351 (398)
T ss_pred             CCCCCEEEEEecCCchhCCHHHcCCCcccEEEEeCCcCHHHHHHHHHHHHhcCCCCc----ccCHHHHHHHcCCCC
Confidence             123567888887541      1   2233688888899988888886654322211    112456677777653

>PRK08116 hypothetical protein; Validated

Probab=97.59  E-value=0.0003  Score=70.68  Aligned_cols=99  Identities=17%  Similarity=0.203  Sum_probs=57.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQM  267 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l  267 (695)
                      .-+.|+|..|+|||.||.++++  .+... ...++++++      .+++..+.........     . .   ...+++.+
T Consensus       115 ~gl~l~G~~GtGKThLa~aia~--~l~~~-~~~v~~~~~------~~ll~~i~~~~~~~~~-----~-~---~~~~~~~l  176 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAACIAN--ELIEK-GVPVIFVNF------PQLLNRIKSTYKSSGK-----E-D---ENEIIRSL  176 (268)
T ss_pred             ceEEEECCCCCCHHHHHHHHHH--HHHHc-CCeEEEEEH------HHHHHHHHHHHhcccc-----c-c---HHHHHHHh
Confidence            4588999999999999999998  44333 233667653      4456666555432110     0 0   11222334


Q ss_pred             CCCcEEEEEeCCCC--CChHHHhh----hcc-CCCCCEEEEEcCC
Q 042541          268 RIEAILLVLDDVWP--GSESLLQK----LGF-QLPDYKILVTSRS  305 (695)
Q Consensus       268 ~~~~~LlVlDdv~~--~~~~~~~~----l~~-~~~gs~iivTtR~  305 (695)
                      .+-. ||||||+..  ..+|....    +.. ...|..+||||..
T Consensus       177 ~~~d-lLviDDlg~e~~t~~~~~~l~~iin~r~~~~~~~IiTsN~  220 (268)
T PRK08116        177 VNAD-LLILDDLGAERDTEWAREKVYNIIDSRYRKGLPTIVTTNL  220 (268)
T ss_pred             cCCC-EEEEecccCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCC
Confidence            4334 899999943  33442211    111 1246679999963

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=97.58  E-value=0.0012  Score=72.59  Aligned_cols=151  Identities=13%  Similarity=0.200  Sum_probs=92.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhccccccccC-CCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHh
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKDDQVQGKF-KDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQ  266 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f-~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~  266 (695)
                      ..+.|+|..|+|||.|++.+++  .....+ ...++|++.      .++...+...+...         ....+.   +.
T Consensus       315 NpL~LyG~sGsGKTHLL~AIa~--~a~~~~~g~~V~Yita------eef~~el~~al~~~---------~~~~f~---~~  374 (617)
T PRK14086        315 NPLFIYGESGLGKTHLLHAIGH--YARRLYPGTRVRYVSS------EEFTNEFINSIRDG---------KGDSFR---RR  374 (617)
T ss_pred             CcEEEECCCCCCHHHHHHHHHH--HHHHhCCCCeEEEeeH------HHHHHHHHHHHHhc---------cHHHHH---HH
Confidence            4589999999999999999998  443322 233566654      33444554443211         011222   22


Q ss_pred             cCCCcEEEEEeCCCCCCh------HHHhhhcc-CCCCCEEEEEcCCCC-------------CCCCCeEecCCCChHHHHH
Q 042541          267 MRIEAILLVLDDVWPGSE------SLLQKLGF-QLPDYKILVTSRSEF-------------PQFGSVHYLKPLTYEAART  326 (695)
Q Consensus       267 l~~~~~LlVlDdv~~~~~------~~~~~l~~-~~~gs~iivTtR~~~-------------~~~~~~~~l~~L~~~ea~~  326 (695)
                      ++ +-=+|||||+.....      .+...+.. ...|..|||||....             ...+..+.+.+.+.+.-.+
T Consensus       375 y~-~~DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~IIITSd~~P~eL~~l~~rL~SRf~~GLvv~I~~PD~EtR~a  453 (617)
T PRK14086        375 YR-EMDILLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIVLSSDRPPKQLVTLEDRLRNRFEWGLITDVQPPELETRIA  453 (617)
T ss_pred             hh-cCCEEEEehhccccCCHHHHHHHHHHHHHHHhcCCCEEEecCCChHhhhhccHHHHhhhhcCceEEcCCCCHHHHHH
Confidence            22 235889999965421      12222221 123567889888651             1234488999999999999


Q ss_pred             HHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHH
Q 042541          327 LFLHSANLQDGNSYIPDENIVSKILRACKGCPLALK  362 (695)
Q Consensus       327 Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~  362 (695)
                      ++.+++.....   .-.++++.-|++.+.+..-.+.
T Consensus       454 IL~kka~~r~l---~l~~eVi~yLa~r~~rnvR~Le  486 (617)
T PRK14086        454 ILRKKAVQEQL---NAPPEVLEFIASRISRNIRELE  486 (617)
T ss_pred             HHHHHHHhcCC---CCCHHHHHHHHHhccCCHHHHH
Confidence            99988754322   2236788888888887654444

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=97.58  E-value=0.00029  Score=63.21  Aligned_cols=89  Identities=20%  Similarity=0.180  Sum_probs=48.2

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQM  267 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l  267 (695)
                      ..+.|+|++|+||||+++.++.  ....... .+++++.+........... ....... ........   .....++..
T Consensus         3 ~~~~l~G~~G~GKTtl~~~l~~--~~~~~~~-~~~~~~~~~~~~~~~~~~~-~~~~~~~-~~~~~~~~---~~~~~~~~~   74 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALAR--ELGPPGG-GVIYIDGEDILEEVLDQLL-LIIVGGK-KASGSGEL---RLRLALALA   74 (148)
T ss_pred             CEEEEECCCCCcHHHHHHHHHh--ccCCCCC-CEEEECCEEccccCHHHHH-hhhhhcc-CCCCCHHH---HHHHHHHHH
Confidence            5789999999999999999987  3433322 2667766654332222211 0111111 11111222   222222222


Q ss_pred             CCC-cEEEEEeCCCCCCh
Q 042541          268 RIE-AILLVLDDVWPGSE  284 (695)
Q Consensus       268 ~~~-~~LlVlDdv~~~~~  284 (695)
                      +.. ..++++|++.....
T Consensus        75 ~~~~~~viiiDei~~~~~   92 (148)
T smart00382       75 RKLKPDVLILDEITSLLD   92 (148)
T ss_pred             HhcCCCEEEEECCcccCC
Confidence            332 59999999987654

AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=97.57  E-value=0.00019  Score=63.87  Aligned_cols=68  Identities=22%  Similarity=0.303  Sum_probs=40.8

Q ss_pred             EEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhc-C
Q 042541          190 IVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQM-R  268 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l-~  268 (695)
                      |.|+|++|+|||++|+.+++.  ..    ..++.++.+...+.                   ...+....+...++.. .
T Consensus         1 ill~G~~G~GKT~l~~~la~~--l~----~~~~~i~~~~~~~~-------------------~~~~~~~~i~~~~~~~~~   55 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQY--LG----FPFIEIDGSELISS-------------------YAGDSEQKIRDFFKKAKK   55 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHH--TT----SEEEEEETTHHHTS-------------------STTHHHHHHHHHHHHHHH
T ss_pred             CEEECcCCCCeeHHHHHHHhh--cc----cccccccccccccc-------------------cccccccccccccccccc
Confidence            579999999999999999984  32    22445544431100                   1122333444444222 2


Q ss_pred             C-CcEEEEEeCCCCC
Q 042541          269 I-EAILLVLDDVWPG  282 (695)
Q Consensus       269 ~-~~~LlVlDdv~~~  282 (695)
                      . ++.+|++||++..
T Consensus        56 ~~~~~vl~iDe~d~l   70 (132)
T PF00004_consen   56 SAKPCVLFIDEIDKL   70 (132)
T ss_dssp             TSTSEEEEEETGGGT
T ss_pred             cccceeeeeccchhc
Confidence            2 4899999998544

Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=97.57  E-value=0.0017  Score=67.45  Aligned_cols=153  Identities=12%  Similarity=0.084  Sum_probs=83.2

Q ss_pred             CCC-CcchHHHHHHHHHcCC-ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcC-
Q 042541          168 SPG-LDVPLKELKMELFKDG-RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKG-  244 (695)
Q Consensus       168 ~vG-r~~~~~~l~~~L~~~~-~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~-  244 (695)
                      ++| -+..++.+...+..+. .....++|+.|+||||+|..+.+.---...... .   .+..+.    ..+.+...-. 
T Consensus         7 i~~~q~~~~~~L~~~~~~~~l~ha~Lf~G~~G~gk~~~a~~la~~l~c~~~~~~-~---~cg~C~----~c~~~~~~~hp   78 (329)
T PRK08058          7 LTALQPVVVKMLQNSIAKNRLSHAYLFEGAKGTGKKATALWLAKSLFCLERNGV-E---PCGTCT----NCKRIDSGNHP   78 (329)
T ss_pred             HHhhHHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHHCCCCCCCC-C---CCCcCH----HHHHHhcCCCC
Confidence            455 5556777777777665 456799999999999999888662100010000 0   000000    0000000000 


Q ss_pred             ---CCCCCCCChHHHHHHHHHHHHh-----cCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCC----
Q 042541          245 ---YPVPEFQTDEAAINDLERFFKQ-----MRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFP----  308 (695)
Q Consensus       245 ---~~~~~~~~~~~~~~~l~~~~~~-----l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~----  308 (695)
                         .-.+.  ......+.++.+.+.     ..+++-++|+|++......    +++.+....+++.+|++|.+...    
T Consensus        79 D~~~i~~~--~~~i~id~ir~l~~~~~~~~~~~~~kvviI~~a~~~~~~a~NaLLK~LEEPp~~~~~Il~t~~~~~ll~T  156 (329)
T PRK08058         79 DVHLVAPD--GQSIKKDQIRYLKEEFSKSGVESNKKVYIIEHADKMTASAANSLLKFLEEPSGGTTAILLTENKHQILPT  156 (329)
T ss_pred             CEEEeccc--cccCCHHHHHHHHHHHhhCCcccCceEEEeehHhhhCHHHHHHHHHHhcCCCCCceEEEEeCChHhCcHH
Confidence               00000  000112223332221     2456678999999776643    55666656667888887766521    


Q ss_pred             --CCCCeEecCCCChHHHHHHHHH
Q 042541          309 --QFGSVHYLKPLTYEAARTLFLH  330 (695)
Q Consensus       309 --~~~~~~~l~~L~~~ea~~Lf~~  330 (695)
                        .-...+++.+++.++..+.+..
T Consensus       157 IrSRc~~i~~~~~~~~~~~~~L~~  180 (329)
T PRK08058        157 ILSRCQVVEFRPLPPESLIQRLQE  180 (329)
T ss_pred             HHhhceeeeCCCCCHHHHHHHHHH
Confidence              1223899999999999888865

>PRK10536 hypothetical protein; Provisional

Probab=97.56  E-value=0.00027  Score=69.00  Aligned_cols=129  Identities=12%  Similarity=0.106  Sum_probs=73.9

Q ss_pred             CCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC----------CHHH--
Q 042541          167 ISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP----------NVKA--  234 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~----------~~~~--  234 (695)
                      .+.+|......+..++.+.  .+|.+.|+.|+|||+||.++..+.-..+.|.. + .+.-+.-.          +..+  
T Consensus        56 ~i~p~n~~Q~~~l~al~~~--~lV~i~G~aGTGKT~La~a~a~~~l~~~~~~k-I-iI~RP~v~~ge~LGfLPG~~~eK~  131 (262)
T PRK10536         56 PILARNEAQAHYLKAIESK--QLIFATGEAGCGKTWISAAKAAEALIHKDVDR-I-IVTRPVLQADEDLGFLPGDIAEKF  131 (262)
T ss_pred             cccCCCHHHHHHHHHHhcC--CeEEEECCCCCCHHHHHHHHHHHHHhcCCeeE-E-EEeCCCCCchhhhCcCCCCHHHHH
Confidence            4567888888888888763  59999999999999999988764222344543 3 43321110          1211  


Q ss_pred             --HHHHHHHhcCCCCCCCCChHHHHHHHH-------HH--HHhcCCCcE---EEEEeCCCCCChHHHhhhc-cCCCCCEE
Q 042541          235 --IVQKVLHHKGYPVPEFQTDEAAINDLE-------RF--FKQMRIEAI---LLVLDDVWPGSESLLQKLG-FQLPDYKI  299 (695)
Q Consensus       235 --~~~~i~~~l~~~~~~~~~~~~~~~~l~-------~~--~~~l~~~~~---LlVlDdv~~~~~~~~~~l~-~~~~gs~i  299 (695)
                        .+.-+...+..-.    .. ...+.+.       ++  +.+++|+.+   ++|+|++.+........+. ..+.+|++
T Consensus       132 ~p~~~pi~D~L~~~~----~~-~~~~~~~~~~~~~Iei~~l~ymRGrtl~~~~vIvDEaqn~~~~~~k~~ltR~g~~sk~  206 (262)
T PRK10536        132 APYFRPVYDVLVRRL----GA-SFMQYCLRPEIGKVEIAPFAYMRGRTFENAVVILDEAQNVTAAQMKMFLTRLGENVTV  206 (262)
T ss_pred             HHHHHHHHHHHHHHh----Ch-HHHHHHHHhccCcEEEecHHHhcCCcccCCEEEEechhcCCHHHHHHHHhhcCCCCEE
Confidence              1222222221100    00 0111110       01  135577765   9999999888765444443 34578999


Q ss_pred             EEEcC
Q 042541          300 LVTSR  304 (695)
Q Consensus       300 ivTtR  304 (695)
                      |+|--
T Consensus       207 v~~GD  211 (262)
T PRK10536        207 IVNGD  211 (262)
T ss_pred             EEeCC
Confidence            98754

>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional

Probab=97.53  E-value=0.00018  Score=76.89  Aligned_cols=163  Identities=14%  Similarity=0.154  Sum_probs=91.7

Q ss_pred             CCCCCCcchHHHHHHHHH----c---------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCH
Q 042541          166 VISPGLDVPLKELKMELF----K---------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNV  232 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~----~---------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~  232 (695)
                      ..+.|.+..+++|.+.+.    .         ...+-|.++|++|+|||++|+.+++  .....|      +.+...   
T Consensus       183 ~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~LAraIA~--el~~~f------i~V~~s---  251 (438)
T PTZ00361        183 ADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVAN--ETSATF------LRVVGS---  251 (438)
T ss_pred             HHhcCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHH--hhCCCE------EEEecc---
Confidence            356789999988888764    1         1245688999999999999999998  343332      222211   


Q ss_pred             HHHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCC-----------hH-------HHhhhcc-
Q 042541          233 KAIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGS-----------ES-------LLQKLGF-  292 (695)
Q Consensus       233 ~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~-----------~~-------~~~~l~~-  292 (695)
                       ++..    ...+         .....+..++ ....+.+.+++||+++...           ..       ++..+.. 
T Consensus       252 -eL~~----k~~G---------e~~~~vr~lF~~A~~~~P~ILfIDEID~l~~kR~~~~sgg~~e~qr~ll~LL~~Ldg~  317 (438)
T PTZ00361        252 -ELIQ----KYLG---------DGPKLVRELFRVAEENAPSIVFIDEIDAIGTKRYDATSGGEKEIQRTMLELLNQLDGF  317 (438)
T ss_pred             -hhhh----hhcc---------hHHHHHHHHHHHHHhCCCcEEeHHHHHHHhccCCCCCCcccHHHHHHHHHHHHHHhhh
Confidence             1111    1100         0112233333 2224678899999974211           00       1111111 


Q ss_pred             -CCCCCEEEEEcCCCC------C---CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCc
Q 042541          293 -QLPDYKILVTSRSEF------P---QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGC  357 (695)
Q Consensus       293 -~~~gs~iivTtR~~~------~---~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~  357 (695)
                       ...+.+||+||....      .   .....+.++..+.++..++|..+..........    ....++..+.|+
T Consensus       318 ~~~~~V~VI~ATNr~d~LDpaLlRpGRfd~~I~~~~Pd~~~R~~Il~~~~~k~~l~~dv----dl~~la~~t~g~  388 (438)
T PTZ00361        318 DSRGDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLAEDV----DLEEFIMAKDEL  388 (438)
T ss_pred             cccCCeEEEEecCChHHhhHHhccCCeeEEEEEeCCCCHHHHHHHHHHHHhcCCCCcCc----CHHHHHHhcCCC
Confidence             123567888776541      1   122378899999999999998765433221111    245566666554

>PRK12608 transcription termination factor Rho; Provisional

Probab=97.52  E-value=0.00047  Score=71.14  Aligned_cols=104  Identities=16%  Similarity=0.167  Sum_probs=66.8

Q ss_pred             HHHHHHHHHc-CCceEEEEEcCCCCcHHHHHHHHhccccccccC-CCcEEEEEeCCCC-CHHHHHHHHHHhcCCCCCCCC
Q 042541          175 LKELKMELFK-DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKF-KDDIFYVTVSKNP-NVKAIVQKVLHHKGYPVPEFQ  251 (695)
Q Consensus       175 ~~~l~~~L~~-~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f-~~~~~wv~~~~~~-~~~~~~~~i~~~l~~~~~~~~  251 (695)
                      ..++++.+.. +..+-+.|+|..|+|||||++.+++  .+.... +..++|+.+.+.. .+.++.+.+...+..+..+..
T Consensus       120 ~~RvID~l~PiGkGQR~LIvG~pGtGKTTLl~~la~--~i~~~~~dv~~vv~lIgER~~EV~df~~~i~~~Vvast~de~  197 (380)
T PRK12608        120 SMRVVDLVAPIGKGQRGLIVAPPRAGKTVLLQQIAA--AVAANHPEVHLMVLLIDERPEEVTDMRRSVKGEVYASTFDRP  197 (380)
T ss_pred             hHhhhhheeecCCCceEEEECCCCCCHHHHHHHHHH--HHHhcCCCceEEEEEecCCCCCHHHHHHHHhhhEEeecCCCC
Confidence            3456777662 3446779999999999999999887  343322 3435687887654 788899998887765443222


Q ss_pred             ChH--HHHHHHHHHHHhc--CCCcEEEEEeCCC
Q 042541          252 TDE--AAINDLERFFKQM--RIEAILLVLDDVW  280 (695)
Q Consensus       252 ~~~--~~~~~l~~~~~~l--~~~~~LlVlDdv~  280 (695)
                      ...  .....+.+..+++  .+++++||+|++.
T Consensus       198 ~~~~~~v~~~~~~~Ae~f~~~GkdVVLvlDslt  230 (380)
T PRK12608        198 PDEHIRVAELVLERAKRLVEQGKDVVILLDSLT  230 (380)
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCCEEEEEeCcH
Confidence            211  1111222222222  5999999999984

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=97.51  E-value=0.0056  Score=62.87  Aligned_cols=169  Identities=13%  Similarity=0.147  Sum_probs=95.5

Q ss_pred             HHHHHHHHHcCC-ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCC-----CC
Q 042541          175 LKELKMELFKDG-RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYP-----VP  248 (695)
Q Consensus       175 ~~~l~~~L~~~~-~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~-----~~  248 (695)
                      -+.+...+..+. ..-..++|+.|+||+++|..++..---...... .   .++.+.    ..+.+... ..+     .+
T Consensus        11 ~~~l~~~~~~~rl~HA~Lf~G~~G~GK~~lA~~~A~~llC~~~~~~-~---~Cg~C~----sC~~~~~g-~HPD~~~i~p   81 (325)
T PRK06871         11 YQQITQAFQQGLGHHALLFKADSGLGTEQLIRALAQWLMCQTPQGD-Q---PCGQCH----SCHLFQAG-NHPDFHILEP   81 (325)
T ss_pred             HHHHHHHHHcCCcceeEEeECCCCCCHHHHHHHHHHHHcCCCCCCC-C---CCCCCH----HHHHHhcC-CCCCEEEEcc
Confidence            456666666655 456779999999999999988762100010000 0   001110    00011000 000     00


Q ss_pred             CCCChHHHHHHHHHHHHh-----cCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCCCC------CCe
Q 042541          249 EFQTDEAAINDLERFFKQ-----MRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFPQF------GSV  313 (695)
Q Consensus       249 ~~~~~~~~~~~l~~~~~~-----l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~~~------~~~  313 (695)
                      . ....-.+++++++.+.     ..+++-++|+|+++.....    +++.+-...+++.+|++|.+...-.      ...
T Consensus        82 ~-~~~~I~id~iR~l~~~~~~~~~~g~~KV~iI~~a~~m~~~AaNaLLKtLEEPp~~~~fiL~t~~~~~llpTI~SRC~~  160 (325)
T PRK06871         82 I-DNKDIGVDQVREINEKVSQHAQQGGNKVVYIQGAERLTEAAANALLKTLEEPRPNTYFLLQADLSAALLPTIYSRCQT  160 (325)
T ss_pred             c-cCCCCCHHHHHHHHHHHhhccccCCceEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhCchHHHhhceE
Confidence            0 0001123333333322     2477778999999877643    6666766777888888877652211      238


Q ss_pred             EecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHH
Q 042541          314 HYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLAL  361 (695)
Q Consensus       314 ~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai  361 (695)
                      +.+.+++.++..+.+......        ....+...+..++|.|+.+
T Consensus       161 ~~~~~~~~~~~~~~L~~~~~~--------~~~~~~~~~~l~~g~p~~A  200 (325)
T PRK06871        161 WLIHPPEEQQALDWLQAQSSA--------EISEILTALRINYGRPLLA  200 (325)
T ss_pred             EeCCCCCHHHHHHHHHHHhcc--------ChHHHHHHHHHcCCCHHHH
Confidence            999999999999888765311        1223667788999999643

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=97.51  E-value=0.001  Score=73.55  Aligned_cols=170  Identities=13%  Similarity=0.160  Sum_probs=92.8

Q ss_pred             CCCCCCcchHHHHHHHHH---c---------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHH
Q 042541          166 VISPGLDVPLKELKMELF---K---------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVK  233 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~---~---------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~  233 (695)
                      +.++|.+...+++.+.+.   .         ...+-+.++|++|+|||+||+.+++.  ....      ++.++..    
T Consensus        55 ~di~g~~~~k~~l~~~~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~la~alA~~--~~~~------~~~i~~~----  122 (495)
T TIGR01241        55 KDVAGIDEAKEELMEIVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGE--AGVP------FFSISGS----  122 (495)
T ss_pred             HHhCCHHHHHHHHHHHHHHHHCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHH--cCCC------eeeccHH----
Confidence            456888877666655443   1         12345889999999999999999873  2111      3333211    


Q ss_pred             HHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCC-----------h---HHHhhhcc------
Q 042541          234 AIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGS-----------E---SLLQKLGF------  292 (695)
Q Consensus       234 ~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~-----------~---~~~~~l~~------  292 (695)
                      ++....   .+.          ....+..++ ......+++|++||++...           .   ..+..+..      
T Consensus       123 ~~~~~~---~g~----------~~~~l~~~f~~a~~~~p~Il~iDEid~l~~~r~~~~~~~~~~~~~~~~~lL~~~d~~~  189 (495)
T TIGR01241       123 DFVEMF---VGV----------GASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFG  189 (495)
T ss_pred             HHHHHH---hcc----------cHHHHHHHHHHHHhcCCCEEEEechhhhhhccccCcCCccHHHHHHHHHHHhhhcccc
Confidence            111111   010          112344444 3334667999999985421           0   11111111      


Q ss_pred             CCCCCEEEEEcCCCC------C---CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCc-hhHHH
Q 042541          293 QLPDYKILVTSRSEF------P---QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGC-PLALK  362 (695)
Q Consensus       293 ~~~gs~iivTtR~~~------~---~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~-PLai~  362 (695)
                      ...+..||.||....      .   .....+.++..+.++-.++|..........    .......+++.+.|. +--|.
T Consensus       190 ~~~~v~vI~aTn~~~~ld~al~r~gRfd~~i~i~~Pd~~~R~~il~~~l~~~~~~----~~~~l~~la~~t~G~sgadl~  265 (495)
T TIGR01241       190 TNTGVIVIAATNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEILKVHAKNKKLA----PDVDLKAVARRTPGFSGADLA  265 (495)
T ss_pred             CCCCeEEEEecCChhhcCHHHhcCCcceEEEEcCCCCHHHHHHHHHHHHhcCCCC----cchhHHHHHHhCCCCCHHHHH
Confidence            112345555665431      1   233478888889988888888766432221    122356788888874 33343


Q ss_pred             HH
Q 042541          363 VV  364 (695)
Q Consensus       363 ~~  364 (695)
                      .+
T Consensus       266 ~l  267 (495)
T TIGR01241       266 NL  267 (495)
T ss_pred             HH
Confidence            33

HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.

>TIGR00763 lon ATP-dependent protease La

Probab=97.50  E-value=0.0028  Score=73.80  Aligned_cols=44  Identities=25%  Similarity=0.249  Sum_probs=36.4

Q ss_pred             CCCCCCcchHHHHHHHHH------cCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          166 VISPGLDVPLKELKMELF------KDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~------~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..++|.+..+++|.+++.      ....+++.++|++|+|||++|+.+++
T Consensus       320 ~~~~G~~~~k~~i~~~~~~~~~~~~~~~~~lll~GppG~GKT~lAk~iA~  369 (775)
T TIGR00763       320 EDHYGLKKVKERILEYLAVQKLRGKMKGPILCLVGPPGVGKTSLGKSIAK  369 (775)
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhcCCCCceEEEECCCCCCHHHHHHHHHH
Confidence            446899999999988765      12346899999999999999999987

This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.

>PRK15386 type III secretion protein GogB; Provisional

Probab=97.49  E-value=0.00018  Score=75.04  Aligned_cols=120  Identities=16%  Similarity=0.237  Sum_probs=75.4

Q ss_pred             CCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccC-CCCCccccccccccc
Q 042541          548 QGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHV-SLPNSLATVRMNHLQ  626 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~-~l~~lp~i~~l~~L~  626 (695)
                      .|++++.|.++.+ ....+|. +  -.+|+.|.+++|... ..++.  .+  ..+|++|.+.+| .++.+|     .+|+
T Consensus        50 ~~~~l~~L~Is~c-~L~sLP~-L--P~sLtsL~Lsnc~nL-tsLP~--~L--P~nLe~L~Ls~Cs~L~sLP-----~sLe  115 (426)
T PRK15386         50 EARASGRLYIKDC-DIESLPV-L--PNELTEITIENCNNL-TTLPG--SI--PEGLEKLTVCHCPEISGLP-----ESVR  115 (426)
T ss_pred             HhcCCCEEEeCCC-CCcccCC-C--CCCCcEEEccCCCCc-ccCCc--hh--hhhhhheEccCcccccccc-----cccc
Confidence            4678889999877 4455562 1  236999999885432 12221  11  247999999998 677777     2355


Q ss_pred             EEeecccc---CCcccccchhhh-------------cccC-CCccEEecccccccccCchhhcCCCCCceeecccc
Q 042541          627 KVSLVMCN---VGQVFRNSTFRI-------------SDAF-PNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNC  685 (695)
Q Consensus       627 ~L~l~~~~---i~~~~~~~~~~l-------------~~~l-~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~  685 (695)
                      .|+++.+.   +..+|++... |             |..| ++|++|++++|..+ .+|..+.  .+|+.|+++.|
T Consensus       116 ~L~L~~n~~~~L~~LPssLk~-L~I~~~n~~~~~~lp~~LPsSLk~L~Is~c~~i-~LP~~LP--~SLk~L~ls~n  187 (426)
T PRK15386        116 SLEIKGSATDSIKNVPNGLTS-LSINSYNPENQARIDNLISPSLKTLSLTGCSNI-ILPEKLP--ESLQSITLHIE  187 (426)
T ss_pred             eEEeCCCCCcccccCcchHhh-eeccccccccccccccccCCcccEEEecCCCcc-cCccccc--ccCcEEEeccc
Confidence            55565553   5555554421 1             1012 47999999998755 4665444  58999998875

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=97.49  E-value=0.0092  Score=61.13  Aligned_cols=157  Identities=16%  Similarity=0.176  Sum_probs=94.9

Q ss_pred             hHHHHHHHHHcCC-ceEEEEEcCCCCcHHHHHHHHhcccccc------------------ccCCCcEEEEEeCCCCCHHH
Q 042541          174 PLKELKMELFKDG-RQFIVVSAPGGYGKTTLVQRLCKDDQVQ------------------GKFKDDIFYVTVSKNPNVKA  234 (695)
Q Consensus       174 ~~~~l~~~L~~~~-~~vv~I~G~gGiGKTtLa~~~~~~~~~~------------------~~f~~~~~wv~~~~~~~~~~  234 (695)
                      .-+++...+..+. ...+.++|+.|+||+++|..++..---.                  +..+. +.|+.-...     
T Consensus        11 ~~~~l~~~~~~~rl~hA~L~~G~~G~Gk~~lA~~~a~~llC~~~~~~~Cg~C~sC~~~~~g~HPD-~~~i~p~~~-----   84 (319)
T PRK06090         11 VWQNWKAGLDAGRIPGALLLQSDEGLGVESLVELFSRALLCQNYQSEACGFCHSCELMQSGNHPD-LHVIKPEKE-----   84 (319)
T ss_pred             HHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHcCCCCC-EEEEecCcC-----
Confidence            3456666666555 4678899999999999998886521000                  01111 223221100     


Q ss_pred             HHHHHHHhcCCCCCCCCChHHHHHHHHHHHHh-----cCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCC
Q 042541          235 IVQKVLHHKGYPVPEFQTDEAAINDLERFFKQ-----MRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRS  305 (695)
Q Consensus       235 ~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~-----l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~  305 (695)
                                       ...-.+++++++.+.     ..++.-++|+|++......    +++.+....+++.+|++|.+
T Consensus        85 -----------------~~~I~vdqiR~l~~~~~~~~~~~~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~  147 (319)
T PRK06090         85 -----------------GKSITVEQIRQCNRLAQESSQLNGYRLFVIEPADAMNESASNALLKTLEEPAPNCLFLLVTHN  147 (319)
T ss_pred             -----------------CCcCCHHHHHHHHHHHhhCcccCCceEEEecchhhhCHHHHHHHHHHhcCCCCCeEEEEEECC
Confidence                             000112222322221     2466679999999877643    66666666677888877766


Q ss_pred             CCC------CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHH
Q 042541          306 EFP------QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVV  364 (695)
Q Consensus       306 ~~~------~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~  364 (695)
                      ...      .-...+.+.+++.+++.+.+....    .    .   .+..++..++|.|+.+..+
T Consensus       148 ~~~lLpTI~SRCq~~~~~~~~~~~~~~~L~~~~----~----~---~~~~~l~l~~G~p~~A~~~  201 (319)
T PRK06090        148 QKRLLPTIVSRCQQWVVTPPSTAQAMQWLKGQG----I----T---VPAYALKLNMGSPLKTLAM  201 (319)
T ss_pred             hhhChHHHHhcceeEeCCCCCHHHHHHHHHHcC----C----c---hHHHHHHHcCCCHHHHHHH
Confidence            521      112278999999999999886531    1    0   2457889999999876554

>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function

Probab=97.48  E-value=0.0025  Score=61.58  Aligned_cols=46  Identities=17%  Similarity=0.094  Sum_probs=37.3

Q ss_pred             CCCCCCCCcchHHHHHHHHH----cCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          164 PPVISPGLDVPLKELKMELF----KDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       164 ~~~~~vGr~~~~~~l~~~L~----~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .-+.++|.+.+.+.|++-..    .....-+.++|..|.|||++++++.+
T Consensus        25 ~l~~L~Gie~Qk~~l~~Nt~~Fl~G~pannvLL~G~rGtGKSSlVkall~   74 (249)
T PF05673_consen   25 RLDDLIGIERQKEALIENTEQFLQGLPANNVLLWGARGTGKSSLVKALLN   74 (249)
T ss_pred             CHHHhcCHHHHHHHHHHHHHHHHcCCCCcceEEecCCCCCHHHHHHHHHH
Confidence            34578999999888876443    34466788999999999999999987

>PF04665 Pox_A32: Poxvirus A32 protein; InterPro: IPR006758 This entry contains uncharacterised proteins belonging to the B354L family which include the pox virus A32 protein

Probab=97.48  E-value=0.00045  Score=67.15  Aligned_cols=36  Identities=36%  Similarity=0.520  Sum_probs=29.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEe
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTV  226 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~  226 (695)
                      -.++|+|..|+|||||+..+..  .....|.. +++++-
T Consensus        14 fr~viIG~sGSGKT~li~~lL~--~~~~~f~~-I~l~t~   49 (241)
T PF04665_consen   14 FRMVIIGKSGSGKTTLIKSLLY--YLRHKFDH-IFLITP   49 (241)
T ss_pred             ceEEEECCCCCCHHHHHHHHHH--hhcccCCE-EEEEec
Confidence            4678999999999999999987  57778865 766644

This is thought to be an ATPase involved in viral DNA packaging [].

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=97.47  E-value=0.0044  Score=64.28  Aligned_cols=170  Identities=17%  Similarity=0.165  Sum_probs=96.5

Q ss_pred             hHHHHHHHHHcCC-ceEEEEEcCCCCcHHHHHHHHhccccc---cccCCCcE----EEEEeCCCCCHHHHHHHHHHhcCC
Q 042541          174 PLKELKMELFKDG-RQFIVVSAPGGYGKTTLVQRLCKDDQV---QGKFKDDI----FYVTVSKNPNVKAIVQKVLHHKGY  245 (695)
Q Consensus       174 ~~~~l~~~L~~~~-~~vv~I~G~gGiGKTtLa~~~~~~~~~---~~~f~~~~----~wv~~~~~~~~~~~~~~i~~~l~~  245 (695)
                      .-+++...+.++. ..-+.++|+.|+||+++|..++..---   ...-.|+.    -++..+..+|+..+          
T Consensus        10 ~~~~l~~~~~~~rl~HA~Lf~G~~G~Gk~~lA~~~A~~LlC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i----------   79 (334)
T PRK07993         10 DYEQLVGSYQAGRGHHALLIQALPGMGDDALIYALSRWLMCQQPQGHKSCGHCRGCQLMQAGTHPDYYTL----------   79 (334)
T ss_pred             HHHHHHHHHHcCCcceEEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCCEEEE----------
Confidence            3466777776655 466789999999999999887652100   00001110    00000000010000          


Q ss_pred             CCCCCCChHHHHHHHHHHHH-----hcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCCC------C
Q 042541          246 PVPEFQTDEAAINDLERFFK-----QMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFPQ------F  310 (695)
Q Consensus       246 ~~~~~~~~~~~~~~l~~~~~-----~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~~------~  310 (695)
                       .++.....-.+++++++.+     ...+++-++|+|+++.....    +++.+....+++.+|.+|.+...-      -
T Consensus        80 -~p~~~~~~I~idqiR~l~~~~~~~~~~g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTIrSR  158 (334)
T PRK07993         80 -TPEKGKSSLGVDAVREVTEKLYEHARLGGAKVVWLPDAALLTDAAANALLKTLEEPPENTWFFLACREPARLLATLRSR  158 (334)
T ss_pred             -ecccccccCCHHHHHHHHHHHhhccccCCceEEEEcchHhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHHhc
Confidence             0000000111233333332     22477889999999877643    666677777778888777765211      1


Q ss_pred             CCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHH
Q 042541          311 GSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALK  362 (695)
Q Consensus       311 ~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~  362 (695)
                      ...+.+.+++.+++.+.+.....        ...+.+..++..++|.|....
T Consensus       159 Cq~~~~~~~~~~~~~~~L~~~~~--------~~~~~a~~~~~la~G~~~~Al  202 (334)
T PRK07993        159 CRLHYLAPPPEQYALTWLSREVT--------MSQDALLAALRLSAGAPGAAL  202 (334)
T ss_pred             cccccCCCCCHHHHHHHHHHccC--------CCHHHHHHHHHHcCCCHHHHH
Confidence            22788999999999888865321        123447788999999996443

>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=97.47  E-value=0.0025  Score=67.91  Aligned_cols=127  Identities=22%  Similarity=0.194  Sum_probs=76.6

Q ss_pred             hHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCCh
Q 042541          174 PLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTD  253 (695)
Q Consensus       174 ~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~  253 (695)
                      -..++.+.+..... ++.|+|+-++||||+++.+..  ...+.    +++++.-+......-                  
T Consensus        25 ~~~~l~~~~~~~~~-i~~i~GpR~~GKTtll~~l~~--~~~~~----~iy~~~~d~~~~~~~------------------   79 (398)
T COG1373          25 LLPRLIKKLDLRPF-IILILGPRQVGKTTLLKLLIK--GLLEE----IIYINFDDLRLDRIE------------------   79 (398)
T ss_pred             hhHHHHhhcccCCc-EEEEECCccccHHHHHHHHHh--hCCcc----eEEEEecchhcchhh------------------
Confidence            34444444443323 999999999999999977665  23222    445554433211111                  


Q ss_pred             HHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH--HHhhhccCCCCCEEEEEcCCCC----------CCCCCeEecCCCCh
Q 042541          254 EAAINDLERFFKQMRIEAILLVLDDVWPGSES--LLQKLGFQLPDYKILVTSRSEF----------PQFGSVHYLKPLTY  321 (695)
Q Consensus       254 ~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~--~~~~l~~~~~gs~iivTtR~~~----------~~~~~~~~l~~L~~  321 (695)
                        ..+.+..+.+.-..++.+++||.|....+|  .+..+....+. +|++|+-+..          .+-+..+.+-||+.
T Consensus        80 --l~d~~~~~~~~~~~~~~yifLDEIq~v~~W~~~lk~l~d~~~~-~v~itgsss~ll~~~~~~~L~GR~~~~~l~PlSF  156 (398)
T COG1373          80 --LLDLLRAYIELKEREKSYIFLDEIQNVPDWERALKYLYDRGNL-DVLITGSSSSLLSKEISESLAGRGKDLELYPLSF  156 (398)
T ss_pred             --HHHHHHHHHHhhccCCceEEEecccCchhHHHHHHHHHccccc-eEEEECCchhhhccchhhhcCCCceeEEECCCCH
Confidence              111122222111227899999999988877  34555555555 8888877662          22234889999999


Q ss_pred             HHHHHHH
Q 042541          322 EAARTLF  328 (695)
Q Consensus       322 ~ea~~Lf  328 (695)
                      .|-..+.
T Consensus       157 ~Efl~~~  163 (398)
T COG1373         157 REFLKLK  163 (398)
T ss_pred             HHHHhhc
Confidence            9887654

>COG4886 Leucine-rich repeat (LRR) protein [Function unknown]

Probab=97.44  E-value=6.8e-05  Score=80.72  Aligned_cols=133  Identities=19%  Similarity=0.308  Sum_probs=90.1

Q ss_pred             CCceEEEEEEccCccccCChhhcCCC-CCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc-ccccccccc
Q 042541          549 GPEVKVVVLNIRTKKYVLPDFLQKMD-ELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL-ATVRMNHLQ  626 (695)
Q Consensus       549 ~~~l~~L~l~~~~~~~~~p~~~~~l~-~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp-~i~~l~~L~  626 (695)
                      .+.+..|.+..+ ....+|.....+. +|+.|++++|.+..  ++  ..+..+++|+.|++++|.+..+| ..+.++.|+
T Consensus       115 ~~~l~~L~l~~n-~i~~i~~~~~~~~~nL~~L~l~~N~i~~--l~--~~~~~l~~L~~L~l~~N~l~~l~~~~~~~~~L~  189 (394)
T COG4886         115 LTNLTSLDLDNN-NITDIPPLIGLLKSNLKELDLSDNKIES--LP--SPLRNLPNLKNLDLSFNDLSDLPKLLSNLSNLN  189 (394)
T ss_pred             ccceeEEecCCc-ccccCccccccchhhcccccccccchhh--hh--hhhhccccccccccCCchhhhhhhhhhhhhhhh
Confidence            356677766554 3345666666674 99999999887631  11  23788999999999999999999 777999999


Q ss_pred             EEeeccccCCcccccchhhhcccCCCccEEecccc----------------------cccccCchhhcCCCCCceeeccc
Q 042541          627 KVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYC----------------------NDLIELPDGLCDIVSMEKLRITN  684 (695)
Q Consensus       627 ~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c----------------------~~l~~lP~~i~~L~~L~~L~l~~  684 (695)
                      .|++++|.+..+|+...     .+..|++|.++++                      +.+..+|..++.+++|+.|++++
T Consensus       190 ~L~ls~N~i~~l~~~~~-----~~~~L~~l~~~~N~~~~~~~~~~~~~~l~~l~l~~n~~~~~~~~~~~l~~l~~L~~s~  264 (394)
T COG4886         190 NLDLSGNKISDLPPEIE-----LLSALEELDLSNNSIIELLSSLSNLKNLSGLELSNNKLEDLPESIGNLSNLETLDLSN  264 (394)
T ss_pred             heeccCCccccCchhhh-----hhhhhhhhhhcCCcceecchhhhhcccccccccCCceeeeccchhccccccceecccc
Confidence            99999999999888642     2333555555543                      22333345556666666666666


Q ss_pred             ccCCCCCC
Q 042541          685 CHRLSALP  692 (695)
Q Consensus       685 ~~~l~~lP  692 (695)
                      |. +..++
T Consensus       265 n~-i~~i~  271 (394)
T COG4886         265 NQ-ISSIS  271 (394)
T ss_pred             cc-ccccc
Confidence            43 44443

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=97.44  E-value=0.005  Score=67.26  Aligned_cols=196  Identities=18%  Similarity=0.186  Sum_probs=119.9

Q ss_pred             CCCCCCCCcchHHHHHHHHH----c-CCceEEEEEcCCCCcHHHHHHHHhcccc------ccccCCCcEEEEEeCCCCCH
Q 042541          164 PPVISPGLDVPLKELKMELF----K-DGRQFIVVSAPGGYGKTTLVQRLCKDDQ------VQGKFKDDIFYVTVSKNPNV  232 (695)
Q Consensus       164 ~~~~~vGr~~~~~~l~~~L~----~-~~~~vv~I~G~gGiGKTtLa~~~~~~~~------~~~~f~~~~~wv~~~~~~~~  232 (695)
                      .|..+-+|+.+..+|..++.    . +..+.+-|.|.+|.|||..+..|.+.-.      --..|+. + .|+.-.-..+
T Consensus       394 vp~sLpcRe~E~~~I~~f~~~~i~~~~~g~~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~y-v-eINgm~l~~~  471 (767)
T KOG1514|consen  394 VPESLPCRENEFSEIEDFLRSFISDQGLGSCMYISGVPGTGKTATVLEVMKELQTSSAQKELPKFDY-V-EINGLRLASP  471 (767)
T ss_pred             ccccccchhHHHHHHHHHHHhhcCCCCCceeEEEecCCCCCceehHHHHHHHHHHHHhhcCCCCccE-E-EEcceeecCH
Confidence            45567899999999988887    2 3356899999999999999999987322      1233543 2 4555555679


Q ss_pred             HHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHH--hcCCCcEEEEEeCCC---CCChHHH-hhhcc-CCCCCEEEEEcCC
Q 042541          233 KAIVQKVLHHKGYPVPEFQTDEAAINDLERFFK--QMRIEAILLVLDDVW---PGSESLL-QKLGF-QLPDYKILVTSRS  305 (695)
Q Consensus       233 ~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~--~l~~~~~LlVlDdv~---~~~~~~~-~~l~~-~~~gs~iivTtR~  305 (695)
                      .++...|..++.+...   .....++.|...+.  .-+.+.+++++|+++   ...+.++ ..|.+ ..++||++|-+=.
T Consensus       472 ~~~Y~~I~~~lsg~~~---~~~~al~~L~~~f~~~k~~~~~~VvLiDElD~Lvtr~QdVlYn~fdWpt~~~sKLvvi~Ia  548 (767)
T KOG1514|consen  472 REIYEKIWEALSGERV---TWDAALEALNFRFTVPKPKRSTTVVLIDELDILVTRSQDVLYNIFDWPTLKNSKLVVIAIA  548 (767)
T ss_pred             HHHHHHHHHhcccCcc---cHHHHHHHHHHhhccCCCCCCCEEEEeccHHHHhcccHHHHHHHhcCCcCCCCceEEEEec
Confidence            9999999999976543   33445555555542  224667899999863   3334433 34444 4578988775543


Q ss_pred             CCC-------------CCC-CeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHH
Q 042541          306 EFP-------------QFG-SVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVV  364 (695)
Q Consensus       306 ~~~-------------~~~-~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~  364 (695)
                      ...             ..| ..+...|.++.+-.++...+..+.....+...+-+++.|+.-.|..-.|+.+.
T Consensus       549 NTmdlPEr~l~nrvsSRlg~tRi~F~pYth~qLq~Ii~~RL~~~~~f~~~aielvarkVAavSGDaRraldic  621 (767)
T KOG1514|consen  549 NTMDLPERLLMNRVSSRLGLTRICFQPYTHEQLQEIISARLKGLDAFENKAIELVARKVAAVSGDARRALDIC  621 (767)
T ss_pred             ccccCHHHHhccchhhhccceeeecCCCCHHHHHHHHHHhhcchhhcchhHHHHHHHHHHhccccHHHHHHHH
Confidence            311             111 25667777777777777665543322111112334445555455444444443

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=97.44  E-value=0.0025  Score=68.15  Aligned_cols=163  Identities=13%  Similarity=0.180  Sum_probs=95.1

Q ss_pred             CCCCCCcchHHHHHHHHH---cC---------CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHH
Q 042541          166 VISPGLDVPLKELKMELF---KD---------GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVK  233 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~---~~---------~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~  233 (695)
                      ..+=|.+..+.++.+++.   .+         .++=|.+||++|+|||.||+++++.  ..      +-++.++..    
T Consensus       190 ~diGG~d~~~~el~~li~~i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAge--l~------vPf~~isAp----  257 (802)
T KOG0733|consen  190 SDIGGLDKTLAELCELIIHIKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAGE--LG------VPFLSISAP----  257 (802)
T ss_pred             hhccChHHHHHHHHHHHHHhcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHHhhh--cC------CceEeecch----
Confidence            356788988888887765   22         2567899999999999999999983  22      324444432    


Q ss_pred             HHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCCh---H--------HHhhhcc-------C-
Q 042541          234 AIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGSE---S--------LLQKLGF-------Q-  293 (695)
Q Consensus       234 ~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~~---~--------~~~~l~~-------~-  293 (695)
                          +|+..+.+         +..+.+++++ +....-++++++|+++-...   +        +...+..       . 
T Consensus       258 ----eivSGvSG---------ESEkkiRelF~~A~~~aPcivFiDeIDAI~pkRe~aqreMErRiVaQLlt~mD~l~~~~  324 (802)
T KOG0733|consen  258 ----EIVSGVSG---------ESEKKIRELFDQAKSNAPCIVFIDEIDAITPKREEAQREMERRIVAQLLTSMDELSNEK  324 (802)
T ss_pred             ----hhhcccCc---------ccHHHHHHHHHHHhccCCeEEEeecccccccchhhHHHHHHHHHHHHHHHhhhcccccc
Confidence                23333322         1245677777 66678899999999865431   0        2222211       1 


Q ss_pred             CCCC-EEEE--EcCCCC-----CCCC---CeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCc
Q 042541          294 LPDY-KILV--TSRSEF-----PQFG---SVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGC  357 (695)
Q Consensus       294 ~~gs-~iiv--TtR~~~-----~~~~---~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~  357 (695)
                      ..|- .++|  |+|-..     ...|   ..+.+.--+..+-.+++...+.+-......    ..++|++.+-|.
T Consensus       325 ~~g~~VlVIgATnRPDslDpaLRRaGRFdrEI~l~vP~e~aR~~IL~~~~~~lrl~g~~----d~~qlA~lTPGf  395 (802)
T KOG0733|consen  325 TKGDPVLVIGATNRPDSLDPALRRAGRFDREICLGVPSETAREEILRIICRGLRLSGDF----DFKQLAKLTPGF  395 (802)
T ss_pred             cCCCCeEEEecCCCCcccCHHHhccccccceeeecCCchHHHHHHHHHHHhhCCCCCCc----CHHHHHhcCCCc
Confidence            1132 3333  455432     2223   366777667776667776655433322222    256677777664

>TIGR00602 rad24 checkpoint protein rad24

Probab=97.43  E-value=0.001  Score=74.19  Aligned_cols=48  Identities=21%  Similarity=0.369  Sum_probs=39.7

Q ss_pred             CCCCCCCCCCcchHHHHHHHHHcC-----CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          162 PDPPVISPGLDVPLKELKMELFKD-----GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       162 ~~~~~~~vGr~~~~~~l~~~L~~~-----~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      |..-+.++|-+..++++..++...     ..+++.|+|++|+||||+++.++.
T Consensus        80 P~~ldel~~~~~ki~~l~~~l~~~~~~~~~~~illL~GP~GsGKTTl~~~la~  132 (637)
T TIGR00602        80 PETQHELAVHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSK  132 (637)
T ss_pred             CCCHHHhcCcHHHHHHHHHHHHhcccccCCCcEEEEECCCCCCHHHHHHHHHH
Confidence            444567899999999999988732     246799999999999999999987

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>KOG1859 consensus Leucine-rich repeat proteins [General function prediction only]

Probab=97.43  E-value=6e-06  Score=88.97  Aligned_cols=109  Identities=22%  Similarity=0.251  Sum_probs=84.7

Q ss_pred             cCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--cccccccccEEeeccccCCcccccc
Q 042541          565 VLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFRNS  642 (695)
Q Consensus       565 ~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~  642 (695)
                      .+.+++.-++.|+.|+|+.|.+..     ...+..|+.|++|||+.|.+..+|  +...+. |+.|+|++|.++.+.. +
T Consensus       178 ~mD~SLqll~ale~LnLshNk~~~-----v~~Lr~l~~LkhLDlsyN~L~~vp~l~~~gc~-L~~L~lrnN~l~tL~g-i  250 (1096)
T KOG1859|consen  178 LMDESLQLLPALESLNLSHNKFTK-----VDNLRRLPKLKHLDLSYNCLRHVPQLSMVGCK-LQLLNLRNNALTTLRG-I  250 (1096)
T ss_pred             hHHHHHHHHHHhhhhccchhhhhh-----hHHHHhcccccccccccchhccccccchhhhh-heeeeecccHHHhhhh-H
Confidence            344577778999999999988742     234788999999999999999999  554555 9999999998876533 3


Q ss_pred             hhhhcccCCCccEEecccccccccCc--hhhcCCCCCceeeccccc
Q 042541          643 TFRISDAFPNLLEMDIDYCNDLIELP--DGLCDIVSMEKLRITNCH  686 (695)
Q Consensus       643 ~~~l~~~l~~L~~L~l~~c~~l~~lP--~~i~~L~~L~~L~l~~~~  686 (695)
                      -     +|.+|+.||+++| .+....  .-++.|..|+.|+|.||+
T Consensus       251 e-----~LksL~~LDlsyN-ll~~hseL~pLwsLs~L~~L~LeGNP  290 (1096)
T KOG1859|consen  251 E-----NLKSLYGLDLSYN-LLSEHSELEPLWSLSSLIVLWLEGNP  290 (1096)
T ss_pred             H-----hhhhhhccchhHh-hhhcchhhhHHHHHHHHHHHhhcCCc
Confidence            3     8999999999985 333322  126788999999999987

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=97.42  E-value=0.00034  Score=80.00  Aligned_cols=149  Identities=15%  Similarity=0.183  Sum_probs=83.4

Q ss_pred             CCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccc---cccccCCCcEEEEEeCCCCCHHHHHHHHHHh
Q 042541          166 VISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDD---QVQGKFKDDIFYVTVSKNPNVKAIVQKVLHH  242 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~---~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~  242 (695)
                      +.++||+.++.++++.|......-+.++|++|+|||++|+.+++..   .+...+....+|. +    +..    .++. 
T Consensus       186 ~~liGR~~ei~~~i~iL~r~~~~n~LLvGppGvGKT~lae~la~~i~~~~vP~~l~~~~~~~-l----~~~----~lla-  255 (758)
T PRK11034        186 DPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYS-L----DIG----SLLA-  255 (758)
T ss_pred             CcCcCCCHHHHHHHHHHhccCCCCeEEECCCCCCHHHHHHHHHHHHHhcCCCchhcCCeEEe-c----cHH----HHhc-
Confidence            3579999999999999986554556789999999999999988731   1111122213231 1    111    1111 


Q ss_pred             cCCCCCCCCChHHHHHHHHHHHHhc-CCCcEEEEEeCCCCC---------ChH---HHhhhccCCCCCEEEEEc-CCCC-
Q 042541          243 KGYPVPEFQTDEAAINDLERFFKQM-RIEAILLVLDDVWPG---------SES---LLQKLGFQLPDYKILVTS-RSEF-  307 (695)
Q Consensus       243 l~~~~~~~~~~~~~~~~l~~~~~~l-~~~~~LlVlDdv~~~---------~~~---~~~~l~~~~~gs~iivTt-R~~~-  307 (695)
                       +..     ...+....+..+++.+ +.++.+|++|++...         ...   .+..+.. ...-++|-+| +.+. 
T Consensus       256 -G~~-----~~Ge~e~rl~~l~~~l~~~~~~ILfIDEIh~L~g~g~~~~g~~d~~nlLkp~L~-~g~i~vIgATt~~E~~  328 (758)
T PRK11034        256 -GTK-----YRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLS-SGKIRVIGSTTYQEFS  328 (758)
T ss_pred             -ccc-----hhhhHHHHHHHHHHHHHhcCCCEEEeccHHHHhccCCCCCcHHHHHHHHHHHHh-CCCeEEEecCChHHHH
Confidence             000     0112223344444332 345789999998532         111   1222221 1223444444 3221 


Q ss_pred             ----------CCCCCeEecCCCChHHHHHHHHHhc
Q 042541          308 ----------PQFGSVHYLKPLTYEAARTLFLHSA  332 (695)
Q Consensus       308 ----------~~~~~~~~l~~L~~~ea~~Lf~~~~  332 (695)
                                ... ..+.+++.+.+++.+++....
T Consensus       329 ~~~~~D~AL~rRF-q~I~v~ePs~~~~~~IL~~~~  362 (758)
T PRK11034        329 NIFEKDRALARRF-QKIDITEPSIEETVQIINGLK  362 (758)
T ss_pred             HHhhccHHHHhhC-cEEEeCCCCHHHHHHHHHHHH
Confidence                      111 278999999999999988643

>KOG1859 consensus Leucine-rich repeat proteins [General function prediction only]

Probab=97.40  E-value=2.6e-05  Score=84.31  Aligned_cols=83  Identities=19%  Similarity=0.232  Sum_probs=62.6

Q ss_pred             cccCCCCcEEEeccCCCCCcccccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCC
Q 042541          597 LSALSKLKKIRLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVS  676 (695)
Q Consensus       597 l~~l~~L~~L~L~~~~l~~lp~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~  676 (695)
                      +.-++.|+.|+|++|.++....+..|++|.+|||+.|.+..+|.-.-.    .+. |+.|.+++| -+..+- ++.+|.+
T Consensus       183 Lqll~ale~LnLshNk~~~v~~Lr~l~~LkhLDlsyN~L~~vp~l~~~----gc~-L~~L~lrnN-~l~tL~-gie~Lks  255 (1096)
T KOG1859|consen  183 LQLLPALESLNLSHNKFTKVDNLRRLPKLKHLDLSYNCLRHVPQLSMV----GCK-LQLLNLRNN-ALTTLR-GIENLKS  255 (1096)
T ss_pred             HHHHHHhhhhccchhhhhhhHHHHhcccccccccccchhccccccchh----hhh-heeeeeccc-HHHhhh-hHHhhhh
Confidence            344667888889888887655666788899999999988877653321    333 888888874 566664 6999999


Q ss_pred             Cceeeccccc
Q 042541          677 MEKLRITNCH  686 (695)
Q Consensus       677 L~~L~l~~~~  686 (695)
                      |++||++.|-
T Consensus       256 L~~LDlsyNl  265 (1096)
T KOG1859|consen  256 LYGLDLSYNL  265 (1096)
T ss_pred             hhccchhHhh
Confidence            9999999864

>CHL00176 ftsH cell division protein; Validated

Probab=97.40  E-value=0.0044  Score=69.74  Aligned_cols=163  Identities=14%  Similarity=0.180  Sum_probs=93.2

Q ss_pred             CCCCCCcchHHHHHHHH---HcC---------CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHH
Q 042541          166 VISPGLDVPLKELKMEL---FKD---------GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVK  233 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L---~~~---------~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~  233 (695)
                      +.++|.++..+++.+.+   ..+         ..+-|.++|++|+|||+||+.+++.  ..      +-++.++..    
T Consensus       183 ~dv~G~~~~k~~l~eiv~~lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAralA~e--~~------~p~i~is~s----  250 (638)
T CHL00176        183 RDIAGIEEAKEEFEEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGE--AE------VPFFSISGS----  250 (638)
T ss_pred             HhccChHHHHHHHHHHHHHHhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHH--hC------CCeeeccHH----
Confidence            45688887666665544   321         1456899999999999999999873  21      223333321    


Q ss_pred             HHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCC-----------h---HHHhhhcc------
Q 042541          234 AIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGS-----------E---SLLQKLGF------  292 (695)
Q Consensus       234 ~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~-----------~---~~~~~l~~------  292 (695)
                      ++....   .+          .....+..++ ......+++|++||++...           .   ..+..+..      
T Consensus       251 ~f~~~~---~g----------~~~~~vr~lF~~A~~~~P~ILfIDEID~l~~~r~~~~~~~~~e~~~~L~~LL~~~dg~~  317 (638)
T CHL00176        251 EFVEMF---VG----------VGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRGAGIGGGNDEREQTLNQLLTEMDGFK  317 (638)
T ss_pred             HHHHHh---hh----------hhHHHHHHHHHHHhcCCCcEEEEecchhhhhcccCCCCCCcHHHHHHHHHHHhhhcccc
Confidence            111100   00          0123344445 4446788999999995431           1   11222221      


Q ss_pred             CCCCCEEEEEcCCC------CC---CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCc
Q 042541          293 QLPDYKILVTSRSE------FP---QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGC  357 (695)
Q Consensus       293 ~~~gs~iivTtR~~------~~---~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~  357 (695)
                      ...+..||.||...      ..   .....+.++..+.++-.++++.++.....    ........+++.+.|.
T Consensus       318 ~~~~ViVIaaTN~~~~LD~ALlRpGRFd~~I~v~lPd~~~R~~IL~~~l~~~~~----~~d~~l~~lA~~t~G~  387 (638)
T CHL00176        318 GNKGVIVIAATNRVDILDAALLRPGRFDRQITVSLPDREGRLDILKVHARNKKL----SPDVSLELIARRTPGF  387 (638)
T ss_pred             CCCCeeEEEecCchHhhhhhhhccccCceEEEECCCCHHHHHHHHHHHHhhccc----chhHHHHHHHhcCCCC
Confidence            12344566666543      11   23347888888999999999887654221    1233467788888873

>PRK10787 DNA-binding ATP-dependent protease La; Provisional

Probab=97.40  E-value=0.017  Score=66.79  Aligned_cols=151  Identities=21%  Similarity=0.157  Sum_probs=84.8

Q ss_pred             CCCCCCcchHHHHHHHHHc------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHH
Q 042541          166 VISPGLDVPLKELKMELFK------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKV  239 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i  239 (695)
                      ...+|.+..+++|.++|..      ....++.++|++|+||||+|+.++.  .....    .+-++++...+..++...-
T Consensus       322 ~~~~g~~~vK~~i~~~l~~~~~~~~~~g~~i~l~GppG~GKTtl~~~ia~--~l~~~----~~~i~~~~~~d~~~i~g~~  395 (784)
T PRK10787        322 TDHYGLERVKDRILEYLAVQSRVNKIKGPILCLVGPPGVGKTSLGQSIAK--ATGRK----YVRMALGGVRDEAEIRGHR  395 (784)
T ss_pred             hhccCHHHHHHHHHHHHHHHHhcccCCCceEEEECCCCCCHHHHHHHHHH--HhCCC----EEEEEcCCCCCHHHhccch
Confidence            4569999999999988871      2356899999999999999999986  33222    2234455544443332221


Q ss_pred             HHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCh--------HHHhhhccC---------------CCC
Q 042541          240 LHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSE--------SLLQKLGFQ---------------LPD  296 (695)
Q Consensus       240 ~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~--------~~~~~l~~~---------------~~g  296 (695)
                      ....+. .+         ..+.+.+......+-+++||.++....        .++..+.+.               ..+
T Consensus       396 ~~~~g~-~~---------G~~~~~l~~~~~~~~villDEidk~~~~~~g~~~~aLlevld~~~~~~~~d~~~~~~~dls~  465 (784)
T PRK10787        396 RTYIGS-MP---------GKLIQKMAKVGVKNPLFLLDEIDKMSSDMRGDPASALLEVLDPEQNVAFSDHYLEVDYDLSD  465 (784)
T ss_pred             hccCCC-CC---------cHHHHHHHhcCCCCCEEEEEChhhcccccCCCHHHHHHHHhccccEEEEecccccccccCCc
Confidence            111111 11         012222222222345788999854432        122222211               123


Q ss_pred             CEEEEEcCCCCCC-----CCCeEecCCCChHHHHHHHHHhc
Q 042541          297 YKILVTSRSEFPQ-----FGSVHYLKPLTYEAARTLFLHSA  332 (695)
Q Consensus       297 s~iivTtR~~~~~-----~~~~~~l~~L~~~ea~~Lf~~~~  332 (695)
                      .-+|.|+.+....     --..+++.+++.+|-.++.+++.
T Consensus       466 v~~i~TaN~~~i~~aLl~R~~ii~~~~~t~eek~~Ia~~~L  506 (784)
T PRK10787        466 VMFVATSNSMNIPAPLLDRMEVIRLSGYTEDEKLNIAKRHL  506 (784)
T ss_pred             eEEEEcCCCCCCCHHHhcceeeeecCCCCHHHHHHHHHHhh
Confidence            3444455433110     01278899999999888887765

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=97.36  E-value=0.015  Score=68.14  Aligned_cols=45  Identities=20%  Similarity=0.245  Sum_probs=36.9

Q ss_pred             CCCCCCCcchHHHHHHHHHc-------C--CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          165 PVISPGLDVPLKELKMELFK-------D--GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~-------~--~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...++|-+..++.+.+.+..       +  ...++.++|+.|+|||.||+.++.
T Consensus       565 ~~~v~GQ~~Av~~v~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKT~lA~~La~  618 (852)
T TIGR03345       565 AERVIGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAE  618 (852)
T ss_pred             cCeEcChHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCCCHHHHHHHHHH
Confidence            35679999999999988751       1  135789999999999999998876

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A

Probab=97.36  E-value=0.0024  Score=58.91  Aligned_cols=116  Identities=16%  Similarity=0.222  Sum_probs=70.3

Q ss_pred             CCcchHHHHHHHHHcCCc-eEEEEEcCCCCcHHHHHHHHhccc---ccc---------------ccCCCcEEEEEeCCC-
Q 042541          170 GLDVPLKELKMELFKDGR-QFIVVSAPGGYGKTTLVQRLCKDD---QVQ---------------GKFKDDIFYVTVSKN-  229 (695)
Q Consensus       170 Gr~~~~~~l~~~L~~~~~-~vv~I~G~gGiGKTtLa~~~~~~~---~~~---------------~~f~~~~~wv~~~~~-  229 (695)
                      |-++..+.|...+..+.. ..+.++|+.|+||+++|..+++.-   ...               ...+. +.|+.-... 
T Consensus         1 gq~~~~~~L~~~~~~~~l~ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~~~c~~c~~c~~~~~~~~~d-~~~~~~~~~~   79 (162)
T PF13177_consen    1 GQEEIIELLKNLIKSGRLPHALLFHGPSGSGKKTLALAFARALLCSNPNEDPCGECRSCRRIEEGNHPD-FIIIKPDKKK   79 (162)
T ss_dssp             S-HHHHHHHHHHHHCTC--SEEEEECSTTSSHHHHHHHHHHHHC-TT-CTT--SSSHHHHHHHTT-CTT-EEEEETTTSS
T ss_pred             CcHHHHHHHHHHHHcCCcceeEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHhccCcc-eEEEeccccc
Confidence            445566777777776664 568999999999999998876621   111               12333 445544432 


Q ss_pred             --CCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEc
Q 042541          230 --PNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTS  303 (695)
Q Consensus       230 --~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTt  303 (695)
                        ..++++. ++...+....                   ..++.-++|+||++.....    +++.+-....++.+|++|
T Consensus        80 ~~i~i~~ir-~i~~~~~~~~-------------------~~~~~KviiI~~ad~l~~~a~NaLLK~LEepp~~~~fiL~t  139 (162)
T PF13177_consen   80 KSIKIDQIR-EIIEFLSLSP-------------------SEGKYKVIIIDEADKLTEEAQNALLKTLEEPPENTYFILIT  139 (162)
T ss_dssp             SSBSHHHHH-HHHHHCTSS--------------------TTSSSEEEEEETGGGS-HHHHHHHHHHHHSTTTTEEEEEEE
T ss_pred             chhhHHHHH-HHHHHHHHHH-------------------hcCCceEEEeehHhhhhHHHHHHHHHHhcCCCCCEEEEEEE
Confidence              2333322 4444433221                   1356789999999877644    556666666789999988


Q ss_pred             CCC
Q 042541          304 RSE  306 (695)
Q Consensus       304 R~~  306 (695)
                      .+.
T Consensus       140 ~~~  142 (162)
T PF13177_consen  140 NNP  142 (162)
T ss_dssp             S-G
T ss_pred             CCh
Confidence            876

...

>KOG4237 consensus Extracellular matrix protein slit, contains leucine-rich and EGF-like repeats [Extracellular structures; Signal transduction mechanisms]

Probab=97.36  E-value=2.3e-05  Score=78.99  Aligned_cols=119  Identities=13%  Similarity=0.181  Sum_probs=88.2

Q ss_pred             ccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--cccccccccEEeecc-ccCCcccc
Q 042541          564 YVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNHLQKVSLVM-CNVGQVFR  640 (695)
Q Consensus       564 ~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L~~L~l~~-~~i~~~~~  640 (695)
                      ..+|..+.  ..-..+.|..|++.  .++. ..|+.+++||.|+|++|.|+.|-  ++..|..|-.|-+.+ |+|+.+|.
T Consensus        59 ~eVP~~LP--~~tveirLdqN~I~--~iP~-~aF~~l~~LRrLdLS~N~Is~I~p~AF~GL~~l~~Lvlyg~NkI~~l~k  133 (498)
T KOG4237|consen   59 TEVPANLP--PETVEIRLDQNQIS--SIPP-GAFKTLHRLRRLDLSKNNISFIAPDAFKGLASLLSLVLYGNNKITDLPK  133 (498)
T ss_pred             ccCcccCC--CcceEEEeccCCcc--cCCh-hhccchhhhceecccccchhhcChHhhhhhHhhhHHHhhcCCchhhhhh
Confidence            34554332  23456677777663  2222 23889999999999999999664  899999887777766 78999999


Q ss_pred             cchhhhcccCCCccEEecccccccccCc-hhhcCCCCCceeecccccCCCCCCC
Q 042541          641 NSTFRISDAFPNLLEMDIDYCNDLIELP-DGLCDIVSMEKLRITNCHRLSALPE  693 (695)
Q Consensus       641 ~~~~~l~~~l~~L~~L~l~~c~~l~~lP-~~i~~L~~L~~L~l~~~~~l~~lP~  693 (695)
                      +.|.    +|..||.|.+.-|. +.-++ ..+..|++|..|.+.+| .+..++.
T Consensus       134 ~~F~----gL~slqrLllNan~-i~Cir~~al~dL~~l~lLslyDn-~~q~i~~  181 (498)
T KOG4237|consen  134 GAFG----GLSSLQRLLLNANH-INCIRQDALRDLPSLSLLSLYDN-KIQSICK  181 (498)
T ss_pred             hHhh----hHHHHHHHhcChhh-hcchhHHHHHHhhhcchhcccch-hhhhhcc
Confidence            9888    89999999888764 44444 45889999999999985 4777665

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

Probab=97.34  E-value=0.0051  Score=61.99  Aligned_cols=163  Identities=15%  Similarity=0.192  Sum_probs=93.7

Q ss_pred             CCCCCcchHHHHHHHHH----c---------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHH
Q 042541          167 ISPGLDVPLKELKMELF----K---------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVK  233 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~----~---------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~  233 (695)
                      .+=|-++.+++|.+.+.    +         +.++=|.+||++|.|||-||++|++  +....|      +.+...    
T Consensus       152 dIGGL~~Qi~EirE~VELPL~~PElF~~~GI~PPKGVLLYGPPGTGKTLLAkAVA~--~T~AtF------IrvvgS----  219 (406)
T COG1222         152 DIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVAN--QTDATF------IRVVGS----  219 (406)
T ss_pred             hccCHHHHHHHHHHHhcccccCHHHHHHcCCCCCCceEeeCCCCCcHHHHHHHHHh--ccCceE------EEeccH----
Confidence            44568888999988876    1         2367799999999999999999999  454443      333332    


Q ss_pred             HHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHh-cCCCcEEEEEeCCCCCC----------h--------HHHhhhccCC
Q 042541          234 AIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQ-MRIEAILLVLDDVWPGS----------E--------SLLQKLGFQL  294 (695)
Q Consensus       234 ~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~-l~~~~~LlVlDdv~~~~----------~--------~~~~~l~~~~  294 (695)
                          ++++..-+.      .   ....+++++. -...++.|.+|.++...          +        .++..+.-+.
T Consensus       220 ----ElVqKYiGE------G---aRlVRelF~lArekaPsIIFiDEIDAIg~kR~d~~t~gDrEVQRTmleLL~qlDGFD  286 (406)
T COG1222         220 ----ELVQKYIGE------G---ARLVRELFELAREKAPSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQLDGFD  286 (406)
T ss_pred             ----HHHHHHhcc------c---hHHHHHHHHHHhhcCCeEEEEechhhhhcccccCCCCchHHHHHHHHHHHHhccCCC
Confidence                222222111      1   1223333321 14678999999985332          1        1333333333


Q ss_pred             C--CCEEEEEcCCCC------CCCC---CeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCch
Q 042541          295 P--DYKILVTSRSEF------PQFG---SVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCP  358 (695)
Q Consensus       295 ~--gs~iivTtR~~~------~~~~---~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~P  358 (695)
                      +  +.|||..|-...      ...|   ..++++.-+.+.-.++|+-++..-.-.....    .+.|++.|.|.-
T Consensus       287 ~~~nvKVI~ATNR~D~LDPALLRPGR~DRkIEfplPd~~gR~~Il~IHtrkM~l~~dvd----~e~la~~~~g~s  357 (406)
T COG1222         287 PRGNVKVIMATNRPDILDPALLRPGRFDRKIEFPLPDEEGRAEILKIHTRKMNLADDVD----LELLARLTEGFS  357 (406)
T ss_pred             CCCCeEEEEecCCccccChhhcCCCcccceeecCCCCHHHHHHHHHHHhhhccCccCcC----HHHHHHhcCCCc
Confidence            3  468888665541      1233   3677775555556677766654333322222    456677777654

>PTZ00494 tuzin-like protein; Provisional

Probab=97.33  E-value=0.28  Score=51.39  Aligned_cols=165  Identities=11%  Similarity=0.031  Sum_probs=99.4

Q ss_pred             CCCCCCCCCCCCCCcchHHHHHHHHHc---CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHH
Q 042541          158 CCSAPDPPVISPGLDVPLKELKMELFK---DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKA  234 (695)
Q Consensus       158 ~~~~~~~~~~~vGr~~~~~~l~~~L~~---~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~  234 (695)
                      ....+..+..+|.|+.+-..+.+.|.+   ..++++++.|.-|.||++|.+.....+    +-+  .++|++...   ++
T Consensus       363 ~~~a~a~~~~~V~R~~eE~~vRqvL~qld~aHPRIvV~TG~~GcGKSslcRsAvrkE----~~p--aV~VDVRg~---ED  433 (664)
T PTZ00494        363 GMLAAAAEAFEVRREDEEALVRSVLTQMAPSHPRIVALAGGSGGGRCVPCRRAVRVE----GVA--LVHVDVGGT---ED  433 (664)
T ss_pred             ccccccccccccchhhHHHHHHHHHhhccCCCCcEEEEecCCCCCchHHHHHHHHHc----CCC--eEEEEecCC---cc
Confidence            344556677889999998888887773   358999999999999999999887632    223  348888765   45


Q ss_pred             HHHHHHHhcCCCCCCCCC-hHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCC-hH---HHhhhccCCCCCEEEEEcCCCCC
Q 042541          235 IVQKVLHHKGYPVPEFQT-DEAAINDLERFF-KQMRIEAILLVLDDVWPGS-ES---LLQKLGFQLPDYKILVTSRSEFP  308 (695)
Q Consensus       235 ~~~~i~~~l~~~~~~~~~-~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~-~~---~~~~l~~~~~gs~iivTtR~~~~  308 (695)
                      -++.+++.++.+..+... .-+.+.+....- ....++.=+||+-==...+ ..   ..-.+.....-|+|++---.+..
T Consensus       434 tLrsVVKALgV~nve~CGDlLdFI~ea~~~A~~~~~g~~P~lVlkLREGssL~RVYnE~vaLacDrRlCHvv~EVplESL  513 (664)
T PTZ00494        434 TLRSVVRALGVSNVEVCGDLLGFVEEAMRGATVKASDGVPFLVMRLREGSDLGRVYGEVVSLVSDCQACHIVLAVPMKAL  513 (664)
T ss_pred             hHHHHHHHhCCCChhhhccHHHHHHHHHHHHHHhcCCCCCEEEEEeccCCcHHHHHHHHHHHHccchhheeeeechHhhh
Confidence            678889999876543211 112222222222 2234555566653211111 00   11223333344788774443321


Q ss_pred             -------CCCCeEecCCCChHHHHHHHHHh
Q 042541          309 -------QFGSVHYLKPLTYEAARTLFLHS  331 (695)
Q Consensus       309 -------~~~~~~~l~~L~~~ea~~Lf~~~  331 (695)
                             .--..|-+++++..+|.++-.+.
T Consensus       514 T~~n~~LPRLDFy~VPnFSr~QAf~YtqH~  543 (664)
T PTZ00494        514 TPLNVSSRRLDFYCIPPFSRRQAFAYAEHT  543 (664)
T ss_pred             chhhccCccceeEecCCcCHHHHHHHHhcc
Confidence                   11127889999999999887654

>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=97.31  E-value=0.0014  Score=71.21  Aligned_cols=154  Identities=16%  Similarity=0.150  Sum_probs=88.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-H
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFF-K  265 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~  265 (695)
                      .+-|.|.|+.|+|||+||+++++  .....-.+++.+++++.-..                   ...+.....+..++ +
T Consensus       431 ~~~Ill~G~~GsGKT~L~kal~~--~~~k~~~~hv~~v~Cs~l~~-------------------~~~e~iQk~l~~vfse  489 (952)
T KOG0735|consen  431 HGNILLNGPKGSGKTNLVKALFD--YYSKDLIAHVEIVSCSTLDG-------------------SSLEKIQKFLNNVFSE  489 (952)
T ss_pred             cccEEEeCCCCCCHhHHHHHHHH--HhccccceEEEEEechhccc-------------------hhHHHHHHHHHHHHHH
Confidence            46789999999999999999998  44343344466666654211                   11222233344444 5


Q ss_pred             hcCCCcEEEEEeCCCCCC--------hH-----HHhhhc------cCCCCC--EEEEEcCCCC---------CCCCCeEe
Q 042541          266 QMRIEAILLVLDDVWPGS--------ES-----LLQKLG------FQLPDY--KILVTSRSEF---------PQFGSVHY  315 (695)
Q Consensus       266 ~l~~~~~LlVlDdv~~~~--------~~-----~~~~l~------~~~~gs--~iivTtR~~~---------~~~~~~~~  315 (695)
                      .+.-.+-++||||++-..        ++     .+..+.      ....+.  .+|.|.....         ........
T Consensus       490 ~~~~~PSiIvLDdld~l~~~s~~e~~q~~~~~~rla~flnqvi~~y~~~~~~ia~Iat~qe~qtl~~~L~s~~~Fq~~~~  569 (952)
T KOG0735|consen  490 ALWYAPSIIVLDDLDCLASASSNENGQDGVVSERLAAFLNQVIKIYLKRNRKIAVIATGQELQTLNPLLVSPLLFQIVIA  569 (952)
T ss_pred             HHhhCCcEEEEcchhhhhccCcccCCcchHHHHHHHHHHHHHHHHHHccCcEEEEEEechhhhhcChhhcCccceEEEEe
Confidence            667889999999984221        11     111111      112233  3445555431         12234788


Q ss_pred             cCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCc-hhHHHHH
Q 042541          316 LKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGC-PLALKVV  364 (695)
Q Consensus       316 l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~-PLai~~~  364 (695)
                      ++.+...+-.++++.........+   ......-+..+|+|. |.-++++
T Consensus       570 L~ap~~~~R~~IL~~~~s~~~~~~---~~~dLd~ls~~TEGy~~~DL~if  616 (952)
T KOG0735|consen  570 LPAPAVTRRKEILTTIFSKNLSDI---TMDDLDFLSVKTEGYLATDLVIF  616 (952)
T ss_pred             cCCcchhHHHHHHHHHHHhhhhhh---hhHHHHHHHHhcCCccchhHHHH
Confidence            999998888888776553332211   223344488889885 4444443

>KOG2739 consensus Leucine-rich acidic nuclear protein [Cell cycle control, cell division, chromosome partitioning; General function prediction only]

Probab=97.31  E-value=9.7e-05  Score=70.94  Aligned_cols=113  Identities=19%  Similarity=0.223  Sum_probs=70.0

Q ss_pred             ccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccC--CCC-Ccc-cccccccccEEeeccccCCccc
Q 042541          564 YVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHV--SLP-NSL-ATVRMNHLQKVSLVMCNVGQVF  639 (695)
Q Consensus       564 ~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~--~l~-~lp-~i~~l~~L~~L~l~~~~i~~~~  639 (695)
                      +.+....-.+..|..|.+.+.+.++     +..+-.|++|++|.++.|  .+. .++ ..-++++|++|++++|+|+.  
T Consensus        33 g~~~gl~d~~~~le~ls~~n~gltt-----~~~~P~Lp~LkkL~lsdn~~~~~~~l~vl~e~~P~l~~l~ls~Nki~~--  105 (260)
T KOG2739|consen   33 GKLGGLTDEFVELELLSVINVGLTT-----LTNFPKLPKLKKLELSDNYRRVSGGLEVLAEKAPNLKVLNLSGNKIKD--  105 (260)
T ss_pred             CCcccccccccchhhhhhhccceee-----cccCCCcchhhhhcccCCcccccccceehhhhCCceeEEeecCCcccc--
Confidence            3444444455666666666655532     122446778888888888  444 555 55566888899998887663  


Q ss_pred             ccchhhhcccCCCccEEecccccccccCc----hhhcCCCCCceeecccc
Q 042541          640 RNSTFRISDAFPNLLEMDIDYCNDLIELP----DGLCDIVSMEKLRITNC  685 (695)
Q Consensus       640 ~~~~~~l~~~l~~L~~L~l~~c~~l~~lP----~~i~~L~~L~~L~l~~~  685 (695)
                      .+....+. .+.+|..|++.+|.... +-    .-+.-|++|.+|+-..+
T Consensus       106 lstl~pl~-~l~nL~~Ldl~n~~~~~-l~dyre~vf~ll~~L~~LD~~dv  153 (260)
T KOG2739|consen  106 LSTLRPLK-ELENLKSLDLFNCSVTN-LDDYREKVFLLLPSLKYLDGCDV  153 (260)
T ss_pred             ccccchhh-hhcchhhhhcccCCccc-cccHHHHHHHHhhhhcccccccc
Confidence            11111222 67788888888885443 22    12556778888776554

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=97.26  E-value=0.038  Score=65.26  Aligned_cols=110  Identities=16%  Similarity=0.224  Sum_probs=62.6

Q ss_pred             CCCCCCCcchHHHHHHHHHcC---------CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHH
Q 042541          165 PVISPGLDVPLKELKMELFKD---------GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAI  235 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~---------~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~  235 (695)
                      ...++|.+..++.+...+...         ...++.++|+.|+|||++|+.+..  .....-.. ++.++++.......+
T Consensus       564 ~~~v~GQ~~av~~v~~~i~~~~~gl~~~~~p~~~~Lf~Gp~GvGKt~lA~~La~--~l~~~~~~-~i~~d~s~~~~~~~~  640 (852)
T TIGR03346       564 HERVVGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELAKALAE--FLFDDEDA-MVRIDMSEYMEKHSV  640 (852)
T ss_pred             hcccCCChHHHHHHHHHHHHHhccCCCCCCCCeEEEEEcCCCCCHHHHHHHHHH--HhcCCCCc-EEEEechhhcccchH
Confidence            346899999999999888731         135688999999999999999987  33222222 445555543321111


Q ss_pred             HHHHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH
Q 042541          236 VQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES  285 (695)
Q Consensus       236 ~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~  285 (695)
                       ..+   +|.+ +.....++ ...+...+.  +....+|+||++......
T Consensus       641 -~~l---~g~~-~g~~g~~~-~g~l~~~v~--~~p~~vlllDeieka~~~  682 (852)
T TIGR03346       641 -ARL---IGAP-PGYVGYEE-GGQLTEAVR--RKPYSVVLFDEVEKAHPD  682 (852)
T ss_pred             -HHh---cCCC-CCccCccc-ccHHHHHHH--cCCCcEEEEeccccCCHH
Confidence             111   2221 21111111 112222221  233459999999877754

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>KOG2035 consensus Replication factor C, subunit RFC3 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=97.25  E-value=0.015  Score=56.56  Aligned_cols=221  Identities=14%  Similarity=0.108  Sum_probs=121.3

Q ss_pred             CCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccc---cc-cccCCCcEEEEEeCC----------CC---
Q 042541          168 SPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDD---QV-QGKFKDDIFYVTVSK----------NP---  230 (695)
Q Consensus       168 ~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~---~~-~~~f~~~~~wv~~~~----------~~---  230 (695)
                      +.++++....+......++.+-..++|++|.||-|.+..+.+.-   .+ +-+-+. .-|.+-+.          ++   
T Consensus        15 l~~~~e~~~~Lksl~~~~d~PHll~yGPSGaGKKTrimclL~elYG~gveklki~~-~t~~tpS~kklEistvsS~yHlE   93 (351)
T KOG2035|consen   15 LIYHEELANLLKSLSSTGDFPHLLVYGPSGAGKKTRIMCLLRELYGVGVEKLKIET-RTFTTPSKKKLEISTVSSNYHLE   93 (351)
T ss_pred             cccHHHHHHHHHHhcccCCCCeEEEECCCCCCchhhHHHHHHHHhCCCchheeeee-EEEecCCCceEEEEEecccceEE
Confidence            56677777777666666678999999999999999887665521   00 001111 11222221          11   


Q ss_pred             --------CHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcE-EEEEeCCCCCChH----HHhhhccCCCCC
Q 042541          231 --------NVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAI-LLVLDDVWPGSES----LLQKLGFQLPDY  297 (695)
Q Consensus       231 --------~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~-LlVlDdv~~~~~~----~~~~l~~~~~gs  297 (695)
                              .-.-+.++++++++...+-               +.-..+.| ++|+-.+++...+    +......-...+
T Consensus        94 itPSDaG~~DRvViQellKevAQt~qi---------------e~~~qr~fKvvvi~ead~LT~dAQ~aLRRTMEkYs~~~  158 (351)
T KOG2035|consen   94 ITPSDAGNYDRVVIQELLKEVAQTQQI---------------ETQGQRPFKVVVINEADELTRDAQHALRRTMEKYSSNC  158 (351)
T ss_pred             eChhhcCcccHHHHHHHHHHHHhhcch---------------hhccccceEEEEEechHhhhHHHHHHHHHHHHHHhcCc
Confidence                    1233455555554432110               11123344 5556555443322    222233334568


Q ss_pred             EEEEEcCCCCC-----CCC-CeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHHHhhC--
Q 042541          298 KILVTSRSEFP-----QFG-SVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGGSLC--  369 (695)
Q Consensus       298 ~iivTtR~~~~-----~~~-~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~~~L~--  369 (695)
                      |+|+..-+-..     ... -.+++...+++|-...+...+...+-..   ..+.+.+|+++++|.-.-...+-...+  
T Consensus       159 RlIl~cns~SriIepIrSRCl~iRvpaps~eeI~~vl~~v~~kE~l~l---p~~~l~rIa~kS~~nLRrAllmlE~~~~~  235 (351)
T KOG2035|consen  159 RLILVCNSTSRIIEPIRSRCLFIRVPAPSDEEITSVLSKVLKKEGLQL---PKELLKRIAEKSNRNLRRALLMLEAVRVN  235 (351)
T ss_pred             eEEEEecCcccchhHHhhheeEEeCCCCCHHHHHHHHHHHHHHhcccC---cHHHHHHHHHHhcccHHHHHHHHHHHHhc
Confidence            88875444321     111 2688999999999999988775544321   278999999999997543333333222  


Q ss_pred             C-------C--CHHHHHHHHHHhcCCCCccCchhhHHHHHHHHHHhc
Q 042541          370 G-------K--HEVFWQRMVKECSRGESVFQSKNDILDCLGSSLDVL  407 (695)
Q Consensus       370 ~-------~--~~~~w~~~l~~~~~~~~~~~~~~~i~~~l~~s~~~L  407 (695)
                      +       .  +.-+|+..+.+....--.......+..+-..-|+-|
T Consensus       236 n~~~~a~~~~i~~~dWe~~i~e~a~~i~~eQs~~~L~~vR~~LYeLL  282 (351)
T KOG2035|consen  236 NEPFTANSQVIPKPDWEIYIQEIARVILKEQSPAKLLEVRGRLYELL  282 (351)
T ss_pred             cccccccCCCCCCccHHHHHHHHHHHHHhccCHHHHHHHHHHHHHHH
Confidence            1       1  346798777765332111223445565555566555

>PRK08118 topology modulation protein; Reviewed

Probab=97.22  E-value=0.00018  Score=66.83  Aligned_cols=35  Identities=26%  Similarity=0.544  Sum_probs=26.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhcccccc-ccCCCcEEE
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKDDQVQ-GKFKDDIFY  223 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~~~~~-~~f~~~~~w  223 (695)
                      +.|.|+|++|+||||||+.+++...+. -+|+. ++|
T Consensus         2 ~rI~I~G~~GsGKSTlak~L~~~l~~~~~~lD~-l~~   37 (167)
T PRK08118          2 KKIILIGSGGSGKSTLARQLGEKLNIPVHHLDA-LFW   37 (167)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCCceecch-hhc
Confidence            358999999999999999999854333 34555 555

>PRK10865 protein disaggregation chaperone; Provisional

Probab=97.19  E-value=0.027  Score=66.23  Aligned_cols=44  Identities=18%  Similarity=0.243  Sum_probs=35.9

Q ss_pred             CCCCCCcchHHHHHHHHHc-------CC--ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          166 VISPGLDVPLKELKMELFK-------DG--RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~-------~~--~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..++|.+..++.+...+..       ++  ..++.++|+.|+|||++|+.+++
T Consensus       568 ~~viGQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~Lf~Gp~G~GKT~lA~aLa~  620 (857)
T PRK10865        568 HRVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKALAN  620 (857)
T ss_pred             CeEeCCHHHHHHHHHHHHHHHhcccCCCCCCceEEEECCCCCCHHHHHHHHHH
Confidence            4578999999998888762       11  24788999999999999999986

>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=97.17  E-value=0.00025  Score=63.89  Aligned_cols=85  Identities=24%  Similarity=0.358  Sum_probs=50.1

Q ss_pred             EEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhcCC
Q 042541          190 IVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRI  269 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~  269 (695)
                      |.|+|++|+|||+||+.+++  ..    ...+.-+.++...+..++....--.-+..  .. ....    +.   .. -.
T Consensus         2 vlL~G~~G~GKt~l~~~la~--~~----~~~~~~i~~~~~~~~~dl~g~~~~~~~~~--~~-~~~~----l~---~a-~~   64 (139)
T PF07728_consen    2 VLLVGPPGTGKTTLARELAA--LL----GRPVIRINCSSDTTEEDLIGSYDPSNGQF--EF-KDGP----LV---RA-MR   64 (139)
T ss_dssp             EEEEESSSSSHHHHHHHHHH--HH----TCEEEEEE-TTTSTHHHHHCEEET-TTTT--CE-EE-C----CC---TT-HH
T ss_pred             EEEECCCCCCHHHHHHHHHH--Hh----hcceEEEEeccccccccceeeeeeccccc--cc-cccc----cc---cc-cc
Confidence            67999999999999999987  33    33356778888888887764332210000  00 0000    00   00 02


Q ss_pred             CcEEEEEeCCCCCChHHHhhhc
Q 042541          270 EAILLVLDDVWPGSESLLQKLG  291 (695)
Q Consensus       270 ~~~LlVlDdv~~~~~~~~~~l~  291 (695)
                      +..++|||++.......+..+.
T Consensus        65 ~~~il~lDEin~a~~~v~~~L~   86 (139)
T PF07728_consen   65 KGGILVLDEINRAPPEVLESLL   86 (139)
T ss_dssp             EEEEEEESSCGG--HHHHHTTH
T ss_pred             ceeEEEECCcccCCHHHHHHHH
Confidence            7899999999877665555543

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of this ATPase AAA domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. This ATPase domain includes some proteins not detected by the IPR003959 from INTERPRO model.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NBX_X 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

>KOG0531 consensus Protein phosphatase 1, regulatory subunit, and related proteins [Signal transduction mechanisms]

Probab=97.17  E-value=0.00014  Score=78.48  Aligned_cols=81  Identities=17%  Similarity=0.346  Sum_probs=36.2

Q ss_pred             cccCCCCcEEEeccCCCCCcccccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchh-hcCCC
Q 042541          597 LSALSKLKKIRLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDG-LCDIV  675 (695)
Q Consensus       597 l~~l~~L~~L~L~~~~l~~lp~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~-i~~L~  675 (695)
                      +..+.+|++|++++|.|..+..+..+..|+.|++++|.|..+....      .+++|+.+++++|. +..++.. +..+.
T Consensus       114 l~~~~~L~~L~ls~N~I~~i~~l~~l~~L~~L~l~~N~i~~~~~~~------~l~~L~~l~l~~n~-i~~ie~~~~~~~~  186 (414)
T KOG0531|consen  114 LSSLVNLQVLDLSFNKITKLEGLSTLTLLKELNLSGNLISDISGLE------SLKSLKLLDLSYNR-IVDIENDELSELI  186 (414)
T ss_pred             hhhhhcchheeccccccccccchhhccchhhheeccCcchhccCCc------cchhhhcccCCcch-hhhhhhhhhhhcc
Confidence            3444555555555555554444444444555555555444322111      24455555555432 2333321 24444


Q ss_pred             CCceeeccc
Q 042541          676 SMEKLRITN  684 (695)
Q Consensus       676 ~L~~L~l~~  684 (695)
                      +|+.+++.+
T Consensus       187 ~l~~l~l~~  195 (414)
T KOG0531|consen  187 SLEELDLGG  195 (414)
T ss_pred             chHHHhccC
Confidence            555555544

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=97.16  E-value=0.007  Score=63.45  Aligned_cols=169  Identities=13%  Similarity=0.128  Sum_probs=96.3

Q ss_pred             CCCCCCCcchHHH-HHHHHH-cC--CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHH
Q 042541          165 PVISPGLDVPLKE-LKMELF-KD--GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVL  240 (695)
Q Consensus       165 ~~~~vGr~~~~~~-l~~~L~-~~--~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~  240 (695)
                      ..+++|-...... +...+. .+  ....+.|+|..|.|||.|++++.+  ......+. ...+.++    .+.....++
T Consensus        87 dnFv~g~~N~~A~aa~~~va~~~g~~~nplfi~G~~GlGKTHLl~Aign--~~~~~~~~-a~v~y~~----se~f~~~~v  159 (408)
T COG0593          87 DNFVVGPSNRLAYAAAKAVAENPGGAYNPLFIYGGVGLGKTHLLQAIGN--EALANGPN-ARVVYLT----SEDFTNDFV  159 (408)
T ss_pred             hheeeCCchHHHHHHHHHHHhccCCcCCcEEEECCCCCCHHHHHHHHHH--HHHhhCCC-ceEEecc----HHHHHHHHH
Confidence            4555665544322 222222 22  267899999999999999999998  55555543 2233333    234444444


Q ss_pred             HhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCC------hHHHhhhccC-CCCCEEEEEcCCCCC-----
Q 042541          241 HHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGS------ESLLQKLGFQ-LPDYKILVTSRSEFP-----  308 (695)
Q Consensus       241 ~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~------~~~~~~l~~~-~~gs~iivTtR~~~~-----  308 (695)
                      ..+..         ...+..+   +..  .-=++++||++...      +.+...|..- ..|-.||+|++....     
T Consensus       160 ~a~~~---------~~~~~Fk---~~y--~~dlllIDDiq~l~gk~~~qeefFh~FN~l~~~~kqIvltsdr~P~~l~~~  225 (408)
T COG0593         160 KALRD---------NEMEKFK---EKY--SLDLLLIDDIQFLAGKERTQEEFFHTFNALLENGKQIVLTSDRPPKELNGL  225 (408)
T ss_pred             HHHHh---------hhHHHHH---Hhh--ccCeeeechHhHhcCChhHHHHHHHHHHHHHhcCCEEEEEcCCCchhhccc
Confidence            44321         1122222   222  33489999985422      1122222221 234489999876632     


Q ss_pred             --------CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCc
Q 042541          309 --------QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGC  357 (695)
Q Consensus       309 --------~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~  357 (695)
                              ..|..+.+.+.+.+....++.+.+.......   .++++.-|++.....
T Consensus       226 ~~rL~SR~~~Gl~~~I~~Pd~e~r~aiL~kka~~~~~~i---~~ev~~~la~~~~~n  279 (408)
T COG0593         226 EDRLRSRLEWGLVVEIEPPDDETRLAILRKKAEDRGIEI---PDEVLEFLAKRLDRN  279 (408)
T ss_pred             cHHHHHHHhceeEEeeCCCCHHHHHHHHHHHHHhcCCCC---CHHHHHHHHHHhhcc
Confidence                    2234899999999999999998765443322   245566666655443

>cd01133 F1-ATPase_beta F1 ATP synthase beta subunit, nucleotide-binding domain

Probab=97.15  E-value=0.0011  Score=65.81  Aligned_cols=94  Identities=13%  Similarity=0.174  Sum_probs=59.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC-CHHHHHHHHHHhcCC-------CCCCCCChH---
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKGY-------PVPEFQTDE---  254 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~~-------~~~~~~~~~---  254 (695)
                      ..+-++|.|.+|+|||||++.+++  .++.+|...++++-+++.. ...++.+++...-..       ...+.....   
T Consensus        68 ~GQr~~If~~~G~GKTtLa~~i~~--~i~~~~~~~~V~~~iGer~~Ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~~  145 (274)
T cd01133          68 KGGKIGLFGGAGVGKTVLIMELIN--NIAKAHGGYSVFAGVGERTREGNDLYHEMKESGVLSKTALVYGQMNEPPGARAR  145 (274)
T ss_pred             cCCEEEEecCCCCChhHHHHHHHH--HHHhcCCCEEEEEEeccCcHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHH
Confidence            357899999999999999999998  5665676657777787655 456666766653211       111111111   


Q ss_pred             --HHHHHHHHHHHhcCCCcEEEEEeCCCC
Q 042541          255 --AAINDLERFFKQMRIEAILLVLDDVWP  281 (695)
Q Consensus       255 --~~~~~l~~~~~~l~~~~~LlVlDdv~~  281 (695)
                        ...-.+.+.+..-.++.+|+++||+-.
T Consensus       146 ~~~~a~~~AEyfr~~~g~~Vl~~~Dsltr  174 (274)
T cd01133         146 VALTGLTMAEYFRDEEGQDVLLFIDNIFR  174 (274)
T ss_pred             HHHHHHHHHHHHHHhcCCeEEEEEeChhH
Confidence              111223344422248999999999843

The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The beta subunit of ATP synthase is catalytic.

>CHL00095 clpC Clp protease ATP binding subunit

Probab=97.15  E-value=0.03  Score=65.85  Aligned_cols=108  Identities=17%  Similarity=0.237  Sum_probs=60.4

Q ss_pred             CCCCCCcchHHHHHHHHHc-------CC--ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHH
Q 042541          166 VISPGLDVPLKELKMELFK-------DG--RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIV  236 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~-------~~--~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~  236 (695)
                      ..++|-+..++.+...+..       ++  ...+.++|+.|+|||+||+.+++  .+-..-.. .+-++.++......+.
T Consensus       509 ~~v~GQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKt~lA~~LA~--~l~~~~~~-~~~~d~s~~~~~~~~~  585 (821)
T CHL00095        509 KRIIGQDEAVVAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTELTKALAS--YFFGSEDA-MIRLDMSEYMEKHTVS  585 (821)
T ss_pred             CcCcChHHHHHHHHHHHHHHhhcccCCCCCceEEEEECCCCCcHHHHHHHHHH--HhcCCccc-eEEEEchhccccccHH
Confidence            4579999999999888761       11  24567999999999999999987  33222122 4455555433222211


Q ss_pred             HHHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCC-cEEEEEeCCCCCChH
Q 042541          237 QKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIE-AILLVLDDVWPGSES  285 (695)
Q Consensus       237 ~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~-~~LlVlDdv~~~~~~  285 (695)
                      .    -+|.+ +.....++ ...+.+   .++.+ ..+++||++......
T Consensus       586 ~----l~g~~-~gyvg~~~-~~~l~~---~~~~~p~~VvllDeieka~~~  626 (821)
T CHL00095        586 K----LIGSP-PGYVGYNE-GGQLTE---AVRKKPYTVVLFDEIEKAHPD  626 (821)
T ss_pred             H----hcCCC-CcccCcCc-cchHHH---HHHhCCCeEEEECChhhCCHH
Confidence            1    12211 11111111 112222   22333 468999999877755

>PRK15386 type III secretion protein GogB; Provisional

Probab=97.11  E-value=0.00046  Score=72.06  Aligned_cols=83  Identities=16%  Similarity=0.345  Sum_probs=53.1

Q ss_pred             hcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCC-CCCcc-cccccccccEEeeccc-cCCcccccchhhh
Q 042541          570 LQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVS-LPNSL-ATVRMNHLQKVSLVMC-NVGQVFRNSTFRI  646 (695)
Q Consensus       570 ~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~-l~~lp-~i~~l~~L~~L~l~~~-~i~~~~~~~~~~l  646 (695)
                      +..+.+++.|++++|.+.  .++.+     ..+|+.|.+++|. ++.+| .+  ..+|++|++++| .+..+|+      
T Consensus        48 ~~~~~~l~~L~Is~c~L~--sLP~L-----P~sLtsL~Lsnc~nLtsLP~~L--P~nLe~L~Ls~Cs~L~sLP~------  112 (426)
T PRK15386         48 IEEARASGRLYIKDCDIE--SLPVL-----PNELTEITIENCNNLTTLPGSI--PEGLEKLTVCHCPEISGLPE------  112 (426)
T ss_pred             HHHhcCCCEEEeCCCCCc--ccCCC-----CCCCcEEEccCCCCcccCCchh--hhhhhheEccCccccccccc------
Confidence            556788999999987442  22221     2358999998754 56777 44  358999999998 5654443      


Q ss_pred             cccCCCccEEeccc--ccccccCchhhc
Q 042541          647 SDAFPNLLEMDIDY--CNDLIELPDGLC  672 (695)
Q Consensus       647 ~~~l~~L~~L~l~~--c~~l~~lP~~i~  672 (695)
                           +|+.|+++.  |..+..+|+++.
T Consensus       113 -----sLe~L~L~~n~~~~L~~LPssLk  135 (426)
T PRK15386        113 -----SVRSLEIKGSATDSIKNVPNGLT  135 (426)
T ss_pred             -----ccceEEeCCCCCcccccCcchHh
Confidence                 344555543  445677777543

>PRK13531 regulatory ATPase RavA; Provisional

Probab=97.08  E-value=0.0031  Score=67.36  Aligned_cols=42  Identities=12%  Similarity=0.101  Sum_probs=36.5

Q ss_pred             CCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          166 VISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..++||++.++.+...+..+  .-|.|.|++|+|||++|+.+..
T Consensus        20 ~~i~gre~vI~lll~aalag--~hVLL~GpPGTGKT~LAraLa~   61 (498)
T PRK13531         20 KGLYERSHAIRLCLLAALSG--ESVFLLGPPGIAKSLIARRLKF   61 (498)
T ss_pred             hhccCcHHHHHHHHHHHccC--CCEEEECCCChhHHHHHHHHHH
Confidence            45799999999998888755  4588999999999999999987

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=97.06  E-value=0.02  Score=57.47  Aligned_cols=55  Identities=16%  Similarity=0.212  Sum_probs=36.1

Q ss_pred             HHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHH
Q 042541          175 LKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQ  237 (695)
Q Consensus       175 ~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~  237 (695)
                      ++++..++..+  .-|.|.|++|+|||+||+.++.  ..    ....+.+++....+..+++.
T Consensus        11 ~~~~l~~l~~g--~~vLL~G~~GtGKT~lA~~la~--~l----g~~~~~i~~~~~~~~~dllg   65 (262)
T TIGR02640        11 TSRALRYLKSG--YPVHLRGPAGTGKTTLAMHVAR--KR----DRPVMLINGDAELTTSDLVG   65 (262)
T ss_pred             HHHHHHHHhcC--CeEEEEcCCCCCHHHHHHHHHH--Hh----CCCEEEEeCCccCCHHHHhh
Confidence            34444444433  4567999999999999999986  22    22355777777666555543

Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728).

>KOG4579 consensus Leucine-rich repeat (LRR) protein associated with apoptosis in muscle tissue [General function prediction only]

Probab=97.05  E-value=8.6e-05  Score=63.88  Aligned_cols=110  Identities=15%  Similarity=0.214  Sum_probs=84.0

Q ss_pred             CCCcEEEEcccCCCCcccC-cccccccCCCCcEEEeccCCCCCcc-ccc-ccccccEEeeccccCCcccccchhhhcccC
Q 042541          574 DELKVLIVTNYGFSPAELN-NFRVLSALSKLKKIRLEHVSLPNSL-ATV-RMNHLQKVSLVMCNVGQVFRNSTFRISDAF  650 (695)
Q Consensus       574 ~~Lr~L~l~~~~~~~~~~~-~~~~l~~l~~L~~L~L~~~~l~~lp-~i~-~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l  650 (695)
                      +.+..++|++|.+.  .+. ....+.....|...+|++|.+..+| .+. +.+-++.|+|.+|.|..+|.+.-     .+
T Consensus        27 kE~h~ldLssc~lm--~i~davy~l~~~~el~~i~ls~N~fk~fp~kft~kf~t~t~lNl~~neisdvPeE~A-----am   99 (177)
T KOG4579|consen   27 KELHFLDLSSCQLM--YIADAVYMLSKGYELTKISLSDNGFKKFPKKFTIKFPTATTLNLANNEISDVPEELA-----AM   99 (177)
T ss_pred             HHhhhcccccchhh--HHHHHHHHHhCCceEEEEecccchhhhCCHHHhhccchhhhhhcchhhhhhchHHHh-----hh
Confidence            34667777776542  011 1122556677888899999999999 554 56689999999999999998855     79


Q ss_pred             CCccEEecccccccccCchhhcCCCCCceeecccccCCCCCC
Q 042541          651 PNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALP  692 (695)
Q Consensus       651 ~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~~l~~lP  692 (695)
                      +.|+.|++++| .+...|.-|..|.+|-.|+..+|. ...+|
T Consensus       100 ~aLr~lNl~~N-~l~~~p~vi~~L~~l~~Lds~~na-~~eid  139 (177)
T KOG4579|consen  100 PALRSLNLRFN-PLNAEPRVIAPLIKLDMLDSPENA-RAEID  139 (177)
T ss_pred             HHhhhcccccC-ccccchHHHHHHHhHHHhcCCCCc-cccCc
Confidence            99999999985 578889888889999999998855 55555

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=97.05  E-value=0.0042  Score=68.86  Aligned_cols=44  Identities=25%  Similarity=0.321  Sum_probs=38.1

Q ss_pred             CCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          166 VISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +.++|.+..++.+...+......-|.|+|++|+|||++|+.+++
T Consensus        65 ~~iiGqs~~i~~l~~al~~~~~~~vLi~Ge~GtGKt~lAr~i~~  108 (531)
T TIGR02902        65 DEIIGQEEGIKALKAALCGPNPQHVIIYGPPGVGKTAAARLVLE  108 (531)
T ss_pred             HHeeCcHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHH
Confidence            45799999999998887766666788999999999999999976

Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.

>KOG1909 consensus Ran GTPase-activating protein [RNA processing and modification; Nuclear structure; Signal transduction mechanisms]

Probab=97.03  E-value=0.00021  Score=71.24  Aligned_cols=138  Identities=15%  Similarity=0.201  Sum_probs=90.6

Q ss_pred             CCceEEEEEEccCc----cccCChhhcCCCCCcEEEEcccCCCCcccC-cccccccCCCCcEEEeccCCCCC-----cc-
Q 042541          549 GPEVKVVVLNIRTK----KYVLPDFLQKMDELKVLIVTNYGFSPAELN-NFRVLSALSKLKKIRLEHVSLPN-----SL-  617 (695)
Q Consensus       549 ~~~l~~L~l~~~~~----~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~-~~~~l~~l~~L~~L~L~~~~l~~-----lp-  617 (695)
                      .++|+++....|..    ...+...|+..+.|+.+.+..|++.+.... ....+..+++|++|+|+.|-++.     +. 
T Consensus       156 ~~~Lrv~i~~rNrlen~ga~~~A~~~~~~~~leevr~~qN~I~~eG~~al~eal~~~~~LevLdl~DNtft~egs~~Lak  235 (382)
T KOG1909|consen  156 KPKLRVFICGRNRLENGGATALAEAFQSHPTLEEVRLSQNGIRPEGVTALAEALEHCPHLEVLDLRDNTFTLEGSVALAK  235 (382)
T ss_pred             CcceEEEEeeccccccccHHHHHHHHHhccccceEEEecccccCchhHHHHHHHHhCCcceeeecccchhhhHHHHHHHH
Confidence            35566666555521    223445677778899999988877655442 12346788899999999988762     33 


Q ss_pred             cccccccccEEeeccccCCcccccc-hhhhcccCCCccEEeccccccccc----CchhhcCCCCCceeeccccc
Q 042541          618 ATVRMNHLQKVSLVMCNVGQVFRNS-TFRISDAFPNLLEMDIDYCNDLIE----LPDGLCDIVSMEKLRITNCH  686 (695)
Q Consensus       618 ~i~~l~~L~~L~l~~~~i~~~~~~~-~~~l~~~l~~L~~L~l~~c~~l~~----lP~~i~~L~~L~~L~l~~~~  686 (695)
                      .+..+++|+.|+++.|.++.---.. ..-+....++|++|.+.+|..-..    +-..+...+.|+.|+|++|.
T Consensus       236 aL~s~~~L~El~l~dcll~~~Ga~a~~~al~~~~p~L~vl~l~gNeIt~da~~~la~~~~ek~dL~kLnLngN~  309 (382)
T KOG1909|consen  236 ALSSWPHLRELNLGDCLLENEGAIAFVDALKESAPSLEVLELAGNEITRDAALALAACMAEKPDLEKLNLNGNR  309 (382)
T ss_pred             HhcccchheeecccccccccccHHHHHHHHhccCCCCceeccCcchhHHHHHHHHHHHHhcchhhHHhcCCccc
Confidence            5557889999999999776422111 111112578899999998743221    23346678899999999976

>PRK04132 replication factor C small subunit; Provisional

Probab=97.00  E-value=0.019  Score=66.09  Aligned_cols=150  Identities=12%  Similarity=0.113  Sum_probs=93.4

Q ss_pred             EEc--CCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhcCC
Q 042541          192 VSA--PGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRI  269 (695)
Q Consensus       192 I~G--~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~  269 (695)
                      +.|  |.++||||+|..++++ -..+.++..++-++.++..+...+ ++++..+....+-                 -..
T Consensus       569 ~~G~lPh~lGKTT~A~ala~~-l~g~~~~~~~lElNASd~rgid~I-R~iIk~~a~~~~~-----------------~~~  629 (846)
T PRK04132        569 IGGNLPTVLHNTTAALALARE-LFGENWRHNFLELNASDERGINVI-REKVKEFARTKPI-----------------GGA  629 (846)
T ss_pred             hcCCCCCcccHHHHHHHHHHh-hhcccccCeEEEEeCCCcccHHHH-HHHHHHHHhcCCc-----------------CCC
Confidence            346  7799999999999983 112334444667777776555533 3333332111000                 012


Q ss_pred             CcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCCC------CCCeEecCCCChHHHHHHHHHhccCCCCCC
Q 042541          270 EAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFPQ------FGSVHYLKPLTYEAARTLFLHSANLQDGNS  339 (695)
Q Consensus       270 ~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~~------~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~  339 (695)
                      +.-++|+|+++.....    ++..+......+++|++|.+....      -...+++.+++.++-...+...+.....  
T Consensus       630 ~~KVvIIDEaD~Lt~~AQnALLk~lEep~~~~~FILi~N~~~kIi~tIrSRC~~i~F~~ls~~~i~~~L~~I~~~Egi--  707 (846)
T PRK04132        630 SFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGL--  707 (846)
T ss_pred             CCEEEEEECcccCCHHHHHHHHHHhhCCCCCeEEEEEeCChhhCchHHhhhceEEeCCCCCHHHHHHHHHHHHHhcCC--
Confidence            4579999999887643    333343344567888777665221      1238999999999998888776543221  


Q ss_pred             CCCchHHHHHHHHhcCCchhHHHH
Q 042541          340 YIPDENIVSKILRACKGCPLALKV  363 (695)
Q Consensus       340 ~~~~~~~~~~I~~~c~G~PLai~~  363 (695)
                       .-.++....|++.|+|-+..+..
T Consensus       708 -~i~~e~L~~Ia~~s~GDlR~AIn  730 (846)
T PRK04132        708 -ELTEEGLQAILYIAEGDMRRAIN  730 (846)
T ss_pred             -CCCHHHHHHHHHHcCCCHHHHHH
Confidence             11366889999999998754443

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=97.00  E-value=0.025  Score=58.59  Aligned_cols=86  Identities=22%  Similarity=0.114  Sum_probs=58.8

Q ss_pred             CCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCC------CCCCeEecCCCChHHHHHHHHHhccCCCC
Q 042541          268 RIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFP------QFGSVHYLKPLTYEAARTLFLHSANLQDG  337 (695)
Q Consensus       268 ~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~------~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~  337 (695)
                      .++.-++|+|+++.....    +++.+....+++.+|++|.+...      .-...+.+.+++.++..+.+....    .
T Consensus       130 ~~~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~LLpTI~SRcq~i~~~~~~~~~~~~~L~~~~----~  205 (342)
T PRK06964        130 RGGARVVVLYPAEALNVAAANALLKTLEEPPPGTVFLLVSARIDRLLPTILSRCRQFPMTVPAPEAAAAWLAAQG----V  205 (342)
T ss_pred             cCCceEEEEechhhcCHHHHHHHHHHhcCCCcCcEEEEEECChhhCcHHHHhcCEEEEecCCCHHHHHHHHHHcC----C
Confidence            466779999999877743    66667667778877776666421      112378999999999999887641    1


Q ss_pred             CCCCCchHHHHHHHHhcCCchhHHHHH
Q 042541          338 NSYIPDENIVSKILRACKGCPLALKVV  364 (695)
Q Consensus       338 ~~~~~~~~~~~~I~~~c~G~PLai~~~  364 (695)
                        +  .   ...++..++|.|..+..+
T Consensus       206 --~--~---~~~~l~~~~Gsp~~Al~~  225 (342)
T PRK06964        206 --A--D---ADALLAEAGGAPLAALAL  225 (342)
T ss_pred             --C--h---HHHHHHHcCCCHHHHHHH
Confidence              0  1   234678899999755444

>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli []

Probab=97.00  E-value=0.00055  Score=65.01  Aligned_cols=124  Identities=15%  Similarity=0.188  Sum_probs=60.7

Q ss_pred             CCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCC----CC-----C----HHHHH
Q 042541          170 GLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSK----NP-----N----VKAIV  236 (695)
Q Consensus       170 Gr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~----~~-----~----~~~~~  236 (695)
                      .+..+.....+.|.  ...+|.+.|++|.|||.||.+.+-+.-..+.|+. ++++.-.-    ..     +    ....+
T Consensus         4 p~~~~Q~~~~~al~--~~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~k-iii~Rp~v~~~~~lGflpG~~~eK~~p~~   80 (205)
T PF02562_consen    4 PKNEEQKFALDALL--NNDLVIVNGPAGTGKTFLALAAALELVKEGEYDK-IIITRPPVEAGEDLGFLPGDLEEKMEPYL   80 (205)
T ss_dssp             --SHHHHHHHHHHH--H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SE-EEEEE-S--TT----SS---------TTT
T ss_pred             CCCHHHHHHHHHHH--hCCeEEEECCCCCcHHHHHHHHHHHHHHhCCCcE-EEEEecCCCCccccccCCCCHHHHHHHHH
Confidence            34556666777777  4579999999999999999887765434567775 65553211    10     0    01111


Q ss_pred             HHHHHhcCCCCCCCCChHHHHHHHHHHH----------HhcCCC---cEEEEEeCCCCCChHHHhhhc-cCCCCCEEEEE
Q 042541          237 QKVLHHKGYPVPEFQTDEAAINDLERFF----------KQMRIE---AILLVLDDVWPGSESLLQKLG-FQLPDYKILVT  302 (695)
Q Consensus       237 ~~i~~~l~~~~~~~~~~~~~~~~l~~~~----------~~l~~~---~~LlVlDdv~~~~~~~~~~l~-~~~~gs~iivT  302 (695)
                      .-+...+..-...        ..+..++          ..++|+   +.++|+|++.+.....+..+. -.+.|||+|++
T Consensus        81 ~p~~d~l~~~~~~--------~~~~~~~~~~~Ie~~~~~~iRGrt~~~~~iIvDEaQN~t~~~~k~ilTR~g~~skii~~  152 (205)
T PF02562_consen   81 RPIYDALEELFGK--------EKLEELIQNGKIEIEPLAFIRGRTFDNAFIIVDEAQNLTPEELKMILTRIGEGSKIIIT  152 (205)
T ss_dssp             HHHHHHHTTTS-T--------TCHHHHHHTTSEEEEEGGGGTT--B-SEEEEE-SGGG--HHHHHHHHTTB-TT-EEEEE
T ss_pred             HHHHHHHHHHhCh--------HhHHHHhhcCeEEEEehhhhcCccccceEEEEecccCCCHHHHHHHHcccCCCcEEEEe
Confidence            2222222211100        0111111          223554   369999999888765455444 34568999997


Q ss_pred             cC
Q 042541          303 SR  304 (695)
Q Consensus       303 tR  304 (695)
                      --
T Consensus       153 GD  154 (205)
T PF02562_consen  153 GD  154 (205)
T ss_dssp             E-
T ss_pred             cC
Confidence            64

; GO: 0005524 ATP binding; PDB: 3B85_A.

>PRK06921 hypothetical protein; Provisional

Probab=97.00  E-value=0.0029  Score=63.45  Aligned_cols=39  Identities=21%  Similarity=0.292  Sum_probs=29.0

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEe
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTV  226 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~  226 (695)
                      ....+.++|..|+|||.||.++++  .+.......++|++.
T Consensus       116 ~~~~l~l~G~~G~GKThLa~aia~--~l~~~~g~~v~y~~~  154 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLLTAAAN--ELMRKKGVPVLYFPF  154 (266)
T ss_pred             CCCeEEEECCCCCcHHHHHHHHHH--HHhhhcCceEEEEEH
Confidence            356799999999999999999998  444332233667765

>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional

Probab=97.00  E-value=0.011  Score=60.63  Aligned_cols=24  Identities=17%  Similarity=0.119  Sum_probs=22.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+..++|||++|+|||.+|+.+++
T Consensus       147 ~PlgllL~GPPGcGKTllAraiA~  170 (413)
T PLN00020        147 VPLILGIWGGKGQGKSFQCELVFK  170 (413)
T ss_pred             CCeEEEeeCCCCCCHHHHHHHHHH
Confidence            368899999999999999999998

>CHL00195 ycf46 Ycf46; Provisional

Probab=96.99  E-value=0.0069  Score=65.93  Aligned_cols=166  Identities=13%  Similarity=0.135  Sum_probs=88.0

Q ss_pred             CCCCCCcchHHHHHHHHH-------c---CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHH
Q 042541          166 VISPGLDVPLKELKMELF-------K---DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAI  235 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~-------~---~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~  235 (695)
                      +.+.|.+..++.+.+...       .   ..++-|.++|++|+|||.+|+.+++.  .    ....+-++.+.       
T Consensus       228 ~dvgGl~~lK~~l~~~~~~~~~~~~~~gl~~pkGILL~GPpGTGKTllAkaiA~e--~----~~~~~~l~~~~-------  294 (489)
T CHL00195        228 SDIGGLDNLKDWLKKRSTSFSKQASNYGLPTPRGLLLVGIQGTGKSLTAKAIAND--W----QLPLLRLDVGK-------  294 (489)
T ss_pred             HHhcCHHHHHHHHHHHHHHhhHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHH--h----CCCEEEEEhHH-------
Confidence            456777666555544221       1   22567899999999999999999873  2    22122333221       


Q ss_pred             HHHHHHhcCCCCCCCCChHHHHHHHHHHHH-hcCCCcEEEEEeCCCCCCh------------HH----HhhhccCCCCCE
Q 042541          236 VQKVLHHKGYPVPEFQTDEAAINDLERFFK-QMRIEAILLVLDDVWPGSE------------SL----LQKLGFQLPDYK  298 (695)
Q Consensus       236 ~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~-~l~~~~~LlVlDdv~~~~~------------~~----~~~l~~~~~gs~  298 (695)
                         +.....         .+....++++++ .-...+++|++|+++....            ..    +..+.....+.-
T Consensus       295 ---l~~~~v---------Gese~~l~~~f~~A~~~~P~IL~IDEID~~~~~~~~~~d~~~~~rvl~~lL~~l~~~~~~V~  362 (489)
T CHL00195        295 ---LFGGIV---------GESESRMRQMIRIAEALSPCILWIDEIDKAFSNSESKGDSGTTNRVLATFITWLSEKKSPVF  362 (489)
T ss_pred             ---hccccc---------ChHHHHHHHHHHHHHhcCCcEEEehhhhhhhccccCCCCchHHHHHHHHHHHHHhcCCCceE
Confidence               111100         011223344442 2235789999999863210            01    111221222334


Q ss_pred             EEEEcCCCC---------CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCch
Q 042541          299 ILVTSRSEF---------PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCP  358 (695)
Q Consensus       299 iivTtR~~~---------~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~P  358 (695)
                      ||.||....         ......+.++.-+.++-.++|..+.........  .......+++.+.|.-
T Consensus       363 vIaTTN~~~~Ld~allR~GRFD~~i~v~lP~~~eR~~Il~~~l~~~~~~~~--~~~dl~~La~~T~GfS  429 (489)
T CHL00195        363 VVATANNIDLLPLEILRKGRFDEIFFLDLPSLEEREKIFKIHLQKFRPKSW--KKYDIKKLSKLSNKFS  429 (489)
T ss_pred             EEEecCChhhCCHHHhCCCcCCeEEEeCCcCHHHHHHHHHHHHhhcCCCcc--cccCHHHHHhhcCCCC
Confidence            555665441         123347888888899999999877644321100  1122566777776653

>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]

Probab=96.99  E-value=0.0013  Score=62.71  Aligned_cols=57  Identities=19%  Similarity=0.328  Sum_probs=39.6

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC-CHHHHHHHHHHhcCCC
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKGYP  246 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~~~  246 (695)
                      ++||.++|+.|+||||.+..++.  +.+.+ ...+..++..... ...+-++...+.++.+
T Consensus         1 p~vi~lvGptGvGKTTt~aKLAa--~~~~~-~~~v~lis~D~~R~ga~eQL~~~a~~l~vp   58 (196)
T PF00448_consen    1 PKVIALVGPTGVGKTTTIAKLAA--RLKLK-GKKVALISADTYRIGAVEQLKTYAEILGVP   58 (196)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHH--HHHHT-T--EEEEEESTSSTHHHHHHHHHHHHHTEE
T ss_pred             CEEEEEECCCCCchHhHHHHHHH--HHhhc-cccceeecCCCCCccHHHHHHHHHHHhccc
Confidence            47999999999999988877776  33333 5557788876433 4556667777777654

SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins []. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 2OG2_A 3B9Q_A 3DM9_B 3DMD_B 3E70_C 3DM5_B 2XXA_C 2J28_9 1ZU5_B 1ZU4_A ....

>PRK12377 putative replication protein; Provisional

Probab=96.98  E-value=0.004  Score=61.46  Aligned_cols=75  Identities=24%  Similarity=0.356  Sum_probs=45.8

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHH
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFK  265 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~  265 (695)
                      +...+.|+|.+|+|||.||.++++  .+...... +.++++.      +++..+-......       ..    ....++
T Consensus       100 ~~~~l~l~G~~GtGKThLa~AIa~--~l~~~g~~-v~~i~~~------~l~~~l~~~~~~~-------~~----~~~~l~  159 (248)
T PRK12377        100 GCTNFVFSGKPGTGKNHLAAAIGN--RLLAKGRS-VIVVTVP------DVMSRLHESYDNG-------QS----GEKFLQ  159 (248)
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHH--HHHHcCCC-eEEEEHH------HHHHHHHHHHhcc-------ch----HHHHHH
Confidence            346789999999999999999998  44333322 5566554      4555554443211       00    112223


Q ss_pred             hcCCCcEEEEEeCCCC
Q 042541          266 QMRIEAILLVLDDVWP  281 (695)
Q Consensus       266 ~l~~~~~LlVlDdv~~  281 (695)
                      .+ .+--||||||+..
T Consensus       160 ~l-~~~dLLiIDDlg~  174 (248)
T PRK12377        160 EL-CKVDLLVLDEIGI  174 (248)
T ss_pred             Hh-cCCCEEEEcCCCC
Confidence            33 3567999999943

>PRK08181 transposase; Validated

Probab=96.98  E-value=0.0017  Score=64.85  Aligned_cols=103  Identities=19%  Similarity=0.215  Sum_probs=56.1

Q ss_pred             HHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHH
Q 042541          180 MELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAIND  259 (695)
Q Consensus       180 ~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~  259 (695)
                      +|+.  ...-+.|+|++|+|||.||..+.+  ....... .++|+++      .+++..+......     ..       
T Consensus       101 ~~~~--~~~nlll~Gp~GtGKTHLa~Aia~--~a~~~g~-~v~f~~~------~~L~~~l~~a~~~-----~~-------  157 (269)
T PRK08181        101 SWLA--KGANLLLFGPPGGGKSHLAAAIGL--ALIENGW-RVLFTRT------TDLVQKLQVARRE-----LQ-------  157 (269)
T ss_pred             HHHh--cCceEEEEecCCCcHHHHHHHHHH--HHHHcCC-ceeeeeH------HHHHHHHHHHHhC-----Cc-------
Confidence            4543  335699999999999999999987  3332222 2556654      4455555433211     01       


Q ss_pred             HHHHHHhcCCCcEEEEEeCCCCCC--hH----HHhhhccCCCCCEEEEEcCCC
Q 042541          260 LERFFKQMRIEAILLVLDDVWPGS--ES----LLQKLGFQLPDYKILVTSRSE  306 (695)
Q Consensus       260 l~~~~~~l~~~~~LlVlDdv~~~~--~~----~~~~l~~~~~gs~iivTtR~~  306 (695)
                      +.+.++.+ .+.-|||+||+....  ++    +..-+...-.+..+||||...
T Consensus       158 ~~~~l~~l-~~~dLLIIDDlg~~~~~~~~~~~Lf~lin~R~~~~s~IiTSN~~  209 (269)
T PRK08181        158 LESAIAKL-DKFDLLILDDLAYVTKDQAETSVLFELISARYERRSILITANQP  209 (269)
T ss_pred             HHHHHHHH-hcCCEEEEeccccccCCHHHHHHHHHHHHHHHhCCCEEEEcCCC
Confidence            11122222 234599999985432  11    222222111235688998744

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=96.97  E-value=0.01  Score=59.20  Aligned_cols=165  Identities=18%  Similarity=0.211  Sum_probs=97.4

Q ss_pred             CCCCCCcchHHHHHHHHH----cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCH-HHHHHHHH
Q 042541          166 VISPGLDVPLKELKMELF----KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNV-KAIVQKVL  240 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~----~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~-~~~~~~i~  240 (695)
                      ..++|-.++.+++-.++.    .++..-|.|+|+.|.|||+|.-....+   .+.|....+-|.+.+..-. .-.+..|.
T Consensus        24 ~~l~g~~~~~~~l~~~lkqt~~~gEsnsviiigprgsgkT~li~~~Ls~---~q~~~E~~l~v~Lng~~~~dk~al~~I~  100 (408)
T KOG2228|consen   24 INLFGVQDEQKHLSELLKQTILHGESNSVIIIGPRGSGKTILIDTRLSD---IQENGENFLLVRLNGELQTDKIALKGIT  100 (408)
T ss_pred             cceeehHHHHHHHHHHHHHHHHhcCCCceEEEccCCCCceEeeHHHHhh---HHhcCCeEEEEEECccchhhHHHHHHHH
Confidence            457899999888888876    344566789999999999999887774   3445444556666655432 22344444


Q ss_pred             Hhc----CCCCCCCCChHHHHHHHHHHHH---hcCCCcEEEEEeCCCCCChH--------HHhhhc-cCCCCCEEEEEcC
Q 042541          241 HHK----GYPVPEFQTDEAAINDLERFFK---QMRIEAILLVLDDVWPGSES--------LLQKLG-FQLPDYKILVTSR  304 (695)
Q Consensus       241 ~~l----~~~~~~~~~~~~~~~~l~~~~~---~l~~~~~LlVlDdv~~~~~~--------~~~~l~-~~~~gs~iivTtR  304 (695)
                      +++    ........+..+....+-..++   ...+.++++|+|.++--...        +.+.-. ...|=|-|-+|||
T Consensus       101 rql~~e~~~~~k~~gsfte~l~~lL~~L~~~~~~t~~~ViFIldEfDlf~~h~rQtllYnlfDisqs~r~Piciig~Ttr  180 (408)
T KOG2228|consen  101 RQLALELNRIVKSFGSFTENLSKLLEALKKGDETTSGKVIFILDEFDLFAPHSRQTLLYNLFDISQSARAPICIIGVTTR  180 (408)
T ss_pred             HHHHHHHhhhheeecccchhHHHHHHHHhcCCCCCCceEEEEeehhhccccchhhHHHHHHHHHHhhcCCCeEEEEeecc
Confidence            443    2221111223334444444442   12345688999887543211        111111 1335577889999


Q ss_pred             CCC---------CCCCC--eEecCCCChHHHHHHHHHhcc
Q 042541          305 SEF---------PQFGS--VHYLKPLTYEAARTLFLHSAN  333 (695)
Q Consensus       305 ~~~---------~~~~~--~~~l~~L~~~ea~~Lf~~~~~  333 (695)
                      -..         ....+  ++-+++++-++...+++....
T Consensus       181 ld~lE~LEKRVKSRFshr~I~m~~~~~l~~yv~l~r~ll~  220 (408)
T KOG2228|consen  181 LDILELLEKRVKSRFSHRVIFMLPSLPLGDYVDLYRKLLS  220 (408)
T ss_pred             ccHHHHHHHHHHhhcccceeeccCCCChHHHHHHHHHHhc
Confidence            761         12222  566777888888888887653

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=96.96  E-value=0.01  Score=69.01  Aligned_cols=164  Identities=15%  Similarity=0.198  Sum_probs=90.5

Q ss_pred             CCCCCCcchHHHHHHHHHc-------------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCH
Q 042541          166 VISPGLDVPLKELKMELFK-------------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNV  232 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~-------------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~  232 (695)
                      ..+.|.+..++.|.+.+.-             ...+-|.++|++|+|||++|+++++.  ....    .+.+..+     
T Consensus       453 ~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g~~~~~giLL~GppGtGKT~lakalA~e--~~~~----fi~v~~~-----  521 (733)
T TIGR01243       453 SDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATE--SGAN----FIAVRGP-----  521 (733)
T ss_pred             hhcccHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHh--cCCC----EEEEehH-----
Confidence            3457877777777766541             12455889999999999999999983  3222    2222221     


Q ss_pred             HHHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCC------------hH----HHhhhcc--C
Q 042541          233 KAIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGS------------ES----LLQKLGF--Q  293 (695)
Q Consensus       233 ~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~------------~~----~~~~l~~--~  293 (695)
                           +++....+         +....++.++ ..-...+++|++|+++...            +.    ++..+..  .
T Consensus       522 -----~l~~~~vG---------ese~~i~~~f~~A~~~~p~iifiDEid~l~~~r~~~~~~~~~~~~~~~lL~~ldg~~~  587 (733)
T TIGR01243       522 -----EILSKWVG---------ESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGARFDTSVTDRIVNQLLTEMDGIQE  587 (733)
T ss_pred             -----HHhhcccC---------cHHHHHHHHHHHHHhcCCEEEEEEChhhhhccCCCCCCccHHHHHHHHHHHHhhcccC
Confidence                 11111110         1122344555 3335678999999985321            11    1222221  1


Q ss_pred             CCCCEEEEEcCCCC------C---CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCch
Q 042541          294 LPDYKILVTSRSEF------P---QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCP  358 (695)
Q Consensus       294 ~~gs~iivTtR~~~------~---~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~P  358 (695)
                      ..+.-||.||....      .   .....+.++..+.++-.++|+.........    .......+++.|.|.-
T Consensus       588 ~~~v~vI~aTn~~~~ld~allRpgRfd~~i~v~~Pd~~~R~~i~~~~~~~~~~~----~~~~l~~la~~t~g~s  657 (733)
T TIGR01243       588 LSNVVVIAATNRPDILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRSMPLA----EDVDLEELAEMTEGYT  657 (733)
T ss_pred             CCCEEEEEeCCChhhCCHhhcCCCccceEEEeCCcCHHHHHHHHHHHhcCCCCC----ccCCHHHHHHHcCCCC
Confidence            12334555664431      1   234478888889999999987654322211    1112566778887753

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=96.96  E-value=0.0012  Score=62.19  Aligned_cols=98  Identities=17%  Similarity=0.281  Sum_probs=65.4

Q ss_pred             CCCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcC
Q 042541          165 PVISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKG  244 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~  244 (695)
                      -..+||-++.++++.-...+++.+-+.|.||+|+||||-+..+++. -+...+..+++=.+.|+...+.-+-..|     
T Consensus        26 l~dIVGNe~tv~rl~via~~gnmP~liisGpPG~GKTTsi~~LAr~-LLG~~~ke~vLELNASdeRGIDvVRn~I-----   99 (333)
T KOG0991|consen   26 LQDIVGNEDTVERLSVIAKEGNMPNLIISGPPGTGKTTSILCLARE-LLGDSYKEAVLELNASDERGIDVVRNKI-----   99 (333)
T ss_pred             HHHhhCCHHHHHHHHHHHHcCCCCceEeeCCCCCchhhHHHHHHHH-HhChhhhhHhhhccCccccccHHHHHHH-----
Confidence            3567999999999987777888999999999999999998888772 2233444445555555544333222222     


Q ss_pred             CCCCCCCChHHHHHHHHHHH-Hh--c-CCCcEEEEEeCCCCCCh
Q 042541          245 YPVPEFQTDEAAINDLERFF-KQ--M-RIEAILLVLDDVWPGSE  284 (695)
Q Consensus       245 ~~~~~~~~~~~~~~~l~~~~-~~--l-~~~~~LlVlDdv~~~~~  284 (695)
                                      +..- +.  + .++--++|||.+++...
T Consensus       100 ----------------K~FAQ~kv~lp~grhKIiILDEADSMT~  127 (333)
T KOG0991|consen  100 ----------------KMFAQKKVTLPPGRHKIIILDEADSMTA  127 (333)
T ss_pred             ----------------HHHHHhhccCCCCceeEEEeeccchhhh
Confidence                            2111 11  1 46677899999987653

>PRK04296 thymidine kinase; Provisional

Probab=96.93  E-value=0.002  Score=61.23  Aligned_cols=110  Identities=9%  Similarity=0.038  Sum_probs=60.8

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCC--CCChHHHHHHHHHHHH
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPE--FQTDEAAINDLERFFK  265 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~--~~~~~~~~~~l~~~~~  265 (695)
                      .++.|+|+.|.||||+|..++.  +...+-.. ++.+.  ..++.......+..+++.....  .....+....+.   +
T Consensus         3 ~i~litG~~GsGKTT~~l~~~~--~~~~~g~~-v~i~k--~~~d~~~~~~~i~~~lg~~~~~~~~~~~~~~~~~~~---~   74 (190)
T PRK04296          3 KLEFIYGAMNSGKSTELLQRAY--NYEERGMK-VLVFK--PAIDDRYGEGKVVSRIGLSREAIPVSSDTDIFELIE---E   74 (190)
T ss_pred             EEEEEECCCCCHHHHHHHHHHH--HHHHcCCe-EEEEe--ccccccccCCcEecCCCCcccceEeCChHHHHHHHH---h
Confidence            5788999999999999988887  44333222 44442  1112222234456666543222  111222222222   2


Q ss_pred             hcCCCcEEEEEeCCCCCChH-HHhhhcc-CCCCCEEEEEcCCC
Q 042541          266 QMRIEAILLVLDDVWPGSES-LLQKLGF-QLPDYKILVTSRSE  306 (695)
Q Consensus       266 ~l~~~~~LlVlDdv~~~~~~-~~~~l~~-~~~gs~iivTtR~~  306 (695)
                       ..++.-+||+|.+...... +.+.+.. ...|..||+|.+..
T Consensus        75 -~~~~~dvviIDEaq~l~~~~v~~l~~~l~~~g~~vi~tgl~~  116 (190)
T PRK04296         75 -EGEKIDCVLIDEAQFLDKEQVVQLAEVLDDLGIPVICYGLDT  116 (190)
T ss_pred             -hCCCCCEEEEEccccCCHHHHHHHHHHHHHcCCeEEEEecCc
Confidence             2345569999999655333 3332322 34688999998865

>KOG2120 consensus SCF ubiquitin ligase, Skp2 component [Posttranslational modification, protein turnover, chaperones]

Probab=96.92  E-value=7.1e-05  Score=72.72  Aligned_cols=61  Identities=20%  Similarity=0.322  Sum_probs=37.3

Q ss_pred             cccccccEEeecccc-CCcccccchhhhcccCCCccEEecccccccccCchh---hcCCCCCceeeccccc
Q 042541          620 VRMNHLQKVSLVMCN-VGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDG---LCDIVSMEKLRITNCH  686 (695)
Q Consensus       620 ~~l~~L~~L~l~~~~-i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~---i~~L~~L~~L~l~~~~  686 (695)
                      .+.++|..|||+.|. ++.   +.+..+- +++.|++|.++.|..+  .|..   +...++|.+|++.+|-
T Consensus       310 ~rcp~l~~LDLSD~v~l~~---~~~~~~~-kf~~L~~lSlsRCY~i--~p~~~~~l~s~psl~yLdv~g~v  374 (419)
T KOG2120|consen  310 RRCPNLVHLDLSDSVMLKN---DCFQEFF-KFNYLQHLSLSRCYDI--IPETLLELNSKPSLVYLDVFGCV  374 (419)
T ss_pred             HhCCceeeeccccccccCc---hHHHHHH-hcchheeeehhhhcCC--ChHHeeeeccCcceEEEEecccc
Confidence            356777777777773 321   2221111 6777888888887643  4433   5666788888887763

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=96.92  E-value=0.0063  Score=70.73  Aligned_cols=164  Identities=12%  Similarity=0.120  Sum_probs=90.5

Q ss_pred             CCCCCcchHHHHHHHHHc-------------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHH
Q 042541          167 ISPGLDVPLKELKMELFK-------------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVK  233 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~~-------------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~  233 (695)
                      .+.|.+..+++|.+++..             ...+-|.++|++|+|||+||+.+++  .....    .+.++.+.     
T Consensus       179 di~G~~~~~~~l~~~i~~~~~~~~~~~~~gi~~~~giLL~GppGtGKT~laraia~--~~~~~----~i~i~~~~-----  247 (733)
T TIGR01243       179 DIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVAN--EAGAY----FISINGPE-----  247 (733)
T ss_pred             HhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCceEEEECCCCCChHHHHHHHHH--HhCCe----EEEEecHH-----
Confidence            468999999998887641             2246788999999999999999987  33221    22332211     


Q ss_pred             HHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCC-----------hH----HHhhhccC-CCC
Q 042541          234 AIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGS-----------ES----LLQKLGFQ-LPD  296 (695)
Q Consensus       234 ~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~-----------~~----~~~~l~~~-~~g  296 (695)
                       +    ....         .......+..++ ......+.+|++|+++...           ..    ++..+... ..+
T Consensus       248 -i----~~~~---------~g~~~~~l~~lf~~a~~~~p~il~iDEid~l~~~r~~~~~~~~~~~~~~Ll~~ld~l~~~~  313 (733)
T TIGR01243       248 -I----MSKY---------YGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRG  313 (733)
T ss_pred             -H----hccc---------ccHHHHHHHHHHHHHHhcCCcEEEeehhhhhcccccCCcchHHHHHHHHHHHHhhccccCC
Confidence             1    1110         001123344444 3335667899999985421           01    12212111 123


Q ss_pred             CEEEE-EcCCCC------C---CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchh
Q 042541          297 YKILV-TSRSEF------P---QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPL  359 (695)
Q Consensus       297 s~iiv-TtR~~~------~---~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PL  359 (695)
                      ..++| ||....      .   .....+.+...+.++-.+++.........    ........+++.+.|.--
T Consensus       314 ~vivI~atn~~~~ld~al~r~gRfd~~i~i~~P~~~~R~~Il~~~~~~~~l----~~d~~l~~la~~t~G~~g  382 (733)
T TIGR01243       314 RVIVIGATNRPDALDPALRRPGRFDREIVIRVPDKRARKEILKVHTRNMPL----AEDVDLDKLAEVTHGFVG  382 (733)
T ss_pred             CEEEEeecCChhhcCHHHhCchhccEEEEeCCcCHHHHHHHHHHHhcCCCC----ccccCHHHHHHhCCCCCH
Confidence            34444 443321      1   12236778888888888888754422111    112236778888888653

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>KOG4579 consensus Leucine-rich repeat (LRR) protein associated with apoptosis in muscle tissue [General function prediction only]

Probab=96.92  E-value=7.7e-05  Score=64.16  Aligned_cols=96  Identities=17%  Similarity=0.157  Sum_probs=74.2

Q ss_pred             ChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc-cccccccccEEeeccccCCcccccchhh
Q 042541          567 PDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL-ATVRMNHLQKVSLVMCNVGQVFRNSTFR  645 (695)
Q Consensus       567 p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp-~i~~l~~L~~L~l~~~~i~~~~~~~~~~  645 (695)
                      +-.+.+...|...+|++|++..-. +.+  -...+.+..|+|.+|.+..+| ++..++.|+.|+++.|++...|..+.  
T Consensus        46 vy~l~~~~el~~i~ls~N~fk~fp-~kf--t~kf~t~t~lNl~~neisdvPeE~Aam~aLr~lNl~~N~l~~~p~vi~--  120 (177)
T KOG4579|consen   46 VYMLSKGYELTKISLSDNGFKKFP-KKF--TIKFPTATTLNLANNEISDVPEELAAMPALRSLNLRFNPLNAEPRVIA--  120 (177)
T ss_pred             HHHHhCCceEEEEecccchhhhCC-HHH--hhccchhhhhhcchhhhhhchHHHhhhHHhhhcccccCccccchHHHH--
Confidence            345667778889999998773110 111  233456888999999999999 99999999999999999999888777  


Q ss_pred             hcccCCCccEEecccccccccCchhh
Q 042541          646 ISDAFPNLLEMDIDYCNDLIELPDGL  671 (695)
Q Consensus       646 l~~~l~~L~~L~l~~c~~l~~lP~~i  671 (695)
                         .|.+|-.|+..++ -...+|-.+
T Consensus       121 ---~L~~l~~Lds~~n-a~~eid~dl  142 (177)
T KOG4579|consen  121 ---PLIKLDMLDSPEN-ARAEIDVDL  142 (177)
T ss_pred             ---HHHhHHHhcCCCC-ccccCcHHH
Confidence               7888888888874 466777653

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=96.91  E-value=0.01  Score=57.02  Aligned_cols=163  Identities=12%  Similarity=0.133  Sum_probs=91.7

Q ss_pred             CCCCCCcchHHH---HHHHHHcCC------ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHH
Q 042541          166 VISPGLDVPLKE---LKMELFKDG------RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIV  236 (695)
Q Consensus       166 ~~~vGr~~~~~~---l~~~L~~~~------~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~  236 (695)
                      +.+||-++...+   |.+.|.+++      ++-|..+|++|.|||-+|+++++  ..+.-|-    -|..      .+  
T Consensus       121 ddViGqEeAK~kcrli~~yLenPe~Fg~WAPknVLFyGppGTGKTm~Akalan--e~kvp~l----~vka------t~--  186 (368)
T COG1223         121 DDVIGQEEAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAKALAN--EAKVPLL----LVKA------TE--  186 (368)
T ss_pred             hhhhchHHHHHHHHHHHHHhhChHHhcccCcceeEEECCCCccHHHHHHHHhc--ccCCceE----Eech------HH--
Confidence            456898876554   445565442      78899999999999999999998  3333221    2211      11  


Q ss_pred             HHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCC-----h-------HHHhhhccC------CCCC
Q 042541          237 QKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGS-----E-------SLLQKLGFQ------LPDY  297 (695)
Q Consensus       237 ~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~-----~-------~~~~~l~~~------~~gs  297 (695)
                       -|-+..          .+...+++++. ..-+.-+|++.+|.++...     +       ....++...      ..|.
T Consensus       187 -liGehV----------Gdgar~Ihely~rA~~~aPcivFiDE~DAiaLdRryQelRGDVsEiVNALLTelDgi~eneGV  255 (368)
T COG1223         187 -LIGEHV----------GDGARRIHELYERARKAAPCIVFIDELDAIALDRRYQELRGDVSEIVNALLTELDGIKENEGV  255 (368)
T ss_pred             -HHHHHh----------hhHHHHHHHHHHHHHhcCCeEEEehhhhhhhhhhhHHHhcccHHHHHHHHHHhccCcccCCce
Confidence             122222          23345566666 4445679999999975332     1       122233221      2244


Q ss_pred             EEEEEcCCC-CC------CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCc
Q 042541          298 KILVTSRSE-FP------QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGC  357 (695)
Q Consensus       298 ~iivTtR~~-~~------~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~  357 (695)
                      ..|-.|... ..      .....++..--+++|-.+++...+..-.    .+.....+.++++.+|+
T Consensus       256 vtIaaTN~p~~LD~aiRsRFEeEIEF~LP~~eEr~~ile~y~k~~P----lpv~~~~~~~~~~t~g~  318 (368)
T COG1223         256 VTIAATNRPELLDPAIRSRFEEEIEFKLPNDEERLEILEYYAKKFP----LPVDADLRYLAAKTKGM  318 (368)
T ss_pred             EEEeecCChhhcCHHHHhhhhheeeeeCCChHHHHHHHHHHHHhCC----CccccCHHHHHHHhCCC
Confidence            444444333 11      1223555555678888888887764322    22233366777777774

>PHA00729 NTP-binding motif containing protein

Probab=96.89  E-value=0.0052  Score=59.14  Aligned_cols=33  Identities=21%  Similarity=0.278  Sum_probs=27.0

Q ss_pred             HHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          177 ELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       177 ~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ++++.+...+...|.|+|.+|+||||||..+.+
T Consensus         7 ~~~~~l~~~~f~nIlItG~pGvGKT~LA~aLa~   39 (226)
T PHA00729          7 KIVSAYNNNGFVSAVIFGKQGSGKTTYALKVAR   39 (226)
T ss_pred             HHHHHHhcCCeEEEEEECCCCCCHHHHHHHHHH
Confidence            445555556667899999999999999999987

>KOG1909 consensus Ran GTPase-activating protein [RNA processing and modification; Nuclear structure; Signal transduction mechanisms]

Probab=96.88  E-value=0.0005  Score=68.62  Aligned_cols=87  Identities=21%  Similarity=0.227  Sum_probs=42.9

Q ss_pred             cCCCCcEEEeccCCCC--C---cc-cccccccccEEeeccccCCcccccchh-hhcccCCCccEEeccccccccc----C
Q 042541          599 ALSKLKKIRLEHVSLP--N---SL-ATVRMNHLQKVSLVMCNVGQVFRNSTF-RISDAFPNLLEMDIDYCNDLIE----L  667 (695)
Q Consensus       599 ~l~~L~~L~L~~~~l~--~---lp-~i~~l~~L~~L~l~~~~i~~~~~~~~~-~l~~~l~~L~~L~l~~c~~l~~----l  667 (695)
                      ..++|+.+.+..|.|.  .   +- .+..++||+.|||+.|-++..-..... .+| .+++|+.|++++|..-..    +
T Consensus       183 ~~~~leevr~~qN~I~~eG~~al~eal~~~~~LevLdl~DNtft~egs~~LakaL~-s~~~L~El~l~dcll~~~Ga~a~  261 (382)
T KOG1909|consen  183 SHPTLEEVRLSQNGIRPEGVTALAEALEHCPHLEVLDLRDNTFTLEGSVALAKALS-SWPHLRELNLGDCLLENEGAIAF  261 (382)
T ss_pred             hccccceEEEecccccCchhHHHHHHHHhCCcceeeecccchhhhHHHHHHHHHhc-ccchheeecccccccccccHHHH
Confidence            3445555555555543  1   12 455666777777776655432211111 111 566677777776642211    1


Q ss_pred             chhh-cCCCCCceeeccccc
Q 042541          668 PDGL-CDIVSMEKLRITNCH  686 (695)
Q Consensus       668 P~~i-~~L~~L~~L~l~~~~  686 (695)
                      -..+ ...++|++|.+.+|.
T Consensus       262 ~~al~~~~p~L~vl~l~gNe  281 (382)
T KOG1909|consen  262 VDALKESAPSLEVLELAGNE  281 (382)
T ss_pred             HHHHhccCCCCceeccCcch
Confidence            1111 235667777766654

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=96.86  E-value=0.014  Score=67.63  Aligned_cols=106  Identities=18%  Similarity=0.203  Sum_probs=61.8

Q ss_pred             CCCCCCcchHHHHHHHHHc-------C--CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHH
Q 042541          166 VISPGLDVPLKELKMELFK-------D--GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIV  236 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~-------~--~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~  236 (695)
                      ..++|-+..++.+...+..       +  ...++.++|+.|+|||+||+.++.  ..   + ...+.++.++......+ 
T Consensus       454 ~~v~GQ~~ai~~l~~~i~~~~~g~~~~~~p~~~~lf~Gp~GvGKT~lA~~la~--~l---~-~~~~~~d~se~~~~~~~-  526 (731)
T TIGR02639       454 AKIFGQDEAIDSLVSSIKRSRAGLGNPNKPVGSFLFTGPTGVGKTELAKQLAE--AL---G-VHLERFDMSEYMEKHTV-  526 (731)
T ss_pred             cceeCcHHHHHHHHHHHHHHhcCCCCCCCCceeEEEECCCCccHHHHHHHHHH--Hh---c-CCeEEEeCchhhhcccH-
Confidence            4678988888888887762       1  134688999999999999999987  33   1 22556776653322111 


Q ss_pred             HHHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH
Q 042541          237 QKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES  285 (695)
Q Consensus       237 ~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~  285 (695)
                         ...++.+ +.....+ ....+.+.++  +....+++||+++.....
T Consensus       527 ---~~lig~~-~gyvg~~-~~~~l~~~~~--~~p~~VvllDEieka~~~  568 (731)
T TIGR02639       527 ---SRLIGAP-PGYVGFE-QGGLLTEAVR--KHPHCVLLLDEIEKAHPD  568 (731)
T ss_pred             ---HHHhcCC-CCCcccc-hhhHHHHHHH--hCCCeEEEEechhhcCHH
Confidence               1112221 1111111 1112222222  234569999999877755

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=96.83  E-value=0.0092  Score=62.25  Aligned_cols=117  Identities=15%  Similarity=0.184  Sum_probs=72.9

Q ss_pred             CCCCcchHHHHHHHHH-cCCceE-EEEEcCCCCcHHHHHHHHhcccccccc---------------------CCCcEEEE
Q 042541          168 SPGLDVPLKELKMELF-KDGRQF-IVVSAPGGYGKTTLVQRLCKDDQVQGK---------------------FKDDIFYV  224 (695)
Q Consensus       168 ~vGr~~~~~~l~~~L~-~~~~~v-v~I~G~gGiGKTtLa~~~~~~~~~~~~---------------------f~~~~~wv  224 (695)
                      ++|-+....++..+.. .++.+. +.++|+.|+||||+|..+++.  +-..                     .+. +..+
T Consensus         3 ~~~~~~~~~~l~~~~~~~~~~~halL~~Gp~G~Gktt~a~~lA~~--l~~~~~~~~~~~~~~~~~~~~~~~~~~d-~lel   79 (325)
T COG0470           3 LVPWQEAVKRLLVQALESGRLPHALLFYGPPGVGKTTAALALAKE--LLCENPTGLLPCGHCRSCKLIPAGNHPD-FLEL   79 (325)
T ss_pred             cccchhHHHHHHHHHHhcCCCCceeeeeCCCCCCHHHHHHHHHHH--HhCCCcccCCcccchhhhhHHhhcCCCc-eEEe
Confidence            5777888888888887 444444 999999999999999999873  3211                     122 4444


Q ss_pred             EeCCCCC---HHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhccCCCCC
Q 042541          225 TVSKNPN---VKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGFQLPDY  297 (695)
Q Consensus       225 ~~~~~~~---~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs  297 (695)
                      +.+....   ..+..+++.+......                   ..++.-++++|+++.....    ++..+......+
T Consensus        80 ~~s~~~~~~i~~~~vr~~~~~~~~~~-------------------~~~~~kviiidead~mt~~A~nallk~lEep~~~~  140 (325)
T COG0470          80 NPSDLRKIDIIVEQVRELAEFLSESP-------------------LEGGYKVVIIDEADKLTEDAANALLKTLEEPPKNT  140 (325)
T ss_pred             cccccCCCcchHHHHHHHHHHhccCC-------------------CCCCceEEEeCcHHHHhHHHHHHHHHHhccCCCCe
Confidence            4444333   2233333333322111                   1367889999999877653    334444455678


Q ss_pred             EEEEEcCCC
Q 042541          298 KILVTSRSE  306 (695)
Q Consensus       298 ~iivTtR~~  306 (695)
                      .+|++|...
T Consensus       141 ~~il~~n~~  149 (325)
T COG0470         141 RFILITNDP  149 (325)
T ss_pred             EEEEEcCCh
Confidence            888888754

>PRK06526 transposase; Provisional

Probab=96.83  E-value=0.0028  Score=63.05  Aligned_cols=24  Identities=33%  Similarity=0.415  Sum_probs=21.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhcc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      ..-+.|+|++|+|||+||..+.+.
T Consensus        98 ~~nlll~Gp~GtGKThLa~al~~~  121 (254)
T PRK06526         98 KENVVFLGPPGTGKTHLAIGLGIR  121 (254)
T ss_pred             CceEEEEeCCCCchHHHHHHHHHH
Confidence            456899999999999999999873

>smart00763 AAA_PrkA PrkA AAA domain

Probab=96.82  E-value=0.0014  Score=67.48  Aligned_cols=46  Identities=20%  Similarity=0.267  Sum_probs=39.3

Q ss_pred             CCCCCCCcchHHHHHHHHHc------CCceEEEEEcCCCCcHHHHHHHHhcc
Q 042541          165 PVISPGLDVPLKELKMELFK------DGRQFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~------~~~~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      ...++|.++.++++++++..      ...+++.++|++|+||||||..+.+.
T Consensus        50 ~~~~~G~~~~i~~lv~~l~~~a~g~~~~r~il~L~GPPGsGKStla~~La~~  101 (361)
T smart00763       50 DHDFFGMEEAIERFVNYFKSAAQGLEERKQILYLLGPVGGGKSSLVECLKRG  101 (361)
T ss_pred             chhccCcHHHHHHHHHHHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            33689999999999999872      23588999999999999999999873

This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.

>PRK09183 transposase/IS protein; Provisional

Probab=96.82  E-value=0.0049  Score=61.69  Aligned_cols=23  Identities=39%  Similarity=0.486  Sum_probs=20.4

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+.|+|++|+|||+||..+.+
T Consensus       102 ~~~v~l~Gp~GtGKThLa~al~~  124 (259)
T PRK09183        102 NENIVLLGPSGVGKTHLAIALGY  124 (259)
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHH
Confidence            35688999999999999999976

>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=96.80  E-value=0.031  Score=62.71  Aligned_cols=167  Identities=13%  Similarity=0.107  Sum_probs=96.8

Q ss_pred             CCCCCCcchH---HHHHHHHHcCC---------ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHH
Q 042541          166 VISPGLDVPL---KELKMELFKDG---------RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVK  233 (695)
Q Consensus       166 ~~~vGr~~~~---~~l~~~L~~~~---------~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~  233 (695)
                      .++.|-++..   ++++.+|.+++         ++=|.++|++|.|||-||++++-..        ++=+++++..    
T Consensus       311 kDVAG~deAK~El~E~V~fLKNP~~Y~~lGAKiPkGvLL~GPPGTGKTLLAKAiAGEA--------gVPF~svSGS----  378 (774)
T KOG0731|consen  311 KDVAGVDEAKEELMEFVKFLKNPEQYQELGAKIPKGVLLVGPPGTGKTLLAKAIAGEA--------GVPFFSVSGS----  378 (774)
T ss_pred             ccccCcHHHHHHHHHHHHHhcCHHHHHHcCCcCcCceEEECCCCCcHHHHHHHHhccc--------CCceeeechH----
Confidence            4567877654   45555565432         5668999999999999999998732        2446666653    


Q ss_pred             HHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCC---------------hHHHhhhc----cC
Q 042541          234 AIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGS---------------ESLLQKLG----FQ  293 (695)
Q Consensus       234 ~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~---------------~~~~~~l~----~~  293 (695)
                          +.++.+.+..         ..+++.++ ..-...++++.+|+++...               +.-+..+.    -.
T Consensus       379 ----EFvE~~~g~~---------asrvr~lf~~ar~~aP~iifideida~~~~r~G~~~~~~~~e~e~tlnQll~emDgf  445 (774)
T KOG0731|consen  379 ----EFVEMFVGVG---------ASRVRDLFPLARKNAPSIIFIDEIDAVGRKRGGKGTGGGQDEREQTLNQLLVEMDGF  445 (774)
T ss_pred             ----HHHHHhcccc---------hHHHHHHHHHhhccCCeEEEecccccccccccccccCCCChHHHHHHHHHHHHhcCC
Confidence                2233322211         23344444 3335778999999874322               11111221    11


Q ss_pred             CCCC-EEEE-EcCCC------CCCCC---CeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhH
Q 042541          294 LPDY-KILV-TSRSE------FPQFG---SVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLA  360 (695)
Q Consensus       294 ~~gs-~iiv-TtR~~------~~~~~---~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLa  360 (695)
                      ..+. .|++ +|...      ....|   ..+.++.-+.....++|..++......  .+..++.+ |+...-|.+=|
T Consensus       446 ~~~~~vi~~a~tnr~d~ld~allrpGRfdr~i~i~~p~~~~r~~i~~~h~~~~~~~--~e~~dl~~-~a~~t~gf~ga  520 (774)
T KOG0731|consen  446 ETSKGVIVLAATNRPDILDPALLRPGRFDRQIQIDLPDVKGRASILKVHLRKKKLD--DEDVDLSK-LASLTPGFSGA  520 (774)
T ss_pred             cCCCcEEEEeccCCccccCHHhcCCCccccceeccCCchhhhHHHHHHHhhccCCC--cchhhHHH-HHhcCCCCcHH
Confidence            2223 3333 33332      12233   377888888888899999887554432  23455566 88888888744

>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A

Probab=96.76  E-value=0.00099  Score=58.23  Aligned_cols=21  Identities=43%  Similarity=0.781  Sum_probs=19.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +|+|.|++|+||||+|+.+.+
T Consensus         1 vI~I~G~~gsGKST~a~~La~   21 (121)
T PF13207_consen    1 VIIISGPPGSGKSTLAKELAE   21 (121)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            689999999999999999987

...

>PHA02244 ATPase-like protein

Probab=96.75  E-value=0.011  Score=61.08  Aligned_cols=49  Identities=6%  Similarity=0.094  Sum_probs=32.1

Q ss_pred             CCCCCCCCCCCCCcchHHH----HHHHHHcCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          159 CSAPDPPVISPGLDVPLKE----LKMELFKDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       159 ~~~~~~~~~~vGr~~~~~~----l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+......++|.......    +..++..+  .-|.|+|++|+|||+||+++++
T Consensus        89 ~~l~~~d~~~ig~sp~~~~~~~ri~r~l~~~--~PVLL~GppGtGKTtLA~aLA~  141 (383)
T PHA02244         89 GDISGIDTTKIASNPTFHYETADIAKIVNAN--IPVFLKGGAGSGKNHIAEQIAE  141 (383)
T ss_pred             CchhhCCCcccCCCHHHHHHHHHHHHHHhcC--CCEEEECCCCCCHHHHHHHHHH
Confidence            3344444556776655443    33333332  3467899999999999999987

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=96.72  E-value=0.0069  Score=58.74  Aligned_cols=47  Identities=17%  Similarity=0.288  Sum_probs=34.6

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQ  237 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~  237 (695)
                      ..++.|+|++|+|||+++.+++..  .... ...++|++... ++...+.+
T Consensus        12 g~i~~i~G~~GsGKT~l~~~~~~~--~~~~-g~~v~yi~~e~-~~~~rl~~   58 (209)
T TIGR02237        12 GTITQIYGPPGSGKTNICMILAVN--AARQ-GKKVVYIDTEG-LSPERFKQ   58 (209)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH--HHhC-CCeEEEEECCC-CCHHHHHH
Confidence            589999999999999999988763  2222 23488999976 66555443

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=96.70  E-value=0.01  Score=58.71  Aligned_cols=50  Identities=18%  Similarity=0.218  Sum_probs=35.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccC---CCcEEEEEeCCCCCHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKF---KDDIFYVTVSKNPNVKAIV  236 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f---~~~~~wv~~~~~~~~~~~~  236 (695)
                      ..++.|+|.+|+|||+||.+++-.......+   ..+++|++..+.++...+.
T Consensus        19 g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~~~~~~rl~   71 (235)
T cd01123          19 GSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEGTFRPERLV   71 (235)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCCCcCHHHHH
Confidence            5789999999999999999887532222211   2358899998877665443

This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

Probab=96.69  E-value=0.0075  Score=65.18  Aligned_cols=181  Identities=18%  Similarity=0.166  Sum_probs=106.6

Q ss_pred             CCCCCCcchHHHHHHHHHcCC-ceEEEEEcCCCCcHHHHHHHHhcccccc--ccCCCcEEEEEeCCCCCHHHHHHHHHHh
Q 042541          166 VISPGLDVPLKELKMELFKDG-RQFIVVSAPGGYGKTTLVQRLCKDDQVQ--GKFKDDIFYVTVSKNPNVKAIVQKVLHH  242 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~~-~~vv~I~G~gGiGKTtLa~~~~~~~~~~--~~f~~~~~wv~~~~~~~~~~~~~~i~~~  242 (695)
                      +.+||-+.-...|...+..+. ..--...|+-|+||||+|+-++.-.--.  ....      .+.++.    ..+.|...
T Consensus        16 ~evvGQe~v~~~L~nal~~~ri~hAYlfsG~RGvGKTt~Ari~AkalNC~~~~~~e------PC~~C~----~Ck~I~~g   85 (515)
T COG2812          16 DDVVGQEHVVKTLSNALENGRIAHAYLFSGPRGVGKTTIARILAKALNCENGPTAE------PCGKCI----SCKEINEG   85 (515)
T ss_pred             HHhcccHHHHHHHHHHHHhCcchhhhhhcCCCCcCchhHHHHHHHHhcCCCCCCCC------cchhhh----hhHhhhcC
Confidence            346999999999999988665 3445688999999999999887521111  1111      111111    11112111


Q ss_pred             cCCCCCCCC-ChHHHHHHHHHHHHhc-----CCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCCCCC-
Q 042541          243 KGYPVPEFQ-TDEAAINDLERFFKQM-----RIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFPQFG-  311 (695)
Q Consensus       243 l~~~~~~~~-~~~~~~~~l~~~~~~l-----~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~~~~-  311 (695)
                      -....-+.+ .....++.++++.+..     +++.-+.|+|+|.-....    +++.+....+..+.|+.|.+...... 
T Consensus        86 ~~~DviEiDaASn~gVddiR~i~e~v~y~P~~~ryKVyiIDEvHMLS~~afNALLKTLEEPP~hV~FIlATTe~~Kip~T  165 (515)
T COG2812          86 SLIDVIEIDAASNTGVDDIREIIEKVNYAPSEGRYKVYIIDEVHMLSKQAFNALLKTLEEPPSHVKFILATTEPQKIPNT  165 (515)
T ss_pred             CcccchhhhhhhccChHHHHHHHHHhccCCccccceEEEEecHHhhhHHHHHHHhcccccCccCeEEEEecCCcCcCchh
Confidence            000000000 0011244455555333     577779999999766543    44444445557777777776632221 


Q ss_pred             -----CeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchh
Q 042541          312 -----SVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPL  359 (695)
Q Consensus       312 -----~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PL  359 (695)
                           -.|.++.++.++-...+...+.....   .-.++....|++..+|...
T Consensus       166 IlSRcq~f~fkri~~~~I~~~L~~i~~~E~I---~~e~~aL~~ia~~a~Gs~R  215 (515)
T COG2812         166 ILSRCQRFDFKRLDLEEIAKHLAAILDKEGI---NIEEDALSLIARAAEGSLR  215 (515)
T ss_pred             hhhccccccccCCCHHHHHHHHHHHHHhcCC---ccCHHHHHHHHHHcCCChh
Confidence                 27899999999988888887754433   2246677888888888554

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=96.68  E-value=0.034  Score=57.45  Aligned_cols=81  Identities=16%  Similarity=0.078  Sum_probs=49.4

Q ss_pred             CCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCCCC------CCeEecCCCChHHHHHHHHHhccCCCCC
Q 042541          269 IEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFPQF------GSVHYLKPLTYEAARTLFLHSANLQDGN  338 (695)
Q Consensus       269 ~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~~~------~~~~~l~~L~~~ea~~Lf~~~~~~~~~~  338 (695)
                      +++-++|+|++...+..    +++.+.....++.+|++|.+.....      ...+.+.+++.+++.+.+....    . 
T Consensus       112 ~~~kV~iiEp~~~Ld~~a~naLLk~LEep~~~~~~Ilvth~~~~ll~ti~SRc~~~~~~~~~~~~~~~~L~~~~----~-  186 (325)
T PRK08699        112 GGLRVILIHPAESMNLQAANSLLKVLEEPPPQVVFLLVSHAADKVLPTIKSRCRKMVLPAPSHEEALAYLRERG----V-  186 (325)
T ss_pred             CCceEEEEechhhCCHHHHHHHHHHHHhCcCCCEEEEEeCChHhChHHHHHHhhhhcCCCCCHHHHHHHHHhcC----C-
Confidence            45556677888776643    4444444445677777777653211      2278899999999988886531    1 


Q ss_pred             CCCCchHHHHHHHHhcCCchhH
Q 042541          339 SYIPDENIVSKILRACKGCPLA  360 (695)
Q Consensus       339 ~~~~~~~~~~~I~~~c~G~PLa  360 (695)
                       .  ...  . .+..++|.|+.
T Consensus       187 -~--~~~--~-~l~~~~g~p~~  202 (325)
T PRK08699        187 -A--EPE--E-RLAFHSGAPLF  202 (325)
T ss_pred             -C--cHH--H-HHHHhCCChhh
Confidence             1  111  1 23568898954

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=96.65  E-value=0.01  Score=61.37  Aligned_cols=57  Identities=18%  Similarity=0.290  Sum_probs=40.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhcccccccc---CCCcEEEEEeCCCCCHHHHHHHHHHhcC
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGK---FKDDIFYVTVSKNPNVKAIVQKVLHHKG  244 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~---f~~~~~wv~~~~~~~~~~~~~~i~~~l~  244 (695)
                      ..++-|+|.+|+|||+++.+++........   -...++||+..+.++.+.+. ++++.++
T Consensus        95 g~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te~~f~~~rl~-~~~~~~g  154 (310)
T TIGR02236        95 QAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTENTFRPERIM-QMAEARG  154 (310)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECCCCCCHHHHH-HHHHHcC
Confidence            578899999999999999988764222111   12248899999988877654 4445544

This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.

>PRK08939 primosomal protein DnaI; Reviewed

Probab=96.65  E-value=0.011  Score=60.60  Aligned_cols=113  Identities=13%  Similarity=0.067  Sum_probs=64.9

Q ss_pred             CCcchHHHHHHHHHc----CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCC
Q 042541          170 GLDVPLKELKMELFK----DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGY  245 (695)
Q Consensus       170 Gr~~~~~~l~~~L~~----~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~  245 (695)
                      +|....+...+++..    ...+-+.|+|..|+|||.||.++++..- ...+.  +.+++++      +++..+....+.
T Consensus       135 ~~~~~~~~~~~fi~~~~~~~~~~gl~L~G~~G~GKThLa~Aia~~l~-~~g~~--v~~~~~~------~l~~~lk~~~~~  205 (306)
T PRK08939        135 DRLDALMAALDFLEAYPPGEKVKGLYLYGDFGVGKSYLLAAIANELA-KKGVS--STLLHFP------EFIRELKNSISD  205 (306)
T ss_pred             HHHHHHHHHHHHHHHhhccCCCCeEEEECCCCCCHHHHHHHHHHHHH-HcCCC--EEEEEHH------HHHHHHHHHHhc
Confidence            344444444555542    1346799999999999999999998422 22333  5577664      455666555432


Q ss_pred             CCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCC--ChHHH----hhhcc-C-CCCCEEEEEcC
Q 042541          246 PVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPG--SESLL----QKLGF-Q-LPDYKILVTSR  304 (695)
Q Consensus       246 ~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~--~~~~~----~~l~~-~-~~gs~iivTtR  304 (695)
                      .     .       +.+.++.+ .+-=||||||+...  .+|..    ..+.. . ..+..+|+||-
T Consensus       206 ~-----~-------~~~~l~~l-~~~dlLiIDDiG~e~~s~~~~~~ll~~Il~~R~~~~~~ti~TSN  259 (306)
T PRK08939        206 G-----S-------VKEKIDAV-KEAPVLMLDDIGAEQMSSWVRDEVLGVILQYRMQEELPTFFTSN  259 (306)
T ss_pred             C-----c-------HHHHHHHh-cCCCEEEEecCCCccccHHHHHHHHHHHHHHHHHCCCeEEEECC
Confidence            1     1       12223333 35668999998543  23322    22211 1 24567888886

>PRK07261 topology modulation protein; Provisional

Probab=96.65  E-value=0.0035  Score=58.53  Aligned_cols=22  Identities=32%  Similarity=0.496  Sum_probs=19.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHhcc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      .|.|+|++|+||||||+.+...
T Consensus         2 ri~i~G~~GsGKSTla~~l~~~   23 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARKLSQH   23 (171)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHH
Confidence            4899999999999999998763

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=96.64  E-value=0.0057  Score=54.86  Aligned_cols=102  Identities=21%  Similarity=0.290  Sum_probs=59.5

Q ss_pred             CCCcchHHHHHHHHH--cCCceEEEEEcCCCCcHHHHHHHHhccccc-cccCCCcEEEEEeCCCCCHHHHHHHHHHhcCC
Q 042541          169 PGLDVPLKELKMELF--KDGRQFIVVSAPGGYGKTTLVQRLCKDDQV-QGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGY  245 (695)
Q Consensus       169 vGr~~~~~~l~~~L~--~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~-~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~  245 (695)
                      ||....++++.+.+.  .....-|.|+|..|+||+++|+.+++.... ...|.. +   ++....               
T Consensus         1 vG~S~~~~~l~~~l~~~a~~~~pvli~GE~GtGK~~~A~~lh~~~~~~~~~~~~-~---~~~~~~---------------   61 (138)
T PF14532_consen    1 VGKSPAMRRLRRQLERLAKSSSPVLITGEPGTGKSLLARALHRYSGRANGPFIV-I---DCASLP---------------   61 (138)
T ss_dssp             --SCHHHHHHHHHHHHHHCSSS-EEEECCTTSSHHHHHHCCHHTTTTCCS-CCC-C---CHHCTC---------------
T ss_pred             CCCCHHHHHHHHHHHHHhCCCCcEEEEcCCCCCHHHHHHHHHhhcCccCCCeEE-e---chhhCc---------------
Confidence            678888888888777  344567899999999999999988763221 112221 0   111100               


Q ss_pred             CCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhccC-CCCCEEEEEcCCC
Q 042541          246 PVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGFQ-LPDYKILVTSRSE  306 (695)
Q Consensus       246 ~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~-~~gs~iivTtR~~  306 (695)
                                     .++++..  +.--|+|+|+......    +...+... ..+.|+|.||...
T Consensus        62 ---------------~~~l~~a--~~gtL~l~~i~~L~~~~Q~~L~~~l~~~~~~~~RlI~ss~~~  110 (138)
T PF14532_consen   62 ---------------AELLEQA--KGGTLYLKNIDRLSPEAQRRLLDLLKRQERSNVRLIASSSQD  110 (138)
T ss_dssp             ---------------HHHHHHC--TTSEEEEECGCCS-HHHHHHHHHHHHHCTTTTSEEEEEECC-
T ss_pred             ---------------HHHHHHc--CCCEEEECChHHCCHHHHHHHHHHHHhcCCCCeEEEEEeCCC
Confidence                           1222222  4556889999877643    33333322 4578999999865

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.63  E-value=0.0062  Score=60.30  Aligned_cols=82  Identities=16%  Similarity=0.381  Sum_probs=49.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccc--cccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDD--QVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFF  264 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~--~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~  264 (695)
                      .++|.++|++|.|||+|++++++.-  |..+.|..++ .+.++.    ..++.+...+-|.      ......+.+++++
T Consensus       177 NRliLlhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~-liEins----hsLFSKWFsESgK------lV~kmF~kI~ELv  245 (423)
T KOG0744|consen  177 NRLILLHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQ-LIEINS----HSLFSKWFSESGK------LVAKMFQKIQELV  245 (423)
T ss_pred             eeEEEEeCCCCCChhHHHHHHHHhheeeecCccccce-EEEEeh----hHHHHHHHhhhhh------HHHHHHHHHHHHH
Confidence            5899999999999999999999864  3456666533 555443    2344444433221      2233344455555


Q ss_pred             HhcCCCcEEEEEeCCC
Q 042541          265 KQMRIEAILLVLDDVW  280 (695)
Q Consensus       265 ~~l~~~~~LlVlDdv~  280 (695)
                      +. ++.-+.+.+|.|.
T Consensus       246 ~d-~~~lVfvLIDEVE  260 (423)
T KOG0744|consen  246 ED-RGNLVFVLIDEVE  260 (423)
T ss_pred             hC-CCcEEEEEeHHHH
Confidence            22 3444566778874

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=96.61  E-value=0.0081  Score=58.98  Aligned_cols=45  Identities=16%  Similarity=0.333  Sum_probs=33.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAI  235 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~  235 (695)
                      ..++.|+|.+|+|||++|.+++..  .... ...++|++.. .++...+
T Consensus        23 g~i~~i~G~~GsGKT~l~~~la~~--~~~~-~~~v~yi~~e-~~~~~r~   67 (225)
T PRK09361         23 GTITQIYGPPGSGKTNICLQLAVE--AAKN-GKKVIYIDTE-GLSPERF   67 (225)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH--HHHC-CCeEEEEECC-CCCHHHH
Confidence            579999999999999999988863  3222 2347899987 5555443

>KOG0743 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.60  E-value=0.17  Score=53.07  Aligned_cols=142  Identities=19%  Similarity=0.265  Sum_probs=78.5

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQM  267 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l  267 (695)
                      |=-.++||+|.|||+++.++++.      .+..|.=+.++...+-.+                         |++++-..
T Consensus       236 RGYLLYGPPGTGKSS~IaAmAn~------L~ydIydLeLt~v~~n~d-------------------------Lr~LL~~t  284 (457)
T KOG0743|consen  236 RGYLLYGPPGTGKSSFIAAMANY------LNYDIYDLELTEVKLDSD-------------------------LRHLLLAT  284 (457)
T ss_pred             ccceeeCCCCCCHHHHHHHHHhh------cCCceEEeeeccccCcHH-------------------------HHHHHHhC
Confidence            45679999999999999999883      222244444443322222                         44444322


Q ss_pred             CCCcEEEEEeCCCCCCh------------H----------HHhhh---ccCCCCCEEEE-EcCCC------CCCCCC---
Q 042541          268 RIEAILLVLDDVWPGSE------------S----------LLQKL---GFQLPDYKILV-TSRSE------FPQFGS---  312 (695)
Q Consensus       268 ~~~~~LlVlDdv~~~~~------------~----------~~~~l---~~~~~gs~iiv-TtR~~------~~~~~~---  312 (695)
                       ..+-+||+.|++...+            .          ++..+   .....+-|||| ||-..      ....|.   
T Consensus       285 -~~kSIivIEDIDcs~~l~~~~~~~~~~~~~~~~~VTlSGLLNfiDGlwSscg~ERIivFTTNh~EkLDPALlRpGRmDm  363 (457)
T KOG0743|consen  285 -PNKSILLIEDIDCSFDLRERRKKKKENFEGDLSRVTLSGLLNFLDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDM  363 (457)
T ss_pred             -CCCcEEEEeecccccccccccccccccccCCcceeehHHhhhhhccccccCCCceEEEEecCChhhcCHhhcCCCccee
Confidence             3455666676643211            0          11111   11112235655 66654      123333   


Q ss_pred             eEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHHHh
Q 042541          313 VHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGGS  367 (695)
Q Consensus       313 ~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~~~  367 (695)
                      .+.+.--+.+.-..||.+......      ...+..+|.+...|.-+.=..++..
T Consensus       364 hI~mgyCtf~~fK~La~nYL~~~~------~h~L~~eie~l~~~~~~tPA~V~e~  412 (457)
T KOG0743|consen  364 HIYMGYCTFEAFKTLASNYLGIEE------DHRLFDEIERLIEETEVTPAQVAEE  412 (457)
T ss_pred             EEEcCCCCHHHHHHHHHHhcCCCC------CcchhHHHHHHhhcCccCHHHHHHH
Confidence            678889999999999998875433      1234556666555554444444443

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=96.59  E-value=0.022  Score=60.27  Aligned_cols=91  Identities=16%  Similarity=0.247  Sum_probs=56.9

Q ss_pred             CCCCCcc---hHHHHHHHHHcCC---------ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHH
Q 042541          167 ISPGLDV---PLKELKMELFKDG---------RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKA  234 (695)
Q Consensus       167 ~~vGr~~---~~~~l~~~L~~~~---------~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~  234 (695)
                      ++-|-|+   |+++|+++|.++.         ++=|.++|++|.|||-||++++-...+.       ||...+..|+.  
T Consensus       305 dVkG~DEAK~ELeEiVefLkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAvAGEA~VP-------FF~~sGSEFdE--  375 (752)
T KOG0734|consen  305 DVKGVDEAKQELEEIVEFLKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAVAGEAGVP-------FFYASGSEFDE--  375 (752)
T ss_pred             cccChHHHHHHHHHHHHHhcCcHHhhhccCcCCCceEEeCCCCCchhHHHHHhhcccCCC-------eEeccccchhh--
Confidence            4567766   5677777777432         5779999999999999999998743221       12222222221  


Q ss_pred             HHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCC
Q 042541          235 IVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPG  282 (695)
Q Consensus       235 ~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~  282 (695)
                          ++            ......+++.++ ..-..-+|+|.+|.++..
T Consensus       376 ----m~------------VGvGArRVRdLF~aAk~~APcIIFIDEiDav  408 (752)
T KOG0734|consen  376 ----MF------------VGVGARRVRDLFAAAKARAPCIIFIDEIDAV  408 (752)
T ss_pred             ----hh------------hcccHHHHHHHHHHHHhcCCeEEEEechhhh
Confidence                11            111234566666 444577999999998543

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.58  E-value=0.028  Score=59.43  Aligned_cols=139  Identities=19%  Similarity=0.233  Sum_probs=80.4

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-H
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFF-K  265 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~  265 (695)
                      ..-+.+.|++|+|||+||..++.    ...|+. +   .+-.   +++       -+|.      +.......+...+ +
T Consensus       538 lvSvLl~Gp~~sGKTaLAA~iA~----~S~FPF-v---KiiS---pe~-------miG~------sEsaKc~~i~k~F~D  593 (744)
T KOG0741|consen  538 LVSVLLEGPPGSGKTALAAKIAL----SSDFPF-V---KIIS---PED-------MIGL------SESAKCAHIKKIFED  593 (744)
T ss_pred             ceEEEEecCCCCChHHHHHHHHh----hcCCCe-E---EEeC---hHH-------ccCc------cHHHHHHHHHHHHHH
Confidence            45678999999999999999875    466775 3   2111   111       0111      2333455666666 6


Q ss_pred             hcCCCcEEEEEeCCCCCChH----------HHhhhc----cCC-CCCEEEE-EcCCC---------CCCCCCeEecCCCC
Q 042541          266 QMRIEAILLVLDDVWPGSES----------LLQKLG----FQL-PDYKILV-TSRSE---------FPQFGSVHYLKPLT  320 (695)
Q Consensus       266 ~l~~~~~LlVlDdv~~~~~~----------~~~~l~----~~~-~gs~iiv-TtR~~---------~~~~~~~~~l~~L~  320 (695)
                      ..+..--.+|+||+...-+|          +++.+.    ... .|-|.+| +|.++         .......|.++.++
T Consensus       594 AYkS~lsiivvDdiErLiD~vpIGPRfSN~vlQaL~VllK~~ppkg~kLli~~TTS~~~vL~~m~i~~~F~~~i~Vpnl~  673 (744)
T KOG0741|consen  594 AYKSPLSIIVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKQPPKGRKLLIFGTTSRREVLQEMGILDCFSSTIHVPNLT  673 (744)
T ss_pred             hhcCcceEEEEcchhhhhcccccCchhhHHHHHHHHHHhccCCCCCceEEEEecccHHHHHHHcCHHHhhhheeecCccC
Confidence            77888899999998654432          222222    122 2445444 33333         12344589999998


Q ss_pred             h-HHHHHHHHHhc-cCCCCCCCCCchHHHHHHHHhc
Q 042541          321 Y-EAARTLFLHSA-NLQDGNSYIPDENIVSKILRAC  354 (695)
Q Consensus       321 ~-~ea~~Lf~~~~-~~~~~~~~~~~~~~~~~I~~~c  354 (695)
                      . ++..+.+...- |.+     ...+.++.+...+|
T Consensus       674 ~~~~~~~vl~~~n~fsd-----~~~~~~~~~~~~~~  704 (744)
T KOG0741|consen  674 TGEQLLEVLEELNIFSD-----DEVRAIAEQLLSKK  704 (744)
T ss_pred             chHHHHHHHHHccCCCc-----chhHHHHHHHhccc
Confidence            7 67777776532 221     22345566666666

>KOG2123 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.56  E-value=0.00016  Score=69.64  Aligned_cols=101  Identities=15%  Similarity=0.166  Sum_probs=57.3

Q ss_pred             CCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcccccccccccEEeeccccCCcccccchhhhcccCCC
Q 042541          573 MDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPN  652 (695)
Q Consensus       573 l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~  652 (695)
                      +.+.+-|++.+|++.     +.+.+..++.|++|.|+-|.|+++-.+..+++|+.|.|+.|.|..+.+-.  .+- +|++
T Consensus        18 l~~vkKLNcwg~~L~-----DIsic~kMp~lEVLsLSvNkIssL~pl~rCtrLkElYLRkN~I~sldEL~--YLk-nlps   89 (388)
T KOG2123|consen   18 LENVKKLNCWGCGLD-----DISICEKMPLLEVLSLSVNKISSLAPLQRCTRLKELYLRKNCIESLDELE--YLK-NLPS   89 (388)
T ss_pred             HHHhhhhcccCCCcc-----HHHHHHhcccceeEEeeccccccchhHHHHHHHHHHHHHhcccccHHHHH--HHh-cCch
Confidence            344555566665542     22335566667777777776666555666677777777777665543211  111 5666


Q ss_pred             ccEEecccccccccCchh-----hcCCCCCceee
Q 042541          653 LLEMDIDYCNDLIELPDG-----LCDIVSMEKLR  681 (695)
Q Consensus       653 L~~L~l~~c~~l~~lP~~-----i~~L~~L~~L~  681 (695)
                      |++|.|..|.-.+.-+..     +.-|++|+.||
T Consensus        90 Lr~LWL~ENPCc~~ag~nYR~~VLR~LPnLkKLD  123 (388)
T KOG2123|consen   90 LRTLWLDENPCCGEAGQNYRRKVLRVLPNLKKLD  123 (388)
T ss_pred             hhhHhhccCCcccccchhHHHHHHHHcccchhcc
Confidence            777777665555554432     44566666655

>PRK06696 uridine kinase; Validated

Probab=96.56  E-value=0.0027  Score=62.27  Aligned_cols=39  Identities=21%  Similarity=0.243  Sum_probs=32.9

Q ss_pred             CcchHHHHHHHHH---cCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          171 LDVPLKELKMELF---KDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       171 r~~~~~~l~~~L~---~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      |++-+++|.+.+.   .+...+|+|.|.+|+||||||+.+..
T Consensus         3 ~~~~~~~la~~~~~~~~~~~~iI~I~G~sgsGKSTlA~~L~~   44 (223)
T PRK06696          3 RKQLIKELAEHILTLNLTRPLRVAIDGITASGKTTFADELAE   44 (223)
T ss_pred             HHHHHHHHHHHHHHhCCCCceEEEEECCCCCCHHHHHHHHHH
Confidence            5666778887775   34578999999999999999999987

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=96.56  E-value=0.017  Score=59.34  Aligned_cols=58  Identities=21%  Similarity=0.229  Sum_probs=41.8

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhcccccc---ccCCCcEEEEEeCCCCCHHHHHHHHHHhcCC
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQ---GKFKDDIFYVTVSKNPNVKAIVQKVLHHKGY  245 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~---~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~  245 (695)
                      ..++-|+|++|+|||+|+..++-.....   ..-...++|++....++++.+.+ +++.++.
T Consensus        96 G~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~~f~~eRi~~-~a~~~g~  156 (313)
T TIGR02238        96 MSITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEGTFRPDRIRA-IAERFGV  156 (313)
T ss_pred             CeEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCCCCCHHHHHH-HHHHcCC
Confidence            4788899999999999998766422222   12234588999999988887754 4566554

This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.

>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=96.48  E-value=0.0093  Score=65.41  Aligned_cols=73  Identities=18%  Similarity=0.360  Sum_probs=55.4

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHh
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQ  266 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~  266 (695)
                      -++..++|++|+||||||+-++++    ..|  .|+=|+.|+..+...+-..|...+....                  .
T Consensus       326 kKilLL~GppGlGKTTLAHViAkq----aGY--sVvEINASDeRt~~~v~~kI~~avq~~s------------------~  381 (877)
T KOG1969|consen  326 KKILLLCGPPGLGKTTLAHVIAKQ----AGY--SVVEINASDERTAPMVKEKIENAVQNHS------------------V  381 (877)
T ss_pred             cceEEeecCCCCChhHHHHHHHHh----cCc--eEEEecccccccHHHHHHHHHHHHhhcc------------------c
Confidence            589999999999999999998863    233  3668888988888777777766653221                  1


Q ss_pred             c--CCCcEEEEEeCCCCCC
Q 042541          267 M--RIEAILLVLDDVWPGS  283 (695)
Q Consensus       267 l--~~~~~LlVlDdv~~~~  283 (695)
                      +  .+++..||+|.++...
T Consensus       382 l~adsrP~CLViDEIDGa~  400 (877)
T KOG1969|consen  382 LDADSRPVCLVIDEIDGAP  400 (877)
T ss_pred             cccCCCcceEEEecccCCc
Confidence            1  3788999999998766

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=96.48  E-value=0.014  Score=57.42  Aligned_cols=48  Identities=19%  Similarity=0.205  Sum_probs=35.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccC-----CCcEEEEEeCCCCCHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKF-----KDDIFYVTVSKNPNVKAIV  236 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f-----~~~~~wv~~~~~~~~~~~~  236 (695)
                      ..++.|+|.+|+|||+||..++..  ....-     +..++|++....++...+.
T Consensus        19 g~v~~I~G~~GsGKT~l~~~ia~~--~~~~~~~~g~~~~v~yi~~e~~~~~~rl~   71 (226)
T cd01393          19 GRITEIFGEFGSGKTQLCLQLAVE--AQLPGELGGLEGKVVYIDTEGAFRPERLV   71 (226)
T ss_pred             CcEEEEeCCCCCChhHHHHHHHHH--hhcccccCCCcceEEEEecCCCCCHHHHH
Confidence            579999999999999999988753  21121     1447899988877765543

RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs radA and radB.

>KOG2739 consensus Leucine-rich acidic nuclear protein [Cell cycle control, cell division, chromosome partitioning; General function prediction only]

Probab=96.47  E-value=0.0014  Score=63.20  Aligned_cols=82  Identities=21%  Similarity=0.261  Sum_probs=57.7

Q ss_pred             ccCCCCcEEEeccCCCC---CcccccccccccEEeeccc--cCCcccccchhhhcccCCCccEEecccccc--cccCchh
Q 042541          598 SALSKLKKIRLEHVSLP---NSLATVRMNHLQKVSLVMC--NVGQVFRNSTFRISDAFPNLLEMDIDYCND--LIELPDG  670 (695)
Q Consensus       598 ~~l~~L~~L~L~~~~l~---~lp~i~~l~~L~~L~l~~~--~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~--l~~lP~~  670 (695)
                      ..+..|++|++.++.++   .+|   .|++|++|.++.|  ++..-.+....    .+++|++|++++|..  +..++. 
T Consensus        40 d~~~~le~ls~~n~gltt~~~~P---~Lp~LkkL~lsdn~~~~~~~l~vl~e----~~P~l~~l~ls~Nki~~lstl~p-  111 (260)
T KOG2739|consen   40 DEFVELELLSVINVGLTTLTNFP---KLPKLKKLELSDNYRRVSGGLEVLAE----KAPNLKVLNLSGNKIKDLSTLRP-  111 (260)
T ss_pred             ccccchhhhhhhccceeecccCC---CcchhhhhcccCCcccccccceehhh----hCCceeEEeecCCccccccccch-
Confidence            34556677777666654   566   8999999999999  54433333333    679999999999642  223332 


Q ss_pred             hcCCCCCceeecccccC
Q 042541          671 LCDIVSMEKLRITNCHR  687 (695)
Q Consensus       671 i~~L~~L~~L~l~~~~~  687 (695)
                      +..+.+|..|++.+|..
T Consensus       112 l~~l~nL~~Ldl~n~~~  128 (260)
T KOG2739|consen  112 LKELENLKSLDLFNCSV  128 (260)
T ss_pred             hhhhcchhhhhcccCCc
Confidence            67888999999999873

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.47  E-value=0.03  Score=61.03  Aligned_cols=160  Identities=18%  Similarity=0.259  Sum_probs=84.6

Q ss_pred             CC-CcchHHHHHHHHH-------------cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHH
Q 042541          169 PG-LDVPLKELKMELF-------------KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKA  234 (695)
Q Consensus       169 vG-r~~~~~~l~~~L~-------------~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~  234 (695)
                      +| .++-..+|.+.+.             -..++=|..+|++|+|||++|+++++  .-.-.|      ++++..     
T Consensus       436 IGGlE~lK~elq~~V~~p~~~pe~F~r~Gi~ppkGVLlyGPPGC~KT~lAkalAn--e~~~nF------lsvkgp-----  502 (693)
T KOG0730|consen  436 IGGLEELKRELQQAVEWPLKHPEKFARFGISPPKGVLLYGPPGCGKTLLAKALAN--EAGMNF------LSVKGP-----  502 (693)
T ss_pred             ccCHHHHHHHHHHHHhhhhhchHHHHHhcCCCCceEEEECCCCcchHHHHHHHhh--hhcCCe------eeccCH-----
Confidence            45 6665555555444             12367899999999999999999998  333333      333321     


Q ss_pred             HHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCC-----------hHHHhhhcc---CC-CCCE
Q 042541          235 IVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGS-----------ESLLQKLGF---QL-PDYK  298 (695)
Q Consensus       235 ~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~-----------~~~~~~l~~---~~-~gs~  298 (695)
                         +++....+      ..   ...++.++ ++-+--++++.||.++...           +.++..+..   +. ....
T Consensus       503 ---EL~sk~vG------eS---Er~ir~iF~kAR~~aP~IiFfDEiDsi~~~R~g~~~~v~~RVlsqLLtEmDG~e~~k~  570 (693)
T KOG0730|consen  503 ---ELFSKYVG------ES---ERAIREVFRKARQVAPCIIFFDEIDALAGSRGGSSSGVTDRVLSQLLTEMDGLEALKN  570 (693)
T ss_pred             ---HHHHHhcC------ch---HHHHHHHHHHHhhcCCeEEehhhHHhHhhccCCCccchHHHHHHHHHHHcccccccCc
Confidence               11211111      11   22334444 2223456899999874322           112222222   11 1223


Q ss_pred             EE-E--EcCCC-----CCCCC---CeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCc
Q 042541          299 IL-V--TSRSE-----FPQFG---SVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGC  357 (695)
Q Consensus       299 ii-v--TtR~~-----~~~~~---~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~  357 (695)
                      |+ |  |-|..     ....|   ..+.++.-+.+.-.++|+.++....-....    ...+|++++.|.
T Consensus       571 V~ViAATNRpd~ID~ALlRPGRlD~iiyVplPD~~aR~~Ilk~~~kkmp~~~~v----dl~~La~~T~g~  636 (693)
T KOG0730|consen  571 VLVIAATNRPDMIDPALLRPGRLDRIIYVPLPDLEARLEILKQCAKKMPFSEDV----DLEELAQATEGY  636 (693)
T ss_pred             EEEEeccCChhhcCHHHcCCcccceeEeecCccHHHHHHHHHHHHhcCCCCccc----cHHHHHHHhccC
Confidence            33 3  33332     12333   367777778888889999887554432221    245566655554

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=96.46  E-value=0.013  Score=62.66  Aligned_cols=91  Identities=16%  Similarity=0.203  Sum_probs=51.1

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCC-CCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHH
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKN-PNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFF  264 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~-~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~  264 (695)
                      .+.+|.++|..|+||||+|..++.  ..... ...+..+++... ....+.+..+.+.++.+........+....+...+
T Consensus        94 ~p~vI~lvG~~GsGKTTtaakLA~--~L~~~-g~kV~lV~~D~~R~aa~eQL~~la~~~gvp~~~~~~~~d~~~i~~~al  170 (437)
T PRK00771         94 KPQTIMLVGLQGSGKTTTAAKLAR--YFKKK-GLKVGLVAADTYRPAAYDQLKQLAEKIGVPFYGDPDNKDAVEIAKEGL  170 (437)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHH--HHHHc-CCeEEEecCCCCCHHHHHHHHHHHHHcCCcEEecCCccCHHHHHHHHH
Confidence            368999999999999999998887  33322 123555655432 22345566666776654322111112223333444


Q ss_pred             HhcCCCcEEEEEeCCC
Q 042541          265 KQMRIEAILLVLDDVW  280 (695)
Q Consensus       265 ~~l~~~~~LlVlDdv~  280 (695)
                      +...+. -++|+|..-
T Consensus       171 ~~~~~~-DvVIIDTAG  185 (437)
T PRK00771        171 EKFKKA-DVIIVDTAG  185 (437)
T ss_pred             HHhhcC-CEEEEECCC
Confidence            333333 567777763

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=96.46  E-value=0.0046  Score=57.97  Aligned_cols=76  Identities=20%  Similarity=0.440  Sum_probs=42.2

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHH
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFK  265 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~  265 (695)
                      ...-+.|+|..|+|||.||..+.+. -+...+.  +.|+++      .+++..+-..-.    . ....   +.+    +
T Consensus        46 ~~~~l~l~G~~G~GKThLa~ai~~~-~~~~g~~--v~f~~~------~~L~~~l~~~~~----~-~~~~---~~~----~  104 (178)
T PF01695_consen   46 NGENLILYGPPGTGKTHLAVAIANE-AIRKGYS--VLFITA------SDLLDELKQSRS----D-GSYE---ELL----K  104 (178)
T ss_dssp             C--EEEEEESTTSSHHHHHHHHHHH-HHHTT----EEEEEH------HHHHHHHHCCHC----C-TTHC---HHH----H
T ss_pred             cCeEEEEEhhHhHHHHHHHHHHHHH-hccCCcc--eeEeec------Cceecccccccc----c-cchh---hhc----C
Confidence            3467999999999999999999873 2223333  667754      345555433211    1 1111   112    2


Q ss_pred             hcCCCcEEEEEeCCCCCC
Q 042541          266 QMRIEAILLVLDDVWPGS  283 (695)
Q Consensus       266 ~l~~~~~LlVlDdv~~~~  283 (695)
                      .+. +-=||||||+....
T Consensus       105 ~l~-~~dlLilDDlG~~~  121 (178)
T PF01695_consen  105 RLK-RVDLLILDDLGYEP  121 (178)
T ss_dssp             HHH-TSSCEEEETCTSS-
T ss_pred             ccc-cccEecccccceee
Confidence            222 34578899986543

They are found associated with IS21 family insertion sequences []. Functionally they have not been characterised, but they may be involved in transposition [].; GO: 0005524 ATP binding; PDB: 3EC2_A 3ECC_A 2W58_A 2QGZ_A.

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=96.44  E-value=0.0025  Score=56.72  Aligned_cols=35  Identities=31%  Similarity=0.479  Sum_probs=26.8

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhcccccccc-CCCcEEEE
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKDDQVQGK-FKDDIFYV  224 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~~~~~~~-f~~~~~wv  224 (695)
                      --|+|.|++|+||||+++.+.+  .++.. |..+-+|.
T Consensus         6 mki~ITG~PGvGKtTl~~ki~e--~L~~~g~kvgGf~t   41 (179)
T COG1618           6 MKIFITGRPGVGKTTLVLKIAE--KLREKGYKVGGFIT   41 (179)
T ss_pred             eEEEEeCCCCccHHHHHHHHHH--HHHhcCceeeeEEe
Confidence            4589999999999999999998  44443 66544454

>PRK05541 adenylylsulfate kinase; Provisional

Probab=96.43  E-value=0.013  Score=55.11  Aligned_cols=36  Identities=25%  Similarity=0.512  Sum_probs=28.2

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEE
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYV  224 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv  224 (695)
                      ...+|.|+|+.|+||||+|+.++.  +....+.. +.++
T Consensus         6 ~~~~I~i~G~~GsGKst~a~~l~~--~l~~~~~~-~~~~   41 (176)
T PRK05541          6 NGYVIWITGLAGSGKTTIAKALYE--RLKLKYSN-VIYL   41 (176)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHH--HHHHcCCc-EEEE
Confidence            356899999999999999999988  55555555 4444

>KOG0531 consensus Protein phosphatase 1, regulatory subunit, and related proteins [Signal transduction mechanisms]

Probab=96.42  E-value=0.0013  Score=70.98  Aligned_cols=108  Identities=17%  Similarity=0.194  Sum_probs=82.9

Q ss_pred             CCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc-cccccccccEEeeccccCCcccccchhhhcccC
Q 042541          572 KMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL-ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAF  650 (695)
Q Consensus       572 ~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp-~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l  650 (695)
                      .+..+..+.++.|.+..    ....++.+.+|.+|++.+|.|..+. .+..+.+|++|++++|.|+.+.+-.      .+
T Consensus        70 ~l~~l~~l~l~~n~i~~----~~~~l~~~~~l~~l~l~~n~i~~i~~~l~~~~~L~~L~ls~N~I~~i~~l~------~l  139 (414)
T KOG0531|consen   70 SLTSLKELNLRQNLIAK----ILNHLSKLKSLEALDLYDNKIEKIENLLSSLVNLQVLDLSFNKITKLEGLS------TL  139 (414)
T ss_pred             HhHhHHhhccchhhhhh----hhcccccccceeeeeccccchhhcccchhhhhcchheeccccccccccchh------hc
Confidence            34555566666655422    1222678899999999999999888 4889999999999999999876543      57


Q ss_pred             CCccEEecccccccccCchhhcCCCCCceeecccccCCCCCC
Q 042541          651 PNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALP  692 (695)
Q Consensus       651 ~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~~l~~lP  692 (695)
                      +.|+.|++++| .+..++ ++..+.+|+.+++++|. +..++
T Consensus       140 ~~L~~L~l~~N-~i~~~~-~~~~l~~L~~l~l~~n~-i~~ie  178 (414)
T KOG0531|consen  140 TLLKELNLSGN-LISDIS-GLESLKSLKLLDLSYNR-IVDIE  178 (414)
T ss_pred             cchhhheeccC-cchhcc-CCccchhhhcccCCcch-hhhhh
Confidence            88999999995 567665 47789999999999976 54443

>TIGR01069 mutS2 MutS2 family protein

Probab=96.41  E-value=0.058  Score=62.45  Aligned_cols=181  Identities=14%  Similarity=0.182  Sum_probs=84.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCC---CCCChHHHHHHHHH
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVP---EFQTDEAAINDLER  262 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~---~~~~~~~~~~~l~~  262 (695)
                      +..++.|+|+.|.|||||.+.+.-.. +..+-.   .+|.+..... ...+.++...++....   ...........+..
T Consensus       321 ~~~~liItGpNg~GKSTlLK~i~~~~-l~aq~G---~~Vpa~~~~~-~~~~d~i~~~i~~~~si~~~LStfS~~m~~~~~  395 (771)
T TIGR01069       321 EKRVLAITGPNTGGKTVTLKTLGLLA-LMFQSG---IPIPANEHSE-IPYFEEIFADIGDEQSIEQNLSTFSGHMKNISA  395 (771)
T ss_pred             CceEEEEECCCCCCchHHHHHHHHHH-HHHHhC---CCccCCcccc-ccchhheeeecChHhHHhhhhhHHHHHHHHHHH
Confidence            35799999999999999999886521 100000   0222111100 0011111111111000   00111223334455


Q ss_pred             HHHhcCCCcEEEEEeCCCCCChH-----H----HhhhccCCCCCEEEEEcCCCCC------CCCC-eEecCCCChHHHHH
Q 042541          263 FFKQMRIEAILLVLDDVWPGSES-----L----LQKLGFQLPDYKILVTSRSEFP------QFGS-VHYLKPLTYEAART  326 (695)
Q Consensus       263 ~~~~l~~~~~LlVlDdv~~~~~~-----~----~~~l~~~~~gs~iivTtR~~~~------~~~~-~~~l~~L~~~ea~~  326 (695)
                      ++..+ ..+-|+++|..-...+.     +    +..+.  ..|+.+|+||.....      ..+. ...+ .++.+ ...
T Consensus       396 il~~~-~~~sLvLlDE~g~GtD~~eg~ala~aiLe~l~--~~g~~viitTH~~eL~~~~~~~~~v~~~~~-~~d~~-~l~  470 (771)
T TIGR01069       396 ILSKT-TENSLVLFDELGAGTDPDEGSALAISILEYLL--KQNAQVLITTHYKELKALMYNNEGVENASV-LFDEE-TLS  470 (771)
T ss_pred             HHHhc-CCCcEEEecCCCCCCCHHHHHHHHHHHHHHHH--hcCCEEEEECChHHHHHHhcCCCCeEEeEE-EEcCC-CCc
Confidence            55444 57899999998654421     1    22222  257899999987511      0010 0111 01110 000


Q ss_pred             HHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHHHhhCCCCHHHHHHHHHHh
Q 042541          327 LFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGGSLCGKHEVFWQRMVKEC  383 (695)
Q Consensus       327 Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~~~L~~~~~~~w~~~l~~~  383 (695)
                       |..+...     ..+....|-+|++++ |+|-.|..-|..+...........+.++
T Consensus       471 -p~Ykl~~-----G~~g~S~a~~iA~~~-Glp~~ii~~A~~~~~~~~~~~~~li~~L  520 (771)
T TIGR01069       471 -PTYKLLK-----GIPGESYAFEIAQRY-GIPHFIIEQAKTFYGEFKEEINVLIEKL  520 (771)
T ss_pred             -eEEEECC-----CCCCCcHHHHHHHHh-CcCHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence             1111110     111244688888888 7888888888776554333444444443

Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=96.40  E-value=0.011  Score=59.79  Aligned_cols=127  Identities=17%  Similarity=0.213  Sum_probs=70.6

Q ss_pred             CCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccc-cccccCCCcEEEEE-----eCCCC-----CHHH----
Q 042541          170 GLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDD-QVQGKFKDDIFYVT-----VSKNP-----NVKA----  234 (695)
Q Consensus       170 Gr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~-~~~~~f~~~~~wv~-----~~~~~-----~~~~----  234 (695)
                      +|..+..--.++|.+++...|.+.|.+|.|||-||.+..-.. -.+..|.. + -|.     ++++.     ..++    
T Consensus       228 prn~eQ~~ALdlLld~dI~lV~L~G~AGtGKTlLALaAgleqv~e~~~y~K-i-iVtRp~vpvG~dIGfLPG~eEeKm~P  305 (436)
T COG1875         228 PRNAEQRVALDLLLDDDIDLVSLGGKAGTGKTLLALAAGLEQVLERKRYRK-I-IVTRPTVPVGEDIGFLPGTEEEKMGP  305 (436)
T ss_pred             cccHHHHHHHHHhcCCCCCeEEeeccCCccHhHHHHHHHHHHHHHHhhhce-E-EEecCCcCcccccCcCCCchhhhccc
Confidence            355555555678889999999999999999999986654321 22445554 3 221     22221     1111    


Q ss_pred             HHHHHHHhc---CCCCCCCCChHHHHHHHHHHH----------HhcCCCc---EEEEEeCCCCCChHHHhh-hccCCCCC
Q 042541          235 IVQKVLHHK---GYPVPEFQTDEAAINDLERFF----------KQMRIEA---ILLVLDDVWPGSESLLQK-LGFQLPDY  297 (695)
Q Consensus       235 ~~~~i~~~l---~~~~~~~~~~~~~~~~l~~~~----------~~l~~~~---~LlVlDdv~~~~~~~~~~-l~~~~~gs  297 (695)
                      -++.|...+   ......   ..   ..+..++          .+++|+.   -++|+|.+.+........ +...++||
T Consensus       306 Wmq~i~DnLE~L~~~~~~---~~---~~l~~~l~~~~iev~alt~IRGRSl~~~FiIIDEaQNLTpheikTiltR~G~Gs  379 (436)
T COG1875         306 WMQAIFDNLEVLFSPNEP---GD---RALEEILSRGRIEVEALTYIRGRSLPDSFIIIDEAQNLTPHELKTILTRAGEGS  379 (436)
T ss_pred             hHHHHHhHHHHHhccccc---ch---HHHHHHHhccceeeeeeeeecccccccceEEEehhhccCHHHHHHHHHhccCCC
Confidence            122222221   111111   11   1222221          2235553   599999998887654444 44567899


Q ss_pred             EEEEEcC
Q 042541          298 KILVTSR  304 (695)
Q Consensus       298 ~iivTtR  304 (695)
                      ||+.|--
T Consensus       380 KIVl~gd  386 (436)
T COG1875         380 KIVLTGD  386 (436)
T ss_pred             EEEEcCC
Confidence            9998764

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=96.39  E-value=0.025  Score=58.62  Aligned_cols=58  Identities=22%  Similarity=0.268  Sum_probs=42.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhcccccc---ccCCCcEEEEEeCCCCCHHHHHHHHHHhcCC
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQ---GKFKDDIFYVTVSKNPNVKAIVQKVLHHKGY  245 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~---~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~  245 (695)
                      ..++-|+|.+|+|||+|+..++-.....   ......++|++....|+++.+.+ +++.++.
T Consensus       126 G~ItEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE~tF~peRl~~-ia~~~g~  186 (344)
T PLN03187        126 RCITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEGTFRPDRIVP-IAERFGM  186 (344)
T ss_pred             CeEEEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcCCCCCHHHHHH-HHHHcCC
Confidence            4788899999999999998876432322   22234589999999999888755 4555554

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=96.38  E-value=0.009  Score=59.48  Aligned_cols=76  Identities=21%  Similarity=0.254  Sum_probs=48.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHH
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFK  265 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~  265 (695)
                      ...-+.++|.+|+|||.||.++.+  ++. .....+.+++++      +++.++.......        .....+.+.+ 
T Consensus       104 ~~~nl~l~G~~G~GKThLa~Ai~~--~l~-~~g~sv~f~~~~------el~~~Lk~~~~~~--------~~~~~l~~~l-  165 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLAIAIGN--ELL-KAGISVLFITAP------DLLSKLKAAFDEG--------RLEEKLLREL-  165 (254)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHHH--HHH-HcCCeEEEEEHH------HHHHHHHHHHhcC--------chHHHHHHHh-
Confidence            556789999999999999999999  444 333346676554      4666666655421        1112233322 


Q ss_pred             hcCCCcEEEEEeCCCCC
Q 042541          266 QMRIEAILLVLDDVWPG  282 (695)
Q Consensus       266 ~l~~~~~LlVlDdv~~~  282 (695)
                         .+-=||||||+...
T Consensus       166 ---~~~dlLIiDDlG~~  179 (254)
T COG1484         166 ---KKVDLLIIDDIGYE  179 (254)
T ss_pred             ---hcCCEEEEecccCc
Confidence               23459999998543

>cd01394 radB RadB

Probab=96.37  E-value=0.013  Score=57.19  Aligned_cols=42  Identities=21%  Similarity=0.377  Sum_probs=31.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCC
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPN  231 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~  231 (695)
                      ..++.|+|.+|+||||+|.+++..  .... ...++|++....+.
T Consensus        19 g~i~~i~G~~GsGKT~l~~~~a~~--~~~~-g~~v~yi~~e~~~~   60 (218)
T cd01394          19 GTVTQVYGPPGTGKTNIAIQLAVE--TAGQ-GKKVAYIDTEGLSS   60 (218)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH--HHhc-CCeEEEEECCCCCH
Confidence            588999999999999999998763  2222 23477988765553

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes

Probab=96.33  E-value=0.0098  Score=55.69  Aligned_cols=53  Identities=19%  Similarity=0.255  Sum_probs=32.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC-CHHHHHHHHHHhcC
Q 042541          189 FIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKG  244 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~  244 (695)
                      ++.++|++|+||||++..++.  ..... ...++.++..... ...+.+....+..+
T Consensus         2 ~~~~~G~~G~GKTt~~~~la~--~~~~~-g~~v~~i~~D~~~~~~~~~l~~~~~~~~   55 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLAL--YLKKK-GKKVLLVAADTYRPAAIEQLRVLGEQVG   55 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHH--HHHHC-CCcEEEEEcCCCChHHHHHHHHhcccCC
Confidence            688999999999999998886  33332 2235556554322 23333444444444

SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.

>PRK07952 DNA replication protein DnaC; Validated

Probab=96.32  E-value=0.017  Score=56.82  Aligned_cols=76  Identities=21%  Similarity=0.338  Sum_probs=44.8

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHh
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQ  266 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~  266 (695)
                      ...+.++|.+|+|||+||.++++.  +...-. .++++++      .+++..+-......  . ..       ...+++.
T Consensus        99 ~~~~~l~G~~GtGKThLa~aia~~--l~~~g~-~v~~it~------~~l~~~l~~~~~~~--~-~~-------~~~~l~~  159 (244)
T PRK07952         99 IASFIFSGKPGTGKNHLAAAICNE--LLLRGK-SVLIITV------ADIMSAMKDTFSNS--E-TS-------EEQLLND  159 (244)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHH--HHhcCC-eEEEEEH------HHHHHHHHHHHhhc--c-cc-------HHHHHHH
Confidence            357899999999999999999984  333222 2556643      44555554443210  0 01       1122233


Q ss_pred             cCCCcEEEEEeCCCCC
Q 042541          267 MRIEAILLVLDDVWPG  282 (695)
Q Consensus       267 l~~~~~LlVlDdv~~~  282 (695)
                      +. +.=+||+||+...
T Consensus       160 l~-~~dlLvIDDig~~  174 (244)
T PRK07952        160 LS-NVDLLVIDEIGVQ  174 (244)
T ss_pred             hc-cCCEEEEeCCCCC
Confidence            44 3458888998554

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=96.29  E-value=0.078  Score=57.27  Aligned_cols=123  Identities=12%  Similarity=0.234  Sum_probs=73.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-H
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFF-K  265 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~  265 (695)
                      +.=|.++|++|+|||-||++|+|  ...-+      |++|...    +++....   |          +....++.++ +
T Consensus       545 PsGvLL~GPPGCGKTLlAKAVAN--Eag~N------FisVKGP----ELlNkYV---G----------ESErAVR~vFqR  599 (802)
T KOG0733|consen  545 PSGVLLCGPPGCGKTLLAKAVAN--EAGAN------FISVKGP----ELLNKYV---G----------ESERAVRQVFQR  599 (802)
T ss_pred             CCceEEeCCCCccHHHHHHHHhh--hccCc------eEeecCH----HHHHHHh---h----------hHHHHHHHHHHH
Confidence            45688999999999999999999  44444      4444432    2222221   1          1123344455 4


Q ss_pred             hcCCCcEEEEEeCCCCCC-----------hHHHhhhcc---CC---CCCEEEEEcCCCC---------CCCCCeEecCCC
Q 042541          266 QMRIEAILLVLDDVWPGS-----------ESLLQKLGF---QL---PDYKILVTSRSEF---------PQFGSVHYLKPL  319 (695)
Q Consensus       266 ~l~~~~~LlVlDdv~~~~-----------~~~~~~l~~---~~---~gs~iivTtR~~~---------~~~~~~~~l~~L  319 (695)
                      .-..-+|+|.||.++...           ..+...+..   +.   .|.-||-.|-...         ......+.++.-
T Consensus       600 AR~saPCVIFFDEiDaL~p~R~~~~s~~s~RvvNqLLtElDGl~~R~gV~viaATNRPDiIDpAiLRPGRlDk~LyV~lP  679 (802)
T KOG0733|consen  600 ARASAPCVIFFDEIDALVPRRSDEGSSVSSRVVNQLLTELDGLEERRGVYVIAATNRPDIIDPAILRPGRLDKLLYVGLP  679 (802)
T ss_pred             hhcCCCeEEEecchhhcCcccCCCCchhHHHHHHHHHHHhcccccccceEEEeecCCCcccchhhcCCCccCceeeecCC
Confidence            446889999999985432           112333322   11   2445555444331         122336777888


Q ss_pred             ChHHHHHHHHHhccC
Q 042541          320 TYEAARTLFLHSANL  334 (695)
Q Consensus       320 ~~~ea~~Lf~~~~~~  334 (695)
                      +.+|-.++++.....
T Consensus       680 n~~eR~~ILK~~tkn  694 (802)
T KOG0733|consen  680 NAEERVAILKTITKN  694 (802)
T ss_pred             CHHHHHHHHHHHhcc
Confidence            888889999887753

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=96.28  E-value=0.02  Score=59.41  Aligned_cols=89  Identities=18%  Similarity=0.233  Sum_probs=50.7

Q ss_pred             ceEEEEEcCCCCcHH-HHHHHHhccccccccCCCcEEEEEeCCCC-CHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKT-TLVQRLCKDDQVQGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFF  264 (695)
Q Consensus       187 ~~vv~I~G~gGiGKT-tLa~~~~~~~~~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~  264 (695)
                      .++|.++|+.|+||| |||+..+......++..  |..++..... ...+-++...+-++.+.....+..+    +...+
T Consensus       203 ~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~k--VaiITtDtYRIGA~EQLk~Ya~im~vp~~vv~~~~e----l~~ai  276 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAKLAARYVMLKKKKK--VAIITTDTYRIGAVEQLKTYADIMGVPLEVVYSPKE----LAEAI  276 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHHhhccCcc--eEEEEeccchhhHHHHHHHHHHHhCCceEEecCHHH----HHHHH
Confidence            799999999999998 56766665321233333  6677665443 4455556666666665433333333    33333


Q ss_pred             HhcCCCcEEEEEeCCCCC
Q 042541          265 KQMRIEAILLVLDDVWPG  282 (695)
Q Consensus       265 ~~l~~~~~LlVlDdv~~~  282 (695)
                      ..+++. =++.+|-+...
T Consensus       277 ~~l~~~-d~ILVDTaGrs  293 (407)
T COG1419         277 EALRDC-DVILVDTAGRS  293 (407)
T ss_pred             HHhhcC-CEEEEeCCCCC
Confidence            344444 45556666433

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=96.28  E-value=0.0039  Score=67.55  Aligned_cols=43  Identities=21%  Similarity=0.358  Sum_probs=38.2

Q ss_pred             CCCCCcchHHHHHHHHH------cCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          167 ISPGLDVPLKELKMELF------KDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~------~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .++|.++.+++|++.|.      ....+++.++|++|+||||||+.+.+
T Consensus        77 d~yGlee~ieriv~~l~~Aa~gl~~~~~IL~LvGPpG~GKSsLa~~la~  125 (644)
T PRK15455         77 EFYGMEEAIEQIVSYFRHAAQGLEEKKQILYLLGPVGGGKSSLAERLKS  125 (644)
T ss_pred             cccCcHHHHHHHHHHHHHHHHhcCCCCceEEEecCCCCCchHHHHHHHH
Confidence            46999999999999993      44568999999999999999999986

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=96.26  E-value=0.035  Score=50.52  Aligned_cols=117  Identities=21%  Similarity=0.197  Sum_probs=61.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCC---CCCHHHHHHHHH--H--hcCCCCC-CCCChHHHHHH
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSK---NPNVKAIVQKVL--H--HKGYPVP-EFQTDEAAIND  259 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~---~~~~~~~~~~i~--~--~l~~~~~-~~~~~~~~~~~  259 (695)
                      .+|-|++..|.||||+|...+-  +...+ ..++.++.+-.   ......++..+-  .  +.+.... ...+.......
T Consensus         3 G~i~vy~g~G~Gkt~~a~g~~~--ra~~~-g~~v~~vQFlKg~~~~gE~~~l~~l~~v~~~~~g~~~~~~~~~~~~~~~~   79 (159)
T cd00561           3 GLIQVYTGNGKGKTTAALGLAL--RALGH-GYRVGVVQFLKGGWKYGELKALERLPNIEIHRMGRGFFWTTENDEEDIAA   79 (159)
T ss_pred             CEEEEECCCCCCHHHHHHHHHH--HHHHC-CCeEEEEEEeCCCCccCHHHHHHhCCCcEEEECCCCCccCCCChHHHHHH
Confidence            5788999999999999987765  33332 22355655533   234444444431  0  0111100 00111222222


Q ss_pred             HHHHH----Hhc-CCCcEEEEEeCCCCC-------ChHHHhhhccCCCCCEEEEEcCCCC
Q 042541          260 LERFF----KQM-RIEAILLVLDDVWPG-------SESLLQKLGFQLPDYKILVTSRSEF  307 (695)
Q Consensus       260 l~~~~----~~l-~~~~~LlVlDdv~~~-------~~~~~~~l~~~~~gs~iivTtR~~~  307 (695)
                      ..+.+    +.+ .+.-=|||||++-..       .+.+.+.+....++..||+|.|+..
T Consensus        80 a~~~~~~a~~~~~~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~p  139 (159)
T cd00561          80 AAEGWAFAKEAIASGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNAP  139 (159)
T ss_pred             HHHHHHHHHHHHhcCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCCC
Confidence            22222    223 355669999997332       1234555555555789999999863

This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.23  E-value=0.066  Score=55.80  Aligned_cols=24  Identities=33%  Similarity=0.444  Sum_probs=21.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +.++|+|+|++|+||||++..++.
T Consensus       240 ~~~vI~LVGptGvGKTTTiaKLA~  263 (436)
T PRK11889        240 EVQTIALIGPTGVGKTTTLAKMAW  263 (436)
T ss_pred             CCcEEEEECCCCCcHHHHHHHHHH
Confidence            357999999999999999998876

>TIGR02012 tigrfam_recA protein RecA

Probab=96.22  E-value=0.018  Score=58.92  Aligned_cols=84  Identities=19%  Similarity=0.226  Sum_probs=51.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCC-----CCCChHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVP-----EFQTDEAAINDLE  261 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~-----~~~~~~~~~~~l~  261 (695)
                      .+++-|+|++|+||||||.++...  .... ...++|++..+.++..     .+++++....     .....++....+.
T Consensus        55 G~iteI~G~~GsGKTtLaL~~~~~--~~~~-g~~v~yId~E~~~~~~-----~a~~lGvd~~~l~v~~p~~~eq~l~~~~  126 (321)
T TIGR02012        55 GRIIEIYGPESSGKTTLALHAIAE--AQKA-GGTAAFIDAEHALDPV-----YARKLGVDIDNLLVSQPDTGEQALEIAE  126 (321)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH--HHHc-CCcEEEEcccchhHHH-----HHHHcCCCHHHeEEecCCCHHHHHHHHH
Confidence            579999999999999999887763  3222 3347899887766653     3444443211     0112333333333


Q ss_pred             HHHHhcCCCcEEEEEeCCC
Q 042541          262 RFFKQMRIEAILLVLDDVW  280 (695)
Q Consensus       262 ~~~~~l~~~~~LlVlDdv~  280 (695)
                      .+++  .+..-++|+|.+-
T Consensus       127 ~li~--~~~~~lIVIDSv~  143 (321)
T TIGR02012       127 TLVR--SGAVDIIVVDSVA  143 (321)
T ss_pred             HHhh--ccCCcEEEEcchh
Confidence            3222  3567799999974

This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage.

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=96.17  E-value=0.013  Score=54.81  Aligned_cols=22  Identities=41%  Similarity=0.679  Sum_probs=19.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHhcc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      .|.|.|++|+||||+|+.+.+.
T Consensus         2 riiilG~pGaGK~T~A~~La~~   23 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKK   23 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999999999884

>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]

Probab=96.16  E-value=0.038  Score=55.26  Aligned_cols=89  Identities=20%  Similarity=0.188  Sum_probs=54.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHH---hcCCCCCCCCChHHHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLH---HKGYPVPEFQTDEAAINDLERF  263 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~---~l~~~~~~~~~~~~~~~~l~~~  263 (695)
                      .+++=|+|+.|+||||+|.+++-.  .+..-.. ++|++.-+.++++.+..-...   .+....+  .+.++....+...
T Consensus        60 g~ItEiyG~~gsGKT~lal~~~~~--aq~~g~~-a~fIDtE~~l~p~r~~~l~~~~~d~l~v~~~--~~~e~q~~i~~~~  134 (279)
T COG0468          60 GRITEIYGPESSGKTTLALQLVAN--AQKPGGK-AAFIDTEHALDPERAKQLGVDLLDNLLVSQP--DTGEQQLEIAEKL  134 (279)
T ss_pred             ceEEEEecCCCcchhhHHHHHHHH--hhcCCCe-EEEEeCCCCCCHHHHHHHHHhhhcceeEecC--CCHHHHHHHHHHH
Confidence            478889999999999999887753  3333223 789999999988766443333   2222111  1233333333333


Q ss_pred             HHhcCCCcEEEEEeCCC
Q 042541          264 FKQMRIEAILLVLDDVW  280 (695)
Q Consensus       264 ~~~l~~~~~LlVlDdv~  280 (695)
                      ......+--|+|+|.+-
T Consensus       135 ~~~~~~~i~LvVVDSva  151 (279)
T COG0468         135 ARSGAEKIDLLVVDSVA  151 (279)
T ss_pred             HHhccCCCCEEEEecCc
Confidence            33333356799999984

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=96.15  E-value=0.028  Score=57.11  Aligned_cols=86  Identities=20%  Similarity=0.307  Sum_probs=48.8

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhcccccc-ccCCCcEEEEEeCCCC-CHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQ-GKFKDDIFYVTVSKNP-NVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFF  264 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~-~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~  264 (695)
                      .++++|+|++|+||||++..++.....+ +.+  .+..++..... ...+.+....+.++.+.....+.    ..+...+
T Consensus       194 ~~vi~~vGptGvGKTTt~~kLa~~~~~~~g~~--~V~li~~D~~r~~a~eql~~~~~~~~~p~~~~~~~----~~l~~~l  267 (282)
T TIGR03499       194 GGVIALVGPTGVGKTTTLAKLAARFVLEHGNK--KVALITTDTYRIGAVEQLKTYAKILGVPVKVARDP----KELRKAL  267 (282)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHHcCCC--eEEEEECCccchhHHHHHHHHHHHhCCceeccCCH----HHHHHHH
Confidence            5799999999999999998887632222 223  36677665422 23334444455555443222222    2344555


Q ss_pred             HhcCCCcEEEEEeCC
Q 042541          265 KQMRIEAILLVLDDV  279 (695)
Q Consensus       265 ~~l~~~~~LlVlDdv  279 (695)
                      +.+.+ .=++++|..
T Consensus       268 ~~~~~-~d~vliDt~  281 (282)
T TIGR03499       268 DRLRD-KDLILIDTA  281 (282)
T ss_pred             HHccC-CCEEEEeCC
Confidence            55543 457777754

>PRK10867 signal recognition particle protein; Provisional

Probab=96.15  E-value=0.015  Score=62.20  Aligned_cols=24  Identities=33%  Similarity=0.396  Sum_probs=20.9

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+.+|.++|++|+||||.+..++.
T Consensus        99 ~p~vI~~vG~~GsGKTTtaakLA~  122 (433)
T PRK10867         99 PPTVIMMVGLQGAGKTTTAGKLAK  122 (433)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHH
Confidence            468999999999999998877765

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=96.14  E-value=0.02  Score=58.60  Aligned_cols=84  Identities=19%  Similarity=0.230  Sum_probs=51.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCC-----CCCChHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVP-----EFQTDEAAINDLE  261 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~-----~~~~~~~~~~~l~  261 (695)
                      .+++-|+|++|+||||||.+++..  .... ...++|++..+.+++.     .++.++....     .....++....+.
T Consensus        55 G~iteI~Gp~GsGKTtLal~~~~~--~~~~-g~~~vyId~E~~~~~~-----~a~~lGvd~~~l~v~~p~~~eq~l~i~~  126 (325)
T cd00983          55 GRIIEIYGPESSGKTTLALHAIAE--AQKL-GGTVAFIDAEHALDPV-----YAKKLGVDLDNLLISQPDTGEQALEIAD  126 (325)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH--HHHc-CCCEEEECccccHHHH-----HHHHcCCCHHHheecCCCCHHHHHHHHH
Confidence            578999999999999999987752  2222 3347899988776653     3334433211     0112333333333


Q ss_pred             HHHHhcCCCcEEEEEeCCC
Q 042541          262 RFFKQMRIEAILLVLDDVW  280 (695)
Q Consensus       262 ~~~~~l~~~~~LlVlDdv~  280 (695)
                      .+++  .+..-++|+|.+-
T Consensus       127 ~li~--s~~~~lIVIDSva  143 (325)
T cd00983         127 SLVR--SGAVDLIVVDSVA  143 (325)
T ss_pred             HHHh--ccCCCEEEEcchH
Confidence            3332  3567799999973

RecA couples ATP hydrolysis to DNA strand exchange.

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=96.13  E-value=0.028  Score=56.12  Aligned_cols=57  Identities=18%  Similarity=0.312  Sum_probs=40.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhcccccc---ccCCCcEEEEEeCCCCCHHHHHHHHHHhcC
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQ---GKFKDDIFYVTVSKNPNVKAIVQKVLHHKG  244 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~---~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~  244 (695)
                      ..+.=|+|.+|+|||+|+..++-...+.   ...+..++|++....++...+. +|++..+
T Consensus        38 g~itEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe~~f~~~Rl~-~i~~~~~   97 (256)
T PF08423_consen   38 GSITEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEGTFSPERLQ-QIAERFG   97 (256)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESSSSS-HHHHH-HHHHHTT
T ss_pred             CcEEEEEEecccccchHHHHHHHHhhcccccccCCCceEEEeCCCCCCHHHHH-HHhhccc
Confidence            4688899999999999998776433332   2335568999999999887775 4555543

It is critical for DNA binding []. Rad51 is a homologue of the bacterial RecA protein. Rad51 and RecA share a core ATPase domain.; PDB: 2ZUC_A 2Z43_C 2ZUD_B 2DFL_A 2ZUB_A 2BKE_A 2KZ3_A 2CVH_B 2CVF_B 1SZP_D ....

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.13  E-value=0.02  Score=59.86  Aligned_cols=89  Identities=17%  Similarity=0.242  Sum_probs=53.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCC-CcEEEEEeCCC-CCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFK-DDIFYVTVSKN-PNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFF  264 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~-~~~~wv~~~~~-~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~  264 (695)
                      ..++.++|+.|+||||++..+..  +....+. ..+..++.... ....+-+....+.++.+........+    +...+
T Consensus       137 g~ii~lvGptGvGKTTtiakLA~--~~~~~~G~~~V~lit~D~~R~ga~EqL~~~a~~~gv~~~~~~~~~~----l~~~l  210 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAKLAA--RCVMRFGASKVALLTTDSYRIGGHEQLRIFGKILGVPVHAVKDGGD----LQLAL  210 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH--HHHHhcCCCeEEEEecccccccHHHHHHHHHHHcCCceEecCCccc----HHHHH
Confidence            47899999999999999999987  3322332 23656664432 24555666667777655432222222    23333


Q ss_pred             HhcCCCcEEEEEeCCCCC
Q 042541          265 KQMRIEAILLVLDDVWPG  282 (695)
Q Consensus       265 ~~l~~~~~LlVlDdv~~~  282 (695)
                      ..+.++ -++++|.....
T Consensus       211 ~~l~~~-DlVLIDTaG~~  227 (374)
T PRK14722        211 AELRNK-HMVLIDTIGMS  227 (374)
T ss_pred             HHhcCC-CEEEEcCCCCC
Confidence            444554 55669998543

>PRK06835 DNA replication protein DnaC; Validated

Probab=96.12  E-value=0.028  Score=58.12  Aligned_cols=38  Identities=21%  Similarity=0.322  Sum_probs=27.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeC
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVS  227 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~  227 (695)
                      ..-+.++|..|+|||.||..+++  .+...- ..|+++++.
T Consensus       183 ~~~Lll~G~~GtGKThLa~aIa~--~l~~~g-~~V~y~t~~  220 (329)
T PRK06835        183 NENLLFYGNTGTGKTFLSNCIAK--ELLDRG-KSVIYRTAD  220 (329)
T ss_pred             CCcEEEECCCCCcHHHHHHHHHH--HHHHCC-CeEEEEEHH
Confidence            37799999999999999999998  333222 236676654

>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed

Probab=96.12  E-value=0.029  Score=55.16  Aligned_cols=25  Identities=32%  Similarity=0.501  Sum_probs=22.7

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +...+|+|.|+.|+|||||++.+..
T Consensus        31 ~~~~iigi~G~~GsGKTTl~~~L~~   55 (229)
T PRK09270         31 QRRTIVGIAGPPGAGKSTLAEFLEA   55 (229)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            4578999999999999999999886

>PRK14974 cell division protein FtsY; Provisional

Probab=96.11  E-value=0.04  Score=56.94  Aligned_cols=92  Identities=14%  Similarity=0.111  Sum_probs=49.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccc-cCCCcEEEEEeCCC-CCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHH
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQG-KFKDDIFYVTVSKN-PNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERF  263 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~-~f~~~~~wv~~~~~-~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~  263 (695)
                      ++.+|.++|+.|+||||++..++.  .... .+.  +..+..... ....+-+......++.+........+....+...
T Consensus       139 ~~~vi~~~G~~GvGKTTtiakLA~--~l~~~g~~--V~li~~Dt~R~~a~eqL~~~a~~lgv~v~~~~~g~dp~~v~~~a  214 (336)
T PRK14974        139 KPVVIVFVGVNGTGKTTTIAKLAY--YLKKNGFS--VVIAAGDTFRAGAIEQLEEHAERLGVKVIKHKYGADPAAVAYDA  214 (336)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHH--HHHHcCCe--EEEecCCcCcHHHHHHHHHHHHHcCCceecccCCCCHHHHHHHH
Confidence            468999999999999998888776  3332 232  445443211 1233445666677765432211111111112222


Q ss_pred             HHh--cCCCcEEEEEeCCCCC
Q 042541          264 FKQ--MRIEAILLVLDDVWPG  282 (695)
Q Consensus       264 ~~~--l~~~~~LlVlDdv~~~  282 (695)
                      ++.  ..+.. ++++|.+...
T Consensus       215 i~~~~~~~~D-vVLIDTaGr~  234 (336)
T PRK14974        215 IEHAKARGID-VVLIDTAGRM  234 (336)
T ss_pred             HHHHHhCCCC-EEEEECCCcc
Confidence            211  12333 9999998654

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=96.11  E-value=0.019  Score=65.97  Aligned_cols=106  Identities=18%  Similarity=0.223  Sum_probs=61.1

Q ss_pred             CCCCCCcchHHHHHHHHHc-------C--CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHH
Q 042541          166 VISPGLDVPLKELKMELFK-------D--GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIV  236 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~-------~--~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~  236 (695)
                      ..++|-++.++.|...+..       .  ....+.++|+.|+|||++|+.++.  ...    ...+.+++++......  
T Consensus       458 ~~ViGQ~~ai~~l~~~i~~~~~gl~~~~kp~~~~Lf~GP~GvGKT~lAk~LA~--~l~----~~~i~id~se~~~~~~--  529 (758)
T PRK11034        458 MLVFGQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSK--ALG----IELLRFDMSEYMERHT--  529 (758)
T ss_pred             ceEeCcHHHHHHHHHHHHHHhccccCCCCCcceEEEECCCCCCHHHHHHHHHH--HhC----CCcEEeechhhccccc--
Confidence            4579999999988888761       1  135788999999999999999987  332    2244666654332111  


Q ss_pred             HHHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH
Q 042541          237 QKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES  285 (695)
Q Consensus       237 ~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~  285 (695)
                        +.+-+|.+ +..... .....+.+.+.  +....+|+||++......
T Consensus       530 --~~~LiG~~-~gyvg~-~~~g~L~~~v~--~~p~sVlllDEieka~~~  572 (758)
T PRK11034        530 --VSRLIGAP-PGYVGF-DQGGLLTDAVI--KHPHAVLLLDEIEKAHPD  572 (758)
T ss_pred             --HHHHcCCC-CCcccc-cccchHHHHHH--hCCCcEEEeccHhhhhHH
Confidence              11112322 111110 00111222221  234579999999877755

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=96.11  E-value=0.022  Score=52.47  Aligned_cols=40  Identities=30%  Similarity=0.498  Sum_probs=29.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCC
Q 042541          189 FIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPN  231 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~  231 (695)
                      ++.|+|++|+||||++..+...  ... ....++|++......
T Consensus         1 ~~~i~G~~G~GKT~l~~~i~~~--~~~-~~~~v~~~~~e~~~~   40 (165)
T cd01120           1 LILVFGPTGSGKTTLALQLALN--IAT-KGGKVVYVDIEEEIE   40 (165)
T ss_pred             CeeEeCCCCCCHHHHHHHHHHH--HHh-cCCEEEEEECCcchH
Confidence            4689999999999999999873  322 334477888876543

This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

>cd03238 ABC_UvrA The excision repair protein UvrA; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion

Probab=96.11  E-value=0.047  Score=51.00  Aligned_cols=23  Identities=35%  Similarity=0.440  Sum_probs=20.6

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|+|||||.+.+..
T Consensus        21 G~~~~l~G~nG~GKSTLl~~il~   43 (176)
T cd03238          21 NVLVVVTGVSGSGKSTLVNEGLY   43 (176)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhh
Confidence            47899999999999999998863

Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins, and UvrB having one ATP binding site that is structurally related to that of helicases.

>KOG1644 consensus U2-associated snRNP A' protein [RNA processing and modification]

Probab=96.08  E-value=0.0086  Score=55.49  Aligned_cols=87  Identities=17%  Similarity=0.212  Sum_probs=41.1

Q ss_pred             hcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc---cccccccccEEeeccccCCcccccchhhh
Q 042541          570 LQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL---ATVRMNHLQKVSLVMCNVGQVFRNSTFRI  646 (695)
Q Consensus       570 ~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp---~i~~l~~L~~L~l~~~~i~~~~~~~~~~l  646 (695)
                      |..++.|.+|.+.+|.+..-. +.+  -..+++|..|.|.+|+|..+.   .+..++.|++|.+-+|+++....--. .+
T Consensus        60 lp~l~rL~tLll~nNrIt~I~-p~L--~~~~p~l~~L~LtnNsi~~l~dl~pLa~~p~L~~Ltll~Npv~~k~~YR~-yv  135 (233)
T KOG1644|consen   60 LPHLPRLHTLLLNNNRITRID-PDL--DTFLPNLKTLILTNNSIQELGDLDPLASCPKLEYLTLLGNPVEHKKNYRL-YV  135 (233)
T ss_pred             CCCccccceEEecCCcceeec-cch--hhhccccceEEecCcchhhhhhcchhccCCccceeeecCCchhcccCcee-EE
Confidence            344556666666665442110 111  123445666666666655443   44455666666666665544321100 00


Q ss_pred             cccCCCccEEeccc
Q 042541          647 SDAFPNLLEMDIDY  660 (695)
Q Consensus       647 ~~~l~~L~~L~l~~  660 (695)
                      -..+++|++||.+.
T Consensus       136 l~klp~l~~LDF~k  149 (233)
T KOG1644|consen  136 LYKLPSLRTLDFQK  149 (233)
T ss_pred             EEecCcceEeehhh
Confidence            00466666666554

>PRK06547 hypothetical protein; Provisional

Probab=96.07  E-value=0.0083  Score=55.87  Aligned_cols=33  Identities=27%  Similarity=0.374  Sum_probs=27.0

Q ss_pred             HHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          177 ELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       177 ~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+...+......+|+|.|++|+||||+|+.+..
T Consensus         5 ~~~~~~~~~~~~~i~i~G~~GsGKTt~a~~l~~   37 (172)
T PRK06547          5 LIAARLCGGGMITVLIDGRSGSGKTTLAGALAA   37 (172)
T ss_pred             HHHHHhhcCCCEEEEEECCCCCCHHHHHHHHHH
Confidence            344445566688999999999999999999986

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=96.07  E-value=0.083  Score=56.26  Aligned_cols=24  Identities=29%  Similarity=0.368  Sum_probs=21.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+.+|.++|+.|+||||++..++.
T Consensus        99 ~~~vi~lvG~~GvGKTTtaaKLA~  122 (429)
T TIGR01425        99 KQNVIMFVGLQGSGKTTTCTKLAY  122 (429)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            368999999999999999988875

This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.

>PTZ00035 Rad51 protein; Provisional

Probab=96.03  E-value=0.063  Score=55.82  Aligned_cols=57  Identities=19%  Similarity=0.259  Sum_probs=39.5

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhcccccc---ccCCCcEEEEEeCCCCCHHHHHHHHHHhcC
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQ---GKFKDDIFYVTVSKNPNVKAIVQKVLHHKG  244 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~---~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~  244 (695)
                      ..++.|+|.+|+|||||+..++-.....   ..-...++|++....++.+.+ .++.+.++
T Consensus       118 G~iteI~G~~GsGKT~l~~~l~~~~qlp~~~gg~~g~vvyIdtE~~f~~eri-~~ia~~~g  177 (337)
T PTZ00035        118 GSITELFGEFRTGKTQLCHTLCVTCQLPIEQGGGEGKVLYIDTEGTFRPERI-VQIAERFG  177 (337)
T ss_pred             CeEEEEECCCCCchhHHHHHHHHHhccccccCCCCceEEEEEccCCCCHHHH-HHHHHHhC
Confidence            5789999999999999998886532321   112334779999888777764 44455544

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=96.01  E-value=0.14  Score=56.91  Aligned_cols=63  Identities=14%  Similarity=0.227  Sum_probs=45.8

Q ss_pred             CCCCCCCcchHHHHHHHHH--cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC
Q 042541          165 PVISPGLDVPLKELKMELF--KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP  230 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~--~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~  230 (695)
                      ...++|....++++.+.+.  .....-|.|+|..|+|||++|+.+++.  -. +-+...+.|++....
T Consensus       186 ~~~iig~s~~~~~~~~~i~~~a~~~~pVlI~Ge~GtGK~~~A~~ih~~--s~-r~~~p~v~v~c~~~~  250 (509)
T PRK05022        186 EGEMIGQSPAMQQLKKEIEVVAASDLNVLILGETGVGKELVARAIHAA--SP-RADKPLVYLNCAALP  250 (509)
T ss_pred             CCceeecCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHh--CC-cCCCCeEEEEcccCC
Confidence            4568999999999988887  344567899999999999999999873  11 122224566666543

>PRK07667 uridine kinase; Provisional

Probab=96.01  E-value=0.0089  Score=57.04  Aligned_cols=35  Identities=29%  Similarity=0.292  Sum_probs=28.2

Q ss_pred             HHHHHHHHH--cCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          175 LKELKMELF--KDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       175 ~~~l~~~L~--~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+.|.+.+.  .+...+|+|.|.+|+||||+|+.+..
T Consensus         3 ~~~~~~~~~~~~~~~~iIgI~G~~gsGKStla~~L~~   39 (193)
T PRK07667          3 TNELINIMKKHKENRFILGIDGLSRSGKTTFVANLKE   39 (193)
T ss_pred             HHHHHHHHHhcCCCCEEEEEECCCCCCHHHHHHHHHH
Confidence            455666665  34467999999999999999999987

>KOG0738 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.01  E-value=0.098  Score=53.48  Aligned_cols=43  Identities=26%  Similarity=0.275  Sum_probs=30.3

Q ss_pred             CCCCCcchHHHHHHHHHc------------CCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          167 ISPGLDVPLKELKMELFK------------DGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~~------------~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+.|..+.++-|.+.+.-            ..-+-|.++|++|.|||-||++|+.
T Consensus       213 DIagl~~AK~lL~EAVvlPi~mPe~F~GirrPWkgvLm~GPPGTGKTlLAKAvAT  267 (491)
T KOG0738|consen  213 DIAGLHEAKKLLKEAVVLPIWMPEFFKGIRRPWKGVLMVGPPGTGKTLLAKAVAT  267 (491)
T ss_pred             hhcchHHHHHHHHHHHhhhhhhHHHHhhcccccceeeeeCCCCCcHHHHHHHHHH
Confidence            345555555555554431            1136688999999999999999998

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=96.01  E-value=0.051  Score=55.02  Aligned_cols=52  Identities=19%  Similarity=0.329  Sum_probs=36.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHh
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHH  242 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~  242 (695)
                      ..++.|.|.+|+||||++.+++..  ........++|+++..  +..++...+...
T Consensus        30 g~~~~i~g~~G~GKT~l~~~~~~~--~~~~~g~~vl~iS~E~--~~~~~~~r~~~~   81 (271)
T cd01122          30 GELIILTAGTGVGKTTFLREYALD--LITQHGVRVGTISLEE--PVVRTARRLLGQ   81 (271)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHH--HHHhcCceEEEEEccc--CHHHHHHHHHHH
Confidence            468899999999999999988763  3222233478988876  445666666554

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>PRK09354 recA recombinase A; Provisional

Probab=95.98  E-value=0.027  Score=58.15  Aligned_cols=84  Identities=18%  Similarity=0.223  Sum_probs=52.5

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCC-----CCCChHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVP-----EFQTDEAAINDLE  261 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~-----~~~~~~~~~~~l~  261 (695)
                      .+++-|+|++|+||||||.+++..  .... ...++|++....++..     .++.++....     .....++....+.
T Consensus        60 G~IteI~G~~GsGKTtLal~~~~~--~~~~-G~~~~yId~E~s~~~~-----~a~~lGvdld~lli~qp~~~Eq~l~i~~  131 (349)
T PRK09354         60 GRIVEIYGPESSGKTTLALHAIAE--AQKA-GGTAAFIDAEHALDPV-----YAKKLGVDIDNLLVSQPDTGEQALEIAD  131 (349)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH--HHHc-CCcEEEECCccchHHH-----HHHHcCCCHHHeEEecCCCHHHHHHHHH
Confidence            578999999999999999887763  2222 3347899998877753     3444443211     0112333333333


Q ss_pred             HHHHhcCCCcEEEEEeCCC
Q 042541          262 RFFKQMRIEAILLVLDDVW  280 (695)
Q Consensus       262 ~~~~~l~~~~~LlVlDdv~  280 (695)
                      .+++  .+..-++|+|.+-
T Consensus       132 ~li~--s~~~~lIVIDSva  148 (349)
T PRK09354        132 TLVR--SGAVDLIVVDSVA  148 (349)
T ss_pred             HHhh--cCCCCEEEEeChh
Confidence            3332  3567799999974

>TIGR00959 ffh signal recognition particle protein

Probab=95.98  E-value=0.021  Score=61.09  Aligned_cols=58  Identities=17%  Similarity=0.178  Sum_probs=34.5

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC-CHHHHHHHHHHhcCC
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKGY  245 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~~  245 (695)
                      .+.++.++|.+|+||||.|..++.  .........+..|++.... ...+-+....+..+.
T Consensus        98 ~p~vi~~vG~~GsGKTTtaakLA~--~l~~~~g~kV~lV~~D~~R~~a~~QL~~~a~~~gv  156 (428)
T TIGR00959        98 PPTVILMVGLQGSGKTTTCGKLAY--YLKKKQGKKVLLVACDLYRPAAIEQLKVLGQQVGV  156 (428)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHH--HHHHhCCCeEEEEeccccchHHHHHHHHHHHhcCC
Confidence            367999999999999999988876  3221112235556554322 223334444555443

This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=95.96  E-value=0.068  Score=50.22  Aligned_cols=23  Identities=35%  Similarity=0.413  Sum_probs=21.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|.|+.|.|||||++.++.
T Consensus        28 Ge~~~i~G~nGsGKStLl~~l~G   50 (178)
T cd03247          28 GEKIALLGRSGSGKSTLLQLLTG   50 (178)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            47899999999999999999986

The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes. CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space. In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism.

>KOG0728 consensus 26S proteasome regulatory complex, ATPase RPT6 [Posttranslational modification, protein turnover, chaperones]

Probab=95.95  E-value=0.078  Score=50.67  Aligned_cols=146  Identities=22%  Similarity=0.298  Sum_probs=80.9

Q ss_pred             CCCCCCCCC-CcchHHHHHHHHHc-------------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeC
Q 042541          162 PDPPVISPG-LDVPLKELKMELFK-------------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVS  227 (695)
Q Consensus       162 ~~~~~~~vG-r~~~~~~l~~~L~~-------------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~  227 (695)
                      |...-.+|| .+..+++|.+.+.-             .+++=|.++|++|.|||-||++|+++       .+ +.++.||
T Consensus       142 PDStYeMiGgLd~QIkeIkEVIeLPvKHPELF~aLGIaQPKGvlLygppgtGktLlaraVahh-------t~-c~firvs  213 (404)
T KOG0728|consen  142 PDSTYEMIGGLDKQIKEIKEVIELPVKHPELFEALGIAQPKGVLLYGPPGTGKTLLARAVAHH-------TD-CTFIRVS  213 (404)
T ss_pred             CccHHHHhccHHHHHHHHHHHHhccccCHHHHHhcCCCCCcceEEecCCCCchhHHHHHHHhh-------cc-eEEEEec
Confidence            333334555 56677777776651             23677899999999999999999983       23 5578887


Q ss_pred             CCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCCh----------H--------HHh
Q 042541          228 KNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGSE----------S--------LLQ  288 (695)
Q Consensus       228 ~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~~----------~--------~~~  288 (695)
                      ..    ++.+..+-.             .....++++ -.-..-+.++..|.+++...          .        ++.
T Consensus       214 gs----elvqk~ige-------------gsrmvrelfvmarehapsiifmdeidsigs~r~e~~~ggdsevqrtmlelln  276 (404)
T KOG0728|consen  214 GS----ELVQKYIGE-------------GSRMVRELFVMAREHAPSIIFMDEIDSIGSSRVESGSGGDSEVQRTMLELLN  276 (404)
T ss_pred             hH----HHHHHHhhh-------------hHHHHHHHHHHHHhcCCceEeeecccccccccccCCCCccHHHHHHHHHHHH
Confidence            64    222222111             112223333 11134567888888754321          1        222


Q ss_pred             hhcc--CCCCCEEEEEc-CCCC-----CCCC---CeEecCCCChHHHHHHHHHhc
Q 042541          289 KLGF--QLPDYKILVTS-RSEF-----PQFG---SVHYLKPLTYEAARTLFLHSA  332 (695)
Q Consensus       289 ~l~~--~~~gs~iivTt-R~~~-----~~~~---~~~~l~~L~~~ea~~Lf~~~~  332 (695)
                      .+..  ...+-+||..| |...     ...|   ..++.++-+.+.-.++++-+.
T Consensus       277 qldgfeatknikvimatnridild~allrpgridrkiefp~p~e~ar~~ilkihs  331 (404)
T KOG0728|consen  277 QLDGFEATKNIKVIMATNRIDILDPALLRPGRIDRKIEFPPPNEEARLDILKIHS  331 (404)
T ss_pred             hccccccccceEEEEeccccccccHhhcCCCcccccccCCCCCHHHHHHHHHHhh
Confidence            2221  22356777755 4331     1223   356666767666666666443

>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=95.94  E-value=0.045  Score=52.23  Aligned_cols=87  Identities=21%  Similarity=0.200  Sum_probs=57.8

Q ss_pred             CCCCCCcchHHHHHHHHH----cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHH
Q 042541          166 VISPGLDVPLKELKMELF----KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLH  241 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~----~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~  241 (695)
                      ..++|.+...+.+++--.    .-..--|.+||..|.|||+|++++.+  .+......   -|.|+..            
T Consensus        60 ~~l~Gvd~qk~~L~~NT~~F~~G~pANnVLLwGaRGtGKSSLVKA~~~--e~~~~glr---LVEV~k~------------  122 (287)
T COG2607          60 ADLVGVDRQKEALVRNTEQFAEGLPANNVLLWGARGTGKSSLVKALLN--EYADEGLR---LVEVDKE------------  122 (287)
T ss_pred             HHHhCchHHHHHHHHHHHHHHcCCcccceEEecCCCCChHHHHHHHHH--HHHhcCCe---EEEEcHH------------
Confidence            457999988888876433    33356789999999999999999998  55555443   3444331            


Q ss_pred             hcCCCCCCCCChHHHHHHHHHHHHhc--CCCcEEEEEeCCCCCC
Q 042541          242 HKGYPVPEFQTDEAAINDLERFFKQM--RIEAILLVLDDVWPGS  283 (695)
Q Consensus       242 ~l~~~~~~~~~~~~~~~~l~~~~~~l--~~~~~LlVlDdv~~~~  283 (695)
                                    .+..|-.+++.|  ...+|+|..||+.-..
T Consensus       123 --------------dl~~Lp~l~~~Lr~~~~kFIlFcDDLSFe~  152 (287)
T COG2607         123 --------------DLATLPDLVELLRARPEKFILFCDDLSFEE  152 (287)
T ss_pred             --------------HHhhHHHHHHHHhcCCceEEEEecCCCCCC
Confidence                          122223333222  4789999999985443

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=95.91  E-value=0.046  Score=56.70  Aligned_cols=57  Identities=18%  Similarity=0.240  Sum_probs=40.4

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhcccccccc---CCCcEEEEEeCCCCCHHHHHHHHHHhcC
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGK---FKDDIFYVTVSKNPNVKAIVQKVLHHKG  244 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~---f~~~~~wv~~~~~~~~~~~~~~i~~~l~  244 (695)
                      ..++-|+|++|+|||+++.+++-.......   -...++|++..+.++...+.+ +++.++
T Consensus       102 g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~~f~~~rl~~-~~~~~g  161 (317)
T PRK04301        102 QSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEGTFRPERIEQ-MAEALG  161 (317)
T ss_pred             CcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCCCcCHHHHHH-HHHHcC
Confidence            578999999999999999888753222211   123488999999888777654 344444

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=95.90  E-value=0.081  Score=58.70  Aligned_cols=143  Identities=15%  Similarity=0.230  Sum_probs=80.8

Q ss_pred             CCCCCcchHHHHHHHHH------c-------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHH
Q 042541          167 ISPGLDVPLKELKMELF------K-------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVK  233 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~------~-------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~  233 (695)
                      .+.|.+...+.+.+.+.      .       ...+.+.++|++|.|||.||+++++  .....|      +.+...    
T Consensus       243 diggl~~~k~~l~e~v~~~~~~~e~~~~~~~~~~~giLl~GpPGtGKT~lAkava~--~~~~~f------i~v~~~----  310 (494)
T COG0464         243 DIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVAL--ESRSRF------ISVKGS----  310 (494)
T ss_pred             hhhcHHHHHHHHHHHHHhHhhChHHHHhcCCCCCCeeEEECCCCCCHHHHHHHHHh--hCCCeE------EEeeCH----
Confidence            33555655555554443      1       2356899999999999999999998  333333      222221    


Q ss_pred             HHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCCh-----------HHHhhhcc----CCC--
Q 042541          234 AIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGSE-----------SLLQKLGF----QLP--  295 (695)
Q Consensus       234 ~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~~-----------~~~~~l~~----~~~--  295 (695)
                          .++...         ..+....+++++ ...+..++.|.+|+++....           .....+..    ...  
T Consensus       311 ----~l~sk~---------vGesek~ir~~F~~A~~~~p~iiFiDEiDs~~~~r~~~~~~~~~r~~~~lL~~~d~~e~~~  377 (494)
T COG0464         311 ----ELLSKW---------VGESEKNIRELFEKARKLAPSIIFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDGIEKAE  377 (494)
T ss_pred             ----HHhccc---------cchHHHHHHHHHHHHHcCCCcEEEEEchhhhhccCCCCCchHHHHHHHHHHHHhcCCCccC
Confidence                111111         112234455555 44468899999999843210           12222221    112  


Q ss_pred             CCEEEEEcCCCC-------C--CCCCeEecCCCChHHHHHHHHHhccC
Q 042541          296 DYKILVTSRSEF-------P--QFGSVHYLKPLTYEAARTLFLHSANL  334 (695)
Q Consensus       296 gs~iivTtR~~~-------~--~~~~~~~l~~L~~~ea~~Lf~~~~~~  334 (695)
                      +..||-||-...       .  .....+.+++-+.++..+.|..+...
T Consensus       378 ~v~vi~aTN~p~~ld~a~lR~gRfd~~i~v~~pd~~~r~~i~~~~~~~  425 (494)
T COG0464         378 GVLVIAATNRPDDLDPALLRPGRFDRLIYVPLPDLEERLEIFKIHLRD  425 (494)
T ss_pred             ceEEEecCCCccccCHhhcccCccceEeecCCCCHHHHHHHHHHHhcc
Confidence            223344444331       1  23347888999999999999988753

>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed

Probab=95.90  E-value=0.12  Score=59.98  Aligned_cols=183  Identities=14%  Similarity=0.136  Sum_probs=85.0

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCC---CChHHHHHHHHH
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEF---QTDEAAINDLER  262 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~---~~~~~~~~~l~~  262 (695)
                      +.+++.|+|+.+.||||+.+.+.-.. +-.+..+   +|.+... ....++..|+..++....-.   .........+..
T Consensus       326 ~~~~~iITGpN~gGKTt~lktigl~~-~maq~G~---~vpa~~~-~~i~~~~~i~~~ig~~~si~~~lStfS~~m~~~~~  400 (782)
T PRK00409        326 DKTVLVITGPNTGGKTVTLKTLGLAA-LMAKSGL---PIPANEP-SEIPVFKEIFADIGDEQSIEQSLSTFSGHMTNIVR  400 (782)
T ss_pred             CceEEEEECCCCCCcHHHHHHHHHHH-HHHHhCC---CcccCCC-ccccccceEEEecCCccchhhchhHHHHHHHHHHH
Confidence            45789999999999999998875320 1111110   2222210 00111111221222111100   111223344444


Q ss_pred             HHHhcCCCcEEEEEeCCCCCChH-----HHhhhcc--CCCCCEEEEEcCCCCC----C--CCC-eEecCCCChHHHHHHH
Q 042541          263 FFKQMRIEAILLVLDDVWPGSES-----LLQKLGF--QLPDYKILVTSRSEFP----Q--FGS-VHYLKPLTYEAARTLF  328 (695)
Q Consensus       263 ~~~~l~~~~~LlVlDdv~~~~~~-----~~~~l~~--~~~gs~iivTtR~~~~----~--~~~-~~~l~~L~~~ea~~Lf  328 (695)
                      ++..+ ..+-|+++|......+.     +...+..  ...|+.+|+||.....    .  .+. ...+. ++. +... +
T Consensus       401 Il~~~-~~~sLvLlDE~~~GtDp~eg~ala~aile~l~~~~~~vIitTH~~el~~~~~~~~~v~~~~~~-~d~-~~l~-~  476 (782)
T PRK00409        401 ILEKA-DKNSLVLFDELGAGTDPDEGAALAISILEYLRKRGAKIIATTHYKELKALMYNREGVENASVE-FDE-ETLR-P  476 (782)
T ss_pred             HHHhC-CcCcEEEecCCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEECChHHHHHHHhcCCCeEEEEEE-Eec-CcCc-E
Confidence            55444 56789999998654421     1111111  1247899999987511    0  010 11111 111 1100 0


Q ss_pred             HHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHHHhhCCCCHHHHHHHHHHh
Q 042541          329 LHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGGSLCGKHEVFWQRMVKEC  383 (695)
Q Consensus       329 ~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~~~L~~~~~~~w~~~l~~~  383 (695)
                      ..... .    ..+....|-+|++.+ |+|-.+..-|..+-..........+.++
T Consensus       477 ~Ykl~-~----G~~g~S~a~~iA~~~-Glp~~ii~~A~~~~~~~~~~~~~li~~l  525 (782)
T PRK00409        477 TYRLL-I----GIPGKSNAFEIAKRL-GLPENIIEEAKKLIGEDKEKLNELIASL  525 (782)
T ss_pred             EEEEe-e----CCCCCcHHHHHHHHh-CcCHHHHHHHHHHHhhhhhHHHHHHHHH
Confidence            01110 0    111245688888888 7888888887766544433444444443

>KOG1644 consensus U2-associated snRNP A' protein [RNA processing and modification]

Probab=95.89  E-value=0.01  Score=55.04  Aligned_cols=100  Identities=13%  Similarity=0.156  Sum_probs=73.5

Q ss_pred             CCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc-ccc-ccccccEEeeccccCCcccc--cchhhhccc
Q 042541          574 DELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL-ATV-RMNHLQKVSLVMCNVGQVFR--NSTFRISDA  649 (695)
Q Consensus       574 ~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp-~i~-~l~~L~~L~l~~~~i~~~~~--~~~~~l~~~  649 (695)
                      .+...+||++|.+     ..++.+..++.|..|.|++|+|+.+- .++ .+++|..|.|.+|+|..+-.  ..-     .
T Consensus        42 d~~d~iDLtdNdl-----~~l~~lp~l~rL~tLll~nNrIt~I~p~L~~~~p~l~~L~LtnNsi~~l~dl~pLa-----~  111 (233)
T KOG1644|consen   42 DQFDAIDLTDNDL-----RKLDNLPHLPRLHTLLLNNNRITRIDPDLDTFLPNLKTLILTNNSIQELGDLDPLA-----S  111 (233)
T ss_pred             cccceecccccch-----hhcccCCCccccceEEecCCcceeeccchhhhccccceEEecCcchhhhhhcchhc-----c
Confidence            4677888888755     23344678889999999999999776 555 46789999999998766432  112     6


Q ss_pred             CCCccEEecccccccccCch----hhcCCCCCceeeccc
Q 042541          650 FPNLLEMDIDYCNDLIELPD----GLCDIVSMEKLRITN  684 (695)
Q Consensus       650 l~~L~~L~l~~c~~l~~lP~----~i~~L~~L~~L~l~~  684 (695)
                      +++|++|.+-+|+ ...-+.    -+.++++|++||+++
T Consensus       112 ~p~L~~Ltll~Np-v~~k~~YR~yvl~klp~l~~LDF~k  149 (233)
T KOG1644|consen  112 CPKLEYLTLLGNP-VEHKKNYRLYVLYKLPSLRTLDFQK  149 (233)
T ss_pred             CCccceeeecCCc-hhcccCceeEEEEecCcceEeehhh
Confidence            8899999888853 444332    277899999999875

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=95.86  E-value=0.6  Score=47.57  Aligned_cols=159  Identities=10%  Similarity=0.057  Sum_probs=91.0

Q ss_pred             HHHHHHHHHcCC-ceEEEEEcCCCCcHHHHHHHHhccccc--------c-ccCCCcEEEEEeCC-CCCHHHHHHHHHHhc
Q 042541          175 LKELKMELFKDG-RQFIVVSAPGGYGKTTLVQRLCKDDQV--------Q-GKFKDDIFYVTVSK-NPNVKAIVQKVLHHK  243 (695)
Q Consensus       175 ~~~l~~~L~~~~-~~vv~I~G~gGiGKTtLa~~~~~~~~~--------~-~~f~~~~~wv~~~~-~~~~~~~~~~i~~~l  243 (695)
                      ++.+...+..+. ..+..++|..|+||+++|..+.+  .+        . +..+..+.+++..+ ....+++ +++.+.+
T Consensus         5 ~~~l~~~i~~~~l~haYLf~G~eg~gk~~~a~~~a~--~l~c~~~~~~~~~~~p~n~~~~d~~g~~i~vd~I-r~l~~~~   81 (299)
T PRK07132          5 IKFLDNSATQNKISHSFLLKSNYNEDIDEKILYFLN--KFNNLQITNLNEQELPANIILFDIFDKDLSKSEF-LSAINKL   81 (299)
T ss_pred             HHHHHHHHHhCCCCeEEEEeCCCCCCHHHHHHHHHH--HHcCcCCCCCCCCCCCcceEEeccCCCcCCHHHH-HHHHHHh
Confidence            345555555554 56677999999999999998876  32        1 11121133432211 1222222 1222222


Q ss_pred             CCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCC------CCCCCe
Q 042541          244 GYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEF------PQFGSV  313 (695)
Q Consensus       244 ~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~------~~~~~~  313 (695)
                      .....                  -.+++-++|+||+......    ++..+....+++.+|++|....      ..-+..
T Consensus        82 ~~~~~------------------~~~~~KvvII~~~e~m~~~a~NaLLK~LEEPp~~t~~il~~~~~~kll~TI~SRc~~  143 (299)
T PRK07132         82 YFSSF------------------VQSQKKILIIKNIEKTSNSLLNALLKTIEEPPKDTYFLLTTKNINKVLPTIVSRCQV  143 (299)
T ss_pred             ccCCc------------------ccCCceEEEEecccccCHHHHHHHHHHhhCCCCCeEEEEEeCChHhChHHHHhCeEE
Confidence            11100                  0257889999998766543    5566666666777777665441      112348


Q ss_pred             EecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHH
Q 042541          314 HYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKV  363 (695)
Q Consensus       314 ~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~  363 (695)
                      +++.++++++..+.+....         ..++.+..++...+|.=.|+..
T Consensus       144 ~~f~~l~~~~l~~~l~~~~---------~~~~~a~~~a~~~~~~~~a~~~  184 (299)
T PRK07132        144 FNVKEPDQQKILAKLLSKN---------KEKEYNWFYAYIFSNFEQAEKY  184 (299)
T ss_pred             EECCCCCHHHHHHHHHHcC---------CChhHHHHHHHHcCCHHHHHHH
Confidence            9999999999988776531         1234567777777773345444

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=95.85  E-value=0.051  Score=56.41  Aligned_cols=58  Identities=17%  Similarity=0.264  Sum_probs=41.4

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhcccccc---ccCCCcEEEEEeCCCCCHHHHHHHHHHhcCC
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQ---GKFKDDIFYVTVSKNPNVKAIVQKVLHHKGY  245 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~---~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~  245 (695)
                      ..++-|+|.+|+|||+|+..++-.....   ..-...++|++....++++.+. ++++.++.
T Consensus       123 g~i~~i~G~~g~GKT~l~~~l~~~~~~~~~~gg~~g~vlyIdtE~~f~~eRl~-qia~~~~~  183 (342)
T PLN03186        123 GSITEIYGEFRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYIDTEGTFRPQRLI-QIAERFGL  183 (342)
T ss_pred             ceEEEEECCCCCCccHHHHHHHHHhhcchhhCCCCceEEEEECCCCccHHHHH-HHHHHcCC
Confidence            5788899999999999998776432221   1122348899999999887764 55666554

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=95.82  E-value=0.012  Score=55.96  Aligned_cols=24  Identities=21%  Similarity=0.354  Sum_probs=21.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +.++|+|+|++|+||||+|+.+..
T Consensus         2 ~~~ii~i~G~~GsGKsTl~~~l~~   25 (188)
T TIGR01360         2 KCKIIFIVGGPGSGKGTQCEKIVE   25 (188)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            357899999999999999999886

Members of this family are adenylate kinase, EC 2.7.4.3. This clade is found only in eukaryotes and includes human adenylate kinase isozyme 1 (myokinase). Within the adenylate kinase superfamily, this set appears specifically closely related to a subfamily of eukaryotic UMP-CMP kinases (TIGR01359), rather than to the large clade of bacterial, archaeal, and eukaryotic adenylate kinase family members in TIGR01351.

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=95.77  E-value=0.03  Score=56.38  Aligned_cols=56  Identities=14%  Similarity=0.236  Sum_probs=35.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC-CHHHHHHHHHHhcC
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKG  244 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~  244 (695)
                      +.++|.++|++|+||||++..++.  ..... ...+.+++..... ...+-+....+..+
T Consensus        71 ~~~vi~l~G~~G~GKTTt~akLA~--~l~~~-g~~V~li~~D~~r~~a~~ql~~~~~~~~  127 (272)
T TIGR00064        71 KPNVILFVGVNGVGKTTTIAKLAN--KLKKQ-GKSVLLAAGDTFRAAAIEQLEEWAKRLG  127 (272)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHH--HHHhc-CCEEEEEeCCCCCHHHHHHHHHHHHhCC
Confidence            358999999999999999988876  33322 2336677665322 12333444555555

There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.

>KOG2120 consensus SCF ubiquitin ligase, Skp2 component [Posttranslational modification, protein turnover, chaperones]

Probab=95.76  E-value=0.0017  Score=63.42  Aligned_cols=38  Identities=18%  Similarity=0.335  Sum_probs=16.7

Q ss_pred             cCCCccEEeccccccccc-CchhhcCCCCCceeeccccc
Q 042541          649 AFPNLLEMDIDYCNDLIE-LPDGLCDIVSMEKLRITNCH  686 (695)
Q Consensus       649 ~l~~L~~L~l~~c~~l~~-lP~~i~~L~~L~~L~l~~~~  686 (695)
                      .+++|..|||++|..+.. +-..|.+++-|++|.++.|.
T Consensus       311 rcp~l~~LDLSD~v~l~~~~~~~~~kf~~L~~lSlsRCY  349 (419)
T KOG2120|consen  311 RCPNLVHLDLSDSVMLKNDCFQEFFKFNYLQHLSLSRCY  349 (419)
T ss_pred             hCCceeeeccccccccCchHHHHHHhcchheeeehhhhc
Confidence            445555555555433321 11223444555555555554

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=95.75  E-value=0.021  Score=55.29  Aligned_cols=23  Identities=17%  Similarity=0.495  Sum_probs=20.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+++.|+|+.|.|||||.+.+..
T Consensus        29 ~~~~~itGpNg~GKStlLk~i~~   51 (213)
T cd03281          29 PSIMVITGPNSSGKSVYLKQVAL   51 (213)
T ss_pred             ceEEEEECCCCCChHHHHHHHHH
Confidence            48899999999999999998874

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]

Probab=95.74  E-value=0.2  Score=55.70  Aligned_cols=92  Identities=17%  Similarity=0.293  Sum_probs=59.4

Q ss_pred             CCCCCcchHHHHHHHHH---------cCC---ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHH
Q 042541          167 ISPGLDVPLKELKMELF---------KDG---RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKA  234 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~---------~~~---~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~  234 (695)
                      ++=|.++.+.+|.+-+.         ..+   ..=|.++|++|.|||-+|++|+..      |.  .-+++|...    +
T Consensus       673 DVGGLeevK~eIldTIqlPL~hpeLfssglrkRSGILLYGPPGTGKTLlAKAVATE------cs--L~FlSVKGP----E  740 (953)
T KOG0736|consen  673 DVGGLEEVKTEILDTIQLPLKHPELFSSGLRKRSGILLYGPPGTGKTLLAKAVATE------CS--LNFLSVKGP----E  740 (953)
T ss_pred             cccCHHHHHHHHHHHhcCcccChhhhhccccccceeEEECCCCCchHHHHHHHHhh------ce--eeEEeecCH----H
Confidence            44567777777877664         222   346889999999999999999872      33  446676653    2


Q ss_pred             HHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCC
Q 042541          235 IVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGS  283 (695)
Q Consensus       235 ~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~  283 (695)
                      ++..-   +|.          ..+.+++.+ ++-.-++|+|.||.+++..
T Consensus       741 LLNMY---VGq----------SE~NVR~VFerAR~A~PCVIFFDELDSlA  777 (953)
T KOG0736|consen  741 LLNMY---VGQ----------SEENVREVFERARSAAPCVIFFDELDSLA  777 (953)
T ss_pred             HHHHH---hcc----------hHHHHHHHHHHhhccCCeEEEeccccccC
Confidence            22221   121          123345555 4446889999999986543

>PF00485 PRK: Phosphoribulokinase / Uridine kinase family; InterPro: IPR006083 Phosphoribulokinase (PRK) 2

Probab=95.73  E-value=0.0071  Score=57.82  Aligned_cols=21  Identities=48%  Similarity=0.797  Sum_probs=19.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ||+|.|++|+||||+|+.+..
T Consensus         1 IIgI~G~sgSGKTTla~~L~~   21 (194)
T PF00485_consen    1 IIGIAGPSGSGKTTLAKRLAQ   21 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            799999999999999999987

7.1.19 from EC catalyses the ATP-dependent phosphorylation of ribulose-5-phosphate to ribulose-1,5-phosphate, a key step in the pentose phosphate pathway where carbon dioxide is assimilated by autotrophic organisms []. In general, plant enzymes are light-activated by the thioredoxin/ferredoxin system, while those from photosynthetic bacteria are regulated by a system that has an absolute requirement for NADH. Thioredoxin/ferredoxin regulation is mediated by the reversible oxidation/reduction of sulphydryl and disulphide groups. Uridine kinase (pyrimidine ribonucleoside kinase) is the rate-limiting enzyme in the pyrimidine salvage pathway. It catalyzes the following reaction: ATP + Uridine = ADP + UMP Pantothenate kinase (2.7.1.33 from EC) catalyzes the rate-limiting step in the biosynthesis of coenzyme A, the conversion of pantothenate to D-4'-phosphopantothenate in the presence of ATP. ; GO: 0005524 ATP binding, 0016301 kinase activity, 0008152 metabolic process; PDB: 2ZSE_A 2ZS7_A 3AF0_A 3AVP_A 2ZS9_A 2ZS8_A 3AEZ_A 2ZSB_A 2ZSD_A 2GEV_A ....

>PF13238 AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB_A 3IIM_A 2AXP_A 3KB2_A 1KHT_A 1NKS_A 3H86_C

Probab=95.73  E-value=0.007  Score=53.33  Aligned_cols=21  Identities=38%  Similarity=0.509  Sum_probs=19.2

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |+|.|..|+||||+|+.+...
T Consensus         1 I~i~G~~GsGKtTia~~L~~~   21 (129)
T PF13238_consen    1 IGISGIPGSGKTTIAKELAER   21 (129)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEECCCCCCHHHHHHHHHHH
Confidence            789999999999999999873

...

>KOG0729 consensus 26S proteasome regulatory complex, ATPase RPT1 [Posttranslational modification, protein turnover, chaperones]

Probab=95.69  E-value=0.05  Score=52.44  Aligned_cols=49  Identities=18%  Similarity=0.247  Sum_probs=37.0

Q ss_pred             CCCCCcchHHHHHHHHHc-------------CCceEEEEEcCCCCcHHHHHHHHhccccccccC
Q 042541          167 ISPGLDVPLKELKMELFK-------------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKF  217 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~~-------------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f  217 (695)
                      .+-|-.++++++.+...-             +.++=|.++|++|.|||-+|++|+|  +....|
T Consensus       178 dvggckeqieklrevve~pll~perfv~lgidppkgvllygppgtgktl~aravan--rtdacf  239 (435)
T KOG0729|consen  178 DVGGCKEQIEKLREVVELPLLHPERFVNLGIDPPKGVLLYGPPGTGKTLCARAVAN--RTDACF  239 (435)
T ss_pred             cccchHHHHHHHHHHHhccccCHHHHhhcCCCCCCceEEeCCCCCchhHHHHHHhc--ccCceE
Confidence            345577778888776551             2357789999999999999999999  555544

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=95.66  E-value=0.051  Score=55.98  Aligned_cols=58  Identities=14%  Similarity=0.126  Sum_probs=39.6

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccC---CCcEEEEEeCCCCCHHHHHHHHHHhcCC
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKF---KDDIFYVTVSKNPNVKAIVQKVLHHKGY  245 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f---~~~~~wv~~~~~~~~~~~~~~i~~~l~~  245 (695)
                      ..++.|+|.+|+|||||+..++.........   ...++|++..+.++...+ .++.+.++.
T Consensus        96 g~i~~i~G~~g~GKT~l~~~~~~~~~~~~~~Gg~~~~vvyIdtE~~f~~~Rl-~~ia~~~~~  156 (316)
T TIGR02239        96 GSITEIFGEFRTGKTQLCHTLAVTCQLPIDQGGGEGKALYIDTEGTFRPERL-LAIAERYGL  156 (316)
T ss_pred             CeEEEEECCCCCCcCHHHHHHHHHHhhhhhcCCCCceEEEEECCCCCCHHHH-HHHHHHcCC
Confidence            5889999999999999998886522221111   124789999888877764 444555443

This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).

>PF12061 DUF3542: Protein of unknown function (DUF3542); InterPro: IPR021929 R1 is a gene for resistance to late blight, the most destructive disease in potato cultivation worldwide

Probab=95.66  E-value=0.014  Score=57.33  Aligned_cols=78  Identities=15%  Similarity=0.307  Sum_probs=68.0

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhhhchHHHHHHHHHHHhhhHHHHHH-HHhhhccCCChHHHHHHHHHHHHHHHHHHhccc
Q 042541            9 ALLGAVFGELLKAVSEEKDKAVTFKDRLEQLESTLRNSIPWIEEI-EKLNQVLDRPKQETENLVRMMEQVEQLVRKCSK   86 (695)
Q Consensus         9 a~~~~v~~kl~~~l~~~~~~~~~~~~~l~~L~~~L~~i~~~l~~a-e~~~~~~~~~~~wl~~l~~~~~d~ed~ld~~~~   86 (695)
                      +.+..+++++-.+...+.....-++.+++.++.+++.+|.||+.. ++.+...+.....+.++...||++|.++|-+..
T Consensus       296 GyVdFlL~NLkdfq~rysdSlaflKnQiqvIQ~elesLqpFLk~V~ee~~nkh~~~ed~a~~ii~kAyevEYVVDaCi~  374 (402)
T PF12061_consen  296 GYVDFLLKNLKDFQGRYSDSLAFLKNQIQVIQTELESLQPFLKHVVEEPHNKHDTNEDCATQIIRKAYEVEYVVDACIS  374 (402)
T ss_pred             cHHHHHHhhHHHHhccccchHHHHHHHHHHHHHHHHHhhHHHHHHHhccchhhhhhhhHHHHHHHHHhheeeeeehhhc
Confidence            357788889988888888888889999999999999999999986 665666666889999999999999999998865

The R1 gene belongs to the class of plant genes for pathogen resistance that have a leucine zipper motif, a putative nucleotide binding domain and a leucine-rich repeat domain []. Most proteins matching this entry are found associated with PF00931 from PFAM.

>cd02025 PanK Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway

Probab=95.65  E-value=0.034  Score=54.12  Aligned_cols=41  Identities=15%  Similarity=0.084  Sum_probs=28.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHhccccccc-cCCCcEEEEEeCCCCC
Q 042541          189 FIVVSAPGGYGKTTLVQRLCKDDQVQG-KFKDDIFYVTVSKNPN  231 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~~~~~~~-~f~~~~~wv~~~~~~~  231 (695)
                      +|+|.|.+|+||||+|+.+..  .+.. .....+..++....+.
T Consensus         1 IigI~G~sGSGKTTla~~L~~--~l~~~~~~~~v~vi~~D~f~~   42 (220)
T cd02025           1 IIGIAGSVAVGKSTTARVLQA--LLSRWPDHPNVELITTDGFLY   42 (220)
T ss_pred             CEEeeCCCCCCHHHHHHHHHH--HHhhcCCCCcEEEEecCcccC
Confidence            589999999999999999987  3321 1222355666655443

The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.

>PF01583 APS_kinase: Adenylylsulphate kinase; InterPro: IPR002891 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases

Probab=95.65  E-value=0.013  Score=52.97  Aligned_cols=37  Identities=22%  Similarity=0.288  Sum_probs=27.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEe
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTV  226 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~  226 (695)
                      ..+|.|+|.+|+||||||+++.+  ++...-.. +++++.
T Consensus         2 g~vIwltGlsGsGKtTlA~~L~~--~L~~~g~~-~~~LDg   38 (156)
T PF01583_consen    2 GFVIWLTGLSGSGKTTLARALER--RLFARGIK-VYLLDG   38 (156)
T ss_dssp             -EEEEEESSTTSSHHHHHHHHHH--HHHHTTS--EEEEEH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH--HHHHcCCc-EEEecC
Confidence            46899999999999999999998  55554333 556543

Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This domain contains an ATP binding P-loop motif [].; GO: 0005524 ATP binding, 0016301 kinase activity, 0016772 transferase activity, transferring phosphorus-containing groups, 0000103 sulfate assimilation; PDB: 1M7H_B 1M7G_B 3CR7_B 1D6J_A 2OFW_G 1X6V_B 1XNJ_A 1XJQ_B 2PEY_A 2PEZ_B ....

>PF10236 DAP3: Mitochondrial ribosomal death-associated protein 3; InterPro: IPR019368 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=95.62  E-value=0.34  Score=49.84  Aligned_cols=49  Identities=24%  Similarity=0.231  Sum_probs=35.6

Q ss_pred             eEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHH
Q 042541          313 VHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLAL  361 (695)
Q Consensus       313 ~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai  361 (695)
                      ++++++++.+|+..++.......--......+...+++.-..+|+|.-+
T Consensus       258 ~i~v~~~s~~E~~~ll~yy~~~~~l~~~~~~~~~~e~~~~~s~GNp~el  306 (309)
T PF10236_consen  258 PIEVPRLSKEEARSLLEYYADSGWLRSRVDEELVLEKLFLSSNGNPREL  306 (309)
T ss_pred             eEEeCCCCHHHHHHHHHHHHHCCccccCCCCHHHHHHHHHhcCCCHHHh
Confidence            6789999999999999887654443222334566777777789999643

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 conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis []. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix [] and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29).

>TIGR01817 nifA Nif-specific regulatory protein

Probab=95.62  E-value=0.18  Score=56.42  Aligned_cols=45  Identities=9%  Similarity=0.106  Sum_probs=37.5

Q ss_pred             CCCCCCCcchHHHHHHHHH--cCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          165 PVISPGLDVPLKELKMELF--KDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~--~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...++|....++++.+.+.  .....-|.|+|..|+|||++|+.+++
T Consensus       195 ~~~liG~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~lA~~ih~  241 (534)
T TIGR01817       195 EDGIIGKSPAMRQVVDQARVVARSNSTVLLRGESGTGKELIAKAIHY  241 (534)
T ss_pred             cCceEECCHHHHHHHHHHHHHhCcCCCEEEECCCCccHHHHHHHHHH
Confidence            4568999999999988876  33345678999999999999999987

This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=95.60  E-value=0.062  Score=55.86  Aligned_cols=44  Identities=16%  Similarity=0.094  Sum_probs=36.5

Q ss_pred             CCCCCCcchHHHHHHHHH--cCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          166 VISPGLDVPLKELKMELF--KDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~--~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +.++|+...++++.+.+.  .....-|.|+|..|+||+++|+.++.
T Consensus         6 ~~liG~S~~~~~~~~~i~~~a~~~~pVlI~GE~GtGK~~lA~~iH~   51 (326)
T PRK11608          6 DNLLGEANSFLEVLEQVSRLAPLDKPVLIIGERGTGKELIASRLHY   51 (326)
T ss_pred             CccEECCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHH
Confidence            457999999999988877  33345688999999999999999875

>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]

Probab=95.59  E-value=0.051  Score=53.30  Aligned_cols=94  Identities=16%  Similarity=0.203  Sum_probs=53.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCC-----CCCHHHHHHHHHHhcCCCCCCCC--ChHHHHH
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSK-----NPNVKAIVQKVLHHKGYPVPEFQ--TDEAAIN  258 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~-----~~~~~~~~~~i~~~l~~~~~~~~--~~~~~~~  258 (695)
                      +..+++|+|.+|+||||+++.+..   +..--...+ ++.-.+     .....+-..++++.++.+.....  ..+-...
T Consensus        38 ~ge~~glVGESG~GKSTlgr~i~~---L~~pt~G~i-~f~g~~i~~~~~~~~~~~v~elL~~Vgl~~~~~~ryPhelSGG  113 (268)
T COG4608          38 EGETLGLVGESGCGKSTLGRLILG---LEEPTSGEI-LFEGKDITKLSKEERRERVLELLEKVGLPEEFLYRYPHELSGG  113 (268)
T ss_pred             CCCEEEEEecCCCCHHHHHHHHHc---CcCCCCceE-EEcCcchhhcchhHHHHHHHHHHHHhCCCHHHhhcCCcccCch
Confidence            357899999999999999999986   333222323 443221     11234455667777664321000  0000112


Q ss_pred             HHHHHH--HhcCCCcEEEEEeCCCCCC
Q 042541          259 DLERFF--KQMRIEAILLVLDDVWPGS  283 (695)
Q Consensus       259 ~l~~~~--~~l~~~~~LlVlDdv~~~~  283 (695)
                      +.+++.  +.+.-++-++|.|..-+..
T Consensus       114 QrQRi~IARALal~P~liV~DEpvSaL  140 (268)
T COG4608         114 QRQRIGIARALALNPKLIVADEPVSAL  140 (268)
T ss_pred             hhhhHHHHHHHhhCCcEEEecCchhhc
Confidence            233333  6677889999999964443

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=95.58  E-value=0.1  Score=51.66  Aligned_cols=47  Identities=19%  Similarity=0.319  Sum_probs=33.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQK  238 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~  238 (695)
                      ..++.|.|.+|+|||++|.++... ..+.  ...++|++..+  +..++.+.
T Consensus        21 gs~~lI~G~pGsGKT~la~~~l~~-~~~~--ge~~lyvs~ee--~~~~i~~~   67 (237)
T TIGR03877        21 RNVVLLSGGPGTGKSIFSQQFLWN-GLQM--GEPGIYVALEE--HPVQVRRN   67 (237)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHH-HHHc--CCcEEEEEeeC--CHHHHHHH
Confidence            589999999999999999887652 2222  22377988866  44555554

Members of this family contain a single copy of the KaiC domain (pfam06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga.

>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=95.57  E-value=0.18  Score=52.71  Aligned_cols=117  Identities=18%  Similarity=0.248  Sum_probs=70.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCC-CCCHHHHHHHHHHhcCCCCCCC--------------
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSK-NPNVKAIVQKVLHHKGYPVPEF--------------  250 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~-~~~~~~~~~~i~~~l~~~~~~~--------------  250 (695)
                      .+.||..+|.-|.||||-|-.+++  .++. ....+.-|++.- .+..-+-++.+.++.+.+....              
T Consensus        99 ~P~vImmvGLQGsGKTTt~~KLA~--~lkk-~~~kvllVaaD~~RpAA~eQL~~La~q~~v~~f~~~~~~~Pv~Iak~al  175 (451)
T COG0541          99 PPTVILMVGLQGSGKTTTAGKLAK--YLKK-KGKKVLLVAADTYRPAAIEQLKQLAEQVGVPFFGSGTEKDPVEIAKAAL  175 (451)
T ss_pred             CCeEEEEEeccCCChHhHHHHHHH--HHHH-cCCceEEEecccCChHHHHHHHHHHHHcCCceecCCCCCCHHHHHHHHH
Confidence            368999999999999999988877  3444 333355555442 2344555666777765433221              


Q ss_pred             -------------------CChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCC-hHHHhhhccCCCCCEEEEEcCC
Q 042541          251 -------------------QTDEAAINDLERFFKQMRIEAILLVLDDVWPGS-ESLLQKLGFQLPDYKILVTSRS  305 (695)
Q Consensus       251 -------------------~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~-~~~~~~l~~~~~gs~iivTtR~  305 (695)
                                         .-+++..+++.++-+.+.....|+|+|-.--.+ ......|....+=+-||+|==+
T Consensus       176 ~~ak~~~~DvvIvDTAGRl~ide~Lm~El~~Ik~~~~P~E~llVvDam~GQdA~~~A~aF~e~l~itGvIlTKlD  250 (451)
T COG0541         176 EKAKEEGYDVVIVDTAGRLHIDEELMDELKEIKEVINPDETLLVVDAMIGQDAVNTAKAFNEALGITGVILTKLD  250 (451)
T ss_pred             HHHHHcCCCEEEEeCCCcccccHHHHHHHHHHHhhcCCCeEEEEEecccchHHHHHHHHHhhhcCCceEEEEccc
Confidence                               113344555555556667777888888763322 2244556655554667776443

>cd02019 NK Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars

Probab=95.57  E-value=0.0094  Score=46.08  Aligned_cols=21  Identities=29%  Similarity=0.624  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +|+|.|..|+||||+++.+.+
T Consensus         1 ~i~i~G~~gsGKst~~~~l~~   21 (69)
T cd02019           1 IIAITGGSGSGKSTVAKKLAE   21 (69)
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            478999999999999999887

Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate.

>PRK05480 uridine/cytidine kinase; Provisional

Probab=95.56  E-value=0.011  Score=57.27  Aligned_cols=25  Identities=24%  Similarity=0.357  Sum_probs=22.6

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+..+|+|.|.+|+|||||++.+..
T Consensus         4 ~~~~iI~I~G~sGsGKTTl~~~l~~   28 (209)
T PRK05480          4 KKPIIIGIAGGSGSGKTTVASTIYE   28 (209)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            3567999999999999999999987

>cd03214 ABC_Iron-Siderophores_B12_Hemin ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea

Probab=95.55  E-value=0.11  Score=49.04  Aligned_cols=115  Identities=17%  Similarity=0.196  Sum_probs=58.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEE---eCCCCCHHH------HHHHHHHhcCCCCC---CCCChH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVT---VSKNPNVKA------IVQKVLHHKGYPVP---EFQTDE  254 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~---~~~~~~~~~------~~~~i~~~l~~~~~---~~~~~~  254 (695)
                      ..+++|+|..|.|||||++.++..   .......+ +++   +.. .+...      ...++++.++....   ......
T Consensus        25 G~~~~l~G~nGsGKStLl~~i~G~---~~~~~G~v-~~~g~~~~~-~~~~~~~~~i~~~~q~l~~~gl~~~~~~~~~~LS   99 (180)
T cd03214          25 GEIVGILGPNGAGKSTLLKTLAGL---LKPSSGEI-LLDGKDLAS-LSPKELARKIAYVPQALELLGLAHLADRPFNELS   99 (180)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC---CCCCCcEE-EECCEECCc-CCHHHHHHHHhHHHHHHHHcCCHhHhcCCcccCC
Confidence            478999999999999999999862   22233323 332   221 12211      11224555543210   001111


Q ss_pred             HHHHHHHHHHHhcCCCcEEEEEeCCCCCCh-----HHHhhhccC-CC-CCEEEEEcCCC
Q 042541          255 AAINDLERFFKQMRIEAILLVLDDVWPGSE-----SLLQKLGFQ-LP-DYKILVTSRSE  306 (695)
Q Consensus       255 ~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~-----~~~~~l~~~-~~-gs~iivTtR~~  306 (695)
                      ....+.-.+...+-..+-++++|+--..-+     .+.+.+... .. |..||++|.+.
T Consensus       100 ~G~~qrl~laral~~~p~llllDEP~~~LD~~~~~~~~~~l~~~~~~~~~tiii~sh~~  158 (180)
T cd03214         100 GGERQRVLLARALAQEPPILLLDEPTSHLDIAHQIELLELLRRLARERGKTVVMVLHDL  158 (180)
T ss_pred             HHHHHHHHHHHHHhcCCCEEEEeCCccCCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            122222223355667889999999743332     122222221 12 66778877654

Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC transporter mediating vitamin B12 uptake. The two ATP-binding cassettes (BtuD) are in close contact with each other, as are the two membrane-spanning subunits (BtuC); this arrangement is distinct from that observed for the E. coli lipid flippase MsbA. The BtuC subunits provide 20 transmembrane helices grouped around a translocation pathway that is closed to the cytoplasm by a gate region, whereas the dimer arrangement of the BtuD subunits resembles the ATP-bound form of the Rad50 DNA repair enzyme. A prominent cytoplasmic loop of BtuC forms the contact region with the ATP-binding cassette and represent a conserved motif among the ABC transporters.

>PTZ00301 uridine kinase; Provisional

Probab=95.55  E-value=0.017  Score=55.55  Aligned_cols=23  Identities=26%  Similarity=0.419  Sum_probs=21.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+|+|.|.+|+||||||+.+.+
T Consensus         3 ~~iIgIaG~SgSGKTTla~~l~~   25 (210)
T PTZ00301          3 CTVIGISGASGSGKSSLSTNIVS   25 (210)
T ss_pred             CEEEEEECCCcCCHHHHHHHHHH
Confidence            46899999999999999998876

>PRK08233 hypothetical protein; Provisional

Probab=95.53  E-value=0.011  Score=55.79  Aligned_cols=23  Identities=43%  Similarity=0.629  Sum_probs=21.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+|+|.|.+|+||||||+.++.
T Consensus         3 ~~iI~I~G~~GsGKtTla~~L~~   25 (182)
T PRK08233          3 TKIITIAAVSGGGKTTLTERLTH   25 (182)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHh
Confidence            47899999999999999999986

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=95.52  E-value=0.018  Score=54.38  Aligned_cols=21  Identities=24%  Similarity=0.362  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ||.|+|++|+||||+|+.++.
T Consensus         1 ~i~i~G~pGsGKst~a~~la~   21 (183)
T TIGR01359         1 VVFVLGGPGSGKGTQCAKIVE   21 (183)
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            588999999999999999876

This subfamily of the adenylate kinase superfamily contains examples of UMP-CMP kinase, as well as others proteins with unknown specificity, some currently designated adenylate kinase. All known members are eukaryotic.

>cd01135 V_A-ATPase_B V/A-type ATP synthase (non-catalytic) subunit B

Probab=95.50  E-value=0.05  Score=54.07  Aligned_cols=95  Identities=11%  Similarity=0.130  Sum_probs=57.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccc--cccCCCcEEEEEeCCCC-CHHHHHHHHHHhcCCC-------CCCCCChH-
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQV--QGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKGYP-------VPEFQTDE-  254 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~--~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~~~-------~~~~~~~~-  254 (695)
                      ..+-++|.|..|+|||+|+..+.+...+  +++-+. ++++-+++.. ...++..++...-...       ..+..... 
T Consensus        68 ~GQR~gIfgg~GvGKt~L~~~i~~~~~~~~~~~~~v-~V~~~IGeR~rev~e~~~~~~~~~~l~~tv~v~~t~~~~~~~r  146 (276)
T cd01135          68 RGQKIPIFSGSGLPHNELAAQIARQAGVVGEEENFA-VVFAAMGITMEDARFFKDDFEETGALERVVLFLNLANDPTIER  146 (276)
T ss_pred             cCCEEEeecCCCCChhHHHHHHHHhhhccccCCCCE-EEEEEeccccHHHHHHHHHhhhcCCcceEEEEEecCCCCHHHH
Confidence            3577899999999999999988874331  112233 6688887654 5677777776642211       11111111 


Q ss_pred             ----HHHHHHHHHHHhcCCCcEEEEEeCCCC
Q 042541          255 ----AAINDLERFFKQMRIEAILLVLDDVWP  281 (695)
Q Consensus       255 ----~~~~~l~~~~~~l~~~~~LlVlDdv~~  281 (695)
                          ...-.+.+.+..-.++++|+++||+..
T Consensus       147 ~~a~~~a~aiAEyfrd~~g~~VLl~~D~ltr  177 (276)
T cd01135         147 IITPRMALTTAEYLAYEKGKHVLVILTDMTN  177 (276)
T ss_pred             HHHHHHHHHHHHHHHhccCCeEEEEEcChhH
Confidence                112234444433248999999999843

These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria. This subfamily consists of the non-catalytic beta subunit.

>cd03222 ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids

Probab=95.50  E-value=0.15  Score=47.75  Aligned_cols=24  Identities=38%  Similarity=0.494  Sum_probs=21.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+++|+|+.|+|||||++.+..
T Consensus        24 ~Ge~~~l~G~nGsGKSTLl~~l~G   47 (177)
T cd03222          24 EGEVIGIVGPNGTGKTTAVKILAG   47 (177)
T ss_pred             CCCEEEEECCCCChHHHHHHHHHc
Confidence            457999999999999999999886

RLI's are not transport proteins, and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains, which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=95.50  E-value=0.018  Score=51.38  Aligned_cols=44  Identities=25%  Similarity=0.418  Sum_probs=32.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCC
Q 042541          189 FIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYP  246 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~  246 (695)
                      +|.|.|++|+||||+|+.++++      +...  .++      .-.+++++++..|.+
T Consensus         2 ~ItIsG~pGsG~TTva~~lAe~------~gl~--~vs------aG~iFR~~A~e~gms   45 (179)
T COG1102           2 VITISGLPGSGKTTVARELAEH------LGLK--LVS------AGTIFREMARERGMS   45 (179)
T ss_pred             EEEeccCCCCChhHHHHHHHHH------hCCc--eee------ccHHHHHHHHHcCCC
Confidence            6899999999999999999873      2211  222      235788888888764

>COG0465 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]

Probab=95.50  E-value=0.13  Score=56.57  Aligned_cols=92  Identities=16%  Similarity=0.216  Sum_probs=55.7

Q ss_pred             CCCCCCCcchHHHH---HHHHHcCC---------ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCH
Q 042541          165 PVISPGLDVPLKEL---KMELFKDG---------RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNV  232 (695)
Q Consensus       165 ~~~~vGr~~~~~~l---~~~L~~~~---------~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~  232 (695)
                      -.+.-|.++..+++   ++.|.++.         ++-|.++|++|.|||.||++++....+.        +.+.|...  
T Consensus       149 F~DVAG~dEakeel~EiVdfLk~p~ky~~lGakiPkGvlLvGpPGTGKTLLAkAvAgEA~VP--------Ff~iSGS~--  218 (596)
T COG0465         149 FADVAGVDEAKEELSELVDFLKNPKKYQALGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVP--------FFSISGSD--  218 (596)
T ss_pred             hhhhcCcHHHHHHHHHHHHHHhCchhhHhcccccccceeEecCCCCCcHHHHHHHhcccCCC--------ceeccchh--
Confidence            34568888765555   45555432         5678999999999999999999843332        22333221  


Q ss_pred             HHHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCC
Q 042541          233 KAIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWP  281 (695)
Q Consensus       233 ~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~  281 (695)
                            .++.+-+-         ...+.+.++ +..+.-++++++|.++.
T Consensus       219 ------FVemfVGv---------GAsRVRdLF~qAkk~aP~IIFIDEiDA  253 (596)
T COG0465         219 ------FVEMFVGV---------GASRVRDLFEQAKKNAPCIIFIDEIDA  253 (596)
T ss_pred             ------hhhhhcCC---------CcHHHHHHHHHhhccCCCeEEEehhhh
Confidence                  11111110         123444555 55567789999998753

>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B

Probab=95.49  E-value=0.011  Score=53.40  Aligned_cols=21  Identities=48%  Similarity=0.857  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +|.++|++|+||||+|+.+..
T Consensus         1 lii~~G~pgsGKSt~a~~l~~   21 (143)
T PF13671_consen    1 LIILCGPPGSGKSTLAKRLAK   21 (143)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            688999999999999999885

...

>TIGR00235 udk uridine kinase

Probab=95.49  E-value=0.011  Score=57.08  Aligned_cols=24  Identities=25%  Similarity=0.412  Sum_probs=21.9

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+|+|+|++|+|||||++.+..
T Consensus         5 ~g~vi~I~G~sGsGKSTl~~~l~~   28 (207)
T TIGR00235         5 KGIIIGIGGGSGSGKTTVARKIYE   28 (207)
T ss_pred             CeEEEEEECCCCCCHHHHHHHHHH
Confidence            457999999999999999999986

Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=95.49  E-value=0.082  Score=54.94  Aligned_cols=42  Identities=17%  Similarity=0.143  Sum_probs=34.1

Q ss_pred             CCCCcchHHHHHHHHH--cCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          168 SPGLDVPLKELKMELF--KDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       168 ~vGr~~~~~~l~~~L~--~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +||....++++.+.+.  .....-|.|+|..|+||+++|+.+++
T Consensus         1 liG~S~~m~~~~~~~~~~a~~~~pVLI~GE~GtGK~~lAr~iH~   44 (329)
T TIGR02974         1 LIGESNAFLEVLEQVSRLAPLDRPVLIIGERGTGKELIAARLHY   44 (329)
T ss_pred             CCcCCHHHHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHH
Confidence            4788888888887776  33345689999999999999999876

Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH

>KOG2982 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.48  E-value=0.0049  Score=60.28  Aligned_cols=85  Identities=18%  Similarity=0.194  Sum_probs=40.0

Q ss_pred             CCCCCcEEEEcccCCCCcccCc-ccccccCCCCcEEEeccCCCCC-cccc-cccccccEEeeccccCCcccccchhhhcc
Q 042541          572 KMDELKVLIVTNYGFSPAELNN-FRVLSALSKLKKIRLEHVSLPN-SLAT-VRMNHLQKVSLVMCNVGQVFRNSTFRISD  648 (695)
Q Consensus       572 ~l~~Lr~L~l~~~~~~~~~~~~-~~~l~~l~~L~~L~L~~~~l~~-lp~i-~~l~~L~~L~l~~~~i~~~~~~~~~~l~~  648 (695)
                      ....++.|||.+|.++.  +.. ...+.+|+.|++|+|+.|++.+ +-+. ..+.+|++|-|.++.+...-..   ...+
T Consensus        69 ~~~~v~elDL~~N~iSd--WseI~~ile~lP~l~~LNls~N~L~s~I~~lp~p~~nl~~lVLNgT~L~w~~~~---s~l~  143 (418)
T KOG2982|consen   69 SVTDVKELDLTGNLISD--WSEIGAILEQLPALTTLNLSCNSLSSDIKSLPLPLKNLRVLVLNGTGLSWTQST---SSLD  143 (418)
T ss_pred             Hhhhhhhhhcccchhcc--HHHHHHHHhcCccceEeeccCCcCCCccccCcccccceEEEEEcCCCCChhhhh---hhhh
Confidence            34556666666665531  111 1224556666666666665541 1111 2355666666666644321110   0111


Q ss_pred             cCCCccEEecccc
Q 042541          649 AFPNLLEMDIDYC  661 (695)
Q Consensus       649 ~l~~L~~L~l~~c  661 (695)
                      .+|.++.|.++.|
T Consensus       144 ~lP~vtelHmS~N  156 (418)
T KOG2982|consen  144 DLPKVTELHMSDN  156 (418)
T ss_pred             cchhhhhhhhccc
Confidence            4555555555553

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=95.48  E-value=0.028  Score=58.98  Aligned_cols=45  Identities=29%  Similarity=0.374  Sum_probs=36.3

Q ss_pred             CCCCCCCcchHHHHHHHHHcC--------------CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          165 PVISPGLDVPLKELKMELFKD--------------GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~--------------~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|.++.++.+...+...              .++-|.++|++|+|||++|+.+..
T Consensus        11 d~~IiGQ~eAkk~lsvAl~n~~~r~~~~~~~~~e~~p~~ILLiGppG~GKT~lAraLA~   69 (441)
T TIGR00390        11 DKYIIGQDNAKKSVAIALRNRYRRSQLNEELKDEVTPKNILMIGPTGVGKTEIARRLAK   69 (441)
T ss_pred             hhhccCHHHHHHHHHHHHHhhhhhhccccccccccCCceEEEECCCCCCHHHHHHHHHH
Confidence            456899998888887666531              146789999999999999999987

This model represents the ATPase subunit of HslVU, while the proteasome-related peptidase subunit is HslV. Residues 54-61 of the model contain a P-loop ATP-binding motif. Cys-287 of E. coli (position 308 in the seed alignment), studied in PubMed:98389714, is Ser in other members of the seed alignment.

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=95.46  E-value=0.1  Score=60.38  Aligned_cols=61  Identities=7%  Similarity=0.061  Sum_probs=43.2

Q ss_pred             CCCCCCcchHHHHHHHHH--cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCC
Q 042541          166 VISPGLDVPLKELKMELF--KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKN  229 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~--~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~  229 (695)
                      ..++|+...++++.+.+.  .....-|.|+|..|+|||++|+.+++.. .+..  ...+.+++...
T Consensus       376 ~~liG~S~~~~~~~~~~~~~a~~~~pVLI~GE~GTGK~~lA~~ih~~s-~r~~--~~~v~i~c~~~  438 (686)
T PRK15429        376 GEIIGRSEAMYSVLKQVEMVAQSDSTVLILGETGTGKELIARAIHNLS-GRNN--RRMVKMNCAAM  438 (686)
T ss_pred             cceeecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHhc-CCCC--CCeEEEecccC
Confidence            357999999988877766  3344578999999999999999998632 1122  22446666543

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.46  E-value=0.06  Score=56.81  Aligned_cols=92  Identities=21%  Similarity=0.294  Sum_probs=53.8

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccc-cCCCcEEEEEeCCCC-CHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHH
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQG-KFKDDIFYVTVSKNP-NVKAIVQKVLHHKGYPVPEFQTDEAAINDLERF  263 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~-~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~  263 (695)
                      ..++|.++|+.|+||||.+..++....... +-...+..+++.... ....-+....+.++.+......    ...+...
T Consensus       173 ~~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQL~~~a~~lgvpv~~~~~----~~~l~~~  248 (388)
T PRK12723        173 KKRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTYGDIMGIPVKAIES----FKDLKEE  248 (388)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHHHHHHhhcCCcceEeeCc----HHHHHHH
Confidence            357999999999999999988876322211 122336566665432 2333366666667665322222    2334444


Q ss_pred             HHhcCCCcEEEEEeCCCCC
Q 042541          264 FKQMRIEAILLVLDDVWPG  282 (695)
Q Consensus       264 ~~~l~~~~~LlVlDdv~~~  282 (695)
                      +..+ .+.-++++|.+...
T Consensus       249 L~~~-~~~DlVLIDTaGr~  266 (388)
T PRK12723        249 ITQS-KDFDLVLVDTIGKS  266 (388)
T ss_pred             HHHh-CCCCEEEEcCCCCC
Confidence            4344 34568889988543

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=95.43  E-value=0.036  Score=52.85  Aligned_cols=42  Identities=24%  Similarity=0.502  Sum_probs=28.1

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhccccccccC-------CCcEEEEEeCCC
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKDDQVQGKF-------KDDIFYVTVSKN  229 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f-------~~~~~wv~~~~~  229 (695)
                      .++.|+|++|+||||++..+..+.-....|       +.+++|++....
T Consensus        33 ~l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~   81 (193)
T PF13481_consen   33 ELTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDS   81 (193)
T ss_dssp             SEEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS-
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCC
Confidence            588999999999999998877642221112       345889888776

>cd01131 PilT Pilus retraction ATPase PilT

Probab=95.42  E-value=0.028  Score=53.88  Aligned_cols=22  Identities=27%  Similarity=0.579  Sum_probs=20.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ++|.|+|+.|+||||++..+..
T Consensus         2 GlilI~GptGSGKTTll~~ll~   23 (198)
T cd01131           2 GLVLVTGPTGSGKSTTLAAMID   23 (198)
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            5799999999999999998776

PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=95.40  E-value=0.12  Score=50.68  Aligned_cols=48  Identities=21%  Similarity=0.408  Sum_probs=31.8

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKV  239 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i  239 (695)
                      ..++.|.|.+|+||||||.+++.. -.+...  .+++++...  +..++++.+
T Consensus        24 g~~~~i~G~~G~GKTtl~~~~~~~-~~~~g~--~~~yi~~e~--~~~~~~~~~   71 (230)
T PRK08533         24 GSLILIEGDESTGKSILSQRLAYG-FLQNGY--SVSYVSTQL--TTTEFIKQM   71 (230)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH-HHhCCC--cEEEEeCCC--CHHHHHHHH
Confidence            469999999999999998666542 222322  356777444  445666655

>PRK06762 hypothetical protein; Provisional

Probab=95.40  E-value=0.013  Score=54.50  Aligned_cols=23  Identities=30%  Similarity=0.580  Sum_probs=21.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +.+|.|+|++|+||||+|+.+.+
T Consensus         2 ~~li~i~G~~GsGKST~A~~L~~   24 (166)
T PRK06762          2 TTLIIIRGNSGSGKTTIAKQLQE   24 (166)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999887

>COG1121 ZnuC ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]

Probab=95.32  E-value=0.12  Score=50.58  Aligned_cols=23  Identities=26%  Similarity=0.505  Sum_probs=21.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|.|||||.+.+..
T Consensus        30 G~~~~iiGPNGaGKSTLlK~iLG   52 (254)
T COG1121          30 GEITALIGPNGAGKSTLLKAILG   52 (254)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhC
Confidence            47899999999999999999876

>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes

Probab=95.30  E-value=0.16  Score=48.56  Aligned_cols=22  Identities=18%  Similarity=0.301  Sum_probs=20.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ++++|+|+.|.|||||.+.+.-
T Consensus        26 ~~~~ltGpNg~GKSTllr~i~~   47 (199)
T cd03283          26 NGILITGSNMSGKSTFLRTIGV   47 (199)
T ss_pred             cEEEEECCCCCChHHHHHHHHH
Confidence            7999999999999999998864

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form slid

>PRK14527 adenylate kinase; Provisional

Probab=95.30  E-value=0.033  Score=53.04  Aligned_cols=25  Identities=28%  Similarity=0.508  Sum_probs=22.1

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ....+|.|+|++|+||||+|+.+++
T Consensus         4 ~~~~~i~i~G~pGsGKsT~a~~La~   28 (191)
T PRK14527          4 TKNKVVIFLGPPGAGKGTQAERLAQ   28 (191)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHH
Confidence            3467899999999999999999876

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=95.29  E-value=0.063  Score=57.69  Aligned_cols=87  Identities=20%  Similarity=0.326  Sum_probs=47.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhcccc-ccccCCCcEEEEEeCCCC-CHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQ-VQGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFF  264 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~-~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~  264 (695)
                      .+++.++|++|+||||++..++.... ....+  .+..++..... ...+-+....+.++.+.......    ..+...+
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~g~--~V~li~~D~~r~~a~eqL~~~a~~~~vp~~~~~~~----~~l~~~l  294 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLYGKK--KVALITLDTYRIGAVEQLKTYAKIMGIPVEVVYDP----KELAKAL  294 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCC--eEEEEECCccHHHHHHHHHHHHHHhCCceEccCCH----HhHHHHH
Confidence            36899999999999999988765222 12222  36677764422 12233344444455443222222    2333444


Q ss_pred             HhcCCCcEEEEEeCCC
Q 042541          265 KQMRIEAILLVLDDVW  280 (695)
Q Consensus       265 ~~l~~~~~LlVlDdv~  280 (695)
                      ..+. ..=++++|..-
T Consensus       295 ~~~~-~~DlVlIDt~G  309 (424)
T PRK05703        295 EQLR-DCDVILIDTAG  309 (424)
T ss_pred             HHhC-CCCEEEEeCCC
Confidence            3333 35688889763

>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]

Probab=95.25  E-value=0.027  Score=53.66  Aligned_cols=43  Identities=28%  Similarity=0.403  Sum_probs=30.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHH
Q 042541          189 FIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVK  233 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~  233 (695)
                      .|+|+|-||+||||+|..++.  ++...=...++-|+...+++..
T Consensus         2 kIaI~GKGG~GKTtiaalll~--~l~~~~~~~VLvVDaDpd~nL~   44 (255)
T COG3640           2 KIAITGKGGVGKTTIAALLLK--RLLSKGGYNVLVVDADPDSNLP   44 (255)
T ss_pred             eEEEecCCCccHHHHHHHHHH--HHHhcCCceEEEEeCCCCCChH
Confidence            589999999999999988555  3332211227788887776644

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=95.24  E-value=0.071  Score=51.62  Aligned_cols=24  Identities=29%  Similarity=0.646  Sum_probs=21.1

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..-.|+|+|++|+|||||.+.++-
T Consensus        28 ~GEfvsilGpSGcGKSTLLriiAG   51 (248)
T COG1116          28 KGEFVAILGPSGCGKSTLLRLIAG   51 (248)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhC
Confidence            347899999999999999999864

>PRK12597 F0F1 ATP synthase subunit beta; Provisional

Probab=95.23  E-value=0.044  Score=58.87  Aligned_cols=95  Identities=12%  Similarity=0.131  Sum_probs=56.1

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC-CHHHHHHHHHHhcCCC-------CCCCCChH--
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKGYP-------VPEFQTDE--  254 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~~~-------~~~~~~~~--  254 (695)
                      ...+-++|.|.+|+|||||+.++.+... +.+-+. ++++-+++.. ...++...+...-...       ..+.+...  
T Consensus       141 gkGQR~gIfa~~G~GKt~Ll~~~~~~~~-~~~~dv-~V~~liGER~rEv~ef~~~~~~~~~l~rsvvv~atsd~~~~~R~  218 (461)
T PRK12597        141 AKGGKTGLFGGAGVGKTVLMMELIFNIS-KQHSGS-SVFAGVGERSREGHELYHEMKESGVLDKTVMVYGQMNEPPGARM  218 (461)
T ss_pred             ccCCEEEeecCCCCChhHHHHHHHHHHH-hhCCCE-EEEEcCCcchHHHHHHHHHHHhcCCcceeEEEecCCCCCHHHHH
Confidence            3457899999999999999988887322 123344 5566666543 5667777776542211       11111111  


Q ss_pred             ---HHHHHHHHHHHhcCCCcEEEEEeCCCC
Q 042541          255 ---AAINDLERFFKQMRIEAILLVLDDVWP  281 (695)
Q Consensus       255 ---~~~~~l~~~~~~l~~~~~LlVlDdv~~  281 (695)
                         .....+.+.++.-.++++||++||+-.
T Consensus       219 ~a~~~a~tiAEyfrd~~G~~VLl~~DslTR  248 (461)
T PRK12597        219 RVVLTGLTIAEYLRDEEKEDVLLFIDNIFR  248 (461)
T ss_pred             HHHHHHHHHHHHHHHhcCCceEEEeccchH
Confidence               112223344432248999999999843

>COG1428 Deoxynucleoside kinases [Nucleotide transport and metabolism]

Probab=95.20  E-value=0.031  Score=52.49  Aligned_cols=47  Identities=34%  Similarity=0.523  Sum_probs=31.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKV  239 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i  239 (695)
                      ..+|+|-||-|+||||||+.+.+  +..  |.  +++-.+.+++=...+..++
T Consensus         4 ~~~IvI~G~IG~GKSTLa~~La~--~l~--~~--~~~E~vednp~L~~FY~d~   50 (216)
T COG1428           4 AMVIVIEGMIGAGKSTLAQALAE--HLG--FK--VFYELVEDNPFLDLFYEDP   50 (216)
T ss_pred             ccEEEEecccccCHHHHHHHHHH--HhC--Cc--eeeecccCChHHHHHHHhH
Confidence            46899999999999999999988  333  22  4455555554444444443

>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor

Probab=95.18  E-value=0.087  Score=48.84  Aligned_cols=127  Identities=17%  Similarity=0.189  Sum_probs=65.6

Q ss_pred             CCCCcchHHHHHHHHH--cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCC
Q 042541          168 SPGLDVPLKELKMELF--KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGY  245 (695)
Q Consensus       168 ~vGr~~~~~~l~~~L~--~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~  245 (695)
                      +||.+..++++.+.+.  .....-|.|+|..|+||+.+|+.+++.  -...-.. .+-|+++. .+.+.+..++.-.-..
T Consensus         1 liG~s~~m~~~~~~~~~~a~~~~pVlI~GE~GtGK~~lA~~IH~~--s~r~~~p-fi~vnc~~-~~~~~~e~~LFG~~~~   76 (168)
T PF00158_consen    1 LIGESPAMKRLREQAKRAASSDLPVLITGETGTGKELLARAIHNN--SPRKNGP-FISVNCAA-LPEELLESELFGHEKG   76 (168)
T ss_dssp             SS--SHHHHHHHHHHHHHTTSTS-EEEECSTTSSHHHHHHHHHHC--STTTTS--EEEEETTT-S-HHHHHHHHHEBCSS
T ss_pred             CEeCCHHHHHHHHHHHHHhCCCCCEEEEcCCCCcHHHHHHHHHHh--hhcccCC-eEEEehhh-hhcchhhhhhhccccc
Confidence            4788888999888777  333456779999999999999999872  2111111 23444443 2444444444433222


Q ss_pred             CCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhcc------CC-----CCCEEEEEcCCC
Q 042541          246 PVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGF------QL-----PDYKILVTSRSE  306 (695)
Q Consensus       246 ~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~------~~-----~gs~iivTtR~~  306 (695)
                      ..........  ..+.      .-..--|+||++......    ++..+..      +.     ...|||.||...
T Consensus        77 ~~~~~~~~~~--G~l~------~A~~GtL~Ld~I~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~st~~~  144 (168)
T PF00158_consen   77 AFTGARSDKK--GLLE------QANGGTLFLDEIEDLPPELQAKLLRVLEEGKFTRLGSDKPVPVDVRIIASTSKD  144 (168)
T ss_dssp             SSTTTSSEBE--HHHH------HTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEECCTSSSEEE--EEEEEEESS-
T ss_pred             cccccccccC--Ccee------eccceEEeecchhhhHHHHHHHHHHHHhhchhccccccccccccceEEeecCcC
Confidence            1111111000  1111      133557889999877643    2222221      11     146899988754

These have a conserved domain of about 230 residues involved in the ATP-dependent [, ] interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction []. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.; GO: 0005524 ATP binding, 0008134 transcription factor binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1NY6_K 3M0E_G 1NY5_A 1OJL_A 3DZD_B 2C9C_A 2C98_A 2C96_A 2BJV_A 2C99_A ....

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=95.17  E-value=0.087  Score=48.84  Aligned_cols=82  Identities=16%  Similarity=0.338  Sum_probs=48.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhcC
Q 042541          189 FIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMR  268 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~  268 (695)
                      ++.|.|.+|+|||++|.++...      ....++|+...+.++. ++...|.+.-......... .+....+.+.++...
T Consensus         1 ~~li~G~~~sGKS~~a~~~~~~------~~~~~~y~at~~~~d~-em~~rI~~H~~~R~~~w~t-~E~~~~l~~~l~~~~   72 (169)
T cd00544           1 IILVTGGARSGKSRFAERLAAE------LGGPVTYIATAEAFDD-EMAERIARHRKRRPAHWRT-IETPRDLVSALKELD   72 (169)
T ss_pred             CEEEECCCCCCHHHHHHHHHHh------cCCCeEEEEccCcCCH-HHHHHHHHHHHhCCCCceE-eecHHHHHHHHHhcC
Confidence            3679999999999999988752      2223778877777654 3444444432222222212 222334555554333


Q ss_pred             CCcEEEEEeCC
Q 042541          269 IEAILLVLDDV  279 (695)
Q Consensus       269 ~~~~LlVlDdv  279 (695)
                       +.-.+++|.+
T Consensus        73 -~~~~VLIDcl   82 (169)
T cd00544          73 -PGDVVLIDCL   82 (169)
T ss_pred             -CCCEEEEEcH
Confidence             3447999986

CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a homotrimer with a propeller-like shape.

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=95.17  E-value=0.03  Score=49.27  Aligned_cols=38  Identities=29%  Similarity=0.341  Sum_probs=28.9

Q ss_pred             chHHHHHHHHHc--CCceEEEEEcCCCCcHHHHHHHHhcc
Q 042541          173 VPLKELKMELFK--DGRQFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       173 ~~~~~l~~~L~~--~~~~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      ++.+++.+.|..  ....+|.+.|.-|+||||+++.++..
T Consensus         6 ~~t~~l~~~l~~~l~~~~~i~l~G~lGaGKTtl~~~l~~~   45 (133)
T TIGR00150         6 KAMDKFGKAFAKPLDFGTVVLLKGDLGAGKTTLVQGLLQG   45 (133)
T ss_pred             HHHHHHHHHHHHhCCCCCEEEEEcCCCCCHHHHHHHHHHH
Confidence            345555555552  33569999999999999999999874

Members of this family have a conserved nucleotide-binding motif GXXGXGKT and a nucleotide-binding fold. Member protein YjeE of Haemophilus influenzae (HI0065) was shown to have ATPase activity.

>TIGR00554 panK_bact pantothenate kinase, bacterial type

Probab=95.16  E-value=0.057  Score=54.61  Aligned_cols=45  Identities=13%  Similarity=0.035  Sum_probs=29.1

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhccccccccC-CCcEEEEEeCCCCC
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKF-KDDIFYVTVSKNPN  231 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f-~~~~~wv~~~~~~~  231 (695)
                      ..+.+|+|.|..|+||||+|+.+..  .+.... ...+..++......
T Consensus        60 ~~p~IIGIaG~~GSGKSTlar~L~~--ll~~~~~~g~V~vi~~D~f~~  105 (290)
T TIGR00554        60 KIPYIISIAGSVAVGKSTTARILQA--LLSRWPEHRKVELITTDGFLH  105 (290)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH--HHhhcCCCCceEEEecccccc
Confidence            3468999999999999999987754  222111 12255555555443

Shown to be a homodimer in E. coli. This enzyme catalyzes the rate-limiting step in the biosynthesis of coenzyme A. It is very well conserved from E. coli to B. subtilis, but differs considerably from known eukaryotic forms, described in a separate model.

>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A

Probab=95.16  E-value=0.019  Score=57.79  Aligned_cols=90  Identities=18%  Similarity=0.231  Sum_probs=47.7

Q ss_pred             HHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHH
Q 042541          176 KELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEA  255 (695)
Q Consensus       176 ~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~  255 (695)
                      ..+++.+...+ +-|.++|+.|+|||++++....  .... ....+.-++.+...+...++..+-..+.....       
T Consensus        23 ~~ll~~l~~~~-~pvLl~G~~GtGKT~li~~~l~--~l~~-~~~~~~~~~~s~~Tts~~~q~~ie~~l~k~~~-------   91 (272)
T PF12775_consen   23 SYLLDLLLSNG-RPVLLVGPSGTGKTSLIQNFLS--SLDS-DKYLVITINFSAQTTSNQLQKIIESKLEKRRG-------   91 (272)
T ss_dssp             HHHHHHHHHCT-EEEEEESSTTSSHHHHHHHHHH--CSTT-CCEEEEEEES-TTHHHHHHHHCCCTTECECTT-------
T ss_pred             HHHHHHHHHcC-CcEEEECCCCCchhHHHHhhhc--cCCc-cccceeEeeccCCCCHHHHHHHHhhcEEcCCC-------
Confidence            44555555554 5678999999999999999876  2221 11113345555544444333222111111000       


Q ss_pred             HHHHHHHHHHhcCCCcEEEEEeCCCCC
Q 042541          256 AINDLERFFKQMRIEAILLVLDDVWPG  282 (695)
Q Consensus       256 ~~~~l~~~~~~l~~~~~LlVlDdv~~~  282 (695)
                            ..+.--.+|+.++.+||+.-.
T Consensus        92 ------~~~gP~~~k~lv~fiDDlN~p  112 (272)
T PF12775_consen   92 ------RVYGPPGGKKLVLFIDDLNMP  112 (272)
T ss_dssp             ------EEEEEESSSEEEEEEETTT-S
T ss_pred             ------CCCCCCCCcEEEEEecccCCC
Confidence                  000111478999999998544

>PRK09280 F0F1 ATP synthase subunit beta; Validated

Probab=95.14  E-value=0.076  Score=56.90  Aligned_cols=94  Identities=14%  Similarity=0.216  Sum_probs=56.1

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC-CHHHHHHHHHHhcCCC-------CCCCCChH--
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKGYP-------VPEFQTDE--  254 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~~~-------~~~~~~~~--  254 (695)
                      ...+-++|.|.+|+|||||+.++...  .....+..++++-+++.. .+.+++.++...-...       ..+.+...  
T Consensus       142 gkGQR~gIfa~~GvGKt~Ll~~i~~~--~~~~~~~v~V~~liGER~rEv~efi~~~~~~~~l~rsvvV~atsd~p~~~r~  219 (463)
T PRK09280        142 AKGGKIGLFGGAGVGKTVLIQELINN--IAKEHGGYSVFAGVGERTREGNDLYHEMKESGVLDKTALVFGQMNEPPGARL  219 (463)
T ss_pred             ccCCEEEeecCCCCChhHHHHHHHHH--HHhcCCCEEEEEEeccCcHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHH
Confidence            34578999999999999999987663  222212335677776544 5677777776642211       11111111  


Q ss_pred             ---HHHHHHHHHHHhcCCCcEEEEEeCCC
Q 042541          255 ---AAINDLERFFKQMRIEAILLVLDDVW  280 (695)
Q Consensus       255 ---~~~~~l~~~~~~l~~~~~LlVlDdv~  280 (695)
                         ...-.+.+.++.-+++++||++||+-
T Consensus       220 ~a~~~a~tiAEyfrd~~G~~VLll~DslT  248 (463)
T PRK09280        220 RVALTGLTMAEYFRDVEGQDVLLFIDNIF  248 (463)
T ss_pred             HHHHHHHHHHHHHHHhcCCceEEEecchH
Confidence               11223444443336899999999984

>PF08433 KTI12: Chromatin associated protein KTI12 ; InterPro: IPR013641 This is a family of chromatin associated proteins which interact with the Elongator complex, a component of the elongating form of RNA polymerase II []

Probab=95.14  E-value=0.055  Score=54.28  Aligned_cols=80  Identities=16%  Similarity=0.263  Sum_probs=36.5

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-Hh
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQ  266 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~  266 (695)
                      +.|.|+|.+|+||||+|+.+...  .... ...+.+++  ..    .+.   +..-.  .............+.... +.
T Consensus         2 pLiil~G~P~SGKTt~a~~L~~~--~~~~-~~~v~~i~--~~----~~~---~~~~~--y~~~~~Ek~~R~~l~s~v~r~   67 (270)
T PF08433_consen    2 PLIILCGLPCSGKTTRAKELKKY--LEEK-GKEVVIIS--DD----SLG---IDRND--YADSKKEKEARGSLKSAVERA   67 (270)
T ss_dssp             -EEEEE--TTSSHHHHHHHHHHH--HHHT-T--EEEE---TH----HHH----TTSS--S--GGGHHHHHHHHHHHHHHH
T ss_pred             EEEEEEcCCCCcHHHHHHHHHHH--HHhc-CCEEEEEc--cc----ccc---cchhh--hhchhhhHHHHHHHHHHHHHh
Confidence            47899999999999999998873  3221 11133333  21    111   11111  111122333444455555 44


Q ss_pred             cCCCcEEEEEeCCCCC
Q 042541          267 MRIEAILLVLDDVWPG  282 (695)
Q Consensus       267 l~~~~~LlVlDdv~~~  282 (695)
                      + ++..++|+||..-.
T Consensus        68 l-s~~~iVI~Dd~nYi   82 (270)
T PF08433_consen   68 L-SKDTIVILDDNNYI   82 (270)
T ss_dssp             H-TT-SEEEE-S---S
T ss_pred             h-ccCeEEEEeCCchH
Confidence            4 55689999998544

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes

Probab=95.13  E-value=0.05  Score=52.28  Aligned_cols=111  Identities=13%  Similarity=0.211  Sum_probs=57.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCC---hHHHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQT---DEAAINDLERF  263 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~---~~~~~~~l~~~  263 (695)
                      ..++.|.|+.|.||||+.+.+.... +..+..+   ++....  ..-.+...|...++........   -.....++..+
T Consensus        29 ~~~~~l~G~n~~GKstll~~i~~~~-~la~~G~---~vpa~~--~~l~~~d~I~~~~~~~d~~~~~~S~fs~e~~~~~~i  102 (204)
T cd03282          29 SRFHIITGPNMSGKSTYLKQIALLA-IMAQIGC---FVPAEY--ATLPIFNRLLSRLSNDDSMERNLSTFASEMSETAYI  102 (204)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHH-HHHHcCC---Ccchhh--cCccChhheeEecCCccccchhhhHHHHHHHHHHHH
Confidence            4789999999999999998886431 1111111   221111  1112333444444332211111   12223334433


Q ss_pred             HHhcCCCcEEEEEeCCCCCChH---------HHhhhccCCCCCEEEEEcCCC
Q 042541          264 FKQMRIEAILLVLDDVWPGSES---------LLQKLGFQLPDYKILVTSRSE  306 (695)
Q Consensus       264 ~~~l~~~~~LlVlDdv~~~~~~---------~~~~l~~~~~gs~iivTtR~~  306 (695)
                      +.. ..++-|+++|......+.         .+..+.  ..|+.+|+||-..
T Consensus       103 l~~-~~~~~lvllDE~~~gt~~~~~~~l~~~il~~l~--~~~~~~i~~TH~~  151 (204)
T cd03282         103 LDY-ADGDSLVLIDELGRGTSSADGFAISLAILECLI--KKESTVFFATHFR  151 (204)
T ss_pred             HHh-cCCCcEEEeccccCCCCHHHHHHHHHHHHHHHH--hcCCEEEEECChH
Confidence            332 356789999998443211         223332  2378899998765

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>cd03221 ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth

Probab=95.12  E-value=0.15  Score=45.94  Aligned_cols=23  Identities=26%  Similarity=0.345  Sum_probs=21.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|..|.|||||++.+..
T Consensus        26 Ge~~~i~G~nGsGKStLl~~l~G   48 (144)
T cd03221          26 GDRIGLVGRNGAGKSTLLKLIAG   48 (144)
T ss_pred             CCEEEEECCCCCCHHHHHHHHcC
Confidence            47899999999999999999986

EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site. The reaction requires ATP hydrolysis. EF-3 contains two ATP nucleotide binding sequence (NBS) motifs. NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.

>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.11  E-value=0.68  Score=51.28  Aligned_cols=91  Identities=21%  Similarity=0.268  Sum_probs=55.4

Q ss_pred             CCCCCcchHHHHHHHHHcC----------C---ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHH
Q 042541          167 ISPGLDVPLKELKMELFKD----------G---RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVK  233 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~~~----------~---~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~  233 (695)
                      .+-|..+..+-+.+.+.-+          .   ..=|.++|++|+|||-||.+++..      +.  .-+++|...    
T Consensus       668 digg~~~~k~~l~~~i~~P~kyp~if~~~plr~~~giLLyGppGcGKT~la~a~a~~------~~--~~fisvKGP----  735 (952)
T KOG0735|consen  668 DIGGLFEAKKVLEEVIEWPSKYPQIFANCPLRLRTGILLYGPPGCGKTLLASAIASN------SN--LRFISVKGP----  735 (952)
T ss_pred             ecccHHHHHHHHHHHHhccccchHHHhhCCcccccceEEECCCCCcHHHHHHHHHhh------CC--eeEEEecCH----
Confidence            3445555666666666511          1   245889999999999999988762      33  336777653    


Q ss_pred             HHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCC
Q 042541          234 AIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPG  282 (695)
Q Consensus       234 ~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~  282 (695)
                      +++.+.   +|.+       +   +.++.++ ++-.-++|+|.||..++.
T Consensus       736 ElL~Ky---IGaS-------E---q~vR~lF~rA~~a~PCiLFFDEfdSi  772 (952)
T KOG0735|consen  736 ELLSKY---IGAS-------E---QNVRDLFERAQSAKPCILFFDEFDSI  772 (952)
T ss_pred             HHHHHH---hccc-------H---HHHHHHHHHhhccCCeEEEecccccc
Confidence            233222   2221       2   2233444 444678999999998654

>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.11  E-value=0.38  Score=47.52  Aligned_cols=91  Identities=20%  Similarity=0.352  Sum_probs=56.4

Q ss_pred             CCCCCcchHHHHHHHHH---------cCC---ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHH
Q 042541          167 ISPGLDVPLKELKMELF---------KDG---RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKA  234 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~---------~~~---~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~  234 (695)
                      .+-|.+...+.|.+.+.         .++   .+-|.++|++|.||+-||++|+..  ...     . +++||..    +
T Consensus       134 DVAGLE~AKeALKEAVILPIKFPqlFtGkR~PwrgiLLyGPPGTGKSYLAKAVATE--AnS-----T-FFSvSSS----D  201 (439)
T KOG0739|consen  134 DVAGLEGAKEALKEAVILPIKFPQLFTGKRKPWRGILLYGPPGTGKSYLAKAVATE--ANS-----T-FFSVSSS----D  201 (439)
T ss_pred             hhccchhHHHHHHhheeecccchhhhcCCCCcceeEEEeCCCCCcHHHHHHHHHhh--cCC-----c-eEEeehH----H
Confidence            45788888888877654         121   477999999999999999999873  211     2 4455543    2


Q ss_pred             HHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCC
Q 042541          235 IVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWP  281 (695)
Q Consensus       235 ~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~  281 (695)
                      +....+   |       ..+..+..|.++-+  ..++-+|.+|.++.
T Consensus       202 LvSKWm---G-------ESEkLVknLFemAR--e~kPSIIFiDEiDs  236 (439)
T KOG0739|consen  202 LVSKWM---G-------ESEKLVKNLFEMAR--ENKPSIIFIDEIDS  236 (439)
T ss_pred             HHHHHh---c-------cHHHHHHHHHHHHH--hcCCcEEEeehhhh
Confidence            222222   1       12222333333332  57899999999853

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=95.11  E-value=0.15  Score=47.51  Aligned_cols=24  Identities=29%  Similarity=0.534  Sum_probs=21.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+++|+|+.|.|||||.+.++.
T Consensus        27 ~G~~~~l~G~nGsGKstLl~~i~G   50 (171)
T cd03228          27 PGEKVAIVGPSGSGKSTLLKLLLR   50 (171)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHc
Confidence            357899999999999999999986

They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities. The MRP-like family, simlar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PTZ00088 adenylate kinase 1; Provisional

Probab=95.08  E-value=0.041  Score=53.77  Aligned_cols=20  Identities=40%  Similarity=0.517  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHhc
Q 042541          190 IVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~  209 (695)
                      |.|.|++|+||||+|+.+++
T Consensus         9 Ivl~G~PGsGK~T~a~~La~   28 (229)
T PTZ00088          9 IVLFGAPGVGKGTFAEILSK   28 (229)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            88999999999999999876

>PF00006 ATP-synt_ab: ATP synthase alpha/beta family, nucleotide-binding domain This Pfam entry corresponds to chains a,b,c,d,e and f; InterPro: IPR000194 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane

Probab=95.08  E-value=0.078  Score=51.15  Aligned_cols=95  Identities=17%  Similarity=0.302  Sum_probs=56.5

Q ss_pred             HHHHH-cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC-CHHHHHHHHHHhcC-------CCCCC
Q 042541          179 KMELF-KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKG-------YPVPE  249 (695)
Q Consensus       179 ~~~L~-~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~-------~~~~~  249 (695)
                      ++.+. -....-++|.|.+|+|||+|+..+.+..  .  -+ .++++-+++.. ...++.+++...-.       ....+
T Consensus         6 ID~l~Pig~Gqr~~I~g~~g~GKt~Ll~~i~~~~--~--~d-~~V~~~iGer~~Ev~~~~~~~~~~~~~~~t~vv~~t~~   80 (215)
T PF00006_consen    6 IDLLFPIGRGQRIGIFGGAGVGKTVLLQEIANNQ--D--AD-VVVYALIGERGREVTEFIEELKGEGALERTVVVAATSD   80 (215)
T ss_dssp             HHHHSCEETTSEEEEEESTTSSHHHHHHHHHHHC--T--TT-EEEEEEESECHHHHHHHHHHHHHTTGGGGEEEEEEETT
T ss_pred             eccccccccCCEEEEEcCcccccchhhHHHHhcc--c--cc-ceeeeeccccchhHHHHHHHHhhcccccccccccccch
Confidence            34444 1234678999999999999999998742  1  12 24678887653 56667776654411       11111


Q ss_pred             CCChHH-----HHHHHHHHHHhcCCCcEEEEEeCC
Q 042541          250 FQTDEA-----AINDLERFFKQMRIEAILLVLDDV  279 (695)
Q Consensus       250 ~~~~~~-----~~~~l~~~~~~l~~~~~LlVlDdv  279 (695)
                      ......     ..-.+.+.+.. +++++|+++||+
T Consensus        81 ~~~~~r~~~~~~a~t~AEyfrd-~G~dVlli~Dsl  114 (215)
T PF00006_consen   81 EPPAARYRAPYTALTIAEYFRD-QGKDVLLIIDSL  114 (215)
T ss_dssp             S-HHHHHHHHHHHHHHHHHHHH-TTSEEEEEEETH
T ss_pred             hhHHHHhhhhccchhhhHHHhh-cCCceeehhhhh
Confidence            111111     11223444433 799999999998

ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The F-ATPases (or F1F0-ATPases), V-ATPases (or V1V0-ATPases) and A-ATPases (or A1A0-ATPases) are composed of two linked complexes: the F1, V1 or A1 complex contains the catalytic core that synthesizes/hydrolyses ATP, and the F0, V0 or A0 complex that forms the membrane-spanning pore. The F-, V- and A-ATPases all contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, ]. In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself driven by the movement of protons through the F0 complex C subunit []. In V- and A-ATPases, the alpha/A and beta/B subunits of the V1 or A1 complex are homologous to the alpha and beta subunits in the F1 complex of F-ATPases, except that the alpha subunit is catalytic and the beta subunit is regulatory. The structure of the alpha and beta subunits is almost identical. Each subunit consists of a N-terminal beta-barrel, a central domain containing the nucleotide-binding site and a C-terminal alpha bundle domain []. This entry represents the central domain. It is found in the alpha and beta subunits from F1, V1, and A1 complexes, as well as in flagellar ATPase and the termination factor Rho. ; GO: 0005524 ATP binding; PDB: 3OEE_N 2HLD_W 3FKS_N 3OE7_O 3OFN_M 2XOK_D 3OEH_V 2WPD_F 3ZRY_D 2OBL_A ....

>KOG2123 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.07  E-value=0.0022  Score=62.11  Aligned_cols=88  Identities=17%  Similarity=0.132  Sum_probs=69.7

Q ss_pred             ccCCCCcEEEeccCCCCCcccccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCch--hhcCCC
Q 042541          598 SALSKLKKIRLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPD--GLCDIV  675 (695)
Q Consensus       598 ~~l~~L~~L~L~~~~l~~lp~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~--~i~~L~  675 (695)
                      +.|.+.+.|+.-||.+..+.-+.+|+.|++|.|+-|+|+.+-|-.      .+++|+.|+|..| .+.+|.+  -+.+|+
T Consensus        16 sdl~~vkKLNcwg~~L~DIsic~kMp~lEVLsLSvNkIssL~pl~------rCtrLkElYLRkN-~I~sldEL~YLknlp   88 (388)
T KOG2123|consen   16 SDLENVKKLNCWGCGLDDISICEKMPLLEVLSLSVNKISSLAPLQ------RCTRLKELYLRKN-CIESLDELEYLKNLP   88 (388)
T ss_pred             hHHHHhhhhcccCCCccHHHHHHhcccceeEEeeccccccchhHH------HHHHHHHHHHHhc-ccccHHHHHHHhcCc
Confidence            346678889999999987765568999999999999999876643      7899999999874 4555543  267899


Q ss_pred             CCceeecccccCCCCCC
Q 042541          676 SMEKLRITNCHRLSALP  692 (695)
Q Consensus       676 ~L~~L~l~~~~~l~~lP  692 (695)
                      +|+.|.|..|+-.+.-|
T Consensus        89 sLr~LWL~ENPCc~~ag  105 (388)
T KOG2123|consen   89 SLRTLWLDENPCCGEAG  105 (388)
T ss_pred             hhhhHhhccCCcccccc
Confidence            99999999988655444

>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional

Probab=95.07  E-value=0.032  Score=56.00  Aligned_cols=37  Identities=16%  Similarity=0.226  Sum_probs=28.6

Q ss_pred             HHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCC
Q 042541          180 MELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFK  218 (695)
Q Consensus       180 ~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~  218 (695)
                      +++...+..+|.|.|.+|+|||||+..+.+  .+.....
T Consensus        97 ~~~~~~~~~~v~l~G~pGsGKTTLl~~l~~--~l~~~~~  133 (290)
T PRK10463         97 ARFAARKQLVLNLVSSPGSGKTTLLTETLM--RLKDSVP  133 (290)
T ss_pred             HHHHhcCCeEEEEECCCCCCHHHHHHHHHH--HhccCCC
Confidence            344456689999999999999999999887  4444443

>cd03230 ABC_DR_subfamily_A This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity

Probab=95.05  E-value=0.11  Score=48.64  Aligned_cols=23  Identities=30%  Similarity=0.457  Sum_probs=21.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|.|||||++.++.
T Consensus        26 Ge~~~i~G~nGsGKStLl~~l~G   48 (173)
T cd03230          26 GEIYGLLGPNGAGKTTLIKIILG   48 (173)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhC
Confidence            46899999999999999999986

In bacteria and archaea, these transporters usually include an ATP-binding protein and one or two integral membrane proteins. Eukaryote systems of the ABCA subfamily display ABC domains that are quite similar to this family. The ATP-binding domain shows the highest similarity between all members of the ABC transporter family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=95.03  E-value=0.014  Score=49.69  Aligned_cols=20  Identities=45%  Similarity=0.708  Sum_probs=18.3

Q ss_pred             EEEEcCCCCcHHHHHHHHhc
Q 042541          190 IVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~  209 (695)
                      |.|+|++|+|||+||+.++.
T Consensus         1 I~i~G~~G~GKS~l~~~l~~   20 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAK   20 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHH
Confidence            56999999999999999887

All of the proteins bind ATP and, consequently, all of them carry the classical Walker A (phosphate-binding loop or P-loop) and Walker B (Mg2+-binding aspartic acid) motifs. Superfamily 3 consists of helicases encoded mainly by small DNA viruses and some large nucleocytoplasmic DNA viruses [, ]. Small viruses are very dependent on the host-cell machinery to replicate. SF3 helicase in small viruses is associated with an origin-binding domain. By pairing a domain that recognises the ori with a helicase, the virus can bypass the host-cell-based regulation pathway and initiate its own replication. The protein binds to the viral ori leading to origin unwinding. Cellular replication proteins are then recruited to the ori and the viral DNA is replicated. In SF3 helicases the Walker A and Walker B motifs are separated by spacers of rather uniform, and relatively short, length. In addition to the A and B motifs this family is characterised by a third motif (C) which resides between the B motif and the C terminus of the conserved region. This motif consists of an Asn residue preceded by a run of hydrophobic residues []. Several structures of SF3 helicases have been solved []. They all possess the same core alpha/beta fold, consisting of a five-stranded parallel beta sheet flanked on both sides by several alpha helices. In contrast to SF1 and SF2 helicases, which have RecA-like core folds, the strand connectivity within the alpha/beta core domain is that of AAA+ proteins []. The SF3 helicase proteins assemble into a hexameric ring. Some proteins known to contain an SF3 helicase domain are listed below: Polyomavirus large T antigen. It initiates DNA unwinding and replication via interactions with the viral origin of replication. Papillomavirus E1 protein. An ATP-dependent DNA helicase required for initiation of viral DNA replication. Parvovirus Rep/NS1 protein, which is also required for the initiation of viral replication. Poxviridae and other large DNA viruses D5 protein. Bacteriophage DNA primase/helicase protein. Bacterial prophage DNA primase/helicase protein. The entry represents the core alpha/beta fold of the SF3 helicase domain found predominantly in DNA viruses.; GO: 0003723 RNA binding, 0003724 RNA helicase activity

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=95.01  E-value=0.097  Score=53.48  Aligned_cols=69  Identities=16%  Similarity=0.142  Sum_probs=45.2

Q ss_pred             CCCCCCCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHH
Q 042541          161 APDPPVISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQ  237 (695)
Q Consensus       161 ~~~~~~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~  237 (695)
                      .|..++.++=..+....+...+..+  +.|.|.|++|+||||+|+.++.  +....    .+.|+++...+..++..
T Consensus        40 ~p~~d~~y~f~~~~~~~vl~~l~~~--~~ilL~G~pGtGKTtla~~lA~--~l~~~----~~rV~~~~~l~~~DliG  108 (327)
T TIGR01650        40 VPDIDPAYLFDKATTKAICAGFAYD--RRVMVQGYHGTGKSTHIEQIAA--RLNWP----CVRVNLDSHVSRIDLVG  108 (327)
T ss_pred             CCCCCCCccCCHHHHHHHHHHHhcC--CcEEEEeCCCChHHHHHHHHHH--HHCCC----eEEEEecCCCChhhcCC
Confidence            3443444444555566677777543  4699999999999999999987  33322    44677776665555443

This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobS gene product, which is a cobalt chelatase subunit, with a MW ~37 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobT (TIGR01651) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobS gene product, the P. denitrificans gene symbol is not used in the name of this model.

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.01  E-value=0.072  Score=57.77  Aligned_cols=88  Identities=20%  Similarity=0.295  Sum_probs=47.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccC-CCcEEEEEeCCCC-CHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKF-KDDIFYVTVSKNP-NVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFF  264 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f-~~~~~wv~~~~~~-~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~  264 (695)
                      ..+|+|+|++|+||||++..+..  ...... ...+..++..... ...+.+....+.++........    ...+...+
T Consensus       350 G~vIaLVGPtGvGKTTtaakLAa--~la~~~~gkkVaLIdtDtyRigA~EQLk~ya~iLgv~v~~a~d----~~~L~~aL  423 (559)
T PRK12727        350 GGVIALVGPTGAGKTTTIAKLAQ--RFAAQHAPRDVALVTTDTQRVGGREQLHSYGRQLGIAVHEADS----AESLLDLL  423 (559)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH--HHHHhcCCCceEEEecccccccHHHHHHHhhcccCceeEecCc----HHHHHHHH
Confidence            57999999999999999988876  222221 1225556553221 2223333333444432221111    12344444


Q ss_pred             HhcCCCcEEEEEeCCCC
Q 042541          265 KQMRIEAILLVLDDVWP  281 (695)
Q Consensus       265 ~~l~~~~~LlVlDdv~~  281 (695)
                      +.+.+ .-+|++|..-.
T Consensus       424 ~~l~~-~DLVLIDTaG~  439 (559)
T PRK12727        424 ERLRD-YKLVLIDTAGM  439 (559)
T ss_pred             HHhcc-CCEEEecCCCc
Confidence            44443 55888898753

>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]

Probab=95.01  E-value=0.02  Score=54.52  Aligned_cols=28  Identities=29%  Similarity=0.374  Sum_probs=23.8

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhcccccccc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGK  216 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~  216 (695)
                      +.+|+|.|.+|+||||+|+.++.  .+...
T Consensus         8 ~iiIgIaG~SgSGKTTva~~l~~--~~~~~   35 (218)
T COG0572           8 VIIIGIAGGSGSGKTTVAKELSE--QLGVE   35 (218)
T ss_pred             eEEEEEeCCCCCCHHHHHHHHHH--HhCcC
Confidence            47899999999999999999987  45444

>PRK12678 transcription termination factor Rho; Provisional

Probab=94.99  E-value=0.07  Score=57.94  Aligned_cols=101  Identities=14%  Similarity=0.154  Sum_probs=54.3

Q ss_pred             HHHHHHH-cCCceEEEEEcCCCCcHHHHHHHHhccccccc-cCCCcEEEEEeCCCC-CHHHHHHHHHHhcCCCCCCCCCh
Q 042541          177 ELKMELF-KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQG-KFKDDIFYVTVSKNP-NVKAIVQKVLHHKGYPVPEFQTD  253 (695)
Q Consensus       177 ~l~~~L~-~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~-~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~~~~~~~~~~  253 (695)
                      ++++.|. -+...-.+|+|++|+|||||++.+++  .+.. +-++.++.+-|.+.. .+.++.+.+-..+-....+....
T Consensus       405 RvIDll~PIGkGQR~LIvgpp~aGKTtLL~~IAn--~i~~n~~~~~~ivvLIgERpeEVtdm~rsVkgeVVasT~D~p~~  482 (672)
T PRK12678        405 RVIDLIMPIGKGQRGLIVSPPKAGKTTILQNIAN--AITTNNPECHLMVVLVDERPEEVTDMQRSVKGEVIASTFDRPPS  482 (672)
T ss_pred             eeeeeecccccCCEeEEeCCCCCCHHHHHHHHHH--HHhhcCCCeEEEEEEEeCchhhHHHHHHhccceEEEECCCCCHH
Confidence            3444444 33457789999999999999999998  3322 334434555566554 33334333311111111111111


Q ss_pred             H-----HHHHHHHHHHHhcCCCcEEEEEeCCC
Q 042541          254 E-----AAINDLERFFKQMRIEAILLVLDDVW  280 (695)
Q Consensus       254 ~-----~~~~~l~~~~~~l~~~~~LlVlDdv~  280 (695)
                      .     ...-.+.+.+.. .++.+||++|++-
T Consensus       483 ~~~~~a~~ai~~Ae~fre-~G~dVlillDSlT  513 (672)
T PRK12678        483 DHTTVAELAIERAKRLVE-LGKDVVVLLDSIT  513 (672)
T ss_pred             HHHHHHHHHHHHHHHHHH-cCCCEEEEEeCch
Confidence            1     111122222211 6899999999984

>PRK03839 putative kinase; Provisional

Probab=94.99  E-value=0.018  Score=54.31  Aligned_cols=21  Identities=33%  Similarity=0.553  Sum_probs=19.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .|.|.|++|+||||+++.+++
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~   22 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAE   22 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            488999999999999999987

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=94.98  E-value=0.025  Score=52.57  Aligned_cols=22  Identities=36%  Similarity=0.594  Sum_probs=20.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +.|.+.|.+|+||||+|++++.
T Consensus         2 pLiIlTGyPgsGKTtfakeLak   23 (261)
T COG4088           2 PLIILTGYPGSGKTTFAKELAK   23 (261)
T ss_pred             ceEEEecCCCCCchHHHHHHHH
Confidence            4678999999999999999987

>cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain

Probab=94.98  E-value=0.11  Score=48.44  Aligned_cols=23  Identities=26%  Similarity=0.475  Sum_probs=21.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|.|||||.+.++.
T Consensus        28 Ge~~~i~G~nGsGKStLl~~l~G   50 (173)
T cd03246          28 GESLAIIGPSGSGKSTLARLILG   50 (173)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHh
Confidence            46899999999999999999986

They export degradative enzymes by using a type I protein secretion system and lack an N-terminal signal peptide, but contain a C-terminal secretion signal. The Type I secretion apparatus is made up of three components, an ABC transporter, a membrane fusion protein (MFP), and an outer membrane protein (OMP). For the HlyA transporter complex, HlyB (ABC transporter) and HlyD (MFP) reside in the inner membrane of E. coli. The OMP component is TolC, which is thought to interact with the MFP to form a continuous channel across the periplasm from the cytoplasm to the exterior. HlyB belongs to the family of ABC transporters, which are ubiquitous, ATP-dependent transmembrane pumps or channels. The spectrum of transport substra

>KOG2982 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.97  E-value=0.0061  Score=59.66  Aligned_cols=85  Identities=14%  Similarity=0.183  Sum_probs=46.7

Q ss_pred             CCceEEEEEEcc--CccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCC--Ccc-cccccc
Q 042541          549 GPEVKVVVLNIR--TKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLP--NSL-ATVRMN  623 (695)
Q Consensus       549 ~~~l~~L~l~~~--~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~--~lp-~i~~l~  623 (695)
                      ++.++-+.|.+|  +....+...+.+|+.|++|+++.|.+.+. +..+|  -.+.+|+.|-|.|+.++  .+. .+..++
T Consensus        70 ~~~v~elDL~~N~iSdWseI~~ile~lP~l~~LNls~N~L~s~-I~~lp--~p~~nl~~lVLNgT~L~w~~~~s~l~~lP  146 (418)
T KOG2982|consen   70 VTDVKELDLTGNLISDWSEIGAILEQLPALTTLNLSCNSLSSD-IKSLP--LPLKNLRVLVLNGTGLSWTQSTSSLDDLP  146 (418)
T ss_pred             hhhhhhhhcccchhccHHHHHHHHhcCccceEeeccCCcCCCc-cccCc--ccccceEEEEEcCCCCChhhhhhhhhcch
Confidence            344555555555  23334445566777777777777666422 11211  23456777777777665  233 455566


Q ss_pred             cccEEeeccccCC
Q 042541          624 HLQKVSLVMCNVG  636 (695)
Q Consensus       624 ~L~~L~l~~~~i~  636 (695)
                      .++.|.++.|++.
T Consensus       147 ~vtelHmS~N~~r  159 (418)
T KOG2982|consen  147 KVTELHMSDNSLR  159 (418)
T ss_pred             hhhhhhhccchhh
Confidence            6666666655433

>PF00560 LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape []

Probab=94.97  E-value=0.011  Score=34.04  Aligned_cols=16  Identities=19%  Similarity=0.156  Sum_probs=7.4

Q ss_pred             ccEEeeccccCCcccc
Q 042541          625 LQKVSLVMCNVGQVFR  640 (695)
Q Consensus       625 L~~L~l~~~~i~~~~~  640 (695)
                      |++|+|++|.++.+|+
T Consensus         2 L~~Ldls~n~l~~ip~   17 (22)
T PF00560_consen    2 LEYLDLSGNNLTSIPS   17 (22)
T ss_dssp             ESEEEETSSEESEEGT
T ss_pred             ccEEECCCCcCEeCCh
Confidence            4445555544444333

LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions [, ].Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response []. Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel beta sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the beta-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins. 3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with alpha-helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions []. Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20- to 30-residue repeats []. ; GO: 0005515 protein binding; PDB: 4ECO_B 2A0Z_A 3ULU_A 1ZIW_A 3ULV_A 1DCE_C 1LTX_A 3J0A_B 3A79_B 4FCG_A ....

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=94.96  E-value=0.15  Score=53.13  Aligned_cols=88  Identities=16%  Similarity=0.131  Sum_probs=52.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC-CHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFK  265 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~  265 (695)
                      .+++.|+|+.|+||||++..++..  .... ...+.+++..... ...+-++...+.++.+.....+..    .+...++
T Consensus       206 ~~ii~lvGptGvGKTTt~akLA~~--l~~~-g~~V~lItaDtyR~gAveQLk~yae~lgvpv~~~~dp~----dL~~al~  278 (407)
T PRK12726        206 HRIISLIGQTGVGKTTTLVKLGWQ--LLKQ-NRTVGFITTDTFRSGAVEQFQGYADKLDVELIVATSPA----ELEEAVQ  278 (407)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH--HHHc-CCeEEEEeCCccCccHHHHHHHHhhcCCCCEEecCCHH----HHHHHHH
Confidence            589999999999999999888763  2221 1236677775432 334455666666665432222222    2333333


Q ss_pred             hcC--CCcEEEEEeCCCC
Q 042541          266 QMR--IEAILLVLDDVWP  281 (695)
Q Consensus       266 ~l~--~~~~LlVlDdv~~  281 (695)
                      .++  +..=++++|-...
T Consensus       279 ~l~~~~~~D~VLIDTAGr  296 (407)
T PRK12726        279 YMTYVNCVDHILIDTVGR  296 (407)
T ss_pred             HHHhcCCCCEEEEECCCC
Confidence            332  3456788888754

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=94.96  E-value=0.039  Score=54.22  Aligned_cols=48  Identities=25%  Similarity=0.608  Sum_probs=31.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQK  238 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~  238 (695)
                      ..++.|.|.+|+|||+|+.++... ..+. +...++|++..+..  ..+.+.
T Consensus        19 gs~~li~G~~GsGKT~l~~q~l~~-~~~~-~ge~vlyvs~ee~~--~~l~~~   66 (226)
T PF06745_consen   19 GSVVLISGPPGSGKTTLALQFLYN-GLKN-FGEKVLYVSFEEPP--EELIEN   66 (226)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHH-HHHH-HT--EEEEESSS-H--HHHHHH
T ss_pred             CcEEEEEeCCCCCcHHHHHHHHHH-hhhh-cCCcEEEEEecCCH--HHHHHH
Confidence            589999999999999999887652 2222 12237798886643  444444

More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria []. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC [].; PDB: 2W0M_A 2ZTS_C 4DUG_B 3K0E_B 3K09_B 3S1A_E 3JZM_E 2GBL_B 3DVL_A 1TF7_C ....

>TIGR03575 selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryotic

Probab=94.95  E-value=0.061  Score=55.55  Aligned_cols=37  Identities=19%  Similarity=0.232  Sum_probs=25.2

Q ss_pred             EEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCC
Q 042541          190 IVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSK  228 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~  228 (695)
                      +++.|++|+||||+++.+.+.......+  .+.+++..+
T Consensus         2 ~~l~Gl~GaGKST~~~~l~~~l~~~~g~--~v~~~~~Dd   38 (340)
T TIGR03575         2 CVLCGLPAAGKSTLARSLSATLRRERGW--AVAVITYDD   38 (340)
T ss_pred             eEEECCCCCCHHHHHHHHHHHHHhccCC--eEEEEcccc
Confidence            6789999999999999998732212222  255666544

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents eukaryotic proteins with this activity.

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=94.95  E-value=0.18  Score=57.54  Aligned_cols=162  Identities=12%  Similarity=0.108  Sum_probs=83.8

Q ss_pred             CCCCCcchHHHHHHHHH---cC---------CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHH
Q 042541          167 ISPGLDVPLKELKMELF---KD---------GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKA  234 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~---~~---------~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~  234 (695)
                      .+.|.+...+++.+.+.   .+         -.+-|.|+|++|+|||++|+.++.  .....    .+.++.++      
T Consensus       153 di~g~~~~~~~l~~i~~~~~~~~~~~~~~~~~~~gill~G~~G~GKt~~~~~~a~--~~~~~----f~~is~~~------  220 (644)
T PRK10733        153 DVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAG--EAKVP----FFTISGSD------  220 (644)
T ss_pred             HHcCHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHH--HcCCC----EEEEehHH------
Confidence            45676666555554432   11         134489999999999999999987  22222    22333221      


Q ss_pred             HHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCC-----------h---HHHhhh----ccC--
Q 042541          235 IVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGS-----------E---SLLQKL----GFQ--  293 (695)
Q Consensus       235 ~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~-----------~---~~~~~l----~~~--  293 (695)
                      +..    ....      .   ....++..+ ......+++|++|+++...           .   ..+..+    ...  
T Consensus       221 ~~~----~~~g------~---~~~~~~~~f~~a~~~~P~IifIDEiD~l~~~r~~~~~g~~~~~~~~ln~lL~~mdg~~~  287 (644)
T PRK10733        221 FVE----MFVG------V---GASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEG  287 (644)
T ss_pred             hHH----hhhc------c---cHHHHHHHHHHHHhcCCcEEEehhHhhhhhccCCCCCCCchHHHHHHHHHHHhhhcccC
Confidence            111    1000      0   112233333 2234568999999985431           0   112222    111  


Q ss_pred             CCCCEEEEEcCCCC------C---CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCc
Q 042541          294 LPDYKILVTSRSEF------P---QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGC  357 (695)
Q Consensus       294 ~~gs~iivTtR~~~------~---~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~  357 (695)
                      ..+.-+|.||....      .   .....+.++..+.++-.+++..+..........    ....+++.+.|.
T Consensus       288 ~~~vivIaaTN~p~~lD~Al~RpgRfdr~i~v~~Pd~~~R~~Il~~~~~~~~l~~~~----d~~~la~~t~G~  356 (644)
T PRK10733        288 NEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDI----DAAIIARGTPGF  356 (644)
T ss_pred             CCCeeEEEecCChhhcCHHHhCCcccceEEEcCCCCHHHHHHHHHHHhhcCCCCCcC----CHHHHHhhCCCC
Confidence            12334444665541      1   233477888888888888888766433221111    134567777663

>PRK04040 adenylate kinase; Provisional

Probab=94.95  E-value=0.02  Score=54.20  Aligned_cols=23  Identities=30%  Similarity=0.496  Sum_probs=21.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+|+|+|++|+||||+++.+..
T Consensus         2 ~~~i~v~G~pG~GKtt~~~~l~~   24 (188)
T PRK04040          2 MKVVVVTGVPGVGKTTVLNKALE   24 (188)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHH
Confidence            36899999999999999999987

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=94.94  E-value=0.13  Score=50.46  Aligned_cols=40  Identities=25%  Similarity=0.451  Sum_probs=28.8

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCC
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKN  229 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~  229 (695)
                      ..++.|.|.+|+|||||+.++... -.+ . ...++|++....
T Consensus        20 G~~~~i~G~~G~GKT~l~~~~~~~-~~~-~-g~~~~~is~e~~   59 (229)
T TIGR03881        20 GFFVAVTGEPGTGKTIFCLHFAYK-GLR-D-GDPVIYVTTEES   59 (229)
T ss_pred             CeEEEEECCCCCChHHHHHHHHHH-HHh-c-CCeEEEEEccCC
Confidence            579999999999999999887652 122 2 223778887543

Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=94.93  E-value=0.19  Score=57.84  Aligned_cols=106  Identities=14%  Similarity=0.239  Sum_probs=64.5

Q ss_pred             CCCCCCcchHHHHHHHHHc------C--CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHH
Q 042541          166 VISPGLDVPLKELKMELFK------D--GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQ  237 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~------~--~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~  237 (695)
                      ..++|-++.+..|.+.+..      .  ......+.|+.|+|||.||++++.  -+-+..+. .+-++.++.      ..
T Consensus       562 ~~V~gQ~eAv~aIa~AI~~sr~gl~~~~~~awflflGpdgvGKt~lAkaLA~--~~Fgse~~-~IriDmse~------~e  632 (898)
T KOG1051|consen  562 ERVIGQDEAVAAIAAAIRRSRAGLKDPNPDAWFLFLGPDGVGKTELAKALAE--YVFGSEEN-FIRLDMSEF------QE  632 (898)
T ss_pred             hhccchHHHHHHHHHHHHhhhcccCCCCCCeEEEEECCCchhHHHHHHHHHH--HHcCCccc-eEEechhhh------hh
Confidence            4568888888888887762      1  245677999999999999999987  45444444 334444432      11


Q ss_pred             HHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcE-EEEEeCCCCCChHH
Q 042541          238 KVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAI-LLVLDDVWPGSESL  286 (695)
Q Consensus       238 ~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~-LlVlDdv~~~~~~~  286 (695)
                        ...+.+..+..... +...+|.   +.++.++| +|+||||...+..+
T Consensus       633 --vskligsp~gyvG~-e~gg~Lt---eavrrrP~sVVLfdeIEkAh~~v  676 (898)
T KOG1051|consen  633 --VSKLIGSPPGYVGK-EEGGQLT---EAVKRRPYSVVLFEEIEKAHPDV  676 (898)
T ss_pred             --hhhccCCCcccccc-hhHHHHH---HHHhcCCceEEEEechhhcCHHH
Confidence              33333333322221 2222333   44555554 77799998887653

>PF07724 AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR013093 ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=94.89  E-value=0.0062  Score=56.65  Aligned_cols=42  Identities=21%  Similarity=0.436  Sum_probs=30.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhcccccc-ccCCCcEEEEEeCCCCC
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQ-GKFKDDIFYVTVSKNPN  231 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~-~~f~~~~~wv~~~~~~~  231 (695)
                      ..++.+.|+.|+|||.||+.+.+  .+. +.... .+-++.+....
T Consensus         3 ~~~~ll~GpsGvGKT~la~~la~--~l~~~~~~~-~~~~d~s~~~~   45 (171)
T PF07724_consen    3 KSNFLLAGPSGVGKTELAKALAE--LLFVGSERP-LIRIDMSEYSE   45 (171)
T ss_dssp             SEEEEEESSTTSSHHHHHHHHHH--HHT-SSCCE-EEEEEGGGHCS
T ss_pred             EEEEEEECCCCCCHHHHHHHHHH--HhccCCccc-hHHHhhhcccc
Confidence            46788999999999999999987  333 33333 55666665444

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of ATPase AAA-2 domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. Some of these ATPases function as a chaperone subunit of a proteasome-like degradation complex. This ATPase family includes some proteins not detected by IPR003959 from INTERPRO.; GO: 0005524 ATP binding; PDB: 1R6B_X 1KSF_X 3PXI_C 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 1HQY_E ....

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=94.88  E-value=0.24  Score=45.70  Aligned_cols=116  Identities=21%  Similarity=0.174  Sum_probs=60.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhcccccc-ccCCCcEEEEEeCC---CCCHHHHHHHHHH---hcCCCCC-CCCChHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQ-GKFKDDIFYVTVSK---NPNVKAIVQKVLH---HKGYPVP-EFQTDEAAIN  258 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~-~~f~~~~~wv~~~~---~~~~~~~~~~i~~---~l~~~~~-~~~~~~~~~~  258 (695)
                      ...|-|++..|.||||.|..++-  +.. ..+.  ++.+.+-.   .......+..+.-   +.+.... ...+......
T Consensus         5 ~Gli~v~~g~GkGKtt~a~g~a~--ra~~~g~~--v~ivQFlKg~~~~GE~~~l~~~~~~~~~~g~g~~~~~~~~~~~~~   80 (173)
T TIGR00708         5 RGIIIVHTGNGKGKTTAAFGMAL--RALGHGKK--VGVIQFIKGAWPNGERAAFEPHGVEFQVMGTGFTWETQNREADTA   80 (173)
T ss_pred             ccEEEEECCCCCChHHHHHHHHH--HHHHCCCe--EEEEEEecCCcccChHHHHHhcCcEEEECCCCCeecCCCcHHHHH
Confidence            46888999999999999977765  332 2222  44443322   2344444444300   0111100 0011112112


Q ss_pred             HHHHHH----Hhc-CCCcEEEEEeCCCCC-------ChHHHhhhccCCCCCEEEEEcCCC
Q 042541          259 DLERFF----KQM-RIEAILLVLDDVWPG-------SESLLQKLGFQLPDYKILVTSRSE  306 (695)
Q Consensus       259 ~l~~~~----~~l-~~~~~LlVlDdv~~~-------~~~~~~~l~~~~~gs~iivTtR~~  306 (695)
                      ...+.+    +.+ .+.--+||||.+-..       .+.+.+.+....++..||+|-|+.
T Consensus        81 ~~~~~~~~a~~~l~~~~~DlvVLDEi~~A~~~gli~~~~v~~lL~~rp~~~evVlTGR~~  140 (173)
T TIGR00708        81 IAKAAWQHAKEMLADPELDLVLLDELTYALKYGYLDVEEVVEALQERPGHQHVIITGRGC  140 (173)
T ss_pred             HHHHHHHHHHHHHhcCCCCEEEehhhHHHHHCCCcCHHHHHHHHHhCCCCCEEEEECCCC
Confidence            222222    333 345569999997321       123455555555578999999977

Alternate name: corrinoid adenosyltransferase.

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=94.88  E-value=0.026  Score=53.47  Aligned_cols=21  Identities=19%  Similarity=0.449  Sum_probs=18.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ++.|+|+.|.||||+.+.+.-
T Consensus         1 ~~~ltG~N~~GKst~l~~i~~   21 (185)
T smart00534        1 VVIITGPNMGGKSTYLRQVGL   21 (185)
T ss_pred             CEEEECCCCCcHHHHHHHHHH
Confidence            478999999999999998874

>cd03223 ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome

Probab=94.87  E-value=0.26  Score=45.63  Aligned_cols=24  Identities=25%  Similarity=0.505  Sum_probs=21.6

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhcc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      ..+++|+|+.|.|||||++.+..-
T Consensus        27 Ge~~~i~G~nGsGKSTLl~~l~G~   50 (166)
T cd03223          27 GDRLLITGPSGTGKSSLFRALAGL   50 (166)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            478999999999999999999863

The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asympt

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=94.85  E-value=0.097  Score=48.36  Aligned_cols=23  Identities=26%  Similarity=0.359  Sum_probs=21.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|.|+.|.|||||.+.++.
T Consensus        26 Ge~~~l~G~nGsGKSTLl~~i~G   48 (163)
T cd03216          26 GEVHALLGENGAGKSTLMKILSG   48 (163)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            47899999999999999999986

The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. Pentoses include xylose, arabinose, and ribose. Important hexoses include glucose, galactose, and fructose. In members of the Carb_monos family, the single hydrophobic gene product forms a homodimer while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=94.83  E-value=0.21  Score=50.02  Aligned_cols=39  Identities=21%  Similarity=0.382  Sum_probs=29.4

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCC
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSK  228 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~  228 (695)
                      ..++.|.|.+|+|||++|.+++.. ..+.  ...+++++...
T Consensus        36 gs~~lI~G~pGtGKT~l~~qf~~~-~a~~--Ge~vlyis~Ee   74 (259)
T TIGR03878        36 YSVINITGVSDTGKSLMVEQFAVT-QASR--GNPVLFVTVES   74 (259)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHH-HHhC--CCcEEEEEecC
Confidence            578999999999999999987652 2222  33477998874

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PRK07276 DNA polymerase III subunit delta'; Validated

Probab=94.83  E-value=1.4  Score=44.62  Aligned_cols=61  Identities=10%  Similarity=0.051  Sum_probs=40.2

Q ss_pred             CCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCCCC------CCeEecCCCChHHHHHHHH
Q 042541          268 RIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFPQF------GSVHYLKPLTYEAARTLFL  329 (695)
Q Consensus       268 ~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~~~------~~~~~l~~L~~~ea~~Lf~  329 (695)
                      .+++-++|+||++.....    +++.+-.+.+++.+|++|.+...-.      ...+.+.+ +.++..+.+.
T Consensus       102 ~~~~kV~II~~ad~m~~~AaNaLLKtLEEPp~~t~~iL~t~~~~~lLpTI~SRcq~i~f~~-~~~~~~~~L~  172 (290)
T PRK07276        102 EGKQQVFIIKDADKMHVNAANSLLKVIEEPQSEIYIFLLTNDENKVLPTIKSRTQIFHFPK-NEAYLIQLLE  172 (290)
T ss_pred             cCCcEEEEeehhhhcCHHHHHHHHHHhcCCCCCeEEEEEECChhhCchHHHHcceeeeCCC-cHHHHHHHHH
Confidence            467789999999877644    5666666666788888777663211      12566766 6666666664

>TIGR01039 atpD ATP synthase, F1 beta subunit

Probab=94.83  E-value=0.078  Score=56.62  Aligned_cols=95  Identities=14%  Similarity=0.199  Sum_probs=56.4

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC-CHHHHHHHHHHhcCCC-------CCCCCChH--
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKGYP-------VPEFQTDE--  254 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~~~-------~~~~~~~~--  254 (695)
                      ...+-++|.|.+|+|||||+..+...  ........++++-+++.. ...+++.++...-...       ..+.+...  
T Consensus       141 g~GQr~~If~~~G~GKt~L~~~~~~~--~~~~~~~v~V~alIGER~rEv~ef~~~~~~~~~l~rtvvV~atsd~p~~~R~  218 (461)
T TIGR01039       141 AKGGKIGLFGGAGVGKTVLIQELINN--IAKEHGGYSVFAGVGERTREGNDLYHEMKESGVIDKTALVYGQMNEPPGARM  218 (461)
T ss_pred             ccCCEEEeecCCCCChHHHHHHHHHH--HHhcCCCeEEEEEecCCchHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHH
Confidence            34578999999999999999998763  222213336677776543 5677777776542111       11111111  


Q ss_pred             ---HHHHHHHHHHHhcCCCcEEEEEeCCCC
Q 042541          255 ---AAINDLERFFKQMRIEAILLVLDDVWP  281 (695)
Q Consensus       255 ---~~~~~l~~~~~~l~~~~~LlVlDdv~~  281 (695)
                         ...-.+.+.++.-+++++||++||+-.
T Consensus       219 ~a~~~a~tiAEyfrd~~G~~VLll~DslTR  248 (461)
T TIGR01039       219 RVALTGLTMAEYFRDEQGQDVLLFIDNIFR  248 (461)
T ss_pred             HHHHHHHHHHHHHHHhcCCeeEEEecchhH
Confidence               112233444433357899999999843

The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. Proton translocating ATP synthase, F1 beta subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), A subunit.

>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional

Probab=94.82  E-value=0.057  Score=56.78  Aligned_cols=45  Identities=27%  Similarity=0.364  Sum_probs=37.0

Q ss_pred             CCCCCCCcchHHHHHHHHHcC--------------CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          165 PVISPGLDVPLKELKMELFKD--------------GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~--------------~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|.++.++.+..++...              ..+.|.++|++|+|||+||+.+..
T Consensus        14 d~~IiGQe~AkkalavAl~~~~~r~~l~~~~~~e~~~~~ILliGp~G~GKT~LAr~LAk   72 (443)
T PRK05201         14 DKYIIGQDDAKRAVAIALRNRWRRMQLPEELRDEVTPKNILMIGPTGVGKTEIARRLAK   72 (443)
T ss_pred             ccccCCHHHHHHHHHHHHHHHHHHhcCCcccccccCCceEEEECCCCCCHHHHHHHHHH
Confidence            456899999999888777530              146789999999999999999987

>PRK06002 fliI flagellum-specific ATP synthase; Validated

Probab=94.81  E-value=0.12  Score=55.29  Aligned_cols=90  Identities=22%  Similarity=0.352  Sum_probs=49.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhc-----CCC-CCCCCCh-----HH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHK-----GYP-VPEFQTD-----EA  255 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l-----~~~-~~~~~~~-----~~  255 (695)
                      ...++|+|..|+|||||++.+....   . .+.+++++.-....++.++....+...     +.- ..+.+..     ..
T Consensus       165 Gqri~I~G~SGsGKTTLL~~Ia~l~---~-pd~gvv~liGergrev~e~~~~~l~~~r~rtI~vV~qsd~~~~~r~~~~~  240 (450)
T PRK06002        165 GQRIGIFAGSGVGKSTLLAMLARAD---A-FDTVVIALVGERGREVREFLEDTLADNLKKAVAVVATSDESPMMRRLAPL  240 (450)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCC---C-CCeeeeeecccCCccHHHHhHHHHHHhhCCeEEEEEcCCCCHHHHHHHHH
Confidence            4689999999999999999887521   1 122344444333445554444333322     110 0111111     11


Q ss_pred             HHHHHHHHHHhcCCCcEEEEEeCCCC
Q 042541          256 AINDLERFFKQMRIEAILLVLDDVWP  281 (695)
Q Consensus       256 ~~~~l~~~~~~l~~~~~LlVlDdv~~  281 (695)
                      ..-.+.+.+.. +++.+|+++||+-.
T Consensus       241 ~a~~iAEyfrd-~G~~Vll~~DslTr  265 (450)
T PRK06002        241 TATAIAEYFRD-RGENVLLIVDSVTR  265 (450)
T ss_pred             HHHHHHHHHHH-cCCCEEEeccchHH
Confidence            12233444422 59999999999843

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=94.81  E-value=0.75  Score=52.85  Aligned_cols=44  Identities=16%  Similarity=0.098  Sum_probs=35.0

Q ss_pred             CCCCCCcchHHHHHHHHH--cCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          166 VISPGLDVPLKELKMELF--KDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~--~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +.++|....+.++.+.+.  .....-|.|+|..|+||+++|+.+.+
T Consensus       325 ~~l~g~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~~A~~ih~  370 (638)
T PRK11388        325 DHMPQDSPQMRRLIHFGRQAAKSSFPVLLCGEEGVGKALLAQAIHN  370 (638)
T ss_pred             cceEECCHHHHHHHHHHHHHhCcCCCEEEECCCCcCHHHHHHHHHH
Confidence            357899988888877766  22234478999999999999999986

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=94.80  E-value=0.018  Score=55.25  Aligned_cols=21  Identities=29%  Similarity=0.502  Sum_probs=19.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +|+|.|++|+|||||++.+..
T Consensus         1 iigi~G~~GsGKSTl~~~l~~   21 (198)
T cd02023           1 IIGIAGGSGSGKTTVAEEIIE   21 (198)
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            589999999999999999876

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine.

>PRK08972 fliI flagellum-specific ATP synthase; Validated

Probab=94.77  E-value=0.11  Score=55.16  Aligned_cols=90  Identities=18%  Similarity=0.260  Sum_probs=53.0

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC-CHHHHHHHHHHhcCCC-------CCCCCCh----
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKGYP-------VPEFQTD----  253 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~~~-------~~~~~~~----  253 (695)
                      ....++|+|..|+|||||++.+...  ..  .+. ++.+-+++.. ...++...++..-+..       ..+.+..    
T Consensus       161 ~GqrigI~G~sG~GKSTLL~~I~~~--~~--~dv-~Vi~lIGER~rEv~efi~~~l~~~~l~rtvvv~atsd~p~~~R~~  235 (444)
T PRK08972        161 KGQRMGLFAGSGVGKSVLLGMMTRG--TT--ADV-IVVGLVGERGREVKEFIEEILGEEGRARSVVVAAPADTSPLMRLK  235 (444)
T ss_pred             CCCEEEEECCCCCChhHHHHHhccC--CC--CCE-EEEEEEcCChHHHHHHHHHhhccCCcccEEEEEECCCCCHHHHHH
Confidence            3578999999999999999998862  11  133 4445566544 4566666665442211       1111111    


Q ss_pred             -HHHHHHHHHHHHhcCCCcEEEEEeCCCC
Q 042541          254 -EAAINDLERFFKQMRIEAILLVLDDVWP  281 (695)
Q Consensus       254 -~~~~~~l~~~~~~l~~~~~LlVlDdv~~  281 (695)
                       ....-.+.+.+.. +++++|+++||+-.
T Consensus       236 a~~~A~tiAEyfrd-~G~~VLl~~DslTR  263 (444)
T PRK08972        236 GCETATTIAEYFRD-QGLNVLLLMDSLTR  263 (444)
T ss_pred             HHHHHHHHHHHHHH-cCCCEEEEEcChHH
Confidence             1112234444432 69999999999843

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=94.77  E-value=0.12  Score=50.97  Aligned_cols=48  Identities=17%  Similarity=0.398  Sum_probs=34.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKV  239 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i  239 (695)
                      ..++.|+|.+|+|||+|+.++... ..+.  ...++|++..+.  ..++.+++
T Consensus        25 g~~~~i~G~~GsGKt~l~~~~~~~-~~~~--g~~~~y~~~e~~--~~~~~~~~   72 (234)
T PRK06067         25 PSLILIEGDHGTGKSVLSQQFVYG-ALKQ--GKKVYVITTENT--SKSYLKQM   72 (234)
T ss_pred             CcEEEEECCCCCChHHHHHHHHHH-HHhC--CCEEEEEEcCCC--HHHHHHHH
Confidence            589999999999999999998652 2232  234779998754  44555543

>PRK06217 hypothetical protein; Validated

Probab=94.76  E-value=0.046  Score=51.65  Aligned_cols=22  Identities=32%  Similarity=0.400  Sum_probs=20.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHhcc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      .|.|.|.+|+||||+|+.+...
T Consensus         3 ~I~i~G~~GsGKSTla~~L~~~   24 (183)
T PRK06217          3 RIHITGASGSGTTTLGAALAER   24 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4899999999999999999873

>PF00154 RecA: recA bacterial DNA recombination protein; InterPro: IPR013765 The recA gene product is a multifunctional enzyme that plays a role in homologous recombination, DNA repair and induction of the SOS response []

Probab=94.76  E-value=0.049  Score=55.57  Aligned_cols=85  Identities=19%  Similarity=0.199  Sum_probs=49.5

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCC-----CCChHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPE-----FQTDEAAINDLE  261 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~-----~~~~~~~~~~l~  261 (695)
                      .+++-|+|+.|+||||||..+..  ..+.. +..++|++....++..     .++++|.+...     ....++....+.
T Consensus        53 G~ivEi~G~~ssGKttLaL~~ia--~~q~~-g~~~a~ID~e~~ld~~-----~a~~lGvdl~rllv~~P~~~E~al~~~e  124 (322)
T PF00154_consen   53 GRIVEIYGPESSGKTTLALHAIA--EAQKQ-GGICAFIDAEHALDPE-----YAESLGVDLDRLLVVQPDTGEQALWIAE  124 (322)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHH--HHHHT-T-EEEEEESSS---HH-----HHHHTT--GGGEEEEE-SSHHHHHHHHH
T ss_pred             CceEEEeCCCCCchhhhHHHHHH--hhhcc-cceeEEecCcccchhh-----HHHhcCccccceEEecCCcHHHHHHHHH
Confidence            57999999999999999988876  33333 3347899998876654     33444432211     113444444444


Q ss_pred             HHHHhcCCCcEEEEEeCCCC
Q 042541          262 RFFKQMRIEAILLVLDDVWP  281 (695)
Q Consensus       262 ~~~~~l~~~~~LlVlDdv~~  281 (695)
                      .+++  .+.--++|+|.|-.
T Consensus       125 ~lir--sg~~~lVVvDSv~a  142 (322)
T PF00154_consen  125 QLIR--SGAVDLVVVDSVAA  142 (322)
T ss_dssp             HHHH--TTSESEEEEE-CTT
T ss_pred             HHhh--cccccEEEEecCcc
Confidence            4443  34455899999843

In homologous recombination, the protein functions as a DNA-dependent ATPase, promoting synapsis, heteroduplex formation and strand exchange between homologous DNAs []. RecA also acts as a protease cofactor that promotes autodigestion of the lexA product and phage repressors. The proteolytic inactivation of the lexA repressor by an activated form of recA may cause a derepression of the 20 or so genes involved in the SOS response, which regulates DNA repair, induced mutagenesis, delayed cell division and prophage induction in response to DNA damage []. RecA is a protein of about 350 amino-acid residues. Its sequence is very well conserved [, , ] among eubacterial species. It is also found in the chloroplast of plants []. RecA-like proteins are found in archaea and diverse eukaryotic organisms, like fission yeast, mouse or human. In the filament visualised by X-ray crystallography, beta-strand 3, the loop C-terminal to beta-strand 2, and alpha-helix D of the core domain form one surface that packs against alpha-helix A and beta-strand 0 (the N-terminal domain) of an adjacent monomer during polymerisation []. The core ATP-binding site domain is well conserved, with 14 invariant residues. It contains the nucleotide binding loop between beta-strand 1 and alpha-helix C. The Escherichia coli sequence GPESSGKT matches the consensus sequence of amino acids (G/A)XXXXGK(T/S) for the Walker A box (also referred to as the P-loop) found in a number of nucleoside triphosphate (NTP)-binding proteins. Another nucleotide binding motif, the Walker B box is found at beta-strand 4 in the RecA structure. The Walker B box is characterised by four hydrophobic amino acids followed by an acidic residue (usually aspartate). Nucleotide specificity and additional ATP binding interactions are contributed by the amino acid residues at beta-strand 2 and the loop C-terminal to that strand, all of which are greater than 90% conserved among bacterial RecA proteins.; GO: 0003697 single-stranded DNA binding, 0005524 ATP binding, 0006281 DNA repair; PDB: 2IN0_A 1MO3_A 3IFJ_A 2IN8_A 2IMZ_B 1G18_A 1MO4_A 3IGD_A 2L8L_A 2IN9_A ....

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=94.73  E-value=0.024  Score=53.42  Aligned_cols=22  Identities=36%  Similarity=0.533  Sum_probs=20.2

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+++|+|++|+|||||++.+..
T Consensus         2 ~~~~i~G~sGsGKttl~~~l~~   23 (179)
T TIGR02322         2 RLIYVVGPSGAGKDTLLDYARA   23 (179)
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            4789999999999999999876

Members of this family resemble PhnN of phosphonate utilization operons, where different such operons confer the ability to use somewhat different profiles of C-P bond-containing compounds (see PubMed:15231805), including phosphites as well as phosphonates. PhnN in E. coli shows considerable homology to guanylate kinases (EC 2.7.4.8), and has actually been shown to act as a ribose 1,5-bisphosphokinase (PRPP forming). This suggests an analogous kinase reaction for phosphonate metabolism, converting 5-phosphoalpha-1-(methylphosphono)ribose to methylphosphono-PRPP.

>PRK00625 shikimate kinase; Provisional

Probab=94.72  E-value=0.022  Score=53.04  Aligned_cols=21  Identities=29%  Similarity=0.301  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .|.|+||+|+||||+++.+.+
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~   22 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAK   22 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            488999999999999999977

>PF13245 AAA_19: Part of AAA domain

Probab=94.71  E-value=0.047  Score=43.01  Aligned_cols=24  Identities=42%  Similarity=0.718  Sum_probs=18.0

Q ss_pred             CceEEEEEcCCCCcHHHHH-HHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLV-QRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa-~~~~~  209 (695)
                      +.+++.|.|++|.|||+++ ..+.+
T Consensus         9 ~~~~~vv~g~pGtGKT~~~~~~i~~   33 (76)
T PF13245_consen    9 GSPLFVVQGPPGTGKTTTLAARIAE   33 (76)
T ss_pred             hCCeEEEECCCCCCHHHHHHHHHHH
Confidence            4578889999999999555 44443

>PRK00131 aroK shikimate kinase; Reviewed

Probab=94.70  E-value=0.026  Score=52.80  Aligned_cols=23  Identities=35%  Similarity=0.306  Sum_probs=21.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...|.|+|++|+||||+|+.++.
T Consensus         4 ~~~i~l~G~~GsGKstla~~La~   26 (175)
T PRK00131          4 GPNIVLIGFMGAGKSTIGRLLAK   26 (175)
T ss_pred             CCeEEEEcCCCCCHHHHHHHHHH
Confidence            46899999999999999999987

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=94.69  E-value=0.31  Score=48.86  Aligned_cols=35  Identities=26%  Similarity=0.323  Sum_probs=26.9

Q ss_pred             HHHHHHHHH-cCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          175 LKELKMELF-KDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       175 ~~~l~~~L~-~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+.+...|. ..+..-++|+|+.|+|||||.+.+..
T Consensus        98 ~~~~l~~l~~~~~~~~~~i~g~~g~GKttl~~~l~~  133 (270)
T TIGR02858        98 ADKLLPYLVRNNRVLNTLIISPPQCGKTTLLRDLAR  133 (270)
T ss_pred             HHHHHHHHHhCCCeeEEEEEcCCCCCHHHHHHHHhC
Confidence            344444444 34457899999999999999999987

Members of this protein are the stage III sporulation protein AA, encoded by one of several genes in the spoIIIA locus. It seems that this protein is found in a species if and only if that species is capable of endospore formation.

>PF08298 AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 This is entry is found at the N terminus of PrkA proteins - bacterial and archaeal serine kinases approximately 630 residues in length

Probab=94.68  E-value=0.053  Score=55.44  Aligned_cols=45  Identities=18%  Similarity=0.290  Sum_probs=39.3

Q ss_pred             CCCCCCCcchHHHHHHHHH------cCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          165 PVISPGLDVPLKELKMELF------KDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~------~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...|+|.++.++++++.+.      +..-+++.++|+.|.|||||+..+-+
T Consensus        60 ~~~~~G~~~~i~~lV~~fk~AA~g~~~~krIl~L~GPvg~GKSsl~~~Lk~  110 (358)
T PF08298_consen   60 EDEFYGMEETIERLVNYFKSAAQGLEERKRILLLLGPVGGGKSSLAELLKR  110 (358)
T ss_pred             cccccCcHHHHHHHHHHHHHHHhccCccceEEEEECCCCCCHHHHHHHHHH
Confidence            4578999999999999987      23468999999999999999988865

PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=94.64  E-value=0.075  Score=56.10  Aligned_cols=58  Identities=19%  Similarity=0.268  Sum_probs=34.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC-CHHHHHHHHHHhcCCC
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKGYP  246 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~~~  246 (695)
                      ..++.|+|++|+||||++..++........+  .+..++..... .....+....+.++.+
T Consensus       223 ~~vi~lvGptGvGKTTtaaKLA~~~~~~~G~--~V~Lit~Dt~R~aA~eQLk~yAe~lgvp  281 (432)
T PRK12724        223 RKVVFFVGPTGSGKTTSIAKLAAKYFLHMGK--SVSLYTTDNYRIAAIEQLKRYADTMGMP  281 (432)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHhcCC--eEEEecccchhhhHHHHHHHHHHhcCCC
Confidence            4689999999999999999888632222222  24444443211 2334444555555543

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=94.63  E-value=0.021  Score=53.71  Aligned_cols=21  Identities=33%  Similarity=0.393  Sum_probs=19.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +|+|.|.+|+||||+|+.+..
T Consensus         1 ii~i~G~sgsGKTtla~~l~~   21 (187)
T cd02024           1 IVGISGVTNSGKTTLAKLLQR   21 (187)
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            589999999999999999987

This enzyme catalyzes the phosphorylation of nicotinamide riboside (NR) to form nicotinamide mononucleotide (NMN). It defines the NR salvage pathway of NAD+ biosynthesis in addition to the pathways through nicotinic acid mononucleotide (NaMN). This enzyme can also phosphorylate the anticancer drug tiazofurin, which is an analog of nicotinamide riboside.

>COG4618 ArpD ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only]

Probab=94.60  E-value=0.089  Score=55.81  Aligned_cols=23  Identities=30%  Similarity=0.472  Sum_probs=20.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...++|+|++|.||||||+.+.-
T Consensus       362 G~~lgIIGPSgSGKSTLaR~lvG  384 (580)
T COG4618         362 GEALGIIGPSGSGKSTLARLLVG  384 (580)
T ss_pred             CceEEEECCCCccHHHHHHHHHc
Confidence            46899999999999999998753

>COG0055 AtpD F0F1-type ATP synthase, beta subunit [Energy production and conversion]

Probab=94.60  E-value=0.072  Score=54.11  Aligned_cols=93  Identities=15%  Similarity=0.211  Sum_probs=58.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCC-CCHHHHHHHHHHhcCCC----------CCCCCC--h
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKN-PNVKAIVQKVLHHKGYP----------VPEFQT--D  253 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~-~~~~~~~~~i~~~l~~~----------~~~~~~--~  253 (695)
                      ..-|++.|-+|+|||.|.+++.+  .+........++.-+++. ..-.++..++.+.--.+          .++...  .
T Consensus       147 GgKiGLFGGAGVGKTVl~~ELI~--Nia~~h~g~SVFaGvGERtREGndLy~Em~es~vl~ktalv~gQMNEpPGaR~RV  224 (468)
T COG0055         147 GGKIGLFGGAGVGKTVLIQELIN--NIAKEHGGYSVFAGVGERTREGNDLYHEMKESGVLDKTALVFGQMNEPPGARMRV  224 (468)
T ss_pred             CceeeeeccCCccceeeHHHHHH--HHHHHcCCeEEEEeccccccchHHHHHHHHhcCCCCceeEEEeecCCCCcceeee
Confidence            46789999999999999999988  454444443557777654 45678888887762211          111111  1


Q ss_pred             HHHHHHHHHHHHhcCCCcEEEEEeCCCC
Q 042541          254 EAAINDLERFFKQMRIEAILLVLDDVWP  281 (695)
Q Consensus       254 ~~~~~~l~~~~~~l~~~~~LlVlDdv~~  281 (695)
                      .-..-.+.+.++.-.++.+|+.+||+..
T Consensus       225 altGlT~AEyfRD~~gqdVLlFIDNIfR  252 (468)
T COG0055         225 ALTGLTMAEYFRDEEGQDVLLFIDNIFR  252 (468)
T ss_pred             hhhhhhHHHHhhcccCCeEEEEehhhhH
Confidence            1111123444544458899999999854

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=94.60  E-value=0.039  Score=55.46  Aligned_cols=53  Identities=15%  Similarity=0.331  Sum_probs=38.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcC
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKG  244 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~  244 (695)
                      ..+++.|+|.+|+|||+++.++..  +...+... ++||+..+.  ..++.+...+ ++
T Consensus        22 ~g~~~lI~G~pGsGKT~f~~qfl~--~~~~~ge~-vlyvs~~e~--~~~l~~~~~~-~g   74 (260)
T COG0467          22 RGSVVLITGPPGTGKTIFALQFLY--EGAREGEP-VLYVSTEES--PEELLENARS-FG   74 (260)
T ss_pred             CCcEEEEEcCCCCcHHHHHHHHHH--HHHhcCCc-EEEEEecCC--HHHHHHHHHH-cC
Confidence            468999999999999999999887  45555554 789998874  3444444433 44

>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]

Probab=94.58  E-value=0.096  Score=54.18  Aligned_cols=86  Identities=17%  Similarity=0.301  Sum_probs=53.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCC-CChHHHHHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEF-QTDEAAINDLERFFK  265 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~-~~~~~~~~~l~~~~~  265 (695)
                      ..+|.|-|.+|||||||..++..  ++...-  .++||+-.+......   --.+.++.+.... --.+...+.+.+.++
T Consensus        93 Gs~iLIgGdPGIGKSTLLLQva~--~lA~~~--~vLYVsGEES~~Qik---lRA~RL~~~~~~l~l~aEt~~e~I~~~l~  165 (456)
T COG1066          93 GSVILIGGDPGIGKSTLLLQVAA--RLAKRG--KVLYVSGEESLQQIK---LRADRLGLPTNNLYLLAETNLEDIIAELE  165 (456)
T ss_pred             ccEEEEccCCCCCHHHHHHHHHH--HHHhcC--cEEEEeCCcCHHHHH---HHHHHhCCCccceEEehhcCHHHHHHHHH
Confidence            47999999999999999999988  555444  377877665432222   2234455433221 112233344444443


Q ss_pred             hcCCCcEEEEEeCCCC
Q 042541          266 QMRIEAILLVLDDVWP  281 (695)
Q Consensus       266 ~l~~~~~LlVlDdv~~  281 (695)
                        ..++-++|+|-+..
T Consensus       166 --~~~p~lvVIDSIQT  179 (456)
T COG1066         166 --QEKPDLVVIDSIQT  179 (456)
T ss_pred             --hcCCCEEEEeccce
Confidence              36789999999743

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=94.56  E-value=0.086  Score=52.89  Aligned_cols=41  Identities=29%  Similarity=0.358  Sum_probs=29.5

Q ss_pred             CCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          169 PGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       169 vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .|...+..+....+......+|.|.|+.|+||||++..+.+
T Consensus        62 lg~~~~~~~~l~~~~~~~~GlilisG~tGSGKTT~l~all~  102 (264)
T cd01129          62 LGLKPENLEIFRKLLEKPHGIILVTGPTGSGKTTTLYSALS  102 (264)
T ss_pred             cCCCHHHHHHHHHHHhcCCCEEEEECCCCCcHHHHHHHHHh
Confidence            45554444444444444457899999999999999998876

It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.

>PF03193 DUF258: Protein of unknown function, DUF258; InterPro: IPR004881 This entry contains Escherichia coli (strain K12) RsgA, which may play a role in 30S ribosomal subunit biogenesis

Probab=94.55  E-value=0.05  Score=49.57  Aligned_cols=35  Identities=29%  Similarity=0.358  Sum_probs=29.1

Q ss_pred             chHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhcc
Q 042541          173 VPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       173 ~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      +.+++|.+.|..   ++++++|..|+|||||+..+..+
T Consensus        24 ~g~~~l~~~l~~---k~~vl~G~SGvGKSSLiN~L~~~   58 (161)
T PF03193_consen   24 EGIEELKELLKG---KTSVLLGQSGVGKSSLINALLPE   58 (161)
T ss_dssp             TTHHHHHHHHTT---SEEEEECSTTSSHHHHHHHHHTS
T ss_pred             cCHHHHHHHhcC---CEEEEECCCCCCHHHHHHHHHhh
Confidence            456777777754   79999999999999999999874

RsgA is an unusual circulary permuted GTPase that catalyzes rapid hydrolysis of GTP with a slow catalytic turnover. It is dispensible for viability, but important for overall fitness. The intrinsic GTPase activity is stimulated by the presence of 30S (160-fold increase in kcat) or 70S (96 fold increase in kcat) ribosomes []. The GTPase is inhibited by aminoglycoside antibiotics such as neomycin and paromycin [] streptomycin and spectinomycin []. This inhibition is not due to competition for binding sites on the 30S or 70S ribosome []. ; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 2YKR_W 2YV5_A 1T9H_A 2RCN_A 4A2I_V 1U0L_B.

>cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2

Probab=94.54  E-value=0.031  Score=52.53  Aligned_cols=21  Identities=33%  Similarity=0.687  Sum_probs=19.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +|+|.|.+|+||||||+.+..
T Consensus         1 ii~i~G~sgsGKttla~~l~~   21 (179)
T cd02028           1 VVGIAGPSGSGKTTFAKKLSN   21 (179)
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            589999999999999999987

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=94.51  E-value=0.068  Score=56.55  Aligned_cols=36  Identities=17%  Similarity=0.296  Sum_probs=28.5

Q ss_pred             HHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhcc
Q 042541          175 LKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       175 ~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      .+.+++.+.......+.|.|.||.|||+|.+.+.+.
T Consensus        10 ~~~v~~~~~~~~~~~~fv~G~~GtGKs~l~~~i~~~   45 (364)
T PF05970_consen   10 FDTVIEAIENEEGLNFFVTGPAGTGKSFLIKAIIDY   45 (364)
T ss_pred             HHHHHHHHHccCCcEEEEEcCCCCChhHHHHHHHHH
Confidence            344455555566788999999999999999998873

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=94.50  E-value=0.028  Score=52.69  Aligned_cols=22  Identities=18%  Similarity=0.427  Sum_probs=20.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ++|.+.|++|+||||+|+.+..
T Consensus         3 ~~i~l~G~~gsGKst~a~~l~~   24 (175)
T cd00227           3 RIIILNGGSSAGKSSIARALQS   24 (175)
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
Confidence            6899999999999999999876

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>PHA02774 E1; Provisional

Probab=94.49  E-value=0.12  Score=56.34  Aligned_cols=36  Identities=28%  Similarity=0.286  Sum_probs=27.3

Q ss_pred             hHHHHHHHHHc-CCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          174 PLKELKMELFK-DGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       174 ~~~~l~~~L~~-~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      -+..+..+|.. ++...+.|+|++|.|||.+|..+.+
T Consensus       420 fl~~lk~~l~~~PKknciv~~GPP~TGKS~fa~sL~~  456 (613)
T PHA02774        420 FLTALKDFLKGIPKKNCLVIYGPPDTGKSMFCMSLIK  456 (613)
T ss_pred             HHHHHHHHHhcCCcccEEEEECCCCCCHHHHHHHHHH
Confidence            34555555543 3346899999999999999999887

>cd01132 F1_ATPase_alpha F1 ATP synthase alpha, central domain

Probab=94.49  E-value=0.098  Score=52.02  Aligned_cols=91  Identities=16%  Similarity=0.193  Sum_probs=53.3

Q ss_pred             CceEEEEEcCCCCcHHHHH-HHHhccccccccCCCcEEEEEeCCCC-CHHHHHHHHHHhcCC-------CCCCCCChH--
Q 042541          186 GRQFIVVSAPGGYGKTTLV-QRLCKDDQVQGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKGY-------PVPEFQTDE--  254 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa-~~~~~~~~~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~~-------~~~~~~~~~--  254 (695)
                      ..+-++|.|..|+|||+|| ..+.+  ..  .-+..++++-+.+.. ...++.+++...-..       ...+.+...  
T Consensus        68 rGQr~~Ifg~~g~GKt~L~l~~i~~--~~--~~~v~~V~~~iGer~~ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~  143 (274)
T cd01132          68 RGQRELIIGDRQTGKTAIAIDTIIN--QK--GKKVYCIYVAIGQKASTVAQVVKTLEEHGAMEYTIVVAATASDPAPLQY  143 (274)
T ss_pred             cCCEEEeeCCCCCCccHHHHHHHHH--hc--CCCeEEEEEecccchHHHHHHHHHHHhcCccceeEEEEeCCCCchhHHH
Confidence            3477999999999999996 55554  21  223323567777654 566777777654211       111111111  


Q ss_pred             ---HHHHHHHHHHHhcCCCcEEEEEeCCCC
Q 042541          255 ---AAINDLERFFKQMRIEAILLVLDDVWP  281 (695)
Q Consensus       255 ---~~~~~l~~~~~~l~~~~~LlVlDdv~~  281 (695)
                         ...-.+.+.+.. +++.+|+++||+-.
T Consensus       144 ~a~~~a~aiAE~fr~-~G~~Vlvl~DslTr  172 (274)
T cd01132         144 LAPYTGCAMGEYFMD-NGKHALIIYDDLSK  172 (274)
T ss_pred             HHHHHHHHHHHHHHH-CCCCEEEEEcChHH
Confidence               112334455533 58999999999843

The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The alpha subunit of the F1 ATP synthase can bind nucleotides, but is non-catalytic.

>PRK05439 pantothenate kinase; Provisional

Probab=94.49  E-value=0.21  Score=50.96  Aligned_cols=46  Identities=15%  Similarity=-0.012  Sum_probs=30.9

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhcccccccc-CCCcEEEEEeCCCCCH
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGK-FKDDIFYVTVSKNPNV  232 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~-f~~~~~wv~~~~~~~~  232 (695)
                      +.+-+|+|.|.+|+||||+|+.+..  ..... ....+.-++..+-...
T Consensus        84 ~~~~iIgIaG~~gsGKSTla~~L~~--~l~~~~~~~~v~vi~~DdFy~~  130 (311)
T PRK05439         84 KVPFIIGIAGSVAVGKSTTARLLQA--LLSRWPEHPKVELVTTDGFLYP  130 (311)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH--HHHhhCCCCceEEEeccccccC
Confidence            3467999999999999999998876  33322 1223555666554433

>PRK04328 hypothetical protein; Provisional

Probab=94.47  E-value=0.19  Score=50.12  Aligned_cols=40  Identities=23%  Similarity=0.357  Sum_probs=30.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCC
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKN  229 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~  229 (695)
                      ..++.|.|.+|+|||+||.++... ..+.. . .++|++..+.
T Consensus        23 gs~ili~G~pGsGKT~l~~~fl~~-~~~~g-e-~~lyis~ee~   62 (249)
T PRK04328         23 RNVVLLSGGPGTGKSIFSQQFLWN-GLQMG-E-PGVYVALEEH   62 (249)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHH-HHhcC-C-cEEEEEeeCC
Confidence            589999999999999999887653 23332 2 3679988774

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=94.47  E-value=0.12  Score=54.46  Aligned_cols=86  Identities=16%  Similarity=0.308  Sum_probs=48.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCC-ChHHHHHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQ-TDEAAINDLERFFK  265 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~-~~~~~~~~l~~~~~  265 (695)
                      ..++.|.|.+|+|||||+.+++..  ....- ..++|++..+.  ...+. .-.+.++....... ..+...+.+.+.++
T Consensus        82 GslvLI~G~pG~GKStLllq~a~~--~a~~g-~~VlYvs~EEs--~~qi~-~Ra~rlg~~~~~l~l~~e~~le~I~~~i~  155 (372)
T cd01121          82 GSVILIGGDPGIGKSTLLLQVAAR--LAKRG-GKVLYVSGEES--PEQIK-LRADRLGISTENLYLLAETNLEDILASIE  155 (372)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHH--HHhcC-CeEEEEECCcC--HHHHH-HHHHHcCCCcccEEEEccCcHHHHHHHHH
Confidence            479999999999999999988863  32222 23778877543  33332 22344543322110 01112233333332


Q ss_pred             hcCCCcEEEEEeCCC
Q 042541          266 QMRIEAILLVLDDVW  280 (695)
Q Consensus       266 ~l~~~~~LlVlDdv~  280 (695)
                        ..+.-++|+|.+.
T Consensus       156 --~~~~~lVVIDSIq  168 (372)
T cd01121         156 --ELKPDLVIIDSIQ  168 (372)
T ss_pred             --hcCCcEEEEcchH
Confidence              2456788999873

This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.

>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model

Probab=94.47  E-value=0.018  Score=49.87  Aligned_cols=27  Identities=33%  Similarity=0.536  Sum_probs=18.6

Q ss_pred             EEEEcCCCCcHHHHHHHHhccccccccCC
Q 042541          190 IVVSAPGGYGKTTLVQRLCKDDQVQGKFK  218 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~~~~~~~f~  218 (695)
                      |.|+|.+|+||||+|+.++.  .+...|.
T Consensus         2 vLleg~PG~GKT~la~~lA~--~~~~~f~   28 (131)
T PF07726_consen    2 VLLEGVPGVGKTTLAKALAR--SLGLSFK   28 (131)
T ss_dssp             EEEES---HHHHHHHHHHHH--HTT--EE
T ss_pred             EeeECCCccHHHHHHHHHHH--HcCCcee
Confidence            67999999999999999998  5555554

AAA ATPases form a large, functionally diverse protein family belonging to the AAA+ superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent unfolding of macromolecules. AAA ATPases contain a P-loop NTPase domain, which is the most abundant class of NTP-binding protein fold, and is found throughout all kingdoms of life []. P-loop NTPase domains act to hydrolyse the beta-gamma phosphate bond of bound nucleoside triphosphate. There are two classes of P-loop domains: the KG (kinase-GTPase) division, and the ASCE division, the latter including the AAA+ group as well as several other ATPases. There are at least six major clades of AAA domains (metalloproteases, meiotic proteins, D1 and D2 domains of ATPases with two AAA domains, proteasome subunits, and BSC1), as well as several minor clades, some of which consist of hypothetical proteins []. The domain organisation of AAA ATPases consists of a non-ATPase N-terminal domain that acts in substrate recognition, followed by one or two AAA domains (D1 and D2), one of which may be degenerate.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 2R44_A.

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=94.46  E-value=1.2  Score=45.06  Aligned_cols=112  Identities=10%  Similarity=-0.016  Sum_probs=61.4

Q ss_pred             HHHHHHHHHcCC-ceEEEEEcCCCCcHHHHHHHHhccccc-----------cccCCCcEEEEEeCCCCCHHHHHHHHHHh
Q 042541          175 LKELKMELFKDG-RQFIVVSAPGGYGKTTLVQRLCKDDQV-----------QGKFKDDIFYVTVSKNPNVKAIVQKVLHH  242 (695)
Q Consensus       175 ~~~l~~~L~~~~-~~vv~I~G~gGiGKTtLa~~~~~~~~~-----------~~~f~~~~~wv~~~~~~~~~~~~~~i~~~  242 (695)
                      -+++...+..+. ..-..++|+.|+||+++|..++..---           ....+. +.|+.-....            
T Consensus         6 ~~~L~~~i~~~rl~HAyLf~G~~G~Gk~~lA~~~A~~llC~~~~~~c~~~~~~~HPD-~~~i~p~~~~------------   72 (290)
T PRK05917          6 WEALIQRVRDQKVPSAIILHGQDLSNLSARAYELASLILKETSPEAAYKISQKIHPD-IHEFSPQGKG------------   72 (290)
T ss_pred             HHHHHHHHHcCCcCeeEeeECCCCCcHHHHHHHHHHHHhCCCCccHHHHHhcCCCCC-EEEEecCCCC------------
Confidence            456667776655 456779999999999999887762100           011122 2222110000            


Q ss_pred             cCCCCCCCCChHHHHHHHHHHH--HhcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCC
Q 042541          243 KGYPVPEFQTDEAAINDLERFF--KQMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSE  306 (695)
Q Consensus       243 l~~~~~~~~~~~~~~~~l~~~~--~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~  306 (695)
                             ..-..+....+.+.+  ....++.-++|+|+++.....    +++.+-...+++.+|++|.+.
T Consensus        73 -------~~I~idqiR~l~~~~~~~p~e~~~kv~ii~~ad~mt~~AaNaLLK~LEEPp~~~~fiL~~~~~  135 (290)
T PRK05917         73 -------RLHSIETPRAIKKQIWIHPYESPYKIYIIHEADRMTLDAISAFLKVLEDPPQHGVIILTSAKP  135 (290)
T ss_pred             -------CcCcHHHHHHHHHHHhhCccCCCceEEEEechhhcCHHHHHHHHHHhhcCCCCeEEEEEeCCh
Confidence                   000111122222222  122466779999999877643    556666666677777777665

>PRK00889 adenylylsulfate kinase; Provisional

Probab=94.45  E-value=0.036  Score=51.98  Aligned_cols=24  Identities=25%  Similarity=0.331  Sum_probs=21.8

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+|+|+|++|+||||+|+.+..
T Consensus         3 ~g~~i~~~G~~GsGKST~a~~la~   26 (175)
T PRK00889          3 RGVTVWFTGLSGAGKTTIARALAE   26 (175)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            356999999999999999999987

>TIGR01351 adk adenylate kinases

Probab=94.45  E-value=0.061  Score=52.12  Aligned_cols=20  Identities=35%  Similarity=0.625  Sum_probs=18.4

Q ss_pred             EEEEcCCCCcHHHHHHHHhc
Q 042541          190 IVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~  209 (695)
                      |.|.|++|+||||+|+.+..
T Consensus         2 I~i~G~pGsGKsT~a~~La~   21 (210)
T TIGR01351         2 LVLLGPPGSGKGTQAKRIAE   21 (210)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            78999999999999999875

Adenylate kinase (EC 2.7.4.3) converts ATP + AMP to ADP + ADP, that is, uses ATP as a phosphate donor for AMP. Most members of this family are known or believed to be adenylate kinase. However, some members accept other nucleotide triphosphates as donors, may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10) is a GTP:AMP phosphotransferase. This family is designated subfamily rather than equivalog for this reason.

>TIGR03263 guanyl_kin guanylate kinase

Probab=94.45  E-value=0.03  Score=52.72  Aligned_cols=22  Identities=50%  Similarity=0.801  Sum_probs=20.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ++|+|+|+.|+|||||++.+..
T Consensus         2 ~ii~l~G~~GsGKsTl~~~L~~   23 (180)
T TIGR03263         2 LLIVISGPSGVGKSTLVKALLE   23 (180)
T ss_pred             cEEEEECCCCCCHHHHHHHHHc
Confidence            5799999999999999999987

Members of this family are the enzyme guanylate kinase, also called GMP kinase. This enzyme transfers a phosphate from ATP to GMP, yielding ADP and GDP.

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=94.44  E-value=0.29  Score=48.57  Aligned_cols=52  Identities=13%  Similarity=0.341  Sum_probs=36.5

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHh
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHH  242 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~  242 (695)
                      ..++.|.|.+|+|||+++.+++.+.-..  ....++|++...  +..++...++..
T Consensus        13 G~l~lI~G~~G~GKT~~~~~~~~~~~~~--~g~~vly~s~E~--~~~~~~~r~~~~   64 (242)
T cd00984          13 GDLIIIAARPSMGKTAFALNIAENIAKK--QGKPVLFFSLEM--SKEQLLQRLLAS   64 (242)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHh--CCCceEEEeCCC--CHHHHHHHHHHH
Confidence            4689999999999999999887632222  133477887776  456666666544

The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=94.43  E-value=0.072  Score=55.61  Aligned_cols=64  Identities=14%  Similarity=0.225  Sum_probs=48.1

Q ss_pred             CCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHH
Q 042541          168 SPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKV  239 (695)
Q Consensus       168 ~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i  239 (695)
                      ++|.++.+..+...+..+  +-+.+.|++|+|||+||+.++.  .+.    ...+++.+.......++....
T Consensus        26 ~~g~~~~~~~~l~a~~~~--~~vll~G~PG~gKT~la~~lA~--~l~----~~~~~i~~t~~l~p~d~~G~~   89 (329)
T COG0714          26 VVGDEEVIELALLALLAG--GHVLLEGPPGVGKTLLARALAR--ALG----LPFVRIQCTPDLLPSDLLGTY   89 (329)
T ss_pred             eeccHHHHHHHHHHHHcC--CCEEEECCCCccHHHHHHHHHH--HhC----CCeEEEecCCCCCHHHhcCch
Confidence            688888887777777654  4588999999999999999987  333    235688888877777665433

>PRK14528 adenylate kinase; Provisional

Probab=94.41  E-value=0.075  Score=50.34  Aligned_cols=22  Identities=36%  Similarity=0.616  Sum_probs=19.7

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +.|.|.|++|+||||+|+.+..
T Consensus         2 ~~i~i~G~pGsGKtt~a~~la~   23 (186)
T PRK14528          2 KNIIFMGPPGAGKGTQAKILCE   23 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            4588999999999999999876

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=94.40  E-value=0.24  Score=52.83  Aligned_cols=87  Identities=16%  Similarity=0.210  Sum_probs=45.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCC-CCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKN-PNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFK  265 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~-~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~  265 (695)
                      ..+|+++|+.|+||||++..++........... +..+..... ....+-+....+.++.+........+    +...+.
T Consensus       191 g~vi~lvGpnG~GKTTtlakLA~~~~~~~~~~~-v~~i~~d~~rigalEQL~~~a~ilGvp~~~v~~~~d----l~~al~  265 (420)
T PRK14721        191 GGVYALIGPTGVGKTTTTAKLAARAVIRHGADK-VALLTTDSYRIGGHEQLRIYGKLLGVSVRSIKDIAD----LQLMLH  265 (420)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCe-EEEEecCCcchhHHHHHHHHHHHcCCceecCCCHHH----HHHHHH
Confidence            479999999999999999877752111111122 434443321 23333355555666654432222222    222233


Q ss_pred             hcCCCcEEEEEeCC
Q 042541          266 QMRIEAILLVLDDV  279 (695)
Q Consensus       266 ~l~~~~~LlVlDdv  279 (695)
                      .+.++ -++++|-.
T Consensus       266 ~l~~~-d~VLIDTa  278 (420)
T PRK14721        266 ELRGK-HMVLIDTV  278 (420)
T ss_pred             HhcCC-CEEEecCC
Confidence            34443 45666765

>TIGR00041 DTMP_kinase thymidylate kinase

Probab=94.40  E-value=0.14  Score=48.82  Aligned_cols=23  Identities=43%  Similarity=0.455  Sum_probs=21.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhcc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      ..|+|.|..|+||||+++.+.+.
T Consensus         4 ~~IvieG~~GsGKsT~~~~L~~~   26 (195)
T TIGR00041         4 MFIVIEGIDGAGKTTQANLLKKL   26 (195)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            57999999999999999999873

Function: phosphorylation of DTMP to form DTDP in both de novo and salvage pathways of DTTP synthesis. Catalytic activity: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate.

>TIGR03305 alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit beta

Probab=94.38  E-value=0.099  Score=55.87  Aligned_cols=94  Identities=10%  Similarity=0.142  Sum_probs=56.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC-CHHHHHHHHHHhcCCC-------CCCCCChH---
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKGYP-------VPEFQTDE---  254 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~~~-------~~~~~~~~---  254 (695)
                      ..+-++|.|.+|+|||+|+..+..... +.+-+. ++++-+++.. ...++..++...-...       ..+.+...   
T Consensus       137 kGQr~~Ifg~~G~GKt~l~~~~~~~~~-~~~~~v-~V~~~iGeR~rEv~e~~~~~~~~~~l~rtvvv~~ts~~~~~~r~~  214 (449)
T TIGR03305       137 RGGKAGLFGGAGVGKTVLLTEMIHNMV-GQHQGV-SIFCGIGERCREGEELYREMKEAGVLDNTVMVFGQMNEPPGARFR  214 (449)
T ss_pred             cCCEEEeecCCCCChhHHHHHHHHHHH-hcCCCE-EEEEEeccCcHHHHHHHHHHhhccccceEEEEEeCCCCCHHHHHH
Confidence            457899999999999999999877422 222344 6688787654 5566777766542111       11111111   


Q ss_pred             --HHHHHHHHHHHhcCCCcEEEEEeCCCC
Q 042541          255 --AAINDLERFFKQMRIEAILLVLDDVWP  281 (695)
Q Consensus       255 --~~~~~l~~~~~~l~~~~~LlVlDdv~~  281 (695)
                        ...-.+.+.++.-+++++|+++||+-.
T Consensus       215 ~~~~a~tiAEyfrd~~G~~VLl~~DslTR  243 (449)
T TIGR03305       215 VGHTALTMAEYFRDDEKQDVLLLIDNIFR  243 (449)
T ss_pred             HHHHHHHHHHHHHHhcCCceEEEecChHH
Confidence              112223344432257999999999843

A small number of taxonomically diverse prokaryotic species have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 beta subunit of this apparent second ATP synthase.

>COG0378 HypB Ni2+-binding GTPase involved in regulation of expression and maturation of urease and hydrogenase [Posttranslational modification, protein turnover, chaperones / Transcription]

Probab=94.38  E-value=0.099  Score=48.51  Aligned_cols=90  Identities=16%  Similarity=0.190  Sum_probs=52.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHH-hcCCCCC--CCCChHHHHHHHHHHH
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLH-HKGYPVP--EFQTDEAAINDLERFF  264 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~-~l~~~~~--~~~~~~~~~~~l~~~~  264 (695)
                      ..|.|-|+.|+|||+|..+.+.  .+++.|+..++=.++-...+...+.+..-. ..+....  ...+.......+.++.
T Consensus        14 ~~i~v~Gp~GSGKTaLie~~~~--~L~~~~~~aVI~~Di~t~~Da~~l~~~~g~~i~~v~TG~~CH~da~m~~~ai~~l~   91 (202)
T COG0378          14 LRIGVGGPPGSGKTALIEKTLR--ALKDEYKIAVITGDIYTKEDADRLRKLPGEPIIGVETGKGCHLDASMNLEAIEELV   91 (202)
T ss_pred             EEEEecCCCCcCHHHHHHHHHH--HHHhhCCeEEEeceeechhhHHHHHhCCCCeeEEeccCCccCCcHHHHHHHHHHHh
Confidence            6899999999999999999988  677778865555444444444444442100 0111111  1224444444555544


Q ss_pred             HhcCCCcEEEEEeCCC
Q 042541          265 KQMRIEAILLVLDDVW  280 (695)
Q Consensus       265 ~~l~~~~~LlVlDdv~  280 (695)
                      ..... -=||++.++.
T Consensus        92 ~~~~~-~Dll~iEs~G  106 (202)
T COG0378          92 LDFPD-LDLLFIESVG  106 (202)
T ss_pred             hcCCc-CCEEEEecCc
Confidence            32222 3577788875

>KOG0727 consensus 26S proteasome regulatory complex, ATPase RPT3 [Posttranslational modification, protein turnover, chaperones]

Probab=94.38  E-value=0.055  Score=51.72  Aligned_cols=44  Identities=27%  Similarity=0.367  Sum_probs=35.3

Q ss_pred             CCCCCcchHHHHHHHHH-------------cCCceEEEEEcCCCCcHHHHHHHHhcc
Q 042541          167 ISPGLDVPLKELKMELF-------------KDGRQFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~-------------~~~~~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      .+-|.+...+++.+...             -+.++-|.++|++|.|||-||++|+++
T Consensus       156 diggld~qkqeireavelplt~~~ly~qigidpprgvllygppg~gktml~kava~~  212 (408)
T KOG0727|consen  156 DIGGLDVQKQEIREAVELPLTHADLYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANH  212 (408)
T ss_pred             ccccchhhHHHHHHHHhccchHHHHHHHhCCCCCcceEEeCCCCCcHHHHHHHHhhc
Confidence            44568888888877765             133677899999999999999999984

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=94.37  E-value=0.027  Score=51.22  Aligned_cols=21  Identities=38%  Similarity=0.526  Sum_probs=19.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ++.|+|++|+||||+|+.+..
T Consensus         1 li~l~G~~GsGKST~a~~l~~   21 (150)
T cd02021           1 IIVVMGVSGSGKSTVGKALAE   21 (150)
T ss_pred             CEEEEcCCCCCHHHHHHHHHh
Confidence            478999999999999999876

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A

Probab=94.34  E-value=0.034  Score=49.83  Aligned_cols=38  Identities=21%  Similarity=0.393  Sum_probs=25.7

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhcccccc-ccCCCcEEEEEeCC
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKDDQVQ-GKFKDDIFYVTVSK  228 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~~~~~-~~f~~~~~wv~~~~  228 (695)
                      ++|.|+|..|+|||||++.+.+  ... ..+.. .+..+...
T Consensus         1 pvv~VvG~~~sGKTTl~~~Li~--~l~~~g~~v-~~ik~~~~   39 (140)
T PF03205_consen    1 PVVQVVGPKNSGKTTLIRKLIN--ELKRRGYRV-AVIKHTDH   39 (140)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHH--HHHHTT--E-EEEEE-ST
T ss_pred             CEEEEECCCCCCHHHHHHHHHH--HHhHcCCce-EEEEEccC
Confidence            5899999999999999999998  443 33443 33555444

>TIGR00073 hypB hydrogenase accessory protein HypB

Probab=94.34  E-value=0.043  Score=53.04  Aligned_cols=30  Identities=33%  Similarity=0.424  Sum_probs=26.0

Q ss_pred             HHHHcCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          180 MELFKDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       180 ~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +.+...++++|+++|..|+|||||..++.+
T Consensus        15 ~~~~~~~~~~i~~~G~~gsGKTTli~~l~~   44 (207)
T TIGR00073        15 ERLDKHGLVVLNFMSSPGSGKTTLIEKLID   44 (207)
T ss_pred             HHhhhcCcEEEEEECCCCCCHHHHHHHHHH
Confidence            344566799999999999999999999887

HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=94.34  E-value=0.052  Score=51.17  Aligned_cols=36  Identities=25%  Similarity=0.306  Sum_probs=27.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEe
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTV  226 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~  226 (695)
                      ..|++|+|++|+|||||.+-+-.-    +.++.+.+|+.-
T Consensus        28 Gevv~iiGpSGSGKSTlLRclN~L----E~~~~G~I~i~g   63 (240)
T COG1126          28 GEVVVIIGPSGSGKSTLLRCLNGL----EEPDSGSITVDG   63 (240)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHCC----cCCCCceEEECC
Confidence            479999999999999999988642    334445667643

>cd03285 ABC_MSH2_euk MutS2 homolog in eukaryotes

Probab=94.33  E-value=0.054  Score=52.86  Aligned_cols=113  Identities=15%  Similarity=0.209  Sum_probs=56.4

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCC---CCChHHHHHHHHH
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPE---FQTDEAAINDLER  262 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~---~~~~~~~~~~l~~  262 (695)
                      +.+++.|+|+.|.||||+.+.+..- .+-.  ..+. +|.....  ...+...++..++.....   .........++..
T Consensus        29 ~~~~~~l~G~n~~GKstll~~i~~~-~~la--~~g~-~vpa~~~--~~~~~~~il~~~~l~d~~~~~lS~~~~e~~~~a~  102 (222)
T cd03285          29 KSRFLIITGPNMGGKSTYIRQIGVI-VLMA--QIGC-FVPCDSA--DIPIVDCILARVGASDSQLKGVSTFMAEMLETAA  102 (222)
T ss_pred             CCeEEEEECCCCCChHHHHHHHHHH-HHHH--HhCC-CcCcccE--EEeccceeEeeeccccchhcCcChHHHHHHHHHH
Confidence            4679999999999999999886532 1111  1100 2222110  011223333333322111   1122233334444


Q ss_pred             HHHhcCCCcEEEEEeCCCC---CChH------HHhhhccCCCCCEEEEEcCCC
Q 042541          263 FFKQMRIEAILLVLDDVWP---GSES------LLQKLGFQLPDYKILVTSRSE  306 (695)
Q Consensus       263 ~~~~l~~~~~LlVlDdv~~---~~~~------~~~~l~~~~~gs~iivTtR~~  306 (695)
                      .++.+ ..+-|+++|..-.   ..+.      .++.+.. ..|+.+|+||-..
T Consensus       103 il~~~-~~~sLvLLDEp~~gT~~lD~~~~~~~il~~l~~-~~~~~vlisTH~~  153 (222)
T cd03285         103 ILKSA-TENSLIIIDELGRGTSTYDGFGLAWAIAEYIAT-QIKCFCLFATHFH  153 (222)
T ss_pred             HHHhC-CCCeEEEEecCcCCCChHHHHHHHHHHHHHHHh-cCCCeEEEEechH
Confidence            44444 5688999999832   2221      1233322 3467888888743

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>PRK08927 fliI flagellum-specific ATP synthase; Validated

Probab=94.33  E-value=0.17  Score=53.93  Aligned_cols=90  Identities=17%  Similarity=0.220  Sum_probs=52.2

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC-CHHHHHHHHHHhcCCC-------CCCCCCh----
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKGYP-------VPEFQTD----  253 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~~~-------~~~~~~~----  253 (695)
                      ....++|+|..|+|||||++.+.+...    .+. ++.+-+++.. ...++..+.+..-+..       ..+.+..    
T Consensus       157 ~Gqri~I~G~sG~GKTtLL~~I~~~~~----~d~-~v~~~iGER~rEv~ef~~~~l~~~~l~rsvvv~atsd~~~~~r~~  231 (442)
T PRK08927        157 RGQRMGIFAGSGVGKSVLLSMLARNAD----ADV-SVIGLIGERGREVQEFLQDDLGPEGLARSVVVVATSDEPALMRRQ  231 (442)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhccC----CCE-EEEEEEecCcHHHHHHHHHHhhccCceeEEEEEECCCCCHHHHHH
Confidence            457899999999999999999886321    123 4456666544 4455555554432211       1111111    


Q ss_pred             -HHHHHHHHHHHHhcCCCcEEEEEeCCCC
Q 042541          254 -EAAINDLERFFKQMRIEAILLVLDDVWP  281 (695)
Q Consensus       254 -~~~~~~l~~~~~~l~~~~~LlVlDdv~~  281 (695)
                       ....-.+.+.+.. +++++|+++||+-.
T Consensus       232 a~~~a~tiAEyfrd-~G~~Vll~~DslTr  259 (442)
T PRK08927        232 AAYLTLAIAEYFRD-QGKDVLCLMDSVTR  259 (442)
T ss_pred             HHHHHHHHHHHHHH-CCCcEEEEEeCcHH
Confidence             1112223444422 59999999999843

>COG0003 ArsA Predicted ATPase involved in chromosome partitioning [Cell division and chromosome partitioning]

Probab=94.33  E-value=0.062  Score=55.03  Aligned_cols=49  Identities=16%  Similarity=0.316  Sum_probs=36.6

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQK  238 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~  238 (695)
                      .+++.+.|.|||||||+|.+.+-  ........ ++-|+.....+..+++..
T Consensus         2 ~riv~f~GKGGVGKTT~aaA~A~--~lA~~g~k-vLlvStDPAhsL~d~f~~   50 (322)
T COG0003           2 TRIVFFTGKGGVGKTTIAAATAV--KLAESGKK-VLLVSTDPAHSLGDVFDL   50 (322)
T ss_pred             cEEEEEecCCcccHHHHHHHHHH--HHHHcCCc-EEEEEeCCCCchHhhhcc
Confidence            47899999999999999988654  34444443 778888877777766654

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=94.30  E-value=0.14  Score=52.67  Aligned_cols=38  Identities=21%  Similarity=0.326  Sum_probs=27.4

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEe
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTV  226 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~  226 (695)
                      ...+++++|++|+||||++..++..  .... ...+..+..
T Consensus       113 ~~~vi~lvGpnGsGKTTt~~kLA~~--l~~~-g~~V~Li~~  150 (318)
T PRK10416        113 KPFVILVVGVNGVGKTTTIGKLAHK--YKAQ-GKKVLLAAG  150 (318)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHH--HHhc-CCeEEEEec
Confidence            4689999999999999999998873  3322 223555554

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=94.29  E-value=0.033  Score=50.48  Aligned_cols=20  Identities=35%  Similarity=0.549  Sum_probs=18.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHh
Q 042541          189 FIVVSAPGGYGKTTLVQRLC  208 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~  208 (695)
                      .|.|.|.+|+||||+++.+.
T Consensus         2 ~I~ITGTPGvGKTT~~~~L~   21 (180)
T COG1936           2 LIAITGTPGVGKTTVCKLLR   21 (180)
T ss_pred             eEEEeCCCCCchHHHHHHHH
Confidence            58999999999999998875

>PRK13947 shikimate kinase; Provisional

Probab=94.27  E-value=0.031  Score=52.13  Aligned_cols=21  Identities=38%  Similarity=0.384  Sum_probs=19.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      -|.|+|++|+||||+|+.+.+
T Consensus         3 ~I~l~G~~GsGKst~a~~La~   23 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVAT   23 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHH
Confidence            488999999999999999987

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=94.26  E-value=0.034  Score=49.69  Aligned_cols=21  Identities=52%  Similarity=0.903  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +|+|+|+.|+|||||++.+..
T Consensus         1 ~i~i~GpsGsGKstl~~~L~~   21 (137)
T cd00071           1 LIVLSGPSGVGKSTLLKRLLE   21 (137)
T ss_pred             CEEEECCCCCCHHHHHHHHHh
Confidence            378999999999999999987

7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.

>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional

Probab=94.25  E-value=0.039  Score=51.05  Aligned_cols=24  Identities=33%  Similarity=0.454  Sum_probs=21.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..++++|+|..|+|||||++.+..
T Consensus         5 ~~~ii~ivG~sgsGKTTLi~~li~   28 (173)
T PRK10751          5 MIPLLAIAAWSGTGKTTLLKKLIP   28 (173)
T ss_pred             CceEEEEECCCCChHHHHHHHHHH
Confidence            357999999999999999999886

>cd03243 ABC_MutS_homologs The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch

Probab=94.21  E-value=0.089  Score=50.62  Aligned_cols=22  Identities=18%  Similarity=0.445  Sum_probs=20.5

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+++|+|+.|.|||||.+.+..
T Consensus        30 ~~~~l~G~Ng~GKStll~~i~~   51 (202)
T cd03243          30 RLLLITGPNMGGKSTYLRSIGL   51 (202)
T ss_pred             eEEEEECCCCCccHHHHHHHHH
Confidence            7999999999999999999874

Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA stru

>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]

Probab=94.21  E-value=0.037  Score=53.14  Aligned_cols=23  Identities=26%  Similarity=0.375  Sum_probs=21.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|.+|+|||||++.+.-
T Consensus        33 Ge~lgivGeSGsGKSTL~r~l~G   55 (252)
T COG1124          33 GETLGIVGESGSGKSTLARLLAG   55 (252)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHhc
Confidence            47899999999999999999975

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=94.20  E-value=0.44  Score=53.43  Aligned_cols=25  Identities=28%  Similarity=0.420  Sum_probs=21.9

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +....++|+|+.|+|||||++.+..
T Consensus       359 ~~G~~vaIvG~SGsGKSTLl~lL~g  383 (529)
T TIGR02868       359 PPGERVAILGPSGSGKSTLLMLLTG  383 (529)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhc
Confidence            3458899999999999999999864

The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex.

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=94.20  E-value=0.051  Score=56.33  Aligned_cols=43  Identities=23%  Similarity=0.207  Sum_probs=36.6

Q ss_pred             CCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          167 ISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+||-+..+..+.-.+.++...-|.|.|..|+|||||++.+..
T Consensus         5 ~ivgq~~~~~al~~~~~~~~~g~vli~G~~G~gKttl~r~~~~   47 (337)
T TIGR02030         5 AIVGQDEMKLALLLNVIDPKIGGVMVMGDRGTGKSTAVRALAA   47 (337)
T ss_pred             ccccHHHHHHHHHHHhcCCCCCeEEEEcCCCCCHHHHHHHHHH
Confidence            4689888888887777777677788999999999999999875

This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria.

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=94.19  E-value=0.073  Score=45.95  Aligned_cols=44  Identities=9%  Similarity=0.064  Sum_probs=32.6

Q ss_pred             CCCCCcchHHHHHHHHH----c---CCceEEEEEcCCCCcHHHHHHHHhcc
Q 042541          167 ISPGLDVPLKELKMELF----K---DGRQFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~----~---~~~~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      .++|-.-..+.+...+.    +   .++-|++.+|.+|+|||.+++.+++.
T Consensus        26 ~l~GQhla~~~v~~ai~~~l~~~~p~KpLVlSfHG~tGtGKn~v~~liA~~   76 (127)
T PF06309_consen   26 NLFGQHLAVEVVVNAIKGHLANPNPRKPLVLSFHGWTGTGKNFVSRLIAEH   76 (127)
T ss_pred             HccCcHHHHHHHHHHHHHHHcCCCCCCCEEEEeecCCCCcHHHHHHHHHHH
Confidence            46776666666666554    2   34678999999999999988887764

Torsion dystonia is an autosomal dominant movement disorder characterised by involuntary, repetitive muscle contractions and twisted postures. The most severe early-onset form of dystonia has been linked to mutations in the human DYT1 (TOR1A) gene encoding a protein termed torsinA. While causative genetic alterations have been identified, the function of torsin proteins and the molecular mechanism underlying dystonia remain unknown. Phylogenetic analysis of the torsin protein family indicates these proteins share distant sequence similarity with the large and diverse family of AAA ATPase, central region containing proteins () proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor

>cd01136 ATPase_flagellum-secretory_path_III Flagellum-specific ATPase/type III secretory pathway virulence-related protein

Probab=94.18  E-value=0.29  Score=50.29  Aligned_cols=90  Identities=17%  Similarity=0.269  Sum_probs=51.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeC-CCCCHHHHHHHHHHhcCCC-------CCCCCChH---
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVS-KNPNVKAIVQKVLHHKGYP-------VPEFQTDE---  254 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~-~~~~~~~~~~~i~~~l~~~-------~~~~~~~~---  254 (695)
                      ....++|+|..|+|||||.+.+...  ..  -+. ....-+. +..+..++.......-+..       ..+.+...   
T Consensus        68 ~Gqri~I~G~sG~GKTtLl~~Ia~~--~~--~~~-~vi~~iGer~~ev~~~~~~~~~~~~l~rtvvv~~t~d~~~~~r~~  142 (326)
T cd01136          68 KGQRLGIFAGSGVGKSTLLGMIARG--TT--ADV-NVIALIGERGREVREFIEKDLGEEGLKRSVVVVATSDESPLLRVK  142 (326)
T ss_pred             CCcEEEEECCCCCChHHHHHHHhCC--CC--CCE-EEEEEEecCCccHHHHHHHHHhcCccceEEEEEcCCCCCHHHHHH
Confidence            3478899999999999999988863  21  122 2234444 3345666666665543211       11111111   


Q ss_pred             --HHHHHHHHHHHhcCCCcEEEEEeCCCC
Q 042541          255 --AAINDLERFFKQMRIEAILLVLDDVWP  281 (695)
Q Consensus       255 --~~~~~l~~~~~~l~~~~~LlVlDdv~~  281 (695)
                        ...-.+.+.+.. +++.+|+++||+-.
T Consensus       143 ~~~~a~~~AEyfr~-~g~~Vll~~Dsltr  170 (326)
T cd01136         143 AAYTATAIAEYFRD-QGKDVLLLMDSLTR  170 (326)
T ss_pred             HHHHHHHHHHHHHH-cCCCeEEEeccchH
Confidence              112223444422 59999999999843

This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they both are proton driven rotary molecular devices. However, the main function of the bacterial flagellar motor is to rotate the flagellar filament for cell motility. Intracellular pathogens such as Salmonella and Chlamydia also have proteins which are similar to the flagellar-specific ATPase, but function in the secretion of virulence-related proteins via the type III secretory pathway.

>PF12780 AAA_8: P-loop containing dynein motor region D4; InterPro: IPR024317 The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases

Probab=94.17  E-value=0.17  Score=50.62  Aligned_cols=94  Identities=18%  Similarity=0.313  Sum_probs=51.0

Q ss_pred             CCCcchHHHHHH---HHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCC
Q 042541          169 PGLDVPLKELKM---ELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGY  245 (695)
Q Consensus       169 vGr~~~~~~l~~---~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~  245 (695)
                      |=.++.++.|..   .|..+ .+-..++|.||+||+|+++.++.-   . .+  .++-+.+++.++..+.          
T Consensus        11 Vlf~~ai~hi~ri~RvL~~~-~Gh~LLvG~~GsGr~sl~rLaa~i---~-~~--~~~~i~~~~~y~~~~f----------   73 (268)
T PF12780_consen   11 VLFDEAIEHIARISRVLSQP-RGHALLVGVGGSGRQSLARLAAFI---C-GY--EVFQIEITKGYSIKDF----------   73 (268)
T ss_dssp             ---HHHHHHHHHHHHHHCST-TEEEEEECTTTSCHHHHHHHHHHH---T-TE--EEE-TTTSTTTHHHHH----------
T ss_pred             eeHHHHHHHHHHHHHHHcCC-CCCeEEecCCCccHHHHHHHHHHH---h-cc--ceEEEEeeCCcCHHHH----------
Confidence            334555554443   34343 466679999999999999987752   1 11  1333334444443333          


Q ss_pred             CCCCCCChHHHHHHHHHHH--HhcCCCcEEEEEeCCCCCChHHHhhh
Q 042541          246 PVPEFQTDEAAINDLERFF--KQMRIEAILLVLDDVWPGSESLLQKL  290 (695)
Q Consensus       246 ~~~~~~~~~~~~~~l~~~~--~~l~~~~~LlVlDdv~~~~~~~~~~l  290 (695)
                                 .+.|+..+  ..+++++..++++|-+-.++..++.+
T Consensus        74 -----------~~dLk~~~~~ag~~~~~~vfll~d~qi~~~~fLe~i  109 (268)
T PF12780_consen   74 -----------KEDLKKALQKAGIKGKPTVFLLTDSQIVDESFLEDI  109 (268)
T ss_dssp             -----------HHHHHHHHHHHHCS-S-EEEEEECCCSSSCHHHHHH
T ss_pred             -----------HHHHHHHHHHHhccCCCeEEEecCcccchHhHHHHH
Confidence                       23344443  44578999999999765554444433

The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four (D1 - D4) correspond to the ATP binding sites with P-loop signatures described previously, and two (D5, D6) are modules in which the P loop has been lost in evolution. This particular entry represents the D4 ATP-binding domain of the motor [].; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

>COG0194 Gmk Guanylate kinase [Nucleotide transport and metabolism]

Probab=94.17  E-value=0.042  Score=50.61  Aligned_cols=24  Identities=50%  Similarity=0.768  Sum_probs=21.8

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhcc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      ..++.|.|++|+|||||+++++.+
T Consensus         4 G~l~vlsgPSG~GKsTl~k~L~~~   27 (191)
T COG0194           4 GLLIVLSGPSGVGKSTLVKALLED   27 (191)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhh
Confidence            468999999999999999999984

>cd00820 PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis

Probab=94.16  E-value=0.044  Score=46.09  Aligned_cols=22  Identities=27%  Similarity=0.450  Sum_probs=19.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHh
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLC  208 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~  208 (695)
                      ...++|+|++|+|||||++.+.
T Consensus        15 ge~v~I~GpSGsGKSTLl~~l~   36 (107)
T cd00820          15 KVGVLITGDSGIGKTELALELI   36 (107)
T ss_pred             CEEEEEEcCCCCCHHHHHHHhh
Confidence            4789999999999999999875

It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (ATP or GTP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity. PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity (the ATP-, and GTP-dependent groups).HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of HPr and its dephosphorylation by phosphorolysis. PEPCK and the C-terminal catalytic domain of HprK/P are structural

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=94.16  E-value=0.24  Score=53.74  Aligned_cols=88  Identities=15%  Similarity=0.182  Sum_probs=47.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCC-CCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKN-PNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFK  265 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~-~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~  265 (695)
                      .+|++++|+.|+||||++..++.....+..- ..+..+..... ....+-+....+.++.+........+.    ...+.
T Consensus       256 g~Vi~LvGpnGvGKTTTiaKLA~~~~~~~G~-~kV~LI~~Dt~RigA~EQLr~~AeilGVpv~~~~~~~Dl----~~aL~  330 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAKLAARCVMRHGA-SKVALLTTDSYRIGGHEQLRIYGKILGVPVHAVKDAADL----RLALS  330 (484)
T ss_pred             CcEEEEECCCCccHHHHHHHHHHHHHHhcCC-CeEEEEeCCccchhHHHHHHHHHHHhCCCeeccCCchhH----HHHHH
Confidence            3799999999999999999888632222111 12555554331 233344555556655443222122111    11223


Q ss_pred             hcCCCcEEEEEeCCC
Q 042541          266 QMRIEAILLVLDDVW  280 (695)
Q Consensus       266 ~l~~~~~LlVlDdv~  280 (695)
                      .+.++ -.+++|-..
T Consensus       331 ~L~d~-d~VLIDTaG  344 (484)
T PRK06995        331 ELRNK-HIVLIDTIG  344 (484)
T ss_pred             hccCC-CeEEeCCCC
Confidence            44444 467777764

>PF00560 LRR_1: Leucine Rich Repeat; InterPro: IPR001611 Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape []

Probab=94.16  E-value=0.019  Score=33.03  Aligned_cols=21  Identities=14%  Similarity=0.157  Sum_probs=15.3

Q ss_pred             CCcEEEeccCCCCCcc-ccccc
Q 042541          602 KLKKIRLEHVSLPNSL-ATVRM  622 (695)
Q Consensus       602 ~L~~L~L~~~~l~~lp-~i~~l  622 (695)
                      +|++|+|++|+++.+| ++++|
T Consensus         1 ~L~~Ldls~n~l~~ip~~~~~l   22 (22)
T PF00560_consen    1 NLEYLDLSGNNLTSIPSSFSNL   22 (22)
T ss_dssp             TESEEEETSSEESEEGTTTTT-
T ss_pred             CccEEECCCCcCEeCChhhcCC
Confidence            4788888888888888 65543

LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions [, ].Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response []. Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel beta sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the beta-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins. 3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with alpha-helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions []. Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20- to 30-residue repeats []. ; GO: 0005515 protein binding; PDB: 4ECO_B 2A0Z_A 3ULU_A 1ZIW_A 3ULV_A 1DCE_C 1LTX_A 3J0A_B 3A79_B 4FCG_A ....

>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor

Probab=94.16  E-value=0.032  Score=50.44  Aligned_cols=21  Identities=38%  Similarity=0.710  Sum_probs=19.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +|.|+|+.|+||||+|+.+..
T Consensus         1 ~I~i~G~~GsGKst~a~~la~   21 (147)
T cd02020           1 IIAIDGPAGSGKSTVAKLLAK   21 (147)
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            589999999999999999886

>PRK00279 adk adenylate kinase; Reviewed

Probab=94.13  E-value=0.087  Score=51.24  Aligned_cols=21  Identities=24%  Similarity=0.411  Sum_probs=19.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .|.|+|++|+||||+|+.++.
T Consensus         2 ~I~v~G~pGsGKsT~a~~la~   22 (215)
T PRK00279          2 RLILLGPPGAGKGTQAKFIAE   22 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            488999999999999998876

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=94.13  E-value=0.11  Score=58.67  Aligned_cols=75  Identities=13%  Similarity=0.158  Sum_probs=49.9

Q ss_pred             CCCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhcccccccc-CCCcEEEEEeCCCCCHHHHHHHHHHhc
Q 042541          165 PVISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGK-FKDDIFYVTVSKNPNVKAIVQKVLHHK  243 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~-f~~~~~wv~~~~~~~~~~~~~~i~~~l  243 (695)
                      -+.++|.++.++.+...+....  -+.++|++|+||||+|+.+.+  .+... |.. ++++ .....+..+++..+...+
T Consensus        17 ~~~viG~~~a~~~l~~a~~~~~--~~ll~G~pG~GKT~la~~la~--~l~~~~~~~-~~~~-~n~~~~~~~~~~~v~~~~   90 (608)
T TIGR00764        17 IDQVIGQEEAVEIIKKAAKQKR--NVLLIGEPGVGKSMLAKAMAE--LLPDEELED-ILVY-PNPEDPNMPRIVEVPAGE   90 (608)
T ss_pred             HhhccCHHHHHHHHHHHHHcCC--CEEEECCCCCCHHHHHHHHHH--HcCchhhee-EEEE-eCCCCCchHHHHHHHHhh
Confidence            3567898888887777776543  566999999999999999987  44433 333 2222 222335556677777666


Q ss_pred             CC
Q 042541          244 GY  245 (695)
Q Consensus       244 ~~  245 (695)
                      +.
T Consensus        91 g~   92 (608)
T TIGR00764        91 GR   92 (608)
T ss_pred             ch
Confidence            53

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=94.12  E-value=0.039  Score=52.29  Aligned_cols=22  Identities=32%  Similarity=0.578  Sum_probs=20.2

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+++|+|+.|+|||||++.++.
T Consensus         3 ~~i~l~G~sGsGKsTl~~~l~~   24 (186)
T PRK10078          3 KLIWLMGPSGSGKDSLLAALRQ   24 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHhc
Confidence            4789999999999999999976

>COG1703 ArgK Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]

Probab=94.10  E-value=0.068  Score=52.91  Aligned_cols=60  Identities=23%  Similarity=0.346  Sum_probs=38.7

Q ss_pred             HHHHHHHH--cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHH
Q 042541          176 KELKMELF--KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIV  236 (695)
Q Consensus       176 ~~l~~~L~--~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~  236 (695)
                      .+++..+.  .++..+|+|.|.+|+|||||.-.+-.....+++ ...|+-|+-|..++--.++
T Consensus        38 ~~ll~~l~p~tG~a~viGITG~PGaGKSTli~~L~~~l~~~G~-rVaVlAVDPSSp~TGGsiL   99 (323)
T COG1703          38 RELLRALYPRTGNAHVIGITGVPGAGKSTLIEALGRELRERGH-RVAVLAVDPSSPFTGGSIL   99 (323)
T ss_pred             HHHHHHHhhcCCCCcEEEecCCCCCchHHHHHHHHHHHHHCCc-EEEEEEECCCCCCCCcccc
Confidence            45555555  556789999999999999999887763322222 2335555556666544443

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=94.10  E-value=0.085  Score=59.36  Aligned_cols=75  Identities=15%  Similarity=0.199  Sum_probs=54.8

Q ss_pred             CCCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccc-cCCCcEEEEEeCCCCCHHHHHHHHHHhc
Q 042541          165 PVISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQG-KFKDDIFYVTVSKNPNVKAIVQKVLHHK  243 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~-~f~~~~~wv~~~~~~~~~~~~~~i~~~l  243 (695)
                      -+.++|.++.++.|...+...  +.+.|+|++|+||||+|+.+.+  .+.. .++. ++|..- ...+...+++.+...+
T Consensus        30 ~~~vigq~~a~~~L~~~~~~~--~~~l~~G~~G~GKttla~~l~~--~l~~~~~~~-~~~~~n-p~~~~~~~~~~v~~~~  103 (637)
T PRK13765         30 IDQVIGQEHAVEVIKKAAKQR--RHVMMIGSPGTGKSMLAKAMAE--LLPKEELQD-ILVYPN-PEDPNNPKIRTVPAGK  103 (637)
T ss_pred             HHHcCChHHHHHHHHHHHHhC--CeEEEECCCCCcHHHHHHHHHH--HcChHhHHH-heEeeC-CCcchHHHHHHHHHhc
Confidence            456789888888887777654  4789999999999999999987  3432 3444 667544 4446777888887776


Q ss_pred             CC
Q 042541          244 GY  245 (695)
Q Consensus       244 ~~  245 (695)
                      |.
T Consensus       104 G~  105 (637)
T PRK13765        104 GK  105 (637)
T ss_pred             CH
Confidence            54

>PRK00300 gmk guanylate kinase; Provisional

Probab=94.07  E-value=0.043  Score=52.93  Aligned_cols=24  Identities=46%  Similarity=0.674  Sum_probs=21.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+|+|+|++|+|||||++.++.
T Consensus         4 ~g~~i~i~G~sGsGKstl~~~l~~   27 (205)
T PRK00300          4 RGLLIVLSGPSGAGKSTLVKALLE   27 (205)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHh
Confidence            347899999999999999999987

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=94.07  E-value=0.21  Score=55.54  Aligned_cols=44  Identities=9%  Similarity=0.021  Sum_probs=34.9

Q ss_pred             CCCCCCcchHHHHHHHHH--cCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          166 VISPGLDVPLKELKMELF--KDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~--~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +.++|....++++.+.+.  .....-|.|+|..|+||+.+|+.+.+
T Consensus       204 ~~~ig~s~~~~~~~~~~~~~A~~~~pvlI~GE~GtGK~~lA~aiH~  249 (520)
T PRK10820        204 SQIVAVSPKMRQVVEQARKLAMLDAPLLITGDTGTGKDLLAYACHL  249 (520)
T ss_pred             cceeECCHHHHHHHHHHHHHhCCCCCEEEECCCCccHHHHHHHHHH
Confidence            467999988888887765  22334588999999999999999765

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=94.07  E-value=0.048  Score=56.39  Aligned_cols=45  Identities=20%  Similarity=0.187  Sum_probs=36.2

Q ss_pred             CCCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          165 PVISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      -..++|.+..++.+.-.+...+..-+.+.|..|+||||+|+.+..
T Consensus         7 f~~i~Gq~~~~~~l~~~~~~~~~~~vLl~G~pG~gKT~lar~la~   51 (334)
T PRK13407          7 FSAIVGQEEMKQAMVLTAIDPGIGGVLVFGDRGTGKSTAVRALAA   51 (334)
T ss_pred             HHHhCCHHHHHHHHHHHHhccCCCcEEEEcCCCCCHHHHHHHHHH
Confidence            345799998888887656545556699999999999999999865

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=94.06  E-value=0.26  Score=56.15  Aligned_cols=59  Identities=19%  Similarity=0.187  Sum_probs=34.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC-CHHHHHHHHHHhcCCC
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKGYP  246 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~~~  246 (695)
                      .++|+++|+.|+||||.+..++..... .+-...|..++..... ...+-+....+.++.+
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~~~~-~~G~kkV~lit~Dt~RigA~eQL~~~a~~~gvp  244 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAARCVA-REGADQLALLTTDSFRIGALEQLRIYGRILGVP  244 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhhHHH-HcCCCeEEEecCcccchHHHHHHHHHHHhCCCC
Confidence            479999999999999999888763211 1111225555543211 2334445555555543

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=94.05  E-value=0.044  Score=62.02  Aligned_cols=147  Identities=14%  Similarity=0.173  Sum_probs=80.0

Q ss_pred             CCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhcccccc-ccCC-----CcEEEEEeCCCCCHHHHHHHH
Q 042541          166 VISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQ-GKFK-----DDIFYVTVSKNPNVKAIVQKV  239 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~-~~f~-----~~~~wv~~~~~~~~~~~~~~i  239 (695)
                      +.++||++|+.++++.|....-.--.++|.+|||||+++.-++.  ++. +.-+     ..++-.+++            
T Consensus       170 DPvIGRd~EI~r~iqIL~RR~KNNPvLiGEpGVGKTAIvEGLA~--rIv~g~VP~~L~~~~i~sLD~g------------  235 (786)
T COG0542         170 DPVIGRDEEIRRTIQILSRRTKNNPVLVGEPGVGKTAIVEGLAQ--RIVNGDVPESLKDKRIYSLDLG------------  235 (786)
T ss_pred             CCCcChHHHHHHHHHHHhccCCCCCeEecCCCCCHHHHHHHHHH--HHhcCCCCHHHcCCEEEEecHH------------
Confidence            34699999999999999833222235789999999999877766  331 1111     112111111            


Q ss_pred             HHhcCCCCCCCCChHHHHHHHHHHHHhcC-CCcEEEEEeCCCCCCh---------HHHhhhccCC-CC-CEEE-EEcCCC
Q 042541          240 LHHKGYPVPEFQTDEAAINDLERFFKQMR-IEAILLVLDDVWPGSE---------SLLQKLGFQL-PD-YKIL-VTSRSE  306 (695)
Q Consensus       240 ~~~l~~~~~~~~~~~~~~~~l~~~~~~l~-~~~~LlVlDdv~~~~~---------~~~~~l~~~~-~g-s~ii-vTtR~~  306 (695)
                       .-..+.    .-..+..++++.+++.++ .++..|++|.+...-.         +....+.+.. .| -+.| .||-++
T Consensus       236 -~LvAGa----kyRGeFEeRlk~vl~ev~~~~~vILFIDEiHtiVGAG~~~G~a~DAaNiLKPaLARGeL~~IGATT~~E  310 (786)
T COG0542         236 -SLVAGA----KYRGEFEERLKAVLKEVEKSKNVILFIDEIHTIVGAGATEGGAMDAANLLKPALARGELRCIGATTLDE  310 (786)
T ss_pred             -HHhccc----cccCcHHHHHHHHHHHHhcCCCeEEEEechhhhcCCCcccccccchhhhhHHHHhcCCeEEEEeccHHH
Confidence             111111    112234456666665443 4489999999743211         0111122211 23 2444 466544


Q ss_pred             CC-------CC---CCeEecCCCChHHHHHHHHHh
Q 042541          307 FP-------QF---GSVHYLKPLTYEAARTLFLHS  331 (695)
Q Consensus       307 ~~-------~~---~~~~~l~~L~~~ea~~Lf~~~  331 (695)
                      ..       +.   -..+.+..-+.+++..+++-.
T Consensus       311 YRk~iEKD~AL~RRFQ~V~V~EPs~e~ti~ILrGl  345 (786)
T COG0542         311 YRKYIEKDAALERRFQKVLVDEPSVEDTIAILRGL  345 (786)
T ss_pred             HHHHhhhchHHHhcCceeeCCCCCHHHHHHHHHHH
Confidence            21       11   116778888888888887653

>PRK14737 gmk guanylate kinase; Provisional

Probab=94.04  E-value=0.047  Score=51.58  Aligned_cols=24  Identities=29%  Similarity=0.560  Sum_probs=21.9

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +..+|.|+|++|+|||||++.+..
T Consensus         3 ~~~~ivl~GpsG~GK~tl~~~l~~   26 (186)
T PRK14737          3 SPKLFIISSVAGGGKSTIIQALLE   26 (186)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHh
Confidence            457899999999999999999986

>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2

Probab=94.03  E-value=0.049  Score=51.49  Aligned_cols=31  Identities=42%  Similarity=0.676  Sum_probs=26.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCC
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKD  219 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~  219 (695)
                      .++|.|+|+.|+|||||++.+..  .....|..
T Consensus         2 ~r~ivl~Gpsg~GK~~l~~~L~~--~~~~~~~~   32 (183)
T PF00625_consen    2 RRPIVLVGPSGSGKSTLAKRLIQ--EFPDKFGR   32 (183)
T ss_dssp             SSEEEEESSTTSSHHHHHHHHHH--HSTTTEEE
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH--hccccccc
Confidence            47899999999999999999987  55666643

7.4.8 from EC) (GK) [] catalyzes the ATP-dependent phosphorylation of GMP into GDP. It is essential for recycling GMP and indirectly, cGMP. In prokaryotes (such as Escherichia coli), lower eukaryotes (such as yeast) and in vertebrates, GK is a highly conserved monomeric protein of about 200 amino acids. GK has been shown [, , ] to be structurally similar to protein A57R (or SalG2R) from various strains of Vaccinia virus. Proteins containing one or more copies of the DHR domain, an SH3 domain as well as a C-terminal GK-like domain, are collectively termed MAGUKs (membrane-associated guanylate kinase homologs) [], and include Drosophila lethal(1)discs large-1 tumor suppressor protein (gene dlg1); mammalian tight junction protein Zo-1; a family of mammalian synaptic proteins that seem to interact with the cytoplasmic tail of NMDA receptor subunits (SAP90/PSD-95, CHAPSYN-110/PSD-93, SAP97/DLG1 and SAP102); vertebrate 55kDa erythrocyte membrane protein (p55); Caenorhabditis elegans protein lin-2; rat protein CASK; and human proteins DLG2 and DLG3. There is an ATP-binding site (P-loop) in the N-terminal section of GK, which is not conserved in the GK-like domain of the above proteins. However these proteins retain the residues known, in GK, to be involved in the binding of GMP.; GO: 0005515 protein binding; PDB: 3UAT_A 3KFV_A 2ANC_F 2F3T_E 2ANB_A 2AN9_A 1S96_A 2F3R_B 3TR0_A 1LVG_A ....

>PF08477 Miro: Miro-like protein; InterPro: IPR013684 Mitochondrial Rho proteins (Miro-1, Q8IXI2 from SWISSPROT and Miro-2, Q8IXI1 from SWISSPROT) are atypical Rho GTPases

Probab=94.03  E-value=0.041  Score=47.67  Aligned_cols=22  Identities=50%  Similarity=0.889  Sum_probs=19.7

Q ss_pred             EEEEcCCCCcHHHHHHHHhccc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKDD  211 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~~  211 (695)
                      |.|+|..|+|||||.+.+....
T Consensus         2 I~V~G~~g~GKTsLi~~l~~~~   23 (119)
T PF08477_consen    2 IVVLGDSGVGKTSLIRRLCGGE   23 (119)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEECcCCCCHHHHHHHHhcCC
Confidence            7899999999999999998753

They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (IPR002048 from INTERPRO), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis []. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 2IWR_A 2BMJ_A 3IHW_A 2ZEJ_A 3D6T_B 3DPU_A.

>PRK14529 adenylate kinase; Provisional

Probab=94.02  E-value=0.18  Score=48.88  Aligned_cols=20  Identities=35%  Similarity=0.424  Sum_probs=18.5

Q ss_pred             EEEEcCCCCcHHHHHHHHhc
Q 042541          190 IVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~  209 (695)
                      |.|.|++|+||||+|+.++.
T Consensus         3 I~l~G~PGsGK~T~a~~La~   22 (223)
T PRK14529          3 ILIFGPNGSGKGTQGALVKK   22 (223)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            78899999999999998876

>PRK08149 ATP synthase SpaL; Validated

Probab=94.02  E-value=0.23  Score=52.94  Aligned_cols=90  Identities=16%  Similarity=0.252  Sum_probs=52.8

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCC-CCCHHHHHHHHHHhcCCC-------CCCCCCh----
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSK-NPNVKAIVQKVLHHKGYP-------VPEFQTD----  253 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~-~~~~~~~~~~i~~~l~~~-------~~~~~~~----  253 (695)
                      ....++|+|..|+|||||+..++....    -+. ++...+.. ..+..++..+........       ..+.+..    
T Consensus       150 ~Gq~i~I~G~sG~GKTTLl~~i~~~~~----~dv-~v~g~Ig~rg~ev~e~~~~~l~~~~~~~~~vV~~~sd~p~~~r~~  224 (428)
T PRK08149        150 VGQRMGIFASAGCGKTSLMNMLIEHSE----ADV-FVIGLIGERGREVTEFVESLRASSRREKCVLVYATSDFSSVDRCN  224 (428)
T ss_pred             cCCEEEEECCCCCChhHHHHHHhcCCC----CCe-EEEEEEeeCCccHHHHHHHHhhcccccceEEEEECCCCCHHHHHh
Confidence            457899999999999999999886321    122 23444543 335666666666643211       1111111    


Q ss_pred             -HHHHHHHHHHHHhcCCCcEEEEEeCCCC
Q 042541          254 -EAAINDLERFFKQMRIEAILLVLDDVWP  281 (695)
Q Consensus       254 -~~~~~~l~~~~~~l~~~~~LlVlDdv~~  281 (695)
                       ......+.+.+.. +++++||++||+-.
T Consensus       225 a~~~a~tiAE~fr~-~G~~Vll~~DslTr  252 (428)
T PRK08149        225 AALVATTVAEYFRD-QGKRVVLFIDSMTR  252 (428)
T ss_pred             HHHHHHHHHHHHHH-cCCCEEEEccchHH
Confidence             1122234444432 59999999999843

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=94.01  E-value=0.43  Score=44.75  Aligned_cols=117  Identities=19%  Similarity=0.206  Sum_probs=62.4

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCC---CCCHHHHHHHHH--Hh--cCCCC-CCCCChHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSK---NPNVKAIVQKVL--HH--KGYPV-PEFQTDEAAIN  258 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~---~~~~~~~~~~i~--~~--l~~~~-~~~~~~~~~~~  258 (695)
                      ...|.|+|..|-||||.|..+.-  +...+ ...|..+.+=.   .......+..+-  .-  .+... ....+......
T Consensus        22 ~g~v~v~~g~GkGKtt~a~g~a~--ra~g~-G~~V~ivQFlKg~~~~GE~~~l~~l~~v~~~~~g~~~~~~~~~~~e~~~   98 (191)
T PRK05986         22 KGLLIVHTGNGKGKSTAAFGMAL--RAVGH-GKKVGVVQFIKGAWSTGERNLLEFGGGVEFHVMGTGFTWETQDRERDIA   98 (191)
T ss_pred             CCeEEEECCCCCChHHHHHHHHH--HHHHC-CCeEEEEEEecCCCccCHHHHHhcCCCcEEEECCCCCcccCCCcHHHHH
Confidence            47899999999999999987765  33222 11244555432   234444444321  10  11110 00112222222


Q ss_pred             HHHHHH----Hhc-CCCcEEEEEeCCCCC-------ChHHHhhhccCCCCCEEEEEcCCC
Q 042541          259 DLERFF----KQM-RIEAILLVLDDVWPG-------SESLLQKLGFQLPDYKILVTSRSE  306 (695)
Q Consensus       259 ~l~~~~----~~l-~~~~~LlVlDdv~~~-------~~~~~~~l~~~~~gs~iivTtR~~  306 (695)
                      ..++.+    +.+ .++--+||||.+-..       .+.+++.+....++..||+|-|..
T Consensus        99 ~~~~~~~~a~~~l~~~~ydlvVLDEi~~Al~~gli~~eevi~~L~~rp~~~evVlTGR~~  158 (191)
T PRK05986         99 AAREGWEEAKRMLADESYDLVVLDELTYALKYGYLDVEEVLEALNARPGMQHVVITGRGA  158 (191)
T ss_pred             HHHHHHHHHHHHHhCCCCCEEEEehhhHHHHCCCccHHHHHHHHHcCCCCCEEEEECCCC
Confidence            233322    333 355669999997322       133555555555578999999976

>COG2019 AdkA Archaeal adenylate kinase [Nucleotide transport and metabolism]

Probab=94.00  E-value=0.046  Score=49.11  Aligned_cols=23  Identities=35%  Similarity=0.551  Sum_probs=20.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .++|+|+|.+|+||||+.+.+..
T Consensus         4 ~kvvvitGVpGvGKTTVl~~~~~   26 (189)
T COG2019           4 RKVVVITGVPGVGKTTVLKIALK   26 (189)
T ss_pred             ceEEEEEcCCCCChHHHHHHHHH
Confidence            57999999999999999988776

>PRK09099 type III secretion system ATPase; Provisional

Probab=94.00  E-value=0.22  Score=53.29  Aligned_cols=92  Identities=18%  Similarity=0.335  Sum_probs=52.9

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCC-------CCCCCCh----
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYP-------VPEFQTD----  253 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~-------~~~~~~~----  253 (695)
                      .....++|.|..|+|||||++.+.....    .+.++++..-.+.....++.+.+...-+..       ..+.+..    
T Consensus       161 ~~Gq~~~I~G~sG~GKTtLl~~ia~~~~----~d~~vi~~iGer~~ev~ef~~~~~~~~~l~rtvvv~~tsd~p~~~r~~  236 (441)
T PRK09099        161 GEGQRMGIFAPAGVGKSTLMGMFARGTQ----CDVNVIALIGERGREVREFIELILGEDGMARSVVVCATSDRSSIERAK  236 (441)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCCCC----CCeEEEEEEccChHHHHHHHHHHhhcCCcceEEEEEECCCCCHHHHHH
Confidence            3457899999999999999999986322    123354443334445666666665442211       1111111    


Q ss_pred             -HHHHHHHHHHHHhcCCCcEEEEEeCCCC
Q 042541          254 -EAAINDLERFFKQMRIEAILLVLDDVWP  281 (695)
Q Consensus       254 -~~~~~~l~~~~~~l~~~~~LlVlDdv~~  281 (695)
                       ....-.+.+.+.. +++++|+++||+-.
T Consensus       237 a~~~a~tiAEyfrd-~G~~VLl~~DslTr  264 (441)
T PRK09099        237 AAYVATAIAEYFRD-RGLRVLLMMDSLTR  264 (441)
T ss_pred             HHHHHHHHHHHHHH-cCCCEEEeccchhH
Confidence             1112223444422 58999999999843

>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]

Probab=93.99  E-value=0.093  Score=47.77  Aligned_cols=34  Identities=24%  Similarity=0.276  Sum_probs=27.1

Q ss_pred             HHHcCCceEEEEEcCCCCcHHHHHHHHhcccccccc
Q 042541          181 ELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGK  216 (695)
Q Consensus       181 ~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~  216 (695)
                      .+......+|.+.|.+|.||||+|.+++.  ++...
T Consensus        17 ~~~~~~~~viW~TGLSGsGKSTiA~ale~--~L~~~   50 (197)
T COG0529          17 ALKGQKGAVIWFTGLSGSGKSTIANALEE--KLFAK   50 (197)
T ss_pred             HHhCCCCeEEEeecCCCCCHHHHHHHHHH--HHHHc
Confidence            34455678999999999999999999987  55443

>PF03308 ArgK: ArgK protein; InterPro: IPR005129 Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components

Probab=93.99  E-value=0.076  Score=51.84  Aligned_cols=61  Identities=23%  Similarity=0.293  Sum_probs=35.0

Q ss_pred             hHHHHHHHHH--cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHH
Q 042541          174 PLKELKMELF--KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAI  235 (695)
Q Consensus       174 ~~~~l~~~L~--~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~  235 (695)
                      +..++++.+.  .++..+|+|.|++|+|||||.-.+...-+- .....+|+-|+-|..++--.+
T Consensus        14 ~~~~ll~~l~~~~g~a~~iGiTG~PGaGKSTli~~l~~~~~~-~g~~VaVlAVDPSSp~tGGAl   76 (266)
T PF03308_consen   14 EARELLKRLYPHTGRAHVIGITGPPGAGKSTLIDALIRELRE-RGKRVAVLAVDPSSPFTGGAL   76 (266)
T ss_dssp             HHHHHHHHHGGGTT-SEEEEEEE-TTSSHHHHHHHHHHHHHH-TT--EEEEEE-GGGGCC---S
T ss_pred             HHHHHHHHHHhhcCCceEEEeeCCCCCcHHHHHHHHHHHHhh-cCCceEEEEECCCCCCCCCcc
Confidence            4456666665  345789999999999999999888763221 223333555555555544333

In Escherichia coli, the arginine-ornithine transport system requires an arginine-ornithine-binding protein and the lysine-arginine-ornithine (LAO) transport system includes a LAO-binding protein. Both periplasmic proteins can be phosphorylated by a single kinase, ArgK [] resulting in reduced levels of transport activity of the periplasmic transport systems that include each of the binding proteins. The ArgK protein acts as an ATPase enzyme and as a kinase.; PDB: 3MD0_A 3P32_A 2QM7_A 2QM8_A 2WWW_D 2P67_A 3NXS_A.

>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]

Probab=93.99  E-value=0.3  Score=55.84  Aligned_cols=25  Identities=24%  Similarity=0.340  Sum_probs=21.4

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +....|+|+|..|+|||||++.+..
T Consensus       497 ~~Ge~vaIvG~SGsGKSTL~KLL~g  521 (709)
T COG2274         497 PPGEKVAIVGRSGSGKSTLLKLLLG  521 (709)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhc
Confidence            3457899999999999999998754

>PRK03846 adenylylsulfate kinase; Provisional

Probab=93.98  E-value=0.051  Score=52.11  Aligned_cols=25  Identities=20%  Similarity=0.246  Sum_probs=22.8

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ....+|+|+|++|+||||||+.+..
T Consensus        22 ~~~~~i~i~G~~GsGKSTla~~l~~   46 (198)
T PRK03846         22 HKGVVLWFTGLSGSGKSTVAGALEE   46 (198)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            4568999999999999999999987

>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes

Probab=93.94  E-value=0.46  Score=46.25  Aligned_cols=113  Identities=14%  Similarity=0.224  Sum_probs=57.4

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCC---CCCChHHHHHHHHH
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVP---EFQTDEAAINDLER  262 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~---~~~~~~~~~~~l~~  262 (695)
                      ..+++.|.|+.|.||||+.+.+.-.. +..+-.. ..|..-..    -....+|...++....   ....-.....++..
T Consensus        30 ~g~~~~itG~N~~GKStll~~i~~~~-~la~~G~-~v~a~~~~----~~~~~~i~~~~~~~d~~~~~~StF~~e~~~~~~  103 (222)
T cd03287          30 GGYCQIITGPNMGGKSSYIRQVALIT-IMAQIGS-FVPASSAT----LSIFDSVLTRMGASDSIQHGMSTFMVELSETSH  103 (222)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHH-HHHhCCC-EEEcCceE----EeccceEEEEecCccccccccchHHHHHHHHHH
Confidence            34788999999999999998876521 1111111 11221000    0111122222221111   11122333455555


Q ss_pred             HHHhcCCCcEEEEEeCCCCCCh---------HHHhhhccCCCCCEEEEEcCCC
Q 042541          263 FFKQMRIEAILLVLDDVWPGSE---------SLLQKLGFQLPDYKILVTSRSE  306 (695)
Q Consensus       263 ~~~~l~~~~~LlVlDdv~~~~~---------~~~~~l~~~~~gs~iivTtR~~  306 (695)
                      +++.. +++-|+++|+......         .+++.+... .++.+|++|...
T Consensus       104 il~~~-~~~sLvllDE~~~gT~~~d~~~i~~~il~~l~~~-~~~~~i~~TH~~  154 (222)
T cd03287         104 ILSNC-TSRSLVILDELGRGTSTHDGIAIAYATLHYLLEE-KKCLVLFVTHYP  154 (222)
T ss_pred             HHHhC-CCCeEEEEccCCCCCChhhHHHHHHHHHHHHHhc-cCCeEEEEcccH
Confidence            55433 5689999999743321         123333322 578899998875

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>KOG1532 consensus GTPase XAB1, interacts with DNA repair protein XPA [Replication, recombination and repair]

Probab=93.94  E-value=0.05  Score=52.79  Aligned_cols=57  Identities=23%  Similarity=0.327  Sum_probs=35.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeC---------CCCCHHHH--HHHHHHhcCCC
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVS---------KNPNVKAI--VQKVLHHKGYP  246 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~---------~~~~~~~~--~~~i~~~l~~~  246 (695)
                      +..|.++||+|+||||..+.++.+.  ...+.. .+-|++.         -+.++.+.  .++.+++-+..
T Consensus        19 p~~ilVvGMAGSGKTTF~QrL~~hl--~~~~~p-pYviNLDPAv~~vpy~aniDIRDtVkYkEvMkqY~LG   86 (366)
T KOG1532|consen   19 PVIILVVGMAGSGKTTFMQRLNSHL--HAKKTP-PYVINLDPAVRNVPYPANIDIRDTVKYKEVMKQYQLG   86 (366)
T ss_pred             CcEEEEEecCCCCchhHHHHHHHHH--hhccCC-CeEEeCCHHHhcCCCccCCchhhhhhHHHHHHHhCCC
Confidence            5678899999999999999998743  333322 2244432         22345444  35677775443

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=93.93  E-value=0.16  Score=47.24  Aligned_cols=83  Identities=18%  Similarity=0.313  Sum_probs=44.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhcC
Q 042541          189 FIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMR  268 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~  268 (695)
                      ++.|.|.+|+||||+|..+...  .    ...++++...... ..+....|..+...........+. -..+.+.++...
T Consensus         3 ~ili~G~~~sGKS~~a~~l~~~--~----~~~~~~iat~~~~-~~e~~~ri~~h~~~R~~~w~t~E~-~~~l~~~i~~~~   74 (170)
T PRK05800          3 LILVTGGARSGKSRFAERLAAQ--S----GLQVLYIATAQPF-DDEMAARIAHHRQRRPAHWQTVEE-PLDLAELLRADA   74 (170)
T ss_pred             EEEEECCCCccHHHHHHHHHHH--c----CCCcEeCcCCCCC-hHHHHHHHHHHHhcCCCCCeEecc-cccHHHHHHhhc
Confidence            6899999999999999988762  2    2224455544433 344555665543322211111111 112444443312


Q ss_pred             CCcEEEEEeCC
Q 042541          269 IEAILLVLDDV  279 (695)
Q Consensus       269 ~~~~LlVlDdv  279 (695)
                      .+.-++++|.+
T Consensus        75 ~~~~~VlID~L   85 (170)
T PRK05800         75 APGRCVLVDCL   85 (170)
T ss_pred             CCCCEEEehhH
Confidence            23337888886

>CHL00060 atpB ATP synthase CF1 beta subunit

Probab=93.93  E-value=0.19  Score=54.17  Aligned_cols=54  Identities=15%  Similarity=0.107  Sum_probs=37.8

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC-CHHHHHHHHHH
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP-NVKAIVQKVLH  241 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~  241 (695)
                      ..+-++|.|.+|+|||||+..+.... .+.+=+. ++++-+++.. ...+++..+..
T Consensus       160 kGQR~gIfgg~GvGKs~L~~~~~~~~-~~~~~dv-~V~~lIGERgrEv~efi~~~~~  214 (494)
T CHL00060        160 RGGKIGLFGGAGVGKTVLIMELINNI-AKAHGGV-SVFGGVGERTREGNDLYMEMKE  214 (494)
T ss_pred             cCCEEeeecCCCCChhHHHHHHHHHH-HHhcCCe-EEEEEeccCchHHHHHHHHHHh
Confidence            35789999999999999999887631 1111134 6677777654 56777777766

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=93.93  E-value=0.18  Score=56.61  Aligned_cols=115  Identities=15%  Similarity=0.124  Sum_probs=58.5

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccC--CCcEEEEEeCCCCCHHHHHHHHHHhcCCC-CCCC--CChHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKF--KDDIFYVTVSKNPNVKAIVQKVLHHKGYP-VPEF--QTDEAAINDLE  261 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f--~~~~~wv~~~~~~~~~~~~~~i~~~l~~~-~~~~--~~~~~~~~~l~  261 (695)
                      .++..|.|.+|.||||++..+..  .+....  ....+.+..........+...+-..+..- .+..  .........+.
T Consensus       167 ~~~~vItGgpGTGKTt~v~~ll~--~l~~~~~~~~~~i~l~APTgkAA~rL~e~~~~~~~~~~~~~~~~~~~~~~a~TiH  244 (615)
T PRK10875        167 RRISVISGGPGTGKTTTVAKLLA--ALIQLADGERCRIRLAAPTGKAAARLTESLGKALRQLPLTDEQKKRIPEEASTLH  244 (615)
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHH--HHHHhcCCCCcEEEEECCcHHHHHHHHHHHHhhhhccccchhhhhcCCCchHHHH
Confidence            47899999999999999988876  222211  11133555555444444444443322110 0000  00000123344


Q ss_pred             HHHHh-cC--------CCc---EEEEEeCCCCCChHHHhhhcc-CCCCCEEEEEc
Q 042541          262 RFFKQ-MR--------IEA---ILLVLDDVWPGSESLLQKLGF-QLPDYKILVTS  303 (695)
Q Consensus       262 ~~~~~-l~--------~~~---~LlVlDdv~~~~~~~~~~l~~-~~~gs~iivTt  303 (695)
                      +++.. ..        +.+   -++|+|.+.-.+-.+...+.. -.+++|+|+--
T Consensus       245 rlLg~~~~~~~~~~~~~~~l~~dvlIvDEaSMvd~~lm~~ll~al~~~~rlIlvG  299 (615)
T PRK10875        245 RLLGAQPGSQRLRYHAGNPLHLDVLVVDEASMVDLPMMARLIDALPPHARVIFLG  299 (615)
T ss_pred             HHhCcCCCccchhhccccCCCCCeEEEChHhcccHHHHHHHHHhcccCCEEEEec
Confidence            44411 11        111   389999987776554443333 33578887744

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=93.91  E-value=0.2  Score=57.36  Aligned_cols=84  Identities=17%  Similarity=0.190  Sum_probs=52.5

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCC-----CCChHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPE-----FQTDEAAINDLE  261 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~-----~~~~~~~~~~l~  261 (695)
                      .+++-|+|++|+|||||+.+++..  .... ...++|++..+.++..     .+++++.....     ....+.....+.
T Consensus        60 GsiteI~G~~GsGKTtLal~~~~~--a~~~-G~~v~yId~E~t~~~~-----~A~~lGvDl~~llv~~~~~~E~~l~~i~  131 (790)
T PRK09519         60 GRVIEIYGPESSGKTTVALHAVAN--AQAA-GGVAAFIDAEHALDPD-----YAKKLGVDTDSLLVSQPDTGEQALEIAD  131 (790)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH--HHHc-CCcEEEECCccchhHH-----HHHHcCCChhHeEEecCCCHHHHHHHHH
Confidence            588999999999999999876552  2222 2337899988877743     56666654221     112233333333


Q ss_pred             HHHHhcCCCcEEEEEeCCC
Q 042541          262 RFFKQMRIEAILLVLDDVW  280 (695)
Q Consensus       262 ~~~~~l~~~~~LlVlDdv~  280 (695)
                      .+++  .++.-|||+|.+.
T Consensus       132 ~lv~--~~~~~LVVIDSI~  148 (790)
T PRK09519        132 MLIR--SGALDIVVIDSVA  148 (790)
T ss_pred             HHhh--cCCCeEEEEcchh
Confidence            3222  3567799999974

>PF03266 NTPase_1: NTPase; InterPro: IPR004948 This entry represents a family of nucleoside-triphosphatases which have activity towards ATP, GTP, CTP, TTP and UTP and may hydrolyse nucleoside diphosphates with lower efficiency []

Probab=93.89  E-value=0.042  Score=50.92  Aligned_cols=21  Identities=38%  Similarity=0.795  Sum_probs=18.1

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |.|.|.+|+|||||++.+++.
T Consensus         2 i~iTG~pG~GKTTll~k~i~~   22 (168)
T PF03266_consen    2 IFITGPPGVGKTTLLKKVIEE   22 (168)
T ss_dssp             EEEES-TTSSHHHHHHHHHHH
T ss_pred             EEEECcCCCCHHHHHHHHHHH
Confidence            789999999999999998873

It includes proteins from bacteria to human, and the function was determined first in a hyperthermophilic bacterium to be an NTPase []. The structure of one member-sequence represents a variation of the RecA fold, and implies that the function might be that of a DNA/RNA modifying enzyme []. The sequence carries both a Walker A and Walker B motif which together are characteristic of ATPases or GTPases. The protein exhibits an increased expression profile in human liver cholangiocarcinoma when compared to normal tissue [].; GO: 0005524 ATP binding, 0016740 transferase activity, 0019204 nucleotide phosphatase activity; PDB: 1YE8_A 2I3B_A.

>PRK13949 shikimate kinase; Provisional

Probab=93.88  E-value=0.044  Score=50.97  Aligned_cols=21  Identities=38%  Similarity=0.376  Sum_probs=19.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      -|.|+|+.|+||||+++.+++
T Consensus         3 ~I~liG~~GsGKstl~~~La~   23 (169)
T PRK13949          3 RIFLVGYMGAGKTTLGKALAR   23 (169)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            489999999999999999987

>PRK13948 shikimate kinase; Provisional

Probab=93.85  E-value=0.052  Score=50.96  Aligned_cols=24  Identities=17%  Similarity=0.267  Sum_probs=21.9

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ....|.++|+.|+||||+++.+.+
T Consensus         9 ~~~~I~LiG~~GsGKSTvg~~La~   32 (182)
T PRK13948          9 PVTWVALAGFMGTGKSRIGWELSR   32 (182)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHH
Confidence            457899999999999999999987

>PF02374 ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_A 3IBG_B 3SJA_A 3H84_B 3SJD_A 3ZS9_A 3A37_A 2WOJ_A 3SJC_B 3A36_B

Probab=93.81  E-value=0.07  Score=54.72  Aligned_cols=47  Identities=17%  Similarity=0.352  Sum_probs=31.5

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHH
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQ  237 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~  237 (695)
                      +++.+.|-||+||||+|.+.+-.  .... ..+++-++.....+..+++.
T Consensus         2 r~~~~~GKGGVGKTT~aaA~A~~--~A~~-G~rtLlvS~Dpa~~L~d~l~   48 (305)
T PF02374_consen    2 RILFFGGKGGVGKTTVAAALALA--LARR-GKRTLLVSTDPAHSLSDVLG   48 (305)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHH--HHHT-TS-EEEEESSTTTHHHHHHT
T ss_pred             eEEEEecCCCCCcHHHHHHHHHH--HhhC-CCCeeEeecCCCccHHHHhC
Confidence            68999999999999999777652  2221 23366777766655555443

...

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=93.79  E-value=0.059  Score=55.87  Aligned_cols=45  Identities=16%  Similarity=0.152  Sum_probs=38.2

Q ss_pred             CCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhcc
Q 042541          166 VISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      ..+||-++.+..|...+.++...-|.|.|..|+||||+|+.+++-
T Consensus        17 ~~ivGq~~~k~al~~~~~~p~~~~vli~G~~GtGKs~~ar~~~~~   61 (350)
T CHL00081         17 TAIVGQEEMKLALILNVIDPKIGGVMIMGDRGTGKSTTIRALVDL   61 (350)
T ss_pred             HHHhChHHHHHHHHHhccCCCCCeEEEEcCCCCCHHHHHHHHHHH
Confidence            457999988888877777877777889999999999999998763

>PRK12339 2-phosphoglycerate kinase; Provisional

Probab=93.76  E-value=0.056  Score=51.51  Aligned_cols=23  Identities=17%  Similarity=0.332  Sum_probs=21.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+|.|.|.+|+||||+|+.++.
T Consensus         3 ~~~i~i~G~~G~GKst~a~~l~~   25 (197)
T PRK12339          3 STIHFIGGIPGVGKTSISGYIAR   25 (197)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999987

>PRK05922 type III secretion system ATPase; Validated

Probab=93.74  E-value=0.45  Score=50.82  Aligned_cols=90  Identities=16%  Similarity=0.234  Sum_probs=50.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCC-CCCHHHHHHHHHHhcCCCC-------CCCCChH---
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSK-NPNVKAIVQKVLHHKGYPV-------PEFQTDE---  254 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~-~~~~~~~~~~i~~~l~~~~-------~~~~~~~---  254 (695)
                      ....++|+|..|+|||||.+.+....    ..+.++ .+-+++ .....+.+.+.........       .+.+...   
T Consensus       156 ~GqrigI~G~nG~GKSTLL~~Ia~~~----~~d~gv-i~liGerg~ev~eyl~q~~~~~~~~rTVlv~atsd~~~~~r~~  230 (434)
T PRK05922        156 KGQRIGVFSEPGSGKSSLLSTIAKGS----KSTINV-IALIGERGREVREYIEQHKEGLAAQRTIIIASPAHETAPTKVI  230 (434)
T ss_pred             CCcEEEEECCCCCChHHHHHHHhccC----CCCceE-EEEeCCCCchHHHHHHHHHhhccccceEEEEECCCCCHHHHHH
Confidence            35679999999999999999998632    123323 333433 3344556655554432211       1111111   


Q ss_pred             --HHHHHHHHHHHhcCCCcEEEEEeCCCC
Q 042541          255 --AAINDLERFFKQMRIEAILLVLDDVWP  281 (695)
Q Consensus       255 --~~~~~l~~~~~~l~~~~~LlVlDdv~~  281 (695)
                        ...-.+.+.++. +++++|+++||+-.
T Consensus       231 a~~~a~tiAEyfrd-~G~~VLl~~DslTR  258 (434)
T PRK05922        231 AGRAAMTIAEYFRD-QGHRVLFIMDSLSR  258 (434)
T ss_pred             HHHHHHHHHHHHHH-cCCCEEEeccchhH
Confidence              112233444422 58999999999843

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=93.72  E-value=0.04  Score=50.95  Aligned_cols=20  Identities=30%  Similarity=0.502  Sum_probs=18.2

Q ss_pred             EEEEcCCCCcHHHHHHHHhc
Q 042541          190 IVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~  209 (695)
                      |.|+|++|+||||+|+.+.+
T Consensus         1 i~l~G~~GsGKSTla~~l~~   20 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAH   20 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999887

This model represents a subfamily of proteins that includes thermoresistant and thermosensitve isozymes of gluconate kinase (gluconokinase) in E. coli and other related proteins; members of this family are often named by similarity to the thermostable isozyme. These proteins show homology to shikimate kinases and adenylate kinases but not to gluconate kinases from the FGGY family of carbohydrate kinases.

>cd00464 SK Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants

Probab=93.71  E-value=0.048  Score=49.79  Aligned_cols=20  Identities=45%  Similarity=0.446  Sum_probs=18.7

Q ss_pred             EEEEcCCCCcHHHHHHHHhc
Q 042541          190 IVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~  209 (695)
                      |.|+|++|+||||+|+.+..
T Consensus         2 i~l~G~~GsGKstla~~la~   21 (154)
T cd00464           2 IVLIGMMGAGKTTVGRLLAK   21 (154)
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            78999999999999999986

Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids, p-aminobenzoic acid, folate and ubiquinone. Shikimate kinase catalyses the phosphorylation of the 3-hydroxyl group of shikimic acid using ATP.

>PRK14530 adenylate kinase; Provisional

Probab=93.70  E-value=0.049  Score=53.01  Aligned_cols=22  Identities=27%  Similarity=0.312  Sum_probs=20.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +.|.|+|++|+||||+|+.++.
T Consensus         4 ~~I~i~G~pGsGKsT~~~~La~   25 (215)
T PRK14530          4 PRILLLGAPGAGKGTQSSNLAE   25 (215)
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
Confidence            4689999999999999999876

>PRK14738 gmk guanylate kinase; Provisional

Probab=93.68  E-value=0.061  Score=51.90  Aligned_cols=24  Identities=29%  Similarity=0.618  Sum_probs=21.5

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+.|.|+|++|+|||||++.+..
T Consensus        12 ~~~~ivi~GpsG~GK~tl~~~L~~   35 (206)
T PRK14738         12 KPLLVVISGPSGVGKDAVLARMRE   35 (206)
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHh
Confidence            468899999999999999999875

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=93.67  E-value=0.38  Score=53.54  Aligned_cols=50  Identities=22%  Similarity=0.318  Sum_probs=35.1

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHH
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKV  239 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i  239 (695)
                      ..+++.|.|.+|+|||+||.++..  ....++...++|++....  ..++.+.+
T Consensus        30 ~Gs~~li~G~pGsGKT~l~~qf~~--~~~~~~ge~~lyis~ee~--~~~i~~~~   79 (509)
T PRK09302         30 KGRPTLVSGTAGTGKTLFALQFLV--NGIKRFDEPGVFVTFEES--PEDIIRNV   79 (509)
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHH--HHHHhcCCCEEEEEccCC--HHHHHHHH
Confidence            358999999999999999998865  222233444789988774  34444443

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=93.63  E-value=0.072  Score=52.32  Aligned_cols=21  Identities=29%  Similarity=0.523  Sum_probs=16.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +..|.|++|.||||++..+..
T Consensus        19 ~~~i~GpPGTGKT~~l~~~i~   39 (236)
T PF13086_consen   19 ITLIQGPPGTGKTTTLASIIA   39 (236)
T ss_dssp             -EEEE-STTSSHHHHHHHHHH
T ss_pred             CEEEECCCCCChHHHHHHHHH
Confidence            788999999999987766665

>KOG0924 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=93.61  E-value=0.32  Score=53.21  Aligned_cols=114  Identities=21%  Similarity=0.281  Sum_probs=65.2

Q ss_pred             CceEEEEEcCCCCcHHH-HHHHHhccccccccC-CCcEEEEEeCCCC--CHHHHHHHHHHhcCCCCCCC----------C
Q 042541          186 GRQFIVVSAPGGYGKTT-LVQRLCKDDQVQGKF-KDDIFYVTVSKNP--NVKAIVQKVLHHKGYPVPEF----------Q  251 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTt-La~~~~~~~~~~~~f-~~~~~wv~~~~~~--~~~~~~~~i~~~l~~~~~~~----------~  251 (695)
                      ...||.|+|..|+|||| |++.+|.+     .| +.+  -|-+.+..  ....+.+.+.+.++......          .
T Consensus       370 ~n~vvvivgETGSGKTTQl~QyL~ed-----GY~~~G--mIGcTQPRRvAAiSVAkrVa~EM~~~lG~~VGYsIRFEdvT  442 (1042)
T KOG0924|consen  370 ENQVVVIVGETGSGKTTQLAQYLYED-----GYADNG--MIGCTQPRRVAAISVAKRVAEEMGVTLGDTVGYSIRFEDVT  442 (1042)
T ss_pred             hCcEEEEEecCCCCchhhhHHHHHhc-----ccccCC--eeeecCchHHHHHHHHHHHHHHhCCccccccceEEEeeecC
Confidence            35899999999999996 56666653     22 223  33444443  34556677777765432110          0


Q ss_pred             Ch------HHHHHHHHHHH-HhcCCCcEEEEEeCCCCCChH------HHhhhccCCCCCEEEEEcCCC
Q 042541          252 TD------EAAINDLERFF-KQMRIEAILLVLDDVWPGSES------LLQKLGFQLPDYKILVTSRSE  306 (695)
Q Consensus       252 ~~------~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~~~------~~~~l~~~~~gs~iivTtR~~  306 (695)
                      ..      ....-.|++.+ +..-.|--.+|+|.+.+..-.      ++.........-|+||||-.-
T Consensus       443 ~~~T~IkymTDGiLLrEsL~d~~L~kYSviImDEAHERslNtDilfGllk~~larRrdlKliVtSATm  510 (1042)
T KOG0924|consen  443 SEDTKIKYMTDGILLRESLKDRDLDKYSVIIMDEAHERSLNTDILFGLLKKVLARRRDLKLIVTSATM  510 (1042)
T ss_pred             CCceeEEEeccchHHHHHhhhhhhhheeEEEechhhhcccchHHHHHHHHHHHHhhccceEEEeeccc
Confidence            00      01122355555 433456678999998665421      233333444578999998764

>PRK06793 fliI flagellum-specific ATP synthase; Validated

Probab=93.59  E-value=0.32  Score=51.91  Aligned_cols=92  Identities=21%  Similarity=0.273  Sum_probs=52.1

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCC-------CCCCCh-----
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPV-------PEFQTD-----  253 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~-------~~~~~~-----  253 (695)
                      ....++|+|..|+|||||++.++....    -+.+++.+.-.+.....+++...+..-+...       .+.+..     
T Consensus       155 ~Gqri~I~G~sG~GKTtLl~~Ia~~~~----~~~gvI~~iGerg~ev~e~~~~~l~~~gl~~tvvv~~tsd~s~~~r~ra  230 (432)
T PRK06793        155 IGQKIGIFAGSGVGKSTLLGMIAKNAK----ADINVISLVGERGREVKDFIRKELGEEGMRKSVVVVATSDESHLMQLRA  230 (432)
T ss_pred             CCcEEEEECCCCCChHHHHHHHhccCC----CCeEEEEeCCCCcccHHHHHHHHhhhcccceeEEEEECCCCCHHHHHHH
Confidence            357889999999999999999886321    1222433222233566677666555432111       111111     


Q ss_pred             HHHHHHHHHHHHhcCCCcEEEEEeCCCCC
Q 042541          254 EAAINDLERFFKQMRIEAILLVLDDVWPG  282 (695)
Q Consensus       254 ~~~~~~l~~~~~~l~~~~~LlVlDdv~~~  282 (695)
                      ......+.+.+.. +++++|+++||+-..
T Consensus       231 ~~~a~~iAEyfr~-~G~~VLlilDslTr~  258 (432)
T PRK06793        231 AKLATSIAEYFRD-QGNNVLLMMDSVTRF  258 (432)
T ss_pred             HHHHHHHHHHHHH-cCCcEEEEecchHHH
Confidence            1112223333321 589999999998544

>TIGR03497 FliI_clade2 flagellar protein export ATPase FliI

Probab=93.58  E-value=0.26  Score=52.51  Aligned_cols=91  Identities=18%  Similarity=0.311  Sum_probs=49.5

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCC-CCHHHHHHHHHHhcCCC-------CCCCCChH--
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKN-PNVKAIVQKVLHHKGYP-------VPEFQTDE--  254 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~-~~~~~~~~~i~~~l~~~-------~~~~~~~~--  254 (695)
                      .....++|+|..|+|||||++.+...  ..  -+.+++. -+++. ....++..+.+.+-+..       ..+.+...  
T Consensus       135 ~~Gqri~I~G~sG~GKTtLl~~i~~~--~~--~~~gvi~-~~Ger~~ev~e~~~~~l~~~~~~~~v~v~~tsd~~~~~r~  209 (413)
T TIGR03497       135 GKGQRVGIFAGSGVGKSTLLGMIARN--AK--ADINVIA-LIGERGREVRDFIEKDLGEEGLKRSVVVVATSDQPALMRL  209 (413)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCC--CC--CCeEEEE-EEccchHHHHHHHHHHhcccccceEEEEEECCCCCHHHHH
Confidence            34578999999999999999988762  21  1232333 33433 24455555544431111       11111111  


Q ss_pred             ---HHHHHHHHHHHhcCCCcEEEEEeCCCC
Q 042541          255 ---AAINDLERFFKQMRIEAILLVLDDVWP  281 (695)
Q Consensus       255 ---~~~~~l~~~~~~l~~~~~LlVlDdv~~  281 (695)
                         ...-.+.+.+.. +++++||++||+-.
T Consensus       210 ~~~~~a~tiAEyfr~-~G~~Vll~~Dsltr  238 (413)
T TIGR03497       210 KAAFTATAIAEYFRD-QGKDVLLMMDSVTR  238 (413)
T ss_pred             HHHHHHHHHHHHHHH-CCCCEEEEEcCcHH
Confidence               112233344422 58999999999843

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

---

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	695
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	3e-57
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-57
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-10
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	7e-48
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	7e-26
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	3e-07
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	4e-07
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	3e-04
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	6e-04

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A* Length = 549

 Score =  202 bits (515), Expect = 3e-57
 Identities = 64/480 (13%), Positives = 137/480 (28%), Gaps = 47/480 (9%)

Query: 99  KKIIKLDTSISDFFRTSLPLQHARDGKLIMV---EVKEIHTMVRRMSGNGNINGWMSNQV 155
           +   +  + +            +     +            ++R +      +  M ++ 
Sbjct: 59  RIYRRQASELGPLIDFFNYNNQSHLADFLEDYIDFAINEPDLLRPVVIAPQFSRQMLDRK 118

Query: 156 GDCCSAPDPPVI--SPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLC-KDDQ 212
               + P              + +   E+      F+ +    G GK+ +  +   K DQ
Sbjct: 119 LLLGNVPKQMTCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQ 178

Query: 213 VQGKFKDDIFYVTVSKNP---------NVKAIVQKVLHHKGYPVPEFQTDEAAINDLERF 263
           + G   D I ++  S            ++  +++       +P  E  T       +   
Sbjct: 179 LIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNA 238

Query: 264 FKQMRIEAILLVLDDVWPGSESLLQKLGFQLPDYKILVTSRSE-----FPQFGSVHYLKP 318
                    L V DDV    E  ++    Q    + LVT+R         Q      +  
Sbjct: 239 LIDRP--NTLFVFDDVV--QEETIRW--AQELRLRCLVTTRDVEISNAASQTCEFIEVTS 292

Query: 319 LTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGGSLCGKHEVFWQR 378
           L  +                    +E++++K +    G P  L +   S   K      +
Sbjct: 293 LEIDECYDFLEAYGMPMPVGE--KEEDVLNKTIELSSGNPATLMMFFKSCEPKTFEKMAQ 350

Query: 379 MVKE------CSRGESVFQSKNDILDCLGSSLDVLNNEVKECYLDLCSFPEDQRIPITAL 432
           +  +               S   +   L   ++VL++E +         P    IP+   
Sbjct: 351 LNNKLESRGLVGVECITPYSYKSLAMALQRCVEVLSDEDRSALAFAVVMPPGVDIPVKLW 410

Query: 433 IDMWM-----ELYELVDDVFAITNLHELSSQNLVDRVVTRKTAGDYGCYNDDFVMQHDLL 487
             +          E +DD      L  LS +     +++ K         D   + H  L
Sbjct: 411 SCVIPVDICSNEEEQLDDE-VADRLKRLSKRGA---LLSGKRMPVLTFKIDH--IIHMFL 464

Query: 488 RELTICRSKSEPINQRKRLVVEISGNNFPKWWMDQKQHPNNASLLSISTDETFSSNWPDM 547
           + +   ++ +  I+  ++ ++EI  NN          H         S  E +     + 
Sbjct: 465 KHVVDAQTIANGISILEQRLLEIGNNNVSVPERHIPSHFQ--KFRRSSASEMYPKTTEET 522

>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 =  209 bits (532), Expect = 5e-57
 Identities = 107/644 (16%), Positives = 220/644 (34%), Gaps = 149/644 (23%)

Query: 31  TFKDRLEQLESTLRNSIPWIEEIEKLNQVLDRPKQ-----ETENLVRMMEQVEQLVRKCS 85
            +KD L   E        +++  +    V D PK      E ++++   + V   +R   
Sbjct: 17  QYKDILSVFED------AFVDNFD-CKDVQDMPKSILSKEEIDHIIMSKDAVSGTLR--- 66

Query: 86  KVKWNCFKRYVYAKKIIKLDTSISDFFRTSLPLQHARDGKLIMVEVKEIHTMVRRMSGNG 145
            + W         +++++       F    L      + K +M     I T  R+ S   
Sbjct: 67  -LFW-TLLSK--QEEMVQ------KFVEEVL----RINYKFLM---SPIKTEQRQPSMMT 109

Query: 146 NINGWMSNQVGDCCSAPDPPVISPGLDV----PLKELKMELFKDGR-QFIVVSAPGGYGK 200
            +      Q     +  D  V +   +V    P  +L+  L +    + +++    G GK
Sbjct: 110 RM---YIEQRDRLYN--DNQVFAK-YNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGK 163

Query: 201 TTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKV--LHHKGYPVPEFQTD----- 253
           T +   +C   +VQ K    IF++ +    + + +++ +  L ++  P    ++D     
Sbjct: 164 TWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNI 223

Query: 254 ----EAAINDLERFFKQMRIEAILLVLDDVWPGSESLLQKLGFQLPDYKILVTSR----- 304
                +   +L R  K    E  LLVL +V   +              KIL+T+R     
Sbjct: 224 KLRIHSIQAELRRLLKSKPYENCLLVLLNVQ--NAKAWNAFNLSC---KILLTTRFKQVT 278

Query: 305 -----SEFPQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPL 359
                +        H+   LT +  ++L L   + +  +  +P E             P 
Sbjct: 279 DFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQD--LPRE--------VLTTNPR 328

Query: 360 ALKVVGGSLCGKHEV----FWQRMVKECSRGESVFQSKNDILDCLGSSLDVLN-NEVKEC 414
            L ++  S+  +  +     W+ +  +             I++   SSL+VL   E ++ 
Sbjct: 329 RLSIIAESI--RDGLATWDNWKHVNCD---------KLTTIIE---SSLNVLEPAEYRKM 374

Query: 415 YLDLCSFPEDQRIPITALIDMWMEL-YELVDDVFAITNLHELSSQNLVDRVVTRKTAGDY 473
           +  L  FP    IP   L  +W ++    V  V     +++L   +LV++     T    
Sbjct: 375 FDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVV-----VNKLHKYSLVEKQPKESTISIP 429

Query: 474 GCYNDDFVMQHDLLREL--TICRSKSEPINQRKRLVVEISGNNFPKWWMDQ------KQH 525
             Y  +  ++ +    L  +I       ++    +      ++    ++DQ        H
Sbjct: 430 SIY-LELKVKLENEYALHRSI-------VDHY-NIPKTFDSDDLIPPYLDQYFYSHIGHH 480

Query: 526 PNNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYG 585
                L +I   E  +           ++V L+ R        FL++    K+   +   
Sbjct: 481 -----LKNIEHPERMT---------LFRMVFLDFR--------FLEQ----KIRHDSTAW 514

Query: 586 FSPAELNNFRVLSALSKLKKIRLEHVSLPNSLATVRMNHLQKVS 629
            +   + N   L  L   K    ++      L    ++ L K+ 
Sbjct: 515 NASGSILN--TLQQLKFYKPYICDNDPKYERLVNAILDFLPKIE 556

>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 = 63.7 bits (154), Expect = 2e-10
 Identities = 75/488 (15%), Positives = 138/488 (28%), Gaps = 152/488 (31%)

Query: 237 QKVLHHKGYPVPEFQTDEAAINDLERFFKQM--------------RIEAILLVLDDVWPG 282
           + +L         F  +     D++   K +               +   L +   +   
Sbjct: 19  KDILSVF---EDAFVDN-FDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSK 74

Query: 283 SESLLQK-LGFQL-PDYKILVTSRSEFPQFGSVHYLKPLTYEAARTLFLHSANLQDGNSY 340
            E ++QK +   L  +YK L++      +  S+       Y   R        L + N  
Sbjct: 75  QEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRM---YIEQRD------RLYNDNQV 125

Query: 341 IPDENI-----VSKILRACKGCPLALKVV----GGSLCGKH------------------E 373
               N+       K+ +A      A  V+     G   GK                   +
Sbjct: 126 FAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLG--SGKTWVALDVCLSYKVQCKMDFK 183

Query: 374 VFWQRMVKECSRGESVFQSKNDILDCLGSSLDVLNNEVKECYLDLCSFPEDQRIPITALI 433
           +FW  + K C+  E+V +               L  ++   +        + ++ I ++ 
Sbjct: 184 IFWLNL-KNCNSPETVLEMLQK-----------LLYQIDPNWTSRSDHSSNIKLRIHSIQ 231

Query: 434 D-----MWMELYE---LV-DDVF--AITNLHELSSQNLV---DRVVTRKTAGDYGCYNDD 479
                 +  + YE   LV  +V      N   LS + L+    + VT   +     +   
Sbjct: 232 AELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTH--- 288

Query: 480 FVMQHDLLRELTICRSKSEPINQRKRLVVEISGNNFPKW-WMDQKQHPNNA---SLLSIS 535
            +        LT    + + +                K+     +  P      +   +S
Sbjct: 289 -ISLDHHSMTLT--PDEVKSL--------------LLKYLDCRPQDLPREVLTTNPRRLS 331

Query: 536 TDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDE--LKVLIVTNYGFSPAEL-N 592
                      +    ++  +      K+V  D L  + E  L VL        PAE   
Sbjct: 332 -----------IIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVL-------EPAEYRK 373

Query: 593 NFRVLSALSKLKKIRLEHVSLPNSL----------ATVR--MNHLQKVSLVMCNVGQVFR 640
            F  LS       +      +P  L          + V   +N L K SLV        +
Sbjct: 374 MFDRLS-------VFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQ----PK 422

Query: 641 NSTFRISD 648
            ST  I  
Sbjct: 423 ESTISIPS 430

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens} Length = 591

 Score =  177 bits (450), Expect = 7e-48
 Identities = 85/504 (16%), Positives = 184/504 (36%), Gaps = 56/504 (11%)

Query: 37  EQLESTLRNSIPWIEEIEKLNQVLDRPKQETENLVRMMEQVEQLVRKCSKVKWNCFKRYV 96
            +  + L      +E+  K + ++D    +    +   E+V     +  +         +
Sbjct: 3   AKARNCLLQHREALEKDIKTSYIMDHMISDGFLTISEEEKVRNEPTQQQRAA-------M 55

Query: 97  YAKKIIKLDTSISDFFRTSLPLQHARDGKLIMVEVKEIHTMVRRMSGNGNINGWMS--NQ 154
             K I+K D      F  +L  +  +D   +   + +   +V   SG  +++G  S    
Sbjct: 56  LIKMILKKDNDSYVSFYNALLHEGYKD---LAALLHDGIPVVSSSSGKDSVSGITSYVRT 112

Query: 155 VGDCCSAPDPPVISPGLDVPLKELKMELFKDGRQFIVVS--APGGYGKTTLVQRLCKDDQ 212
           V      P  PV+       +  ++ +L K   +   V+     G GK+ L     +D  
Sbjct: 113 VLCEGGVPQRPVVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHS 172

Query: 213 VQGKFKDD-IFYVTVSKNPNV------KAIVQKVLHHKGYPVPEFQTDEAAINDLERFFK 265
           +        + +V+V K          + +  ++   + +        E A + L R   
Sbjct: 173 LLEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRL-RILM 231

Query: 266 QMRIEAILLVLDDVWPGSESLLQKLGFQLPDYKILVTSRSE------FPQFGSVHYLKPL 319
             +    LL+LDDVW     +L+    Q    +IL+T+R +            V     L
Sbjct: 232 LRKHPRSLLILDDVW--DSWVLKAFDSQ---CQILLTTRDKSVTDSVMGPKYVVPVESSL 286

Query: 320 TYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGGSLCGKHEV--FWQ 377
             E    +     N++  +           I++ CKG PL + ++G  L        ++ 
Sbjct: 287 GKEKGLEILSLFVNMKKADL----PEQAHSIIKECKGSPLVVSLIGALLRDFPNRWEYYL 342

Query: 378 RMVKE---CSRGESVFQSKNDILDCLGSSLDVLNNEVKECYLDLCSFPEDQRIPITALID 434
           + ++        +S       + + +  S+++L  ++K+ Y DL    +D ++P   L  
Sbjct: 343 KQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCI 402

Query: 435 MWMELYELVDDVFAITNLHELSSQNLVDRVVTRKTAGDYGCYNDDFVMQHDLLRELTICR 494
           +W    E V+D+       E  +++L+      K+          + + HDL  +    +
Sbjct: 403 LWDMETEEVEDIL-----QEFVNKSLLFCDRNGKS--------FRYYL-HDLQVDFLTEK 448

Query: 495 SKSEPINQRKRLVVEISGNNFPKW 518
           + S+  +  K+++ +    + P  
Sbjct: 449 NCSQLQDLHKKIITQFQRYHQPHT 472

>3sfz_A APAF-1, apoptotic peptidase activating factor 1; apoptosis, caspase activation, cytochrome C, procaspase-9, A nucleotide, cytosol; HET: ADP; 3.00A {Mus musculus} PDB: 3shf_A* 3iyt_A* 3iza_A* Length = 1249

 Score =  112 bits (283), Expect = 7e-26
 Identities = 70/379 (18%), Positives = 145/379 (38%), Gaps = 44/379 (11%)

Query: 161 APDPPVISPGLDVPLKELKMELFK--DGRQFIVVSAPGGYGKTTLVQRLCKD-DQVQGKF 217
            P  PVI       +  ++ +L+K      ++ +    G GK+ L     +D   ++G F
Sbjct: 119 VPQRPVIFVTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCF 178

Query: 218 KDDIFYVTVSKNPNVK------AIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEA 271
              + +V++ K            +  ++   + +        E A + L R     +   
Sbjct: 179 SGGVHWVSIGKQDKSGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRL-RVLMLRKHPR 237

Query: 272 ILLVLDDVWPGSESLLQKLGFQLPDYKILVTSRSEFPQFG------SVHYLKPLTYEAAR 325
            LL+LDDVW     +L+    Q    +IL+T+R +            V     L  E   
Sbjct: 238 SLLILDDVW--DPWVLKAFDNQC---QILLTTRDKSVTDSVMGPKHVVPVESGLGREKGL 292

Query: 326 TLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGGSLCGKHEVFWQRMVKECSR 385
            +     N++     +P E     I++ CKG PL + ++G  L      +   + +  ++
Sbjct: 293 EILSLFVNMKK--EDLPAE--AHSIIKECKGSPLVVSLIGALLRDFPNRWAYYLRQLQNK 348

Query: 386 GESVFQSK-----NDILDCLGSSLDVLNNEVKECYLDLCSFPEDQRIPITALIDMWMELY 440
                +         + + +  S+++L  ++K+ Y DL    +D ++P   L  +W    
Sbjct: 349 QFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLWDLET 408

Query: 441 ELVDDVFAITNLHELSSQNLVDRVVTRKTAGDYGCYNDDFVMQHDLLRELTICRSKSEPI 500
           E V+D+     L E  +++L+      K+   Y          HDL  +    +++S+  
Sbjct: 409 EEVEDI-----LQEFVNKSLLFCNRNGKSFCYY---------LHDLQVDFLTEKNRSQLQ 454

Query: 501 NQRKRLVVEISGNNFPKWW 519
           +  +++V +      P   
Sbjct: 455 DLHRKMVTQFQRYYQPHTL 473

>4fcg_A Uncharacterized protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, LRR, N- and C-terminal helices; 2.00A {Xanthomonas campestris PV} Length = 328

 Score = 52.3 bits (126), Expect = 3e-07
 Identities = 31/149 (20%), Positives = 52/149 (34%), Gaps = 36/149 (24%)

Query: 566 LPDFLQKMDELKVLIVTNYGFS-----PAELNNFRV---LSALSKLKKIRLEH---VSLP 614
           LP  +  ++ L+ L +           P  L +         L  L+ +RLE     SLP
Sbjct: 142 LPASIASLNRLRELSI--RACPELTELPEPLASTDASGEHQGLVNLQSLRLEWTGIRSLP 199

Query: 615 NSLAT--------VRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIE 666
            S+A         +R + L  +   + +                P L E+D+  C  L  
Sbjct: 200 ASIANLQNLKSLKIRNSPLSALGPAIHH---------------LPKLEELDLRGCTALRN 244

Query: 667 LPDGLCDIVSMEKLRITNCHRLSALPEGI 695
            P        +++L + +C  L  LP  I
Sbjct: 245 YPPIFGGRAPLKRLILKDCSNLLTLPLDI 273

>4fcg_A Uncharacterized protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, LRR, N- and C-terminal helices; 2.00A {Xanthomonas campestris PV} Length = 328

 Score = 51.5 bits (124), Expect = 4e-07
 Identities = 29/143 (20%), Positives = 53/143 (37%), Gaps = 33/143 (23%)

Query: 566 LPDFLQKMDELKVLIVTNYGFS--PAELNNFRVLSALSKLKKIRLEH---VSLPNSLATV 620
                Q +  L+ L +   G    PA + N      L  LK +++ +    +L  ++   
Sbjct: 175 ASGEHQGLVNLQSLRLEWTGIRSLPASIAN------LQNLKSLKIRNSPLSALGPAIH-- 226

Query: 621 RMNHLQKVSLVMCN--------VGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLC 672
            +  L+++ L  C          G                L  + +  C++L+ LP  + 
Sbjct: 227 HLPKLEELDLRGCTALRNYPPIFGG------------RAPLKRLILKDCSNLLTLPLDIH 274

Query: 673 DIVSMEKLRITNCHRLSALPEGI 695
            +  +EKL +  C  LS LP  I
Sbjct: 275 RLTQLEKLDLRGCVNLSRLPSLI 297

>4fcg_A Uncharacterized protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, LRR, N- and C-terminal helices; 2.00A {Xanthomonas campestris PV} Length = 328

 Score = 42.6 bits (101), Expect = 3e-04
 Identities = 23/154 (14%), Positives = 45/154 (29%), Gaps = 35/154 (22%)

Query: 566 LPDFLQKMDELKVLIVTNYG--FSPAELNNFRVLS-----------ALSKLKKIRLEH-- 610
             D L +           +   +  A  NN ++ +            L    +       
Sbjct: 28  YHDVLSQWQRHYNADRNRWHSAWRQANSNNPQIETRTGRALKATADLLEDATQPGRVALE 87

Query: 611 ------VSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAF---PNLLEMDIDYC 661
                    P+     R++HLQ +++               + D       L  + +   
Sbjct: 88  LRSVPLPQFPDQAF--RLSHLQHMTI--------DAAGLMELPDTMQQFAGLETLTLARN 137

Query: 662 NDLIELPDGLCDIVSMEKLRITNCHRLSALPEGI 695
             L  LP  +  +  + +L I  C  L+ LPE +
Sbjct: 138 P-LRALPASIASLNRLRELSIRACPELTELPEPL 170

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1 Length = 198

 Score = 40.6 bits (96), Expect = 6e-04
 Identities = 13/38 (34%), Positives = 22/38 (57%), Gaps = 7/38 (18%)

Query: 190 IVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVS 227
           +V+S P G GK+TL+++L ++          IF  +VS
Sbjct: 7   VVLSGPSGAGKSTLLKKLFQEH-------SSIFGFSVS 37

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	695
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	100.0
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	100.0
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	100.0
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	100.0
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	99.71
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	99.67
2fna_A	357	Conserved hypothetical protein; structural genomic	99.67
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	99.62
4fcg_A	328	Uncharacterized protein; structural genomics, PSI-	99.62
3qfl_A	115	MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-	99.58
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	99.51
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	99.49
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	99.47
2o6q_A	270	Variable lymphocyte receptor A; leucine-rich repea	99.46
2ell_A	168	Acidic leucine-rich nuclear phosphoprotein 32 FAM	99.46
3m19_A	251	Variable lymphocyte receptor A diversity region; a	99.45
1ozn_A	285	Reticulon 4 receptor; NOGO receptor, MAD, myelinat	99.43
3rfs_A	272	Internalin B, repeat modules, variable lymphocyte	99.43
3m19_A	251	Variable lymphocyte receptor A diversity region; a	99.43
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	99.42
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	99.4
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	99.4
2o6s_A	208	Variable lymphocyte receptor B; leucine-rich repea	99.4
1p9a_G	290	Platelet glycoprotein IB alpha chain precursor; pl	99.39
2v9t_B	220	SLIT homolog 2 protein N-product; structural prote	99.39
1p9a_G	290	Platelet glycoprotein IB alpha chain precursor; pl	99.39
3rfs_A	272	Internalin B, repeat modules, variable lymphocyte	99.38
1ozn_A	285	Reticulon 4 receptor; NOGO receptor, MAD, myelinat	99.38
3e6j_A	229	Variable lymphocyte receptor diversity region; var	99.38
2o6q_A	270	Variable lymphocyte receptor A; leucine-rich repea	99.38
1ogq_A	313	PGIP-2, polygalacturonase inhibiting protein; inhi	99.38
1ogq_A	313	PGIP-2, polygalacturonase inhibiting protein; inhi	99.37
2xwt_C	239	Thyrotropin receptor; signaling protein-immune sys	99.37
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	99.36
3zyi_A	452	Leucine-rich repeat-containing protein 4; cell adh	99.35
2v70_A	220	SLIT-2, SLIT homolog 2 protein N-product; neurogen	99.35
2je0_A	149	Acidic leucine-rich nuclear phosphoprotein 32 FAM	99.35
4ezg_A	197	Putative uncharacterized protein; internalin-A, le	99.34
3rgz_A	768	Protein brassinosteroid insensitive 1; phytohormon	99.33
2o6s_A	208	Variable lymphocyte receptor B; leucine-rich repea	99.32
3e6j_A	229	Variable lymphocyte receptor diversity region; var	99.31
3zyi_A	452	Leucine-rich repeat-containing protein 4; cell adh	99.31
2xwt_C	239	Thyrotropin receptor; signaling protein-immune sys	99.31
2z62_A	276	TOLL-like receptor 4, variable lymphocyte recepto;	99.3
2xot_A	361	Amphoterin-induced protein 1; cell adhesion, neuro	99.3
3zyj_A	440	Leucine-rich repeat-containing protein 4C; cell ad	99.3
1h6u_A	308	Internalin H; cell adhesion, leucine rich repeat,	99.29
1h6t_A	291	Internalin B; cell adhesion, leucine rich repeat,	99.29
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	99.28
4g8a_A	635	TOLL-like receptor 4; leucine rich repeat MD-2 rel	99.28
2z66_A	306	Variable lymphocyte receptor B, TOLL-like recepto;	99.28
2z62_A	276	TOLL-like receptor 4, variable lymphocyte recepto;	99.28
2z66_A	306	Variable lymphocyte receptor B, TOLL-like recepto;	99.27
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	99.27
1h6t_A	291	Internalin B; cell adhesion, leucine rich repeat,	99.27
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	99.27
4b8c_D	727	Glucose-repressible alcohol dehydrogenase transcr	99.27
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	99.26
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	99.26
1w8a_A	192	SLIT protein; signaling protein, secreted protein,	99.26
2chg_A	226	Replication factor C small subunit; DNA-binding pr	99.26
1a9n_A	176	U2A', U2A'; complex (nuclear protein/RNA), RNA, sn	99.26
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	99.26
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	99.26
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	99.25
1wwl_A	312	Monocyte differentiation antigen CD14; LPS, immune	99.25
3vq2_A	606	TLR4, TOLL-like receptor 4; leucine rich repeat MD	99.25
4glp_A	310	Monocyte differentiation antigen CD14; alpha beta	99.24
2id5_A	477	Lingo-1, leucine rich repeat neuronal 6A; CNS-spec	99.24
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	99.24
3oja_B	597	Anopheles plasmodium-responsive leucine-rich REPE	99.24
2z80_A	353	TOLL-like receptor 2, variable lymphocyte recepto;	99.24
4eco_A	636	Uncharacterized protein; leucine-rich repeats, pro	99.24
2v9t_B	220	SLIT homolog 2 protein N-product; structural prote	99.24
4ecn_A	876	Leucine-rich repeat protein; leucine-rich repeats,	99.23
1h6u_A	308	Internalin H; cell adhesion, leucine rich repeat,	99.23
3o6n_A	390	APL1; leucine-rich repeat, protein binding; HET: N	99.23
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	99.22
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	99.22
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	99.22
1m9s_A	605	Internalin B; cell invasion, GW domains, SH3 domai	99.22
1m9s_A	605	Internalin B; cell invasion, GW domains, SH3 domai	99.21
1a9n_A	176	U2A', U2A'; complex (nuclear protein/RNA), RNA, sn	99.21
3oja_A	487	Leucine-rich immune molecule 1; coiled-coil, helix	99.21
2v70_A	220	SLIT-2, SLIT homolog 2 protein N-product; neurogen	99.21
1wwl_A	312	Monocyte differentiation antigen CD14; LPS, immune	99.2
3v47_A	455	TOLL-like receptor 5B and variable lymphocyte REC	99.2
2xot_A	361	Amphoterin-induced protein 1; cell adhesion, neuro	99.2
3v47_A	455	TOLL-like receptor 5B and variable lymphocyte REC	99.19
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	99.19
1xku_A	330	Decorin; proteoglycan, leucine-rich repeat, struct	99.18
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	99.18
2ell_A	168	Acidic leucine-rich nuclear phosphoprotein 32 FAM	99.18
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	99.18
1xeu_A	263	Internalin C; cellular invasion, leucine-rich repe	99.17
4glp_A	310	Monocyte differentiation antigen CD14; alpha beta	99.17
2ft3_A	332	Biglycan; proteoglycan, dimer interface, structura	99.17
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	99.17
2z63_A	570	TOLL-like receptor 4, variable lymphocyte recepto;	99.17
3t6q_A	606	CD180 antigen; protein-protein complex, leucine ri	99.17
2je0_A	149	Acidic leucine-rich nuclear phosphoprotein 32 FAM	99.17
2wfh_A	193	SLIT homolog 2 protein C-product; developmental pr	99.16
2z7x_B	520	TOLL-like receptor 1, variable lymphocyte recepto;	99.16
2z81_A	549	CD282 antigen, TOLL-like receptor 2, variable lymp	99.16
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	99.15
3j0a_A	844	TOLL-like receptor 5; membrane protein, leucine-ri	99.15
1ziw_A	680	TOLL-like receptor 3; innate immunity, immune syst	99.15
4b8c_D	727	Glucose-repressible alcohol dehydrogenase transcr	99.14
3a79_B	562	TLR6, VLRB.59, TOLL-like receptor 6, variable lymp	99.13
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	99.12
4fmz_A	347	Internalin; leucine rich repeat, structural genomi	99.11
2o6r_A	177	Variable lymphocyte receptor B; leucine-rich repea	99.1
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	99.1
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	99.08
3o53_A	317	Protein LRIM1, AGAP006348-PA; leucine-rich repeat,	99.08
2z7x_B	520	TOLL-like receptor 1, variable lymphocyte recepto;	99.07
1xeu_A	263	Internalin C; cellular invasion, leucine-rich repe	99.06
4g8a_A	635	TOLL-like receptor 4; leucine rich repeat MD-2 rel	99.06
3a79_B	562	TLR6, VLRB.59, TOLL-like receptor 6, variable lymp	99.05
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	99.04
2r9u_A	174	Variable lymphocyte receptor; adaptive immunity, V	99.03
3bz5_A	457	Internalin-J, INLJ; leucine rich repeat (LRR), cys	99.03
3bz5_A	457	Internalin-J, INLJ; leucine rich repeat (LRR), cys	99.03
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	99.01
1ds9_A	198	Outer arm dynein; leucine-rich repeat, beta-BETA-a	99.01
2ast_B	336	S-phase kinase-associated protein 2; SCF-substrate	99.01
1o6v_A	466	Internalin A; bacterial infection, extracellular r	99.01
2wfh_A	193	SLIT homolog 2 protein C-product; developmental pr	99.0
2ast_B	336	S-phase kinase-associated protein 2; SCF-substrate	98.99
3g39_A	170	Variable lymphocyte receptor VLRB.2D; antibody, X-	98.99
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	98.96
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	98.96
2o6r_A	177	Variable lymphocyte receptor B; leucine-rich repea	98.96
3cvr_A	571	Invasion plasmid antigen; leucine rich repeat and	98.95
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	98.92
1ds9_A	198	Outer arm dynein; leucine-rich repeat, beta-BETA-a	98.91
1o6v_A	466	Internalin A; bacterial infection, extracellular r	98.9
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	98.9
1w8a_A	192	SLIT protein; signaling protein, secreted protein,	98.89
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	98.87
3g06_A	622	SSPH2 (leucine-rich repeat protein); E3 ubiquitin	98.86
4ay9_X	350	Follicle-stimulating hormone receptor; hormone-rec	98.84
2ca6_A	386	RAN GTPase-activating protein 1; GAP, GTPase activ	98.8
1jl5_A	454	Outer protein YOPM; leucine-rich repeat, molecular	98.8
2ca6_A	386	RAN GTPase-activating protein 1; GAP, GTPase activ	98.79
2r9u_A	174	Variable lymphocyte receptor; adaptive immunity, V	98.78
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	98.76
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	98.75
3g39_A	170	Variable lymphocyte receptor VLRB.2D; antibody, X-	98.73
2chq_A	319	Replication factor C small subunit; DNA-binding pr	98.7
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	98.64
2ifg_A	347	High affinity nerve growth factor receptor; TRK, T	98.63
3goz_A	362	Leucine-rich repeat-containing protein; LEGL7, NES	98.59
3goz_A	362	Leucine-rich repeat-containing protein; LEGL7, NES	98.58
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	98.53
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	98.52
1z7x_W	461	Ribonuclease inhibitor; leucine-rich repeat, enzym	98.51
2ifg_A	347	High affinity nerve growth factor receptor; TRK, T	98.49
3bos_A	242	Putative DNA replication factor; P-loop containing	98.48
1z7x_W	461	Ribonuclease inhibitor; leucine-rich repeat, enzym	98.45
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	98.41
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	98.4
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	98.4
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	98.37
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	98.36
3pvs_A	447	Replication-associated recombination protein A; ma	98.31
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	98.29
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	98.28
2p1m_B	594	Transport inhibitor response 1 protein; F-BOX, leu	98.26
3un9_A	372	NLR family member X1; leucine rich repeat (LRR), a	98.23
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	98.21
3sb4_A	329	Hypothetical leucine rich repeat protein; LRR, rig	98.2
3ogk_B	592	Coronatine-insensitive protein 1; leucine rich rep	98.19
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	98.18
2p1m_B	594	Transport inhibitor response 1 protein; F-BOX, leu	98.17
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	98.16
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	98.15
3ogk_B	592	Coronatine-insensitive protein 1; leucine rich rep	98.14
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	98.14
3un9_A	372	NLR family member X1; leucine rich repeat (LRR), a	98.13
2ra8_A	362	Uncharacterized protein Q64V53_bacfr; WGR domain,	98.12
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	98.1
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	98.1
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	98.07
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	98.05
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	98.03
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	98.02
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	98.02
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	98.01
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	98.01
3e4g_A	176	ATP synthase subunit S, mitochondrial; leucine-ric	97.98
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	97.94
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	97.93
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	97.93
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	97.92
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	97.9
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	97.85
3e4g_A	176	ATP synthase subunit S, mitochondrial; leucine-ric	97.82
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	97.81
1io0_A	185	Tropomodulin; LRR protein, right-handed super-heli	97.81
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	97.8
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	97.78
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	97.74
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	97.73
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	97.73
3co5_A	143	Putative two-component system transcriptional RES	97.69
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	97.68
3sb4_A	329	Hypothetical leucine rich repeat protein; LRR, rig	97.68
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	97.66
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	97.63
2ra8_A	362	Uncharacterized protein Q64V53_bacfr; WGR domain,	97.62
3rw6_A	267	Nuclear RNA export factor 1; retroviral constituti	97.61
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	97.6
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	97.56
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	97.55
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	97.55
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	97.52
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	97.51
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	97.41
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	97.41
3rw6_A	267	Nuclear RNA export factor 1; retroviral constituti	97.38
1io0_A	185	Tropomodulin; LRR protein, right-handed super-heli	97.36
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	97.28
4fdw_A	401	Leucine rich hypothetical protein; putative cell s	97.22
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	97.11
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	97.09
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	97.09
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	96.99
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	96.92
2qgz_A	308	Helicase loader, putative primosome component; str	96.84
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	96.77
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	96.76
2cvh_A	220	DNA repair and recombination protein RADB; filamen	96.73
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	96.64
4fdw_A	401	Leucine rich hypothetical protein; putative cell s	96.54
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	96.52
2z43_A	324	DNA repair and recombination protein RADA; archaea	96.46
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	96.43
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	96.34
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	96.3
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	96.3
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	96.29
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	96.23
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	96.19
3io5_A	333	Recombination and repair protein; storage dimer, i	96.18
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	96.09
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	96.08
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	96.0
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	95.93
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	95.83
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	95.76
1xp8_A	366	RECA protein, recombinase A; recombination, radior	95.68
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	95.66
1u94_A	356	RECA protein, recombinase A; homologous recombinat	95.62
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	95.56
4a74_A	231	DNA repair and recombination protein RADA; hydrola	95.53
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	95.48
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	95.47
3ice_A	422	Transcription termination factor RHO; transcriptio	95.46
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	95.45
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	95.38
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	95.33
2xxa_A	433	Signal recognition particle protein; protein trans	95.31
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	95.25
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	95.23
3rfe_A	130	Platelet glycoprotein IB beta chain; platelet surf	95.21
2r44_A	331	Uncharacterized protein; putative ATPase, structur	95.2
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	95.19
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	95.15
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	95.09
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	95.08
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	95.07
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	95.06
2ck3_D	482	ATP synthase subunit beta\, mitochondrial; hydrola	95.03
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	95.02
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	95.01
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	94.98
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	94.96
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	94.88
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	94.87
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	94.86
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	94.86
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	94.86
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	94.81
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	94.8
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	94.8
2hf9_A	226	Probable hydrogenase nickel incorporation protein	94.78
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	94.73
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	94.71
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	94.7
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	94.69
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	94.66
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	94.6
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	94.6
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	94.58
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	94.58
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	94.56
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	94.53
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	94.49
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	94.46
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	94.44
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	94.39
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	94.39
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	94.39
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	94.36
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	94.34
4fs7_A	394	Uncharacterized protein; leucine-rich repeats, pro	94.33
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	94.33
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	94.32
3fwy_A	314	Light-independent protochlorophyllide reductase I	94.32
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	94.29
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	94.25
1fx0_B	498	ATP synthase beta chain; latent ATPase, thermal st	94.23
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	94.22
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	94.22
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	94.22
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	94.18
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	94.18
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	94.18
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	94.18
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	94.18
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	94.17
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	94.16
3rfe_A	130	Platelet glycoprotein IB beta chain; platelet surf	94.15
1via_A	175	Shikimate kinase; structural genomics, transferase	94.15
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	94.1
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	94.1
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	94.09
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	94.08
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	94.07
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	94.05
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	94.01
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	93.99
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	93.95
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	93.95
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	93.93
3l0o_A	427	Transcription termination factor RHO; helicase, RH	93.92
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	93.92
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	93.9
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	93.87
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	93.87
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	93.82
1tue_A	212	Replication protein E1; helicase, replication, E1E	93.82
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	93.81
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	93.79
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	93.79
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	93.78
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	93.77
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	93.76
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	93.74
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	93.74
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	93.72
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	93.72
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	93.7
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	93.66
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	93.64
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	93.63
1pgv_A	197	TMD-1, tropomodulin TMD-1; structural genomics, PS	93.61
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	93.59
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	93.58
2vli_A	183	Antibiotic resistance protein; transferase, tunica	93.54
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	93.54
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	93.49
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	93.44
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	93.43
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	93.41
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	93.41
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	93.41
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	93.41
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	93.36
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	93.18
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	93.17
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	93.15
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	93.15
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	93.12
3end_A	307	Light-independent protochlorophyllide reductase ir	93.12
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	93.11
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	93.05
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	93.03
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	93.01
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	93.0
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	92.96
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	92.96
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	92.95
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	92.94
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	92.89
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	92.88
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	92.87
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	92.84
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	92.82
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	92.81
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	92.81
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	92.78
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	92.76
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	92.72
4gt6_A	394	Cell surface protein; leucine rich repeats, putati	92.71
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	92.67
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	92.66
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	92.64
3io3_A	348	DEHA2D07832P; chaperone, membrane traffic, ATPase;	92.6
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	92.59
3gqb_B	464	V-type ATP synthase beta chain; A3B3, V-ATPase, AT	92.56
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	92.55
1b0u_A	262	Histidine permease; ABC transporter, transport pro	92.52
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	92.5
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	92.48
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	92.47
3vr4_D	465	V-type sodium ATPase subunit D; V-ATPase, rotary m	92.47
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	92.37
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	92.36
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	92.36
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	92.35
4h09_A	379	Hypothetical leucine rich repeat protein; two LRR_	92.33
4gzl_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	92.32
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	92.32
2ck3_A	510	ATP synthase subunit alpha\, mitochondrial; hydrol	92.31
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	92.3
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	92.26
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	92.24
1ji0_A	240	ABC transporter; ATP binding protein, structural g	92.24
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	92.18
1sgw_A	214	Putative ABC transporter; structural genomics, P p	92.18
4hlc_A	205	DTMP kinase, thymidylate kinase; TMK, MRSA, pipiri	92.17
1g6h_A	257	High-affinity branched-chain amino acid transport	92.16
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	92.15
3iqw_A	334	Tail-anchored protein targeting factor GET3; ATPas	92.12
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	92.1
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	92.09
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	92.07
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	92.05
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	92.05
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	92.03
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	92.03
4fs7_A	394	Uncharacterized protein; leucine-rich repeats, pro	92.02
2ghi_A	260	Transport protein; multidrug resistance protein, M	92.01
2og2_A	359	Putative signal recognition particle receptor; nuc	92.01
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	91.99
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	91.99
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	91.98
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	91.98
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	91.94
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	91.91
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	91.86
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	91.85
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	91.84
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	91.84
2qe7_A	502	ATP synthase subunit alpha; blockage of ATP hydrol	91.82
2eyu_A	261	Twitching motility protein PILT; pilus retraction	91.76
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	91.74
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	91.73
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	91.73
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	91.72
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	91.71
2wji_A	165	Ferrous iron transport protein B homolog; membrane	91.66
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	91.65
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	91.64
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	91.63
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	91.63
4dzz_A	206	Plasmid partitioning protein PARF; deviant walker	91.59
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	91.58
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	91.48
4h09_A	379	Hypothetical leucine rich repeat protein; two LRR_	91.42
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	91.35
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	91.34
2c61_A	469	A-type ATP synthase non-catalytic subunit B; hydro	91.31
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	91.3
1p9r_A	418	General secretion pathway protein E; bacterial typ	91.28
1fx0_A	507	ATP synthase alpha chain; latent ATPase, thermal s	91.15
2r9v_A	515	ATP synthase subunit alpha; TM1612, structural gen	91.06
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	91.04
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	91.02
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	90.97
2afh_E	289	Nitrogenase iron protein 1; nitrogen fixation, iro	90.96
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	90.95
2ged_A	193	SR-beta, signal recognition particle receptor beta	90.9
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	90.88
4gt6_A	394	Cell surface protein; leucine rich repeats, putati	90.84
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	90.84
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	90.82
1cp2_A	269	CP2, nitrogenase iron protein; oxidoreductase; 1.9	90.79
3oaa_A	513	ATP synthase subunit alpha; rossmann fold, hydrola	90.77
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	90.75
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	90.74
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	90.73
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	90.71
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	90.67
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	90.66
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	90.57
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	90.57
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	90.56
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	90.54
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	90.54
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	90.48
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	90.46
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	90.42
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	90.4
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	90.38
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	90.37
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	90.36
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	90.33

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A*

Probab=100.00  E-value=2e-46  Score=417.65  Aligned_cols=316  Identities=13%  Similarity=0.107  Sum_probs=239.2

Q ss_pred             CCCCCCCCCCCCcchHHHHHHHHHcC---CceEEEEEcCCCCcHHHHHHHHhc--cccccccCCCcEEEEEeCCCC--CH
Q 042541          160 SAPDPPVISPGLDVPLKELKMELFKD---GRQFIVVSAPGGYGKTTLVQRLCK--DDQVQGKFKDDIFYVTVSKNP--NV  232 (695)
Q Consensus       160 ~~~~~~~~~vGr~~~~~~l~~~L~~~---~~~vv~I~G~gGiGKTtLa~~~~~--~~~~~~~f~~~~~wv~~~~~~--~~  232 (695)
                      .+|..+.. |||+.++++|.++|..+   +.++|+|+||||+||||||+++|+  +.+++.+|+. ++||++++.+  +.
T Consensus       123 ~~p~~~~~-~GR~~~~~~l~~~L~~~~~~~~~vv~I~G~gGvGKTtLA~~v~~~~~~~~~~~F~~-~~wv~vs~~~~~~~  200 (549)
T 2a5y_B          123 NVPKQMTC-YIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDS-IVWLKDSGTAPKST  200 (549)
T ss_dssp             TCBCCCCS-CCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSE-EEEEECCCCSTTHH
T ss_pred             CCCCCCcc-CCchHHHHHHHHHHhcccCCCceEEEEEcCCCCCHHHHHHHHHHhhhHHHhccCCc-EEEEEECCCCCCCH
Confidence            45555544 59999999999999843   579999999999999999999998  6789999987 8899999985  89


Q ss_pred             HHHHHHHHHhcCCCCC--CCCC-hHHHHHHHHHHH-HhcCCC-cEEEEEeCCCCCChHHHhhhccCCCCCEEEEEcCCCC
Q 042541          233 KAIVQKVLHHKGYPVP--EFQT-DEAAINDLERFF-KQMRIE-AILLVLDDVWPGSESLLQKLGFQLPDYKILVTSRSEF  307 (695)
Q Consensus       233 ~~~~~~i~~~l~~~~~--~~~~-~~~~~~~l~~~~-~~l~~~-~~LlVlDdv~~~~~~~~~~l~~~~~gs~iivTtR~~~  307 (695)
                      ..++..|+.+++....  ...+ .......+...+ +.++++ |+||||||||+.....|.    ..+||+||||||+..
T Consensus       201 ~~~~~~il~~l~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~~kr~LlVLDdv~~~~~~~~~----~~~gs~ilvTTR~~~  276 (549)
T 2a5y_B          201 FDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWA----QELRLRCLVTTRDVE  276 (549)
T ss_dssp             HHHHHHHHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHHHHHH----HHTTCEEEEEESBGG
T ss_pred             HHHHHHHHHHHhcCcccccccccccccHHHHHHHHHHHHcCCCcEEEEEECCCCchhhccc----ccCCCEEEEEcCCHH
Confidence            9999999999986521  1111 111123343444 677886 999999999996543222    238999999999974


Q ss_pred             CC--CC---CeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHHHhhCCCCHHHHHHHHHH
Q 042541          308 PQ--FG---SVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGGSLCGKHEVFWQRMVKE  382 (695)
Q Consensus       308 ~~--~~---~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~~~L~~~~~~~w~~~l~~  382 (695)
                      +.  .+   ..|++++|+.++||+||.+.++....  +....+++++|+++|+|+||||+++|+.|+.+.. +|...+..
T Consensus       277 v~~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~--~~~~~~~~~~I~~~c~GlPLAl~~~g~~l~~~~w-~~~~~l~~  353 (549)
T 2a5y_B          277 ISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMPV--GEKEEDVLNKTIELSSGNPATLMMFFKSCEPKTF-EKMAQLNN  353 (549)
T ss_dssp             GGGGCCSCEEEEECCCCCHHHHHHHHHHTSCCCC----CHHHHHHHHHHHHHTTCHHHHHHHHTTCCSSSH-HHHHHHHH
T ss_pred             HHHHcCCCCeEEECCCCCHHHHHHHHHHHhcCCCC--chhHHHHHHHHHHHhCCChHHHHHHHHHhccchH-HHHHHhHH
Confidence            32  22   37999999999999999999876532  2446789999999999999999999999987742 33333332


Q ss_pred             hcCCCCccCchhhHHHHHHHHHHhccHHHHHHHh-----------hhcccCCCcccChHHHHHHHHHh--hCCChh----
Q 042541          383 CSRGESVFQSKNDILDCLGSSLDVLNNEVKECYL-----------DLCSFPEDQRIPITALIDMWMEL--YELVDD----  445 (695)
Q Consensus       383 ~~~~~~~~~~~~~i~~~l~~s~~~L~~~~k~cf~-----------~ls~fp~~~~i~~~~Li~~W~~~--~~~~~~----  445 (695)
                      .....    ...++..++.+||+.||+++|.||+           |||+||+++.|+    +.+|+++  |++...    
T Consensus       354 ~l~~~----~~~~i~~~l~~Sy~~L~~~lk~~f~~Ls~~er~l~~~ls~fp~~~~i~----i~~w~a~~~G~i~~~~~~~  425 (549)
T 2a5y_B          354 KLESR----GLVGVECITPYSYKSLAMALQRCVEVLSDEDRSALAFAVVMPPGVDIP----VKLWSCVIPVDICSNEEEQ  425 (549)
T ss_dssp             HHHHH----CSSTTCCCSSSSSSSHHHHHHHHHHTSCHHHHHHTTGGGSSCTTCCEE----HHHHHHHSCC-------CC
T ss_pred             Hhhcc----cHHHHHHHHhcccccccHHHHHHHhccchhhhhHhhheeeeCCCCeee----eeeeeeeccceeccCCCCC
Confidence            21100    1235667788899999888999988           999999999999    7899998  666421    


Q ss_pred             --HHHHHHHHHHhhccccchhhccccCCCCCCCCCcceehhHHHHHHHHHhccCCCcc
Q 042541          446 --VFAITNLHELSSQNLVDRVVTRKTAGDYGCYNDDFVMQHDLLRELTICRSKSEPIN  501 (695)
Q Consensus       446 --~~~~~~l~~L~~~sLl~~~~~~~~~~~~~~~~~~~~~mHdlv~~~a~~~~~~e~~~  501 (695)
                        +.+.++|++|+++|||++...         ....+|+|||+||++|+.++.++++.
T Consensus       426 ~~~~~~~~l~~L~~rsLl~~~~~---------~~~~~~~mHdlv~~~a~~~~~~~~~~  474 (549)
T 2a5y_B          426 LDDEVADRLKRLSKRGALLSGKR---------MPVLTFKIDHIIHMFLKHVVDAQTIA  474 (549)
T ss_dssp             CTHHHHHHHHHTTTBSSCSEEEC---------SSSCEEECCHHHHHHHHTTSCTHHHH
T ss_pred             CHHHHHHHHHHHHHcCCeeEecC---------CCceEEEeChHHHHHHHHHHHHHHHH
Confidence              234449999999999997432         13467999999999999999887653

>3sfz_A APAF-1, apoptotic peptidase activating factor 1; apoptosis, caspase activation, cytochrome C, procaspase-9, A nucleotide, cytosol; HET: ADP; 3.00A {Mus musculus} PDB: 3shf_A* 3iyt_A* 3iza_A*

Probab=100.00  E-value=9.1e-40  Score=401.93  Aligned_cols=317  Identities=19%  Similarity=0.270  Sum_probs=246.4

Q ss_pred             CCCCCCCCCCCCCCcchHHHHHHHHH--cCCceEEEEEcCCCCcHHHHHHHHhccccc-cccCCCcEEEEEeCCCCC--H
Q 042541          158 CCSAPDPPVISPGLDVPLKELKMELF--KDGRQFIVVSAPGGYGKTTLVQRLCKDDQV-QGKFKDDIFYVTVSKNPN--V  232 (695)
Q Consensus       158 ~~~~~~~~~~~vGr~~~~~~l~~~L~--~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~-~~~f~~~~~wv~~~~~~~--~  232 (695)
                      ...+|..+..||||++++++|.++|.  +++.++|+|+||||+||||||+++|++.+. ..+|..+++|+++++..+  .
T Consensus       116 ~~~~p~~~~~~vgR~~~~~~l~~~l~~~~~~~~~v~i~G~gG~GKTtLa~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~  195 (1249)
T 3sfz_A          116 EGGVPQRPVIFVTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGL  195 (1249)
T ss_dssp             HTTCCCCCSSCCCCHHHHHHHHHHHHTTTTSCEEEEEECSTTSSHHHHHHHHTCCHHHHTTTSTTCEEEEECCSCCHHHH
T ss_pred             cCCCCCCCceeccHHHHHHHHHHHHhhccCCCCEEEEEeCCCCCHHHHHHHHhcChhHHHhhCCCeEEEEEECCcCchHH
Confidence            35677788889999999999999997  456899999999999999999999996543 667888799999998654  3


Q ss_pred             HHHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCC--cEEEEEeCCCCCChHHHhhhccCCCCCEEEEEcCCCCCC
Q 042541          233 KAIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIE--AILLVLDDVWPGSESLLQKLGFQLPDYKILVTSRSEFPQ  309 (695)
Q Consensus       233 ~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~--~~LlVlDdv~~~~~~~~~~l~~~~~gs~iivTtR~~~~~  309 (695)
                      ...+..++..+..............+.+...+ ..+.++  |+||||||||+..  .+..   ..+||+||||||++...
T Consensus       196 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LlvlDd~~~~~--~~~~---~~~~~~ilvTtR~~~~~  270 (1249)
T 3sfz_A          196 LMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDPW--VLKA---FDNQCQILLTTRDKSVT  270 (1249)
T ss_dssp             HHHHHHHHHHHTTTCTTCSSCCSSHHHHHHHHHHHTSSSSCSCEEEEESCCCHH--HHTT---TCSSCEEEEEESSTTTT
T ss_pred             HHHHHHHHHHhhhhcccccCCCCCHHHHHHHHHHHHhccCCCEEEEEecCCCHH--HHHh---hcCCCEEEEEcCCHHHH
Confidence            44466777777654322111111223334444 556666  9999999999753  2333   46899999999998543


Q ss_pred             -----CCCeEecCC-CChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHHHhhCCCCHHHHHHHHHHh
Q 042541          310 -----FGSVHYLKP-LTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGGSLCGKHEVFWQRMVKEC  383 (695)
Q Consensus       310 -----~~~~~~l~~-L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~~~L~~~~~~~w~~~l~~~  383 (695)
                           ....+++++ |+++||++||...++...    ...++.+++|+++|+|+||||+++|++|+.++ ..|...++.+
T Consensus       271 ~~~~~~~~~~~~~~~l~~~~a~~l~~~~~~~~~----~~~~~~~~~i~~~~~glPLal~~~~~~l~~~~-~~~~~~l~~l  345 (1249)
T 3sfz_A          271 DSVMGPKHVVPVESGLGREKGLEILSLFVNMKK----EDLPAEAHSIIKECKGSPLVVSLIGALLRDFP-NRWAYYLRQL  345 (1249)
T ss_dssp             TTCCSCBCCEECCSSCCHHHHHHHHHHHHTSCS----TTCCTHHHHHHHHTTTCHHHHHHHHHHHHHSS-SCHHHHHHHH
T ss_pred             HhhcCCceEEEecCCCCHHHHHHHHHHhhCCCh----hhCcHHHHHHHHHhCCCHHHHHHHHHHhhcCh-hHHHHHHHHH
Confidence                 224789996 999999999998885432    23567899999999999999999999998776 4688788776


Q ss_pred             cCCC-Cc-----cCchhhHHHHHHHHHHhccHHHHHHHhhhcccCCCcccChHHHHHHHHHhhCCChhHHHHHHHHHHhh
Q 042541          384 SRGE-SV-----FQSKNDILDCLGSSLDVLNNEVKECYLDLCSFPEDQRIPITALIDMWMELYELVDDVFAITNLHELSS  457 (695)
Q Consensus       384 ~~~~-~~-----~~~~~~i~~~l~~s~~~L~~~~k~cf~~ls~fp~~~~i~~~~Li~~W~~~~~~~~~~~~~~~l~~L~~  457 (695)
                      .... ..     ....+.+..++.+||+.||+++|.||+|||+||+++.|+.+.++.+|.++    + +.++++|++|++
T Consensus       346 ~~~~~~~~~~~~~~~~~~~~~~l~~s~~~L~~~~~~~~~~l~~f~~~~~i~~~~~~~~~~~~----~-~~~~~~l~~L~~  420 (1249)
T 3sfz_A          346 QNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLWDLE----T-EEVEDILQEFVN  420 (1249)
T ss_dssp             HSCCCCCSSCTTCTTHHHHHHHHHHHHHTSCTTTHHHHHHGGGSCTTCCEEHHHHHHHHTCC----H-HHHHHHHHHHHH
T ss_pred             hhhhhhhcccccccchHHHHHHHHHHHHhCCHHHHHHHHHhCccCCCCeeCHHHHHHHhCCC----H-HHHHHHHHHHHh
Confidence            4432 11     11234799999999999999999999999999999999999999999542    3 388999999999


Q ss_pred             ccccchhhccccCCCCCCCCCcceehhHHHHHHHHHhccCC
Q 042541          458 QNLVDRVVTRKTAGDYGCYNDDFVMQHDLLRELTICRSKSE  498 (695)
Q Consensus       458 ~sLl~~~~~~~~~~~~~~~~~~~~~mHdlv~~~a~~~~~~e  498 (695)
                      +|||+...         .+...+|+||++||++|+..+.++
T Consensus       421 ~sl~~~~~---------~~~~~~~~~h~l~~~~~~~~~~~~  452 (1249)
T 3sfz_A          421 KSLLFCNR---------NGKSFCYYLHDLQVDFLTEKNRSQ  452 (1249)
T ss_dssp             TTSCEEEE---------SSSSEEEECCHHHHHHHHHHTGGG
T ss_pred             ccceEEec---------CCCceEEEecHHHHHHHHhhhhHH
Confidence            99998632         233457999999999999987765

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=100.00  E-value=7.8e-40  Score=367.88  Aligned_cols=284  Identities=18%  Similarity=0.266  Sum_probs=224.8

Q ss_pred             CCCCCCcchHHHHHHHHHc-CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcC
Q 042541          166 VISPGLDVPLKELKMELFK-DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKG  244 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~-~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~  244 (695)
                      ...|||+.++++|.++|.. ++.++|+|+||||+||||||+++|++.+++.+|+.+++|+++++.++...++..|+..++
T Consensus       128 k~~VGRe~eLeeL~elL~~~d~~RVV~IvGmGGIGKTTLAk~Vy~d~rV~~~Fd~gV~WVsVs~~~d~~~IL~~Ll~lL~  207 (1221)
T 1vt4_I          128 KYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLY  207 (1221)
T ss_dssp             CSCCCCHHHHHHHHHHHHHCCSSCEEEECCSTTSSHHHHHHHHHHHCHHHHHHSSCEEEEECCCSSSHHHHHHHHHHHHH
T ss_pred             CCCCCcHHHHHHHHHHHhccCCCeEEEEEcCCCccHHHHHHHHHHhhHHHHhCCCcEEEEEeCCCCCHHHHHHHHHHHHh
Confidence            3459999999999999985 558999999999999999999999987889999988999999999998888888777542


Q ss_pred             CCC---CCC----CCh----HHHHHHHHHHHHhcCCCcEEEEEeCCCCCChHHHhhhccCCCCCEEEEEcCCCCCC---C
Q 042541          245 YPV---PEF----QTD----EAAINDLERFFKQMRIEAILLVLDDVWPGSESLLQKLGFQLPDYKILVTSRSEFPQ---F  310 (695)
Q Consensus       245 ~~~---~~~----~~~----~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~~~~~l~~~~~gs~iivTtR~~~~~---~  310 (695)
                      ...   ...    ...    +...+.+...++.+.++++||||||||+..  .+..+.   +||+||||||++...   .
T Consensus       208 ~i~~~~~~~~d~~~~ip~~leeL~e~Lr~lL~~l~~KRvLLVLDDVwd~e--qLe~f~---pGSRILVTTRd~~Va~~l~  282 (1221)
T 1vt4_I          208 QIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAK--AWNAFN---LSCKILLTTRFKQVTDFLS  282 (1221)
T ss_dssp             HHCSSSTTTSCCCSSHHHHHHHHHHHHHHHHHHSTTSSCEEEEESCCCHH--HHHHHH---SSCCEEEECSCSHHHHHHH
T ss_pred             hcCcccccccccccCCCCCHHHHHHHHHHHHHhhcCCCEEEEEeCcChHH--HHHhhC---CCeEEEEeccChHHHHhcC
Confidence            211   000    011    222344444444558999999999999843  355553   899999999998532   1


Q ss_pred             -CCeEecC------CCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHHHhhCCC--CHHHHHHHHH
Q 042541          311 -GSVHYLK------PLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGGSLCGK--HEVFWQRMVK  381 (695)
Q Consensus       311 -~~~~~l~------~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~~~L~~~--~~~~w~~~l~  381 (695)
                       ...|.++      +|+.+|||+||.+.....       ..++..+|   |+|+||||+++|+.|+.+  +.++|...  
T Consensus       283 g~~vy~LeL~d~dL~LS~eEA~eLF~~~~g~~-------~eeL~~eI---CgGLPLALkLaGs~Lr~k~~s~eeW~~~--  350 (1221)
T 1vt4_I          283 AATTTHISLDHHSMTLTPDEVKSLLLKYLDCR-------PQDLPREV---LTTNPRRLSIIAESIRDGLATWDNWKHV--  350 (1221)
T ss_dssp             HHSSCEEEECSSSSCCCHHHHHHHHHHHHCCC-------TTTHHHHH---CCCCHHHHHHHHHHHHHSCSSHHHHHHC--
T ss_pred             CCeEEEecCccccCCcCHHHHHHHHHHHcCCC-------HHHHHHHH---hCCCHHHHHHHHHHHhCCCCCHHHHhcC--
Confidence             1256666      999999999999884221       23344444   999999999999999877  67888631  


Q ss_pred             HhcCCCCccCchhhHHHHHHHHHHhccHHH-HHHHhhhcccCCCcccChHHHHHHHHHhhCCChhHHHHHHHHHHhhccc
Q 042541          382 ECSRGESVFQSKNDILDCLGSSLDVLNNEV-KECYLDLCSFPEDQRIPITALIDMWMELYELVDDVFAITNLHELSSQNL  460 (695)
Q Consensus       382 ~~~~~~~~~~~~~~i~~~l~~s~~~L~~~~-k~cf~~ls~fp~~~~i~~~~Li~~W~~~~~~~~~~~~~~~l~~L~~~sL  460 (695)
                                ....+..++.+||+.||++. |+||++||+||+++.|+.+.++.+|++++   ++ .++.+|++|+++||
T Consensus       351 ----------~~~~I~aaLelSYd~Lp~eelK~cFL~LAIFPed~~I~~elLa~LW~aeG---ee-dAe~~L~eLvdRSL  416 (1221)
T 1vt4_I          351 ----------NCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVI---KS-DVMVVVNKLHKYSL  416 (1221)
T ss_dssp             ----------SCHHHHHHHHHHHHHSCTTHHHHHHHHTTSSCTTSCEEHHHHHHHHCSSC---SH-HHHHHHHHHHTSSS
T ss_pred             ----------ChhHHHHHHHHHHHhCCHHHHHHHHHHHhCCCCCCCCCHHHHHHHhcCCC---HH-HHHHHHHHHHhhCC
Confidence                      23689999999999999999 99999999999999999999999998765   22 68899999999999


Q ss_pred             cchhhccccCCCCCCCCCcceehhHHHHHHH
Q 042541          461 VDRVVTRKTAGDYGCYNDDFVMQHDLLRELT  491 (695)
Q Consensus       461 l~~~~~~~~~~~~~~~~~~~~~mHdlv~~~a  491 (695)
                      |+..           .+..+|+|||++++++
T Consensus       417 Lq~d-----------~~~~rYrMHDLllELr  436 (1221)
T 1vt4_I          417 VEKQ-----------PKESTISIPSIYLELK  436 (1221)
T ss_dssp             SSBC-----------SSSSEEBCCCHHHHHH
T ss_pred             EEEe-----------CCCCEEEehHHHHHHh
Confidence            9962           1246799999999966

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=100.00  E-value=3.1e-36  Score=340.46  Aligned_cols=312  Identities=20%  Similarity=0.301  Sum_probs=234.3

Q ss_pred             CCCCCCCCCCCCCcchHHHHHHHHH--cCCceEEEEEcCCCCcHHHHHHHHhccccc-cccCCCcEEEEEeCCCCCHHHH
Q 042541          159 CSAPDPPVISPGLDVPLKELKMELF--KDGRQFIVVSAPGGYGKTTLVQRLCKDDQV-QGKFKDDIFYVTVSKNPNVKAI  235 (695)
Q Consensus       159 ~~~~~~~~~~vGr~~~~~~l~~~L~--~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~-~~~f~~~~~wv~~~~~~~~~~~  235 (695)
                      .++|..+..||||+.++++|.++|.  .++.++|+|+||||+||||||++++++.++ ..+|+.+++|++++.. +...+
T Consensus       117 ~~~P~~~~~~vGR~~~l~~L~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~~~~f~~~v~wv~~~~~-~~~~~  195 (591)
T 1z6t_A          117 GGVPQRPVVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQ-DKSGL  195 (591)
T ss_dssp             TTCCCCCSSCCCCHHHHHHHHHHHTTSTTSCEEEEEECCTTSSHHHHHHHHHCCHHHHHHHCTTCEEEEEEESC-CHHHH
T ss_pred             CCCCCCCCeecccHHHHHHHHHHHhcccCCCceEEEEcCCCCCHHHHHHHHHhchhHHHhhCCCceEEEECCCC-chHHH
Confidence            3566777889999999999999997  346799999999999999999999997655 7889766999999876 33333


Q ss_pred             HHH---HHHhcCCCC----CCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChHHHhhhccCCCCCEEEEEcCCCCC
Q 042541          236 VQK---VLHHKGYPV----PEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSESLLQKLGFQLPDYKILVTSRSEFP  308 (695)
Q Consensus       236 ~~~---i~~~l~~~~----~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~~~~~l~~~~~gs~iivTtR~~~~  308 (695)
                      +..   +...++...    ............+...+.. +.+++||||||+|+..  .+..+   .+|++||||||+...
T Consensus       196 ~~~l~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~-~~~~~LLVLDdv~~~~--~l~~l---~~~~~ilvTsR~~~~  269 (591)
T 1z6t_A          196 LMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLR-KHPRSLLILDDVWDSW--VLKAF---DSQCQILLTTRDKSV  269 (591)
T ss_dssp             HHHHHHHHHHHCSSCCSCSSCCCSHHHHHHHHHHHHHH-TCTTCEEEEEEECCHH--HHHTT---CSSCEEEEEESCGGG
T ss_pred             HHHHHHHHHHhccccccccCCCCCHHHHHHHHHHHHcc-CCCCeEEEEeCCCCHH--HHHHh---cCCCeEEEECCCcHH
Confidence            333   344554211    1112333344444444421 3479999999999742  34433   678999999999843


Q ss_pred             C---CCCeEec---CCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHHHhhCCCCHHHHHHHHHH
Q 042541          309 Q---FGSVHYL---KPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGGSLCGKHEVFWQRMVKE  382 (695)
Q Consensus       309 ~---~~~~~~l---~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~~~L~~~~~~~w~~~l~~  382 (695)
                      .   .+..+++   ++|+.+|+++||...++...    ....+.+.+|+++|+|+||||.++|+.++..+ ..|...+..
T Consensus       270 ~~~~~~~~~~v~~l~~L~~~ea~~L~~~~~~~~~----~~~~~~~~~i~~~~~G~PLal~~~a~~l~~~~-~~w~~~l~~  344 (591)
T 1z6t_A          270 TDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKK----ADLPEQAHSIIKECKGSPLVVSLIGALLRDFP-NRWEYYLKQ  344 (591)
T ss_dssp             GTTCCSCEEEEECCSSCCHHHHHHHHHHHHTSCG----GGSCTHHHHHHHHHTTCHHHHHHHHHHHHHST-TCHHHHHHH
T ss_pred             HHhcCCCceEeecCCCCCHHHHHHHHHHHhCCCc----ccccHHHHHHHHHhCCCcHHHHHHHHHHhcCc-hhHHHHHHH
Confidence            2   2345555   58999999999999886421    12356799999999999999999999998764 368777776


Q ss_pred             hcCCCC------ccCchhhHHHHHHHHHHhccHHHHHHHhhhcccCCCcccChHHHHHHHHHhhCCChhHHHHHHHHHHh
Q 042541          383 CSRGES------VFQSKNDILDCLGSSLDVLNNEVKECYLDLCSFPEDQRIPITALIDMWMELYELVDDVFAITNLHELS  456 (695)
Q Consensus       383 ~~~~~~------~~~~~~~i~~~l~~s~~~L~~~~k~cf~~ls~fp~~~~i~~~~Li~~W~~~~~~~~~~~~~~~l~~L~  456 (695)
                      +.....      ......++..++..||+.||++.|.||++||+||+++.|+.+.+..+|..    +.+ .+..++++|+
T Consensus       345 l~~~~~~~~~~~~~~~~~~l~~~l~~s~~~L~~~~~~~l~~la~f~~~~~i~~~~l~~l~~~----~~~-~~~~~l~~L~  419 (591)
T 1z6t_A          345 LQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCILWDM----ETE-EVEDILQEFV  419 (591)
T ss_dssp             HHSCCCCCSSCCCSSCCHHHHHHHHHHHHTSCTTTHHHHHHGGGCCTTCCEEHHHHHHHHTC----CHH-HHHHHHHHHH
T ss_pred             HHHhHHHHhhhccccchHHHHHHHHHHHHhCCHHHHHHHHHccccCCCCccCHHHHHHHhcc----CHH-HHHHHHHHHH
Confidence            653221      11233579999999999999999999999999999999999999999953    233 6889999999


Q ss_pred             hccccchhhccccCCCCCCCCCcceehhHHHHHHHHHhcc
Q 042541          457 SQNLVDRVVTRKTAGDYGCYNDDFVMQHDLLRELTICRSK  496 (695)
Q Consensus       457 ~~sLl~~~~~~~~~~~~~~~~~~~~~mHdlv~~~a~~~~~  496 (695)
                      ++|||+...         .+...+|+||+++|++++....
T Consensus       420 ~~~Ll~~~~---------~~~~~~~~~H~lv~~~~~~~~~  450 (591)
T 1z6t_A          420 NKSLLFCDR---------NGKSFRYYLHDLQVDFLTEKNC  450 (591)
T ss_dssp             HTTSSEEEE---------ETTEEEEECCHHHHHHHHHHTG
T ss_pred             hCcCeEEec---------CCCccEEEEcHHHHHHHHhhhh
Confidence            999998532         1234579999999999988744

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=99.71  E-value=1.6e-15  Score=159.15  Aligned_cols=287  Identities=11%  Similarity=0.054  Sum_probs=177.9

Q ss_pred             CCCCCCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC------CHHHH
Q 042541          162 PDPPVISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP------NVKAI  235 (695)
Q Consensus       162 ~~~~~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~------~~~~~  235 (695)
                      +..+..|+||+.++++|.+++..+  +++.|+|++|+|||||++++++.  .    +  ++|+++....      +...+
T Consensus         8 ~~~~~~~~gR~~el~~L~~~l~~~--~~v~i~G~~G~GKT~Ll~~~~~~--~----~--~~~~~~~~~~~~~~~~~~~~~   77 (350)
T 2qen_A            8 KTRREDIFDREEESRKLEESLENY--PLTLLLGIRRVGKSSLLRAFLNE--R----P--GILIDCRELYAERGHITREEL   77 (350)
T ss_dssp             CCSGGGSCSCHHHHHHHHHHHHHC--SEEEEECCTTSSHHHHHHHHHHH--S----S--EEEEEHHHHHHTTTCBCHHHH
T ss_pred             CCChHhcCChHHHHHHHHHHHhcC--CeEEEECCCcCCHHHHHHHHHHH--c----C--cEEEEeecccccccCCCHHHH
Confidence            345567899999999999988764  79999999999999999999873  2    1  6688876542      56677


Q ss_pred             HHHHHHhcCCC----------------CCC--CCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCh-------HH---H
Q 042541          236 VQKVLHHKGYP----------------VPE--FQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSE-------SL---L  287 (695)
Q Consensus       236 ~~~i~~~l~~~----------------~~~--~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~-------~~---~  287 (695)
                      +..+.+.+...                ...  ........+.+.....  ..++++||+||++....       ..   +
T Consensus        78 ~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~--~~~~~vlvlDe~~~~~~~~~~~~~~~~~~L  155 (350)
T 2qen_A           78 IKELQSTISPFQKFQSKFKISLNLKFLTLEPRKLSLREVFRELNDLGE--ELGEFIVAFDEAQYLRFYGSRGGKELLALF  155 (350)
T ss_dssp             HHHHHHHSCSHHHHHHHHTCCCCCGGGTSCGGGCCHHHHHHHHHHHHH--HHSCEEEEEETGGGGGGBTTTTTHHHHHHH
T ss_pred             HHHHHHHHHHHHhHhhhceeEEEecceeeccccchHHHHHHHHHHHHh--ccCCEEEEEeCHHHHhccCccchhhHHHHH
Confidence            77777665420                000  0111222222222221  11389999999976432       22   2


Q ss_pred             hhhccCCCCCEEEEEcCCCC-------------CCC---CCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHH
Q 042541          288 QKLGFQLPDYKILVTSRSEF-------------PQF---GSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKIL  351 (695)
Q Consensus       288 ~~l~~~~~gs~iivTtR~~~-------------~~~---~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~  351 (695)
                      ..+....++.++|+|++...             .-.   ...+.+.+|+.+|+.+++.........   ....+.+.+|+
T Consensus       156 ~~~~~~~~~~~~il~g~~~~~l~~~l~~~~~~~~l~~~~~~~i~l~pl~~~e~~~~l~~~~~~~~~---~~~~~~~~~i~  232 (350)
T 2qen_A          156 AYAYDSLPNLKIILTGSEVGLLHDFLKITDYESPLYGRIAGEVLVKPFDKDTSVEFLKRGFREVNL---DVPENEIEEAV  232 (350)
T ss_dssp             HHHHHHCTTEEEEEEESSHHHHHHHHCTTCTTSTTTTCCCEEEECCCCCHHHHHHHHHHHHHTTTC---CCCHHHHHHHH
T ss_pred             HHHHHhcCCeEEEEECCcHHHHHHHHhhcCCCCccccCccceeeCCCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHH
Confidence            22222235788999876531             011   127899999999999999875432211   12356789999


Q ss_pred             HhcCCchhHHHHHHHhhCC-CCHHHHHHHHHHhcCCCCccCchhhHHHHHHHHHHhc---cHHHHHHHhhhcccCCCccc
Q 042541          352 RACKGCPLALKVVGGSLCG-KHEVFWQRMVKECSRGESVFQSKNDILDCLGSSLDVL---NNEVKECYLDLCSFPEDQRI  427 (695)
Q Consensus       352 ~~c~G~PLai~~~~~~L~~-~~~~~w~~~l~~~~~~~~~~~~~~~i~~~l~~s~~~L---~~~~k~cf~~ls~fp~~~~i  427 (695)
                      +.|+|+|+++..++..+.. .+...+   +....         +.+...+...+..+   ++..+..+..+|.  ..  +
T Consensus       233 ~~tgG~P~~l~~~~~~~~~~~~~~~~---~~~~~---------~~~~~~~~~~l~~l~~~~~~~~~~l~~la~--g~--~  296 (350)
T 2qen_A          233 ELLDGIPGWLVVFGVEYLRNGDFGRA---MKRTL---------EVAKGLIMGELEELRRRSPRYVDILRAIAL--GY--N  296 (350)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCCHHHH---HHHHH---------HHHHHHHHHHHHHHHHHCHHHHHHHHHHHT--TC--C
T ss_pred             HHhCCCHHHHHHHHHHHhccccHhHH---HHHHH---------HHHHHHHHHHHHHHHhCChhHHHHHHHHHh--CC--C
Confidence            9999999999998875422 222222   11110         11122222233344   7888999988887  22  3


Q ss_pred             ChHHHHHHHHHhh-CCChhHHHHHHHHHHhhccccchhhccccCCCCCCCCCcceehhHHHHHHHH
Q 042541          428 PITALIDMWMELY-ELVDDVFAITNLHELSSQNLVDRVVTRKTAGDYGCYNDDFVMQHDLLRELTI  492 (695)
Q Consensus       428 ~~~~Li~~W~~~~-~~~~~~~~~~~l~~L~~~sLl~~~~~~~~~~~~~~~~~~~~~mHdlv~~~a~  492 (695)
                      +...+........ .+... ....+++.|.+.+||...            +..|.-.|++++++.+
T Consensus       297 ~~~~l~~~~~~~~~~~~~~-~~~~~l~~L~~~gli~~~------------~~~y~~~~p~~~~~~~  349 (350)
T 2qen_A          297 RWSLIRDYLAVKGTKIPEP-RLYALLENLKKMNWIVEE------------DNTYKIADPVVATVLR  349 (350)
T ss_dssp             SHHHHHHHHHHTTCCCCHH-HHHHHHHHHHHTTSEEEE------------TTEEEESSHHHHHHHT
T ss_pred             CHHHHHHHHHHHhCCCCHH-HHHHHHHHHHhCCCEEec------------CCEEEEecHHHHHHHc
Confidence            4455544432221 34443 778999999999999852            1233345888888753

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=99.67  E-value=6.1e-16  Score=166.25  Aligned_cols=284  Identities=17%  Similarity=0.067  Sum_probs=177.8

Q ss_pred             CCCCCCCcchHHHHHHHH-H----c--CCceEEEE--EcCCCCcHHHHHHHHhccccccc-----cCCCcEEEEEeCCCC
Q 042541          165 PVISPGLDVPLKELKMEL-F----K--DGRQFIVV--SAPGGYGKTTLVQRLCKDDQVQG-----KFKDDIFYVTVSKNP  230 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L-~----~--~~~~vv~I--~G~gGiGKTtLa~~~~~~~~~~~-----~f~~~~~wv~~~~~~  230 (695)
                      +..++||+.++++|..++ .    .  ...+.+.|  +|++|+||||||+.+++.  ...     .+...++|+++....
T Consensus        21 p~~l~gR~~el~~l~~~l~~~~~~~~~~~~~~~li~i~G~~G~GKT~L~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~   98 (412)
T 1w5s_A           21 PPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKR--VSEAAAKEGLTVKQAYVNAFNAP   98 (412)
T ss_dssp             CSSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHH--HHHHHHHTTCCEEEEEEEGGGCC
T ss_pred             CCCCCChHHHHHHHHHHHhHHHhcCCCCCCCEEEEeCcCcCCCCHHHHHHHHHHH--HHHHHhccCCceeEEEEECCCCC
Confidence            467899999999999988 4    2  34567777  999999999999999984  322     234446788887778


Q ss_pred             CHHHHHHHHHHhcCCCCCCC-CChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCC------hHHHh----hhccC---C--
Q 042541          231 NVKAIVQKVLHHKGYPVPEF-QTDEAAINDLERFFKQMRIEAILLVLDDVWPGS------ESLLQ----KLGFQ---L--  294 (695)
Q Consensus       231 ~~~~~~~~i~~~l~~~~~~~-~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~------~~~~~----~l~~~---~--  294 (695)
                      +...++..++.+++...+.. .........+...+.. .+++++|||||++...      ...+.    .+...   .  
T Consensus        99 ~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~-~~~~~llvlDe~~~l~~~~~~~~~~l~~l~~~~~~~~~~~~~  177 (412)
T 1w5s_A           99 NLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYV-ENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGV  177 (412)
T ss_dssp             SHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHH-HTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCTTSC
T ss_pred             CHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHh-cCCeEEEEEeCHHHHhhccCcchHHHHHHHHHHHhcccCCCC
Confidence            89999999999987654321 1223334444444421 3679999999997632      22222    22111   1  


Q ss_pred             CCCEEEEEcCCCC-------------CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcC------
Q 042541          295 PDYKILVTSRSEF-------------PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACK------  355 (695)
Q Consensus       295 ~gs~iivTtR~~~-------------~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~------  355 (695)
                      .+..+|+||+...             ......+.+++++.++++++|...+..... ......+.+..|++.|+      
T Consensus       178 ~~v~lI~~~~~~~~~~~l~~~~~~~~~~~~~~i~l~~l~~~e~~~ll~~~~~~~~~-~~~~~~~~~~~i~~~~~~~~~~~  256 (412)
T 1w5s_A          178 NRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLR-DTVWEPRHLELISDVYGEDKGGD  256 (412)
T ss_dssp             CBEEEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHHBC-TTSCCHHHHHHHHHHHCGGGTSC
T ss_pred             ceEEEEEEeccccHHHHHhhhcchhhhhcCCeeeeCCCCHHHHHHHHHHHHHhcCC-CCCCChHHHHHHHHHHHHhccCC
Confidence            3345777886431             112234999999999999999765431111 11123678899999999      


Q ss_pred             CchhHHHHHHHhh------CCC---CHHHHHHHHHHhcCCCCccCchhhHHHHHHHHHHhccHHHHHHHhhhcccC--CC
Q 042541          356 GCPLALKVVGGSL------CGK---HEVFWQRMVKECSRGESVFQSKNDILDCLGSSLDVLNNEVKECYLDLCSFP--ED  424 (695)
Q Consensus       356 G~PLai~~~~~~L------~~~---~~~~w~~~l~~~~~~~~~~~~~~~i~~~l~~s~~~L~~~~k~cf~~ls~fp--~~  424 (695)
                      |.|..+..++...      ...   +.+.+...+.....           ...+..++..||++.+.++..++.+.  .+
T Consensus       257 G~p~~~~~l~~~a~~~a~~~~~~~i~~~~v~~~~~~~~~-----------~~~~~~~l~~l~~~~~~~l~aia~l~~~~~  325 (412)
T 1w5s_A          257 GSARRAIVALKMACEMAEAMGRDSLSEDLVRKAVSENEA-----------ASIQTHELEALSIHELIILRLIAEATLGGM  325 (412)
T ss_dssp             CCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHC-----------------CCSSSSSCHHHHHHHHHHHHHHHTTC
T ss_pred             CcHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhc-----------cchHHHHHHcCCHHHHHHHHHHHHHHhcCC
Confidence            9997665554321      111   12333322222100           12334456789999999998888654  33


Q ss_pred             cccChHHHHHHHHHhh----C---CChhHHHHHHHHHHhhccccchh
Q 042541          425 QRIPITALIDMWMELY----E---LVDDVFAITNLHELSSQNLVDRV  464 (695)
Q Consensus       425 ~~i~~~~Li~~W~~~~----~---~~~~~~~~~~l~~L~~~sLl~~~  464 (695)
                      ..++...+...+....    .   +.. .....++++|++.+||...
T Consensus       326 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~l~~L~~~gli~~~  371 (412)
T 1w5s_A          326 EWINAGLLRQRYEDASLTMYNVKPRGY-TQYHIYLKHLTSLGLVDAK  371 (412)
T ss_dssp             SSBCHHHHHHHHHHHHHHHSCCCCCCH-HHHHHHHHHHHHTTSEEEE
T ss_pred             CCccHHHHHHHHHHHHHhhcCCCCCCH-HHHHHHHHHHHhCCCEEee
Confidence            3555655555443211    1   222 3677899999999999864

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=99.67  E-value=4.1e-15  Score=156.39  Aligned_cols=287  Identities=15%  Similarity=0.100  Sum_probs=169.7

Q ss_pred             CCCCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCC-----CCHHHHHHH
Q 042541          164 PPVISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKN-----PNVKAIVQK  238 (695)
Q Consensus       164 ~~~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~-----~~~~~~~~~  238 (695)
                      .+..|+||+.+++.|.+ +..   +++.|+|++|+|||||++++++.  ...    .++|+++...     .+...++..
T Consensus        11 ~~~~~~gR~~el~~L~~-l~~---~~v~i~G~~G~GKT~L~~~~~~~--~~~----~~~~~~~~~~~~~~~~~~~~~~~~   80 (357)
T 2fna_A           11 NRKDFFDREKEIEKLKG-LRA---PITLVLGLRRTGKSSIIKIGINE--LNL----PYIYLDLRKFEERNYISYKDFLLE   80 (357)
T ss_dssp             SGGGSCCCHHHHHHHHH-TCS---SEEEEEESTTSSHHHHHHHHHHH--HTC----CEEEEEGGGGTTCSCCCHHHHHHH
T ss_pred             CHHHhcChHHHHHHHHH-hcC---CcEEEECCCCCCHHHHHHHHHHh--cCC----CEEEEEchhhccccCCCHHHHHHH
Confidence            45678999999999999 654   69999999999999999999873  322    2569988743     344555544


Q ss_pred             HHHhcC--------------C----CCCCCC-C------hHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCh-------HH
Q 042541          239 VLHHKG--------------Y----PVPEFQ-T------DEAAINDLERFFKQMRIEAILLVLDDVWPGSE-------SL  286 (695)
Q Consensus       239 i~~~l~--------------~----~~~~~~-~------~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~-------~~  286 (695)
                      +.+.+.              .    +.+... .      .......+.+.+.....++++|||||++....       ..
T Consensus        81 l~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~vlvlDe~~~~~~~~~~~~~~~  160 (357)
T 2fna_A           81 LQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASKDNVIIVLDEAQELVKLRGVNLLPA  160 (357)
T ss_dssp             HHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCSSCEEEEEETGGGGGGCTTCCCHHH
T ss_pred             HHHHHHHHhhhhhHHHHHhcccceEEecceEEEeccCCcchhhHHHHHHHHHhcCCCCeEEEEECHHHhhccCchhHHHH
Confidence            443321              0    000000 0      00112233333322222499999999965321       12


Q ss_pred             HhhhccCCCCCEEEEEcCCCC--------C-----CC---CCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHH
Q 042541          287 LQKLGFQLPDYKILVTSRSEF--------P-----QF---GSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKI  350 (695)
Q Consensus       287 ~~~l~~~~~gs~iivTtR~~~--------~-----~~---~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I  350 (695)
                      +..+....++.++|+|++...        .     ..   ...+.+.+|+.+|+.+++..........  .  .+ ...|
T Consensus       161 l~~~~~~~~~~~~i~~g~~~~~l~~~l~~~~~~~~l~~r~~~~i~l~~l~~~e~~~~l~~~~~~~~~~--~--~~-~~~i  235 (357)
T 2fna_A          161 LAYAYDNLKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADID--F--KD-YEVV  235 (357)
T ss_dssp             HHHHHHHCTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHHTCC--C--CC-HHHH
T ss_pred             HHHHHHcCCCeEEEEEcCchHHHHHHHhccCCCCccccCccceeecCCCCHHHHHHHHHHHHHHcCCC--C--Cc-HHHH
Confidence            333322235788999988641        0     11   2378999999999999998754211111  1  11 2889


Q ss_pred             HHhcCCchhHHHHHHHhhCC-CCHHHHHHHHHHhcCCCCccCchhhHHHHHHHHH---HhccHHHHHHHhhhcccCCCcc
Q 042541          351 LRACKGCPLALKVVGGSLCG-KHEVFWQRMVKECSRGESVFQSKNDILDCLGSSL---DVLNNEVKECYLDLCSFPEDQR  426 (695)
Q Consensus       351 ~~~c~G~PLai~~~~~~L~~-~~~~~w~~~l~~~~~~~~~~~~~~~i~~~l~~s~---~~L~~~~k~cf~~ls~fp~~~~  426 (695)
                      ++.|+|+|+++..++..+.. .+...|-..+.+.        ....+...+.-.+   ..||+..+..+..+|.   +. 
T Consensus       236 ~~~t~G~P~~l~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~l~~~~~~~~~l~~~~~~~l~~la~---g~-  303 (357)
T 2fna_A          236 YEKIGGIPGWLTYFGFIYLDNKNLDFAINQTLEY--------AKKLILKEFENFLHGREIARKRYLNIMRTLSK---CG-  303 (357)
T ss_dssp             HHHHCSCHHHHHHHHHHHHHHCCHHHHHHHHHHH--------HHHHHHHHHHHHHTTCGGGHHHHHHHHHHHTT---CB-
T ss_pred             HHHhCCCHHHHHHHHHHHccccchHHHHHHHHHH--------HHHHHHHHHHHHhhccccccHHHHHHHHHHHc---CC-
Confidence            99999999999999876542 2333332111000        0011112222111   1688899999999988   22 


Q ss_pred             cChHHHHHHHHHhhC--CChhHHHHHHHHHHhhccccchhhccccCCCCCCCCCcceehhHHHHHHH
Q 042541          427 IPITALIDMWMELYE--LVDDVFAITNLHELSSQNLVDRVVTRKTAGDYGCYNDDFVMQHDLLRELT  491 (695)
Q Consensus       427 i~~~~Li~~W~~~~~--~~~~~~~~~~l~~L~~~sLl~~~~~~~~~~~~~~~~~~~~~mHdlv~~~a  491 (695)
                       +...+.........  +... ....+++.|++.+||....            ..|.-.|++++++.
T Consensus       304 -~~~~l~~~~~~~~g~~~~~~-~~~~~L~~L~~~gli~~~~------------~~y~f~~~~~~~~l  356 (357)
T 2fna_A          304 -KWSDVKRALELEEGIEISDS-EIYNYLTQLTKHSWIIKEG------------EKYCPSEPLISLAF  356 (357)
T ss_dssp             -CHHHHHHHHHHHHCSCCCHH-HHHHHHHHHHHTTSEEESS------------SCEEESSHHHHHHT
T ss_pred             -CHHHHHHHHHHhcCCCCCHH-HHHHHHHHHHhCCCEEecC------------CEEEecCHHHHHhh
Confidence             44444432211112  4443 7789999999999998521            12333688988764

>4fcg_A Uncharacterized protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, LRR, N- and C-terminal helices; 2.00A {Xanthomonas campestris PV}

Probab=99.62  E-value=3.4e-15  Score=154.93  Aligned_cols=159  Identities=19%  Similarity=0.270  Sum_probs=110.8

Q ss_pred             cceEEeeecCCcccCCCCC-CCCCceEEEEEEccCccccCChhhcC---------CCCCcEEEEcccCCCCcccCccccc
Q 042541          528 NASLLSISTDETFSSNWPD-MQGPEVKVVVLNIRTKKYVLPDFLQK---------MDELKVLIVTNYGFSPAELNNFRVL  597 (695)
Q Consensus       528 ~~r~l~~~~~~~~~~~~~~-~~~~~l~~L~l~~~~~~~~~p~~~~~---------l~~Lr~L~l~~~~~~~~~~~~~~~l  597 (695)
                      ..++|.+..+... ..+.. ..+++|+.|.++.|...+.+|..+..         +++|++|++++|.+.  .++  ..+
T Consensus       128 ~L~~L~Ls~n~l~-~lp~~l~~l~~L~~L~L~~n~~~~~~p~~~~~~~~~~~~~~l~~L~~L~L~~n~l~--~lp--~~l  202 (328)
T 4fcg_A          128 GLETLTLARNPLR-ALPASIASLNRLRELSIRACPELTELPEPLASTDASGEHQGLVNLQSLRLEWTGIR--SLP--ASI  202 (328)
T ss_dssp             TCSEEEEESCCCC-CCCGGGGGCTTCCEEEEEEETTCCCCCSCSEEEC-CCCEEESTTCCEEEEEEECCC--CCC--GGG
T ss_pred             CCCEEECCCCccc-cCcHHHhcCcCCCEEECCCCCCccccChhHhhccchhhhccCCCCCEEECcCCCcC--cch--Hhh
Confidence            4555555544322 11211 24566666666666555556654433         666777777666553  222  236


Q ss_pred             ccCCCCcEEEeccCCCCCcc-cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCC
Q 042541          598 SALSKLKKIRLEHVSLPNSL-ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVS  676 (695)
Q Consensus       598 ~~l~~L~~L~L~~~~l~~lp-~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~  676 (695)
                      +.+++|++|+|++|.+..+| .++++++|++|+|++|.+.+..|..+.    .+++|++|++++|+.++.+|..++++++
T Consensus       203 ~~l~~L~~L~L~~N~l~~l~~~l~~l~~L~~L~Ls~n~~~~~~p~~~~----~l~~L~~L~L~~n~~~~~~p~~~~~l~~  278 (328)
T 4fcg_A          203 ANLQNLKSLKIRNSPLSALGPAIHHLPKLEELDLRGCTALRNYPPIFG----GRAPLKRLILKDCSNLLTLPLDIHRLTQ  278 (328)
T ss_dssp             GGCTTCCEEEEESSCCCCCCGGGGGCTTCCEEECTTCTTCCBCCCCTT----CCCCCCEEECTTCTTCCBCCTTGGGCTT
T ss_pred             cCCCCCCEEEccCCCCCcCchhhccCCCCCEEECcCCcchhhhHHHhc----CCCCCCEEECCCCCchhhcchhhhcCCC
Confidence            77788888888888888777 788888888888888776666665554    7888999999988888888988899999


Q ss_pred             CceeecccccCCCCCCCCC
Q 042541          677 MEKLRITNCHRLSALPEGI  695 (695)
Q Consensus       677 L~~L~l~~~~~l~~lP~~i  695 (695)
                      |++|+|++|+.++.+|.++
T Consensus       279 L~~L~L~~n~~~~~iP~~l  297 (328)
T 4fcg_A          279 LEKLDLRGCVNLSRLPSLI  297 (328)
T ss_dssp             CCEEECTTCTTCCCCCGGG
T ss_pred             CCEEeCCCCCchhhccHHH
Confidence            9999999988888888753

>4fcg_A Uncharacterized protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, LRR, N- and C-terminal helices; 2.00A {Xanthomonas campestris PV}

Probab=99.62  E-value=3.1e-15  Score=155.19  Aligned_cols=161  Identities=16%  Similarity=0.237  Sum_probs=112.8

Q ss_pred             ccceEEeeecCCcccCCCCC-CCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcc------ccccc
Q 042541          527 NNASLLSISTDETFSSNWPD-MQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNF------RVLSA  599 (695)
Q Consensus       527 ~~~r~l~~~~~~~~~~~~~~-~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~------~~l~~  599 (695)
                      ...++|.+..+... ..+.. ..+++|+.|.++.+... .+|..+.++++|++|++++|.........+      ..++.
T Consensus       104 ~~L~~L~L~~n~l~-~lp~~~~~l~~L~~L~Ls~n~l~-~lp~~l~~l~~L~~L~L~~n~~~~~~p~~~~~~~~~~~~~~  181 (328)
T 4fcg_A          104 SHLQHMTIDAAGLM-ELPDTMQQFAGLETLTLARNPLR-ALPASIASLNRLRELSIRACPELTELPEPLASTDASGEHQG  181 (328)
T ss_dssp             TTCSEEEEESSCCC-CCCSCGGGGTTCSEEEEESCCCC-CCCGGGGGCTTCCEEEEEEETTCCCCCSCSEEEC-CCCEEE
T ss_pred             CCCCEEECCCCCcc-chhHHHhccCCCCEEECCCCccc-cCcHHHhcCcCCCEEECCCCCCccccChhHhhccchhhhcc
Confidence            35667776655433 22222 35777888888777555 677778888888888888765432211111      11345


Q ss_pred             CCCCcEEEeccCCCCCcc-cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCc
Q 042541          600 LSKLKKIRLEHVSLPNSL-ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSME  678 (695)
Q Consensus       600 l~~L~~L~L~~~~l~~lp-~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~  678 (695)
                      +++|++|++++|.++.+| .++++++|++|+|++|.++.+|+.+.     .+++|++|++++|+..+.+|..++.+++|+
T Consensus       182 l~~L~~L~L~~n~l~~lp~~l~~l~~L~~L~L~~N~l~~l~~~l~-----~l~~L~~L~Ls~n~~~~~~p~~~~~l~~L~  256 (328)
T 4fcg_A          182 LVNLQSLRLEWTGIRSLPASIANLQNLKSLKIRNSPLSALGPAIH-----HLPKLEELDLRGCTALRNYPPIFGGRAPLK  256 (328)
T ss_dssp             STTCCEEEEEEECCCCCCGGGGGCTTCCEEEEESSCCCCCCGGGG-----GCTTCCEEECTTCTTCCBCCCCTTCCCCCC
T ss_pred             CCCCCEEECcCCCcCcchHhhcCCCCCCEEEccCCCCCcCchhhc-----cCCCCCEEECcCCcchhhhHHHhcCCCCCC
Confidence            778888888888888888 78888888888888888877776544     778888888888877778888888888888


Q ss_pred             eeecccccCCCCCCCC
Q 042541          679 KLRITNCHRLSALPEG  694 (695)
Q Consensus       679 ~L~l~~~~~l~~lP~~  694 (695)
                      +|++++|+.++.+|..
T Consensus       257 ~L~L~~n~~~~~~p~~  272 (328)
T 4fcg_A          257 RLILKDCSNLLTLPLD  272 (328)
T ss_dssp             EEECTTCTTCCBCCTT
T ss_pred             EEECCCCCchhhcchh
Confidence            8888888777777764

>3qfl_A MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-binding domain, L rich repeat containing receptors, protein binding; 2.00A {Hordeum vulgare}

Probab=99.58  E-value=1.4e-15  Score=129.69  Aligned_cols=78  Identities=18%  Similarity=0.176  Sum_probs=73.0

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhhhchHHHHHHHHHHHhhhHHHHHHHHh--hhccCCChHHHHHHHHHHHHHHHHHHhccc
Q 042541            9 ALLGAVFGELLKAVSEEKDKAVTFKDRLEQLESTLRNSIPWIEEIEKL--NQVLDRPKQETENLVRMMEQVEQLVRKCSK   86 (695)
Q Consensus         9 a~~~~v~~kl~~~l~~~~~~~~~~~~~l~~L~~~L~~i~~~l~~ae~~--~~~~~~~~~wl~~l~~~~~d~ed~ld~~~~   86 (695)
                      |+++++++|+.+++.+|+.+..++++++++|+++|+.|+++|.||+.+  +..+..++.|+++||+++||+|||||+|.+
T Consensus         1 a~v~~ll~KL~~ll~~E~~l~~gv~~~i~~Lk~eL~~m~a~L~da~~~~~~~~d~~vk~W~~~vrdlaYD~ED~iD~f~~   80 (115)
T 3qfl_A            1 AAISNLIPKLGELLTEEFKLHKGVKKNIEDLGKELESMNAALIKIGEVPREQLDSQDKLWADEVRELSYVIEDVVDKFLV   80 (115)
T ss_dssp             CTTCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCGGGCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHHHHHHHHHhccccCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            357889999999999999999999999999999999999999999987  456777899999999999999999999997

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=99.51  E-value=1.9e-12  Score=137.79  Aligned_cols=284  Identities=17%  Similarity=0.128  Sum_probs=181.4

Q ss_pred             CCCCCCCcchHHHHHHHHHc----CCce--EEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHH
Q 042541          165 PVISPGLDVPLKELKMELFK----DGRQ--FIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQK  238 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~----~~~~--vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~  238 (695)
                      |+.++||+.+++++..++..    ....  .+.|+|++|+|||||++.+++  .........++|++++...+...++..
T Consensus        16 p~~l~gr~~~~~~l~~~l~~~~~~~~~~~~~~li~G~~G~GKTtl~~~l~~--~~~~~~~~~~~~i~~~~~~~~~~~~~~   93 (389)
T 1fnn_A           16 PKRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWE--LYKDKTTARFVYINGFIYRNFTAIIGE   93 (389)
T ss_dssp             CSCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHH--HHTTSCCCEEEEEETTTCCSHHHHHHH
T ss_pred             CCCCCChHHHHHHHHHHHHHHHcCCCCCCCeEEEECCCCCCHHHHHHHHHH--HHhhhcCeeEEEEeCccCCCHHHHHHH
Confidence            36789999999999998873    3334  899999999999999999987  333322334678888888888999999


Q ss_pred             HHHhcCCCCCCC-CChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChHHHhhhcc---C--C---CCCEEEEEcCCCC--
Q 042541          239 VLHHKGYPVPEF-QTDEAAINDLERFFKQMRIEAILLVLDDVWPGSESLLQKLGF---Q--L---PDYKILVTSRSEF--  307 (695)
Q Consensus       239 i~~~l~~~~~~~-~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~~~~~l~~---~--~---~gs~iivTtR~~~--  307 (695)
                      ++..++...+.. .........+...+.. .+++.+|||||++.........+..   .  .   .+..+|++|+...  
T Consensus        94 l~~~l~~~~~~~~~~~~~~~~~l~~~l~~-~~~~~vlilDE~~~l~~~~~~~L~~~~~~~~~~~~~~~~iI~~~~~~~~~  172 (389)
T 1fnn_A           94 IARSLNIPFPRRGLSRDEFLALLVEHLRE-RDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVL  172 (389)
T ss_dssp             HHHHTTCCCCSSCCCHHHHHHHHHHHHHH-TTCCEEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESSTHHH
T ss_pred             HHHHhCccCCCCCCCHHHHHHHHHHHHhh-cCCeEEEEEECccccchHHHHHHHHHHHhCCCCCcCCEEEEEEECCchHH
Confidence            999987654322 1233444444444432 4678999999998776443333321   1  1   3667888777551  


Q ss_pred             -C-------C-CCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhc---------CCchhHHHHHHHhhC
Q 042541          308 -P-------Q-FGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRAC---------KGCPLALKVVGGSLC  369 (695)
Q Consensus       308 -~-------~-~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c---------~G~PLai~~~~~~L~  369 (695)
                       .       . ....+.+++++.++..+++...+..... ...-..+....|++.+         +|.|..+..+.....
T Consensus       173 ~~l~~~~~~r~~~~~i~~~pl~~~~~~~~l~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~~~G~~r~~~~~l~~a~  251 (389)
T 1fnn_A          173 NNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAGLA-EGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILYRSA  251 (389)
T ss_dssp             HTSCHHHHHHHTTCEEECCCCBHHHHHHHHHHHHHHHBC-TTSSCHHHHHHHHHHHSBSSTTCTTSCCHHHHHHHHHHHH
T ss_pred             HHhCHHhhhcCCCceEEeCCCCHHHHHHHHHHHHHhhcC-CCCCCHHHHHHHHHHHhhcccCCCCCCcHHHHHHHHHHHH
Confidence             1       0 1126999999999999999887542111 0122467888999999         788765544432211


Q ss_pred             ------CC---CHHHHHHHHHHhcCCCCccCchhhHHHHHHHHHHhccHHHHHHHhhhcccC---CCcccChHHHHHHHH
Q 042541          370 ------GK---HEVFWQRMVKECSRGESVFQSKNDILDCLGSSLDVLNNEVKECYLDLCSFP---EDQRIPITALIDMWM  437 (695)
Q Consensus       370 ------~~---~~~~w~~~l~~~~~~~~~~~~~~~i~~~l~~s~~~L~~~~k~cf~~ls~fp---~~~~i~~~~Li~~W~  437 (695)
                            +.   +.+.....+.....            ..+...+..||++.+.++..++.+.   .+..+....+...+.
T Consensus       252 ~~a~~~~~~~i~~~~v~~~~~~~~~------------~~~~~~l~~l~~~~~~~L~~l~~~~~~~~~~~~~~~~i~~~~~  319 (389)
T 1fnn_A          252 YAAQQNGRKHIAPEDVRKSSKEVLF------------GISEEVLIGLPLHEKLFLLAIVRSLKISHTPYITFGDAEESYK  319 (389)
T ss_dssp             HHHHHTTCSSCCHHHHHHHHHHHSC------------CCCHHHHHHSCHHHHHHHHHHHHHHHHHCSSCEEHHHHHHHHH
T ss_pred             HHHHHhCCCCcCHHHHHHHHHHHhh------------hhHHHHHHcCCHHHHHHHHHHHHHHhhccCCCccHHHHHHHHH
Confidence                  11   22222223322211            1123446788888888887777654   222456666666554


Q ss_pred             Hh----h--CCChhHHHHHHHHHHhhccccchhh
Q 042541          438 EL----Y--ELVDDVFAITNLHELSSQNLVDRVV  465 (695)
Q Consensus       438 ~~----~--~~~~~~~~~~~l~~L~~~sLl~~~~  465 (695)
                      ..    +  .+.. ....+++++|...++|....
T Consensus       320 ~~~~~~~~~~~~~-~~~~~~l~~L~~~gli~~~~  352 (389)
T 1fnn_A          320 IVCEEYGERPRVH-SQLWSYLNDLREKGIVETRQ  352 (389)
T ss_dssp             HHHHHTTCCCCCH-HHHHHHHHHHHHTTSSEEEE
T ss_pred             HHHHHcCCCCCCH-HHHHHHHHHHHhCCCeEEee
Confidence            31    1  1223 37789999999999998744

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=99.49  E-value=3.1e-12  Score=135.79  Aligned_cols=283  Identities=15%  Similarity=0.112  Sum_probs=174.8

Q ss_pred             CCCCCCCcchHHHHHHHHH----cCCceEEEEEcCCCCcHHHHHHHHhccccc----cccC-CCcEEEEEeCCCC-CHHH
Q 042541          165 PVISPGLDVPLKELKMELF----KDGRQFIVVSAPGGYGKTTLVQRLCKDDQV----QGKF-KDDIFYVTVSKNP-NVKA  234 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~----~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~----~~~f-~~~~~wv~~~~~~-~~~~  234 (695)
                      |+.++||+.+++++..++.    ....+.+.|+|++|+||||||+.+++...-    ...+ ...++|+++.... +...
T Consensus        19 p~~l~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~   98 (384)
T 2qby_B           19 FKEIPFREDILRDAAIAIRYFVKNEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNCREVGGTPQA   98 (384)
T ss_dssp             CSSCTTCHHHHHHHHHHHHHHHTTCCCCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEEHHHHCSCHHH
T ss_pred             CCCCCChHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEECccCCCCHHH
Confidence            3678999999999988776    334678999999999999999999983211    1123 4447788887777 8888


Q ss_pred             HHHHHHHhc-CCCCCCC-CChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCC----hHH-HhhhccCCCCCEEEEEcCCCC
Q 042541          235 IVQKVLHHK-GYPVPEF-QTDEAAINDLERFFKQMRIEAILLVLDDVWPGS----ESL-LQKLGFQLPDYKILVTSRSEF  307 (695)
Q Consensus       235 ~~~~i~~~l-~~~~~~~-~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~----~~~-~~~l~~~~~gs~iivTtR~~~  307 (695)
                      ++..++..+ +...+.. .........   +.+.+..++.+|||||++...    ... +..+.....+..+|+||+...
T Consensus        99 ~~~~l~~~l~~~~~~~~~~~~~~~~~~---l~~~l~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~~~~~iI~~t~~~~  175 (384)
T 2qby_B           99 VLSSLAGKLTGFSVPKHGINLGEYIDK---IKNGTRNIRAIIYLDEVDTLVKRRGGDIVLYQLLRSDANISVIMISNDIN  175 (384)
T ss_dssp             HHHHHHHHHHCSCCCSSSSCTHHHHHH---HHHHHSSSCEEEEEETTHHHHHSTTSHHHHHHHHTSSSCEEEEEECSSTT
T ss_pred             HHHHHHHHhcCCCCCCCCCCHHHHHHH---HHHHhccCCCEEEEECHHHhccCCCCceeHHHHhcCCcceEEEEEECCCc
Confidence            999988887 3222111 112222333   334455555699999996532    122 333333236788998988652


Q ss_pred             ----------CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcC---Cchh-HHHHHHHh--hC-C
Q 042541          308 ----------PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACK---GCPL-ALKVVGGS--LC-G  370 (695)
Q Consensus       308 ----------~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~---G~PL-ai~~~~~~--L~-~  370 (695)
                                ...+..+.+++++.++..++|...+...... ..-..+..+.|++.|+   |.|. ++..+-..  +. +
T Consensus       176 ~~~~l~~~l~sr~~~~i~l~~l~~~~~~~il~~~~~~~~~~-~~~~~~~~~~i~~~~~~~~G~~r~a~~~l~~a~~~a~~  254 (384)
T 2qby_B          176 VRDYMEPRVLSSLGPSVIFKPYDAEQLKFILSKYAEYGLIK-GTYDDEILSYIAAISAKEHGDARKAVNLLFRAAQLASG  254 (384)
T ss_dssp             TTTTSCHHHHHTCCCEEEECCCCHHHHHHHHHHHHHHTSCT-TSCCSHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHTTS
T ss_pred             hHhhhCHHHHhcCCCeEEECCCCHHHHHHHHHHHHHhhccc-CCcCHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHhcC
Confidence                      1223489999999999999999875321110 1123566788888888   9887 33333222  22 1


Q ss_pred             ---CCHHHHHHHHHHhcCCCCccCchhhHHHHHHHHHHhccHHHHHHHhhhcccCCCcccChHHHHHHHHHhh--CCChh
Q 042541          371 ---KHEVFWQRMVKECSRGESVFQSKNDILDCLGSSLDVLNNEVKECYLDLCSFPEDQRIPITALIDMWMELY--ELVDD  445 (695)
Q Consensus       371 ---~~~~~w~~~l~~~~~~~~~~~~~~~i~~~l~~s~~~L~~~~k~cf~~ls~fp~~~~i~~~~Li~~W~~~~--~~~~~  445 (695)
                         -+.+.+...+.+..            ...+..++..|+++.+..+..++....+..+. .......-..+  .... 
T Consensus       255 ~~~i~~~~v~~~~~~~~------------~~~~~~~~~~l~~~~~~~l~al~~~~~~~~~~-~~~~~~~~~~g~~~~~~-  320 (384)
T 2qby_B          255 GGIIRKEHVDKAIVDYE------------QERLIEAVKALPFHYKLALRSLIESEDVMSAH-KMYTDLCNKFKQKPLSY-  320 (384)
T ss_dssp             SSCCCHHHHHHHHHHHH------------HHHHHHHHHSSCHHHHHHHHHHHTCCBHHHHH-HHHHHHHHHTTCCCCCH-
T ss_pred             CCccCHHHHHHHHHHHh------------cchHHHHHHcCCHHHHHHHHHHHHhcccChHH-HHHHHHHHHcCCCCCCH-
Confidence               14556655554321            23466678889988888777776611101111 11111111122  1222 


Q ss_pred             HHHHHHHHHHhhccccchhh
Q 042541          446 VFAITNLHELSSQNLVDRVV  465 (695)
Q Consensus       446 ~~~~~~l~~L~~~sLl~~~~  465 (695)
                      ....++++.|...|+++...
T Consensus       321 ~~~~~~l~~L~~~gli~~~~  340 (384)
T 2qby_B          321 RRFSDIISELDMFGIVKIRI  340 (384)
T ss_dssp             HHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHHhCCCEEEEe
Confidence            47889999999999998643

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=99.47  E-value=2.4e-12  Score=136.71  Aligned_cols=284  Identities=14%  Similarity=0.084  Sum_probs=176.2

Q ss_pred             CCCCCCCcchHHHHHHHHH----cCCceEEEEEcCCCCcHHHHHHHHhcccccccc-----CCCcEEEEEeCCCCCHHHH
Q 042541          165 PVISPGLDVPLKELKMELF----KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGK-----FKDDIFYVTVSKNPNVKAI  235 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~----~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~-----f~~~~~wv~~~~~~~~~~~  235 (695)
                      ++.++||+.+++++..++.    ....+.+.|+|++|+||||||+.+++.  ....     ....++|+++....+...+
T Consensus        18 p~~~~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~l~~~~~~~--~~~~~~~~~~~~~~~~i~~~~~~~~~~~   95 (387)
T 2v1u_A           18 PDVLPHREAELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRR--LEARASSLGVLVKPIYVNARHRETPYRV   95 (387)
T ss_dssp             CSCCTTCHHHHHHHHHTTGGGTSSCCCCCEEECBCTTSSHHHHHHHHHHH--HHHHHHHHTCCEEEEEEETTTSCSHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHH--HHHHHhccCCCeEEEEEECCcCCCHHHH
Confidence            4678999999999999885    245678999999999999999999873  3221     1334678888888899999


Q ss_pred             HHHHHHhcCCCCCCCCC-hHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCh-----HHHhh-hccC-----CCCCEEEEEc
Q 042541          236 VQKVLHHKGYPVPEFQT-DEAAINDLERFFKQMRIEAILLVLDDVWPGSE-----SLLQK-LGFQ-----LPDYKILVTS  303 (695)
Q Consensus       236 ~~~i~~~l~~~~~~~~~-~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~-----~~~~~-l~~~-----~~gs~iivTt  303 (695)
                      +..++..++...+.... .......+...+.. .+++.+|||||++....     ..+.. +...     ..+..+|+||
T Consensus        96 ~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~-~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~I~~t  174 (387)
T 2v1u_A           96 ASAIAEAVGVRVPFTGLSVGEVYERLVKRLSR-LRGIYIIVLDEIDFLPKRPGGQDLLYRITRINQELGDRVWVSLVGIT  174 (387)
T ss_dssp             HHHHHHHHSCCCCSSCCCHHHHHHHHHHHHTT-SCSEEEEEEETTTHHHHSTTHHHHHHHHHHGGGCC-----CEEEEEC
T ss_pred             HHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhc-cCCeEEEEEccHhhhcccCCCChHHHhHhhchhhcCCCceEEEEEEE
Confidence            99999998765433221 22323333333321 46789999999975421     22222 2111     3456777777


Q ss_pred             CCCCC----------CCCC-eEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcC---CchhHHH-HHHHhh
Q 042541          304 RSEFP----------QFGS-VHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACK---GCPLALK-VVGGSL  368 (695)
Q Consensus       304 R~~~~----------~~~~-~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~---G~PLai~-~~~~~L  368 (695)
                      +....          ..+. .+.+++++.++..+++...+...... ..-..+..+.|++.++   |.|..+. .+..+.
T Consensus       175 ~~~~~~~~l~~~l~~r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~G~~r~~~~~l~~a~  253 (387)
T 2v1u_A          175 NSLGFVENLEPRVKSSLGEVELVFPPYTAPQLRDILETRAEEAFNP-GVLDPDVVPLCAALAAREHGDARRALDLLRVAG  253 (387)
T ss_dssp             SCSTTSSSSCHHHHTTTTSEECCBCCCCHHHHHHHHHHHHHHHBCT-TTBCSSHHHHHHHHHHSSSCCHHHHHHHHHHHH
T ss_pred             CCCchHhhhCHHHHhcCCCeEEeeCCCCHHHHHHHHHHHHHhhccC-CCCCHHHHHHHHHHHHHhccCHHHHHHHHHHHH
Confidence            76511          1222 78999999999999998875321110 1112456788888888   9994333 322221


Q ss_pred             C-----C-C--CHHHHHHHHHHhcCCCCccCchhhHHHHHHHHHHhccHHHHHHHhhhc-ccCCCcccChHHHHHHHHH-
Q 042541          369 C-----G-K--HEVFWQRMVKECSRGESVFQSKNDILDCLGSSLDVLNNEVKECYLDLC-SFPEDQRIPITALIDMWME-  438 (695)
Q Consensus       369 ~-----~-~--~~~~w~~~l~~~~~~~~~~~~~~~i~~~l~~s~~~L~~~~k~cf~~ls-~fp~~~~i~~~~Li~~W~~-  438 (695)
                      .     + .  +.+.+...+....            ...+.-++..|+++.+..+..++ ++-....+....+.+.... 
T Consensus       254 ~~a~~~~~~~i~~~~v~~a~~~~~------------~~~~~~~~~~l~~~~~~~l~a~~~~~~~~~~~~~~~~~~~~~~~  321 (387)
T 2v1u_A          254 EIAERRREERVRREHVYSARAEIE------------RDRVSEVVRTLPLHAKLVLLSIMMLEDGGRPASTGEIYERYKEL  321 (387)
T ss_dssp             HHHHHTTCSCBCHHHHHHHHHHHH------------HHHHHHHHHSSCHHHHHHHHHHHHHSSSSCCEEHHHHHHHHHHH
T ss_pred             HHHHHcCCCCcCHHHHHHHHHHHh------------hchHHHHHHcCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHH
Confidence            1     1 1  3445544444321            22455677889998887776665 4432234555544444322 


Q ss_pred             ---hh--CCChhHHHHHHHHHHhhccccchhh
Q 042541          439 ---LY--ELVDDVFAITNLHELSSQNLVDRVV  465 (695)
Q Consensus       439 ---~~--~~~~~~~~~~~l~~L~~~sLl~~~~  465 (695)
                         .+  .... ..+.+++++|...|+++...
T Consensus       322 ~~~~~~~~~~~-~~~~~~l~~L~~~gli~~~~  352 (387)
T 2v1u_A          322 TSTLGLEHVTL-RRVSGIISELDMLGIVKSRV  352 (387)
T ss_dssp             HHHTTCCCCCH-HHHHHHHHHHHHTTSEEEEE
T ss_pred             HHhcCCCCCCH-HHHHHHHHHHHhCCCeEEEe
Confidence               11  1122 47889999999999998743

>2o6q_A Variable lymphocyte receptor A; leucine-rich repeat protein, LRR, immune system; 2.50A {Eptatretus burgeri}

Probab=99.46  E-value=8.8e-13  Score=132.74  Aligned_cols=158  Identities=17%  Similarity=0.255  Sum_probs=87.0

Q ss_pred             ccceEEeeecCCcccCCC-CCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcE
Q 042541          527 NNASLLSISTDETFSSNW-PDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKK  605 (695)
Q Consensus       527 ~~~r~l~~~~~~~~~~~~-~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~  605 (695)
                      ...++|.+..+....... ....+++|+.|.++.+......+..+.++++|++|++++|.+...  + ...+..+++|++
T Consensus        37 ~~l~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~i~~~~~~~l~~L~~L~l~~n~l~~~--~-~~~~~~l~~L~~  113 (270)
T 2o6q_A           37 ADTKKLDLQSNKLSSLPSKAFHRLTKLRLLYLNDNKLQTLPAGIFKELKNLETLWVTDNKLQAL--P-IGVFDQLVNLAE  113 (270)
T ss_dssp             TTCSEEECCSSCCSCCCTTSSSSCTTCCEEECCSSCCSCCCTTTTSSCTTCCEEECCSSCCCCC--C-TTTTTTCSSCCE
T ss_pred             CCCCEEECcCCCCCeeCHHHhcCCCCCCEEECCCCccCeeChhhhcCCCCCCEEECCCCcCCcC--C-HhHcccccCCCE
Confidence            455666665543322111 122566677777766644433333456667777777776654311  1 112455666666


Q ss_pred             EEeccCCCCCcc--cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchh-hcCCCCCceeec
Q 042541          606 IRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDG-LCDIVSMEKLRI  682 (695)
Q Consensus       606 L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~-i~~L~~L~~L~l  682 (695)
                      |++++|.++.+|  .++.+++|++|+|++|.++.+++..+.    .+++|+.|++++| .+..+|.. +.++++|++|++
T Consensus       114 L~l~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~----~l~~L~~L~L~~n-~l~~~~~~~~~~l~~L~~L~L  188 (270)
T 2o6q_A          114 LRLDRNQLKSLPPRVFDSLTKLTYLSLGYNELQSLPKGVFD----KLTSLKELRLYNN-QLKRVPEGAFDKLTELKTLKL  188 (270)
T ss_dssp             EECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTT----TCTTCCEEECCSS-CCSCCCTTTTTTCTTCCEEEC
T ss_pred             EECCCCccCeeCHHHhCcCcCCCEEECCCCcCCccCHhHcc----CCcccceeEecCC-cCcEeChhHhccCCCcCEEEC
Confidence            666666666555  455666666666666666666655444    5666666666654 34444433 556666666666


Q ss_pred             ccccCCCCCCC
Q 042541          683 TNCHRLSALPE  693 (695)
Q Consensus       683 ~~~~~l~~lP~  693 (695)
                      ++|. +..+|.
T Consensus       189 ~~N~-l~~~~~  198 (270)
T 2o6q_A          189 DNNQ-LKRVPE  198 (270)
T ss_dssp             CSSC-CSCCCT
T ss_pred             CCCc-CCcCCH
Confidence            6643 555554

>2ell_A Acidic leucine-rich nuclear phosphoprotein 32 FAM B; phapi2 protein, silver-stainable protein SSP29, acidic prote in leucines, structural genomics; NMR {Homo sapiens} PDB: 2rr6_A 2jqd_A

Probab=99.46  E-value=1.9e-13  Score=126.88  Aligned_cols=136  Identities=17%  Similarity=0.197  Sum_probs=114.2

Q ss_pred             CCCceEEEEEEccCcc-ccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCC-cc-ccccccc
Q 042541          548 QGPEVKVVVLNIRTKK-YVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPN-SL-ATVRMNH  624 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~-~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~-lp-~i~~l~~  624 (695)
                      .+++++.|.++.+... +.+|..+..+++|++|++++|.+...     ..++.+++|++|++++|.+.. +| .++++++
T Consensus        22 ~~~~L~~L~l~~n~l~~~~i~~~~~~l~~L~~L~l~~n~l~~~-----~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~   96 (168)
T 2ell_A           22 TPAAVRELVLDNCKSNDGKIEGLTAEFVNLEFLSLINVGLISV-----SNLPKLPKLKKLELSENRIFGGLDMLAEKLPN   96 (168)
T ss_dssp             CTTSCSEEECCSCBCBTTBCSSCCGGGGGCCEEEEESSCCCCC-----SSCCCCSSCCEEEEESCCCCSCCCHHHHHCTT
T ss_pred             CcccCCEEECCCCCCChhhHHHHHHhCCCCCEEeCcCCCCCCh-----hhhccCCCCCEEECcCCcCchHHHHHHhhCCC
Confidence            3467888888887655 57888889999999999999877432     448899999999999999996 77 7778999


Q ss_pred             ccEEeeccccCCcccc-cchhhhcccCCCccEEecccccccccCch----hhcCCCCCceeecccccCCCCCCCC
Q 042541          625 LQKVSLVMCNVGQVFR-NSTFRISDAFPNLLEMDIDYCNDLIELPD----GLCDIVSMEKLRITNCHRLSALPEG  694 (695)
Q Consensus       625 L~~L~l~~~~i~~~~~-~~~~~l~~~l~~L~~L~l~~c~~l~~lP~----~i~~L~~L~~L~l~~~~~l~~lP~~  694 (695)
                      |++|++++|.++.++. ..+.    .+++|++|++++| .+..+|.    .+..+++|++|++++|. ...+|.+
T Consensus        97 L~~L~Ls~N~l~~~~~~~~l~----~l~~L~~L~l~~N-~l~~~~~~~~~~~~~l~~L~~L~l~~n~-~~~~~~~  165 (168)
T 2ell_A           97 LTHLNLSGNKLKDISTLEPLK----KLECLKSLDLFNC-EVTNLNDYRESVFKLLPQLTYLDGYDRE-DQEAPDS  165 (168)
T ss_dssp             CCEEECBSSSCCSSGGGGGGS----SCSCCCEEECCSS-GGGTSTTHHHHHHTTCSSCCEETTEETT-SCBCCSS
T ss_pred             CCEEeccCCccCcchhHHHHh----cCCCCCEEEeeCC-cCcchHHHHHHHHHhCccCcEecCCCCC-hhhcccc
Confidence            9999999999998763 3343    8999999999997 5677776    79999999999999976 7888864

>3m19_A Variable lymphocyte receptor A diversity region; adaptive immunity, antibody, T cell, leucine-rich repeat, immune system; 1.70A {Petromyzon marinus} PDB: 3m18_A

Probab=99.45  E-value=7.2e-13  Score=131.80  Aligned_cols=154  Identities=13%  Similarity=0.159  Sum_probs=122.0

Q ss_pred             CccceEEeeecCCcccCCCC-CCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCc
Q 042541          526 PNNASLLSISTDETFSSNWP-DMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLK  604 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~~~~~-~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~  604 (695)
                      +...+.|.+..+........ ...+++|+.|.++.+......|..+..+++|++|++++|.+...  + ...+..+++|+
T Consensus        34 ~~~l~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~--~-~~~~~~l~~L~  110 (251)
T 3m19_A           34 PADTEKLDLQSTGLATLSDATFRGLTKLTWLNLDYNQLQTLSAGVFDDLTELGTLGLANNQLASL--P-LGVFDHLTQLD  110 (251)
T ss_dssp             CTTCCEEECTTSCCCCCCTTTTTTCTTCCEEECTTSCCCCCCTTTTTTCTTCCEEECTTSCCCCC--C-TTTTTTCTTCC
T ss_pred             CCCCCEEEccCCCcCccCHhHhcCcccCCEEECCCCcCCccCHhHhccCCcCCEEECCCCccccc--C-hhHhcccCCCC
Confidence            45677888776554332222 23688999999998877777777889999999999999877421  1 12367889999


Q ss_pred             EEEeccCCCCCcc--cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCch-hhcCCCCCceee
Q 042541          605 KIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPD-GLCDIVSMEKLR  681 (695)
Q Consensus       605 ~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~-~i~~L~~L~~L~  681 (695)
                      +|+|++|.++.+|  .++.+++|++|+|++|.++.+++..+.    .+++|++|+|++| .+..+|. .+..+++|++|+
T Consensus       111 ~L~L~~N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~----~l~~L~~L~L~~N-~l~~~~~~~~~~l~~L~~L~  185 (251)
T 3m19_A          111 KLYLGGNQLKSLPSGVFDRLTKLKELRLNTNQLQSIPAGAFD----KLTNLQTLSLSTN-QLQSVPHGAFDRLGKLQTIT  185 (251)
T ss_dssp             EEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTT----TCTTCCEEECCSS-CCSCCCTTTTTTCTTCCEEE
T ss_pred             EEEcCCCcCCCcChhHhccCCcccEEECcCCcCCccCHHHcC----cCcCCCEEECCCC-cCCccCHHHHhCCCCCCEEE
Confidence            9999999999888  568899999999999999999887665    8999999999996 4566665 688999999999


Q ss_pred             cccccC
Q 042541          682 ITNCHR  687 (695)
Q Consensus       682 l~~~~~  687 (695)
                      +++|+.
T Consensus       186 l~~N~~  191 (251)
T 3m19_A          186 LFGNQF  191 (251)
T ss_dssp             CCSCCB
T ss_pred             eeCCce
Confidence            999773

>1ozn_A Reticulon 4 receptor; NOGO receptor, MAD, myelination inhibition, OMGP, MAG, NOGO- signal transduction, neuronal regeneration, ligand binding; HET: NDG MAN NAG BMA; 1.52A {Homo sapiens} SCOP: c.10.2.7 PDB: 1p8t_A* 3kj4_A*

Probab=99.43  E-value=1.4e-12  Score=132.42  Aligned_cols=137  Identities=16%  Similarity=0.142  Sum_probs=80.4

Q ss_pred             CCCceEEEEEEccC-ccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--ccccccc
Q 042541          548 QGPEVKVVVLNIRT-KKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNH  624 (695)
Q Consensus       548 ~~~~l~~L~l~~~~-~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~  624 (695)
                      .+++|+.|.++.+. .....|..+..+++|++|++++|.+....   ...+..+++|++|++++|.+..+|  .++++++
T Consensus        78 ~l~~L~~L~l~~n~~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~---~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~  154 (285)
T 1ozn_A           78 GLALLEQLDLSDNAQLRSVDPATFHGLGRLHTLHLDRCGLQELG---PGLFRGLAALQYLYLQDNALQALPDDTFRDLGN  154 (285)
T ss_dssp             TCTTCCEEECCSCTTCCCCCTTTTTTCTTCCEEECTTSCCCCCC---TTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTT
T ss_pred             CccCCCEEeCCCCCCccccCHHHhcCCcCCCEEECCCCcCCEEC---HhHhhCCcCCCEEECCCCcccccCHhHhccCCC
Confidence            45666666666654 33333555666666666666666543110   122556666666666666666555  4666666


Q ss_pred             ccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccccCCCCCC
Q 042541          625 LQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALP  692 (695)
Q Consensus       625 L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~~l~~lP  692 (695)
                      |++|++++|.++.+++..+.    .+++|+.|++++|......|..++++++|+.|++++|. +..+|
T Consensus       155 L~~L~l~~n~l~~~~~~~~~----~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~-l~~~~  217 (285)
T 1ozn_A          155 LTHLFLHGNRISSVPERAFR----GLHSLDRLLLHQNRVAHVHPHAFRDLGRLMTLYLFANN-LSALP  217 (285)
T ss_dssp             CCEEECCSSCCCEECTTTTT----TCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSC-CSCCC
T ss_pred             ccEEECCCCcccccCHHHhc----CccccCEEECCCCcccccCHhHccCcccccEeeCCCCc-CCcCC
Confidence            77777766666666665444    56666666666654333345566666666666666654 44444

>3rfs_A Internalin B, repeat modules, variable lymphocyte B; LRR, protein binding, plasma; 1.70A {Listeria monocytogenes} PDB: 3rfj_A

Probab=99.43  E-value=1e-12  Score=132.34  Aligned_cols=158  Identities=13%  Similarity=0.161  Sum_probs=123.8

Q ss_pred             CccceEEeeecCCcccCCCCCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcE
Q 042541          526 PNNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKK  605 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~~~~~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~  605 (695)
                      ....++|.+..+.... ......+++|+.|.++.+......|..+..+++|++|++++|.+...  . ...++.+++|++
T Consensus        62 l~~L~~L~l~~n~l~~-~~~l~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~--~-~~~~~~l~~L~~  137 (272)
T 3rfs_A           62 LPNVRYLALGGNKLHD-ISALKELTNLTYLILTGNQLQSLPNGVFDKLTNLKELVLVENQLQSL--P-DGVFDKLTNLTY  137 (272)
T ss_dssp             CTTCCEEECTTSCCCC-CGGGTTCTTCCEEECTTSCCCCCCTTTTTTCTTCCEEECTTSCCCCC--C-TTTTTTCTTCCE
T ss_pred             CCCCcEEECCCCCCCC-chhhcCCCCCCEEECCCCccCccChhHhcCCcCCCEEECCCCcCCcc--C-HHHhccCCCCCE
Confidence            3567788876654322 22234788999999988877666666789999999999999877421  1 122678999999


Q ss_pred             EEeccCCCCCcc--cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCch-hhcCCCCCceeec
Q 042541          606 IRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPD-GLCDIVSMEKLRI  682 (695)
Q Consensus       606 L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~-~i~~L~~L~~L~l  682 (695)
                      |++++|.++.+|  .++++++|++|++++|.++.+++..+.    .+++|++|++++|. +..+|. .++.+++|++|++
T Consensus       138 L~L~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~----~l~~L~~L~L~~N~-l~~~~~~~~~~l~~L~~L~l  212 (272)
T 3rfs_A          138 LNLAHNQLQSLPKGVFDKLTNLTELDLSYNQLQSLPEGVFD----KLTQLKDLRLYQNQ-LKSVPDGVFDRLTSLQYIWL  212 (272)
T ss_dssp             EECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTT----TCTTCCEEECCSSC-CSCCCTTTTTTCTTCCEEEC
T ss_pred             EECCCCccCccCHHHhccCccCCEEECCCCCcCccCHHHhc----CCccCCEEECCCCc-CCccCHHHHhCCcCCCEEEc
Confidence            999999999887  578999999999999999998888766    89999999999975 555554 4789999999999


Q ss_pred             ccccCCCCCC
Q 042541          683 TNCHRLSALP  692 (695)
Q Consensus       683 ~~~~~l~~lP  692 (695)
                      ++|+..+..|
T Consensus       213 ~~N~~~~~~~  222 (272)
T 3rfs_A          213 HDNPWDCTCP  222 (272)
T ss_dssp             CSSCBCCCTT
T ss_pred             cCCCccccCc
Confidence            9988665554

>3m19_A Variable lymphocyte receptor A diversity region; adaptive immunity, antibody, T cell, leucine-rich repeat, immune system; 1.70A {Petromyzon marinus} PDB: 3m18_A

Probab=99.43  E-value=1.5e-12  Score=129.41  Aligned_cols=136  Identities=13%  Similarity=0.179  Sum_probs=116.9

Q ss_pred             CCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--ccccccccc
Q 042541          549 GPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNHLQ  626 (695)
Q Consensus       549 ~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L~  626 (695)
                      .++++.|.++.+......|..+.++++|++|++++|.+...   ....+..+++|++|+|++|.++.+|  .++.+++|+
T Consensus        34 ~~~l~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~---~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~  110 (251)
T 3m19_A           34 PADTEKLDLQSTGLATLSDATFRGLTKLTWLNLDYNQLQTL---SAGVFDDLTELGTLGLANNQLASLPLGVFDHLTQLD  110 (251)
T ss_dssp             CTTCCEEECTTSCCCCCCTTTTTTCTTCCEEECTTSCCCCC---CTTTTTTCTTCCEEECTTSCCCCCCTTTTTTCTTCC
T ss_pred             CCCCCEEEccCCCcCccCHhHhcCcccCCEEECCCCcCCcc---CHhHhccCCcCCEEECCCCcccccChhHhcccCCCC
Confidence            36799999988877777777899999999999999877432   1223788999999999999999888  778999999


Q ss_pred             EEeeccccCCcccccchhhhcccCCCccEEecccccccccCch-hhcCCCCCceeecccccCCCCCCC
Q 042541          627 KVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPD-GLCDIVSMEKLRITNCHRLSALPE  693 (695)
Q Consensus       627 ~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~-~i~~L~~L~~L~l~~~~~l~~lP~  693 (695)
                      +|+|++|.++.+++..+.    .+++|++|+|++| .+..+|. .++.+++|++|+|++|. +..+|+
T Consensus       111 ~L~L~~N~l~~~~~~~~~----~l~~L~~L~Ls~N-~l~~~~~~~~~~l~~L~~L~L~~N~-l~~~~~  172 (251)
T 3m19_A          111 KLYLGGNQLKSLPSGVFD----RLTKLKELRLNTN-QLQSIPAGAFDKLTNLQTLSLSTNQ-LQSVPH  172 (251)
T ss_dssp             EEECCSSCCCCCCTTTTT----TCTTCCEEECCSS-CCCCCCTTTTTTCTTCCEEECCSSC-CSCCCT
T ss_pred             EEEcCCCcCCCcChhHhc----cCCcccEEECcCC-cCCccCHHHcCcCcCCCEEECCCCc-CCccCH
Confidence            999999999999998776    8999999999996 5777876 58999999999999976 777775

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=99.42  E-value=4.4e-12  Score=134.66  Aligned_cols=283  Identities=13%  Similarity=0.114  Sum_probs=172.3

Q ss_pred             CCCCCCCcchHHHHHHHHH----cCCceEEEEEcCCCCcHHHHHHHHhccccccccC--CCcEEEEEeCCCCCHHHHHHH
Q 042541          165 PVISPGLDVPLKELKMELF----KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKF--KDDIFYVTVSKNPNVKAIVQK  238 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~----~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f--~~~~~wv~~~~~~~~~~~~~~  238 (695)
                      ++.|+||+.+++.+.+++.    ....+.+.|+|++|+||||||+.+++  .....+  ...++|+++....+...++..
T Consensus        19 p~~~~gr~~e~~~l~~~l~~~~~~~~~~~vli~G~~G~GKTtl~~~l~~--~~~~~~~~~~~~~~i~~~~~~~~~~~~~~   96 (386)
T 2qby_A           19 PDELPHREDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLS--KLHKKFLGKFKHVYINTRQIDTPYRVLAD   96 (386)
T ss_dssp             CSCCTTCHHHHHHHHHSSGGGGGTCCCCCEEEEECTTSSHHHHHHHHHH--HHHHHTCSSCEEEEEEHHHHCSHHHHHHH
T ss_pred             CCCCCChHHHHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHH--HHHHHhcCCceEEEEECCCCCCHHHHHHH
Confidence            4678999999999999887    34467899999999999999999998  443333  334678888777788888888


Q ss_pred             HHHhcCCCCCCCC-ChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCC----hHHHhhh---c-c-CCCCCEEEEEcCCCC-
Q 042541          239 VLHHKGYPVPEFQ-TDEAAINDLERFFKQMRIEAILLVLDDVWPGS----ESLLQKL---G-F-QLPDYKILVTSRSEF-  307 (695)
Q Consensus       239 i~~~l~~~~~~~~-~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~----~~~~~~l---~-~-~~~gs~iivTtR~~~-  307 (695)
                      ++..++...+... ........+...+.. .+++.+||+|+++...    ...+..+   . . ...+..+|+||+... 
T Consensus        97 i~~~l~~~~~~~~~~~~~~~~~l~~~l~~-~~~~~vlilDE~~~l~~~~~~~~l~~l~~~~~~~~~~~~~~I~~~~~~~~  175 (386)
T 2qby_A           97 LLESLDVKVPFTGLSIAELYRRLVKAVRD-YGSQVVIVLDEIDAFVKKYNDDILYKLSRINSEVNKSKISFIGITNDVKF  175 (386)
T ss_dssp             HTTTTSCCCCSSSCCHHHHHHHHHHHHHT-CCSCEEEEEETHHHHHHSSCSTHHHHHHHHHHSCCC--EEEEEEESCGGG
T ss_pred             HHHHhCCCCCCCCCCHHHHHHHHHHHHhc-cCCeEEEEEcChhhhhccCcCHHHHHHhhchhhcCCCeEEEEEEECCCCh
Confidence            8888865433211 223334444444432 4568999999985421    1112222   1 1 223456677776541 


Q ss_pred             ---C------CCC-CeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcC---CchhHHHHHHHhh-C----
Q 042541          308 ---P------QFG-SVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACK---GCPLALKVVGGSL-C----  369 (695)
Q Consensus       308 ---~------~~~-~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~---G~PLai~~~~~~L-~----  369 (695)
                         .      ... ..+.+++++.++..+++...+..... ...-..+....|++.++   |.|..+..+.... .    
T Consensus       176 ~~~~~~~~~~r~~~~~i~l~~l~~~~~~~il~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~G~~r~~~~ll~~a~~~a~~  254 (386)
T 2qby_A          176 VDLLDPRVKSSLSEEEIIFPPYNAEELEDILTKRAQMAFK-PGVLPDNVIKLCAALAAREHGDARRALDLLRVSGEIAER  254 (386)
T ss_dssp             GGGCTTHHHHTTTTEEEEECCCCHHHHHHHHHHHHHHHBC-SSCSCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             HhhhCHHHhccCCCeeEEeCCCCHHHHHHHHHHHHHhhcc-CCCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHh
Confidence               0      111 37999999999999999876532111 11224667788888888   9998444332221 0    


Q ss_pred             -CC---CHHHHHHHHHHhcCCCCccCchhhHHHHHHHHHHhccHHHHHHHhhhcccCC-C-cccChHHHHHHHHH----h
Q 042541          370 -GK---HEVFWQRMVKECSRGESVFQSKNDILDCLGSSLDVLNNEVKECYLDLCSFPE-D-QRIPITALIDMWME----L  439 (695)
Q Consensus       370 -~~---~~~~w~~~l~~~~~~~~~~~~~~~i~~~l~~s~~~L~~~~k~cf~~ls~fp~-~-~~i~~~~Li~~W~~----~  439 (695)
                       +.   +.+.+...+.+.            ....+...+..||++.+..+..++.+.+ + ..+....+.+....    .
T Consensus       255 ~~~~~i~~~~v~~a~~~~------------~~~~~~~~~~~l~~~~~~il~ai~~~~~~g~~~~~~~~l~~~~~~~~~~~  322 (386)
T 2qby_A          255 MKDTKVKEEYVYMAKEEI------------ERDRVRDIILTLPFHSKLVLMAVVSISSEENVVSTTGAVYETYLNICKKL  322 (386)
T ss_dssp             TTCSSCCHHHHHHHHHHH------------HHHHHHHHHHTSCHHHHHHHHHHHHHC-----CEEHHHHHHHHHHHHHHH
T ss_pred             cCCCccCHHHHHHHHHHH------------hhchHHHHHHcCCHHHHHHHHHHHHHHhcCCCceeHHHHHHHHHHHHHhc
Confidence             11   234444333321            1234566678888887777766663321 1 22334444333221    1


Q ss_pred             hCCCh--hHHHHHHHHHHhhccccchh
Q 042541          440 YELVD--DVFAITNLHELSSQNLVDRV  464 (695)
Q Consensus       440 ~~~~~--~~~~~~~l~~L~~~sLl~~~  464 (695)
                      + ..+  ......+++.|...++|+..
T Consensus       323 g-~~~~~~~~~~~~l~~L~~~gli~~~  348 (386)
T 2qby_A          323 G-VEAVTQRRVSDIINELDMVGILTAK  348 (386)
T ss_dssp             T-CCCCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             C-CCCCCHHHHHHHHHHHHhCCCEEEE
Confidence            2 221  13678899999999999864

>3rgz_A Protein brassinosteroid insensitive 1; phytohormone, leucine-rich RE receptor-like kinases, leucine-rich repeat; HET: NAG BLD; 2.28A {Arabidopsis thaliana} PDB: 3rgx_A* 3riz_A* 3rj0_A*

Probab=99.40  E-value=8.1e-13  Score=153.31  Aligned_cols=164  Identities=12%  Similarity=0.062  Sum_probs=129.9

Q ss_pred             ccceEEeeecCCcccCCCCC-CCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCC---cccC----------
Q 042541          527 NNASLLSISTDETFSSNWPD-MQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSP---AELN----------  592 (695)
Q Consensus       527 ~~~r~l~~~~~~~~~~~~~~-~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~---~~~~----------  592 (695)
                      ...+.+.+..+......+.. ..+++|+.|.++.|...+.+|..+..+++|++|++++|.+.+   ..+.          
T Consensus       490 ~~L~~L~L~~N~l~~~~p~~~~~l~~L~~L~L~~N~l~~~~p~~l~~l~~L~~L~Ls~N~l~g~ip~~~~~~~~~~~~~~  569 (768)
T 3rgz_A          490 TNLNWISLSNNRLTGEIPKWIGRLENLAILKLSNNSFSGNIPAELGDCRSLIWLDLNTNLFNGTIPAAMFKQSGKIAANF  569 (768)
T ss_dssp             TTCCEEECCSSCCCSCCCGGGGGCTTCCEEECCSSCCEEECCGGGGGCTTCCEEECCSSEEESBCCGGGGTTTTCBCCST
T ss_pred             CCCCEEEccCCccCCcCChHHhcCCCCCEEECCCCcccCcCCHHHcCCCCCCEEECCCCccCCcCChHHhcccchhhhhc
Confidence            45667777655433222222 257888888888888888888888899999999998875431   1100          


Q ss_pred             ------------------------------------------------------cccccccCCCCcEEEeccCCCC-Ccc
Q 042541          593 ------------------------------------------------------NFRVLSALSKLKKIRLEHVSLP-NSL  617 (695)
Q Consensus       593 ------------------------------------------------------~~~~l~~l~~L~~L~L~~~~l~-~lp  617 (695)
                                                                            .++.++.+++|++|+|++|.++ .+|
T Consensus       570 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~~~~g~~~~~~~~l~~L~~LdLs~N~l~g~ip  649 (768)
T 3rgz_A          570 IAGKRYVYIKNDGMKKECHGAGNLLEFQGIRSEQLNRLSTRNPCNITSRVYGGHTSPTFDNNGSMMFLDMSYNMLSGYIP  649 (768)
T ss_dssp             TCSCEEEEEECCSCCTTCCSSEEEEECTTCCGGGGGGGGGTCCSCTTSCEEEEECCCSCSSSBCCCEEECCSSCCBSCCC
T ss_pred             cccccccccccccccccccccccccccccccchhhhccccccccccccceecccCchhhhccccccEEECcCCcccccCC
Confidence                                                                  0112455778999999999998 889


Q ss_pred             -cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccccCCCCCCCC
Q 042541          618 -ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPEG  694 (695)
Q Consensus       618 -~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~~l~~lP~~  694 (695)
                       .++++++|++|+|++|.+++..|..+.    .+++|+.|+|++|...+.+|..+++|++|++|++++|+..|.+|.+
T Consensus       650 ~~l~~l~~L~~L~Ls~N~l~g~ip~~l~----~L~~L~~LdLs~N~l~g~ip~~l~~l~~L~~L~ls~N~l~g~iP~~  723 (768)
T 3rgz_A          650 KEIGSMPYLFILNLGHNDISGSIPDEVG----DLRGLNILDLSSNKLDGRIPQAMSALTMLTEIDLSNNNLSGPIPEM  723 (768)
T ss_dssp             GGGGGCTTCCEEECCSSCCCSCCCGGGG----GCTTCCEEECCSSCCEECCCGGGGGCCCCSEEECCSSEEEEECCSS
T ss_pred             HHHhccccCCEEeCcCCccCCCCChHHh----CCCCCCEEECCCCcccCcCChHHhCCCCCCEEECcCCcccccCCCc
Confidence             999999999999999999977777666    8999999999999888899999999999999999999988889864

>4ezg_A Putative uncharacterized protein; internalin-A, leucine-rich repeat protein, structural genomi center for structural genomics, JCSG; HET: MSE; 1.50A {Listeria monocytogenes}

Probab=99.40  E-value=1e-12  Score=125.41  Aligned_cols=148  Identities=12%  Similarity=0.192  Sum_probs=114.0

Q ss_pred             ccceEEeeecCCcccCCCCCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEE
Q 042541          527 NNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKI  606 (695)
Q Consensus       527 ~~~r~l~~~~~~~~~~~~~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L  606 (695)
                      ...+++.+...... ..+.-..+++|+.|.++.+.  ...+..+..+++|++|++++|.+....   ++.++.+++|++|
T Consensus        44 ~~L~~L~l~~n~i~-~l~~l~~l~~L~~L~l~~n~--~~~~~~l~~l~~L~~L~l~~n~l~~~~---~~~l~~l~~L~~L  117 (197)
T 4ezg_A           44 NSLTYITLANINVT-DLTGIEYAHNIKDLTINNIH--ATNYNPISGLSNLERLRIMGKDVTSDK---IPNLSGLTSLTLL  117 (197)
T ss_dssp             HTCCEEEEESSCCS-CCTTGGGCTTCSEEEEESCC--CSCCGGGTTCTTCCEEEEECTTCBGGG---SCCCTTCTTCCEE
T ss_pred             CCccEEeccCCCcc-ChHHHhcCCCCCEEEccCCC--CCcchhhhcCCCCCEEEeECCccCccc---ChhhcCCCCCCEE
Confidence            35778888765433 22223468899999999882  233447889999999999998774222   2347889999999


Q ss_pred             EeccCCCCC-cc-cccccccccEEeecccc-CCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecc
Q 042541          607 RLEHVSLPN-SL-ATVRMNHLQKVSLVMCN-VGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRIT  683 (695)
Q Consensus       607 ~L~~~~l~~-lp-~i~~l~~L~~L~l~~~~-i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~  683 (695)
                      ++++|.+.. .| .++++++|++|++++|. ++.++ ...     .+++|+.|++++| .+..+| .+..+++|++|+++
T Consensus       118 ~Ls~n~i~~~~~~~l~~l~~L~~L~L~~n~~i~~~~-~l~-----~l~~L~~L~l~~n-~i~~~~-~l~~l~~L~~L~l~  189 (197)
T 4ezg_A          118 DISHSAHDDSILTKINTLPKVNSIDLSYNGAITDIM-PLK-----TLPELKSLNIQFD-GVHDYR-GIEDFPKLNQLYAF  189 (197)
T ss_dssp             ECCSSBCBGGGHHHHTTCSSCCEEECCSCTBCCCCG-GGG-----GCSSCCEEECTTB-CCCCCT-TGGGCSSCCEEEEC
T ss_pred             EecCCccCcHhHHHHhhCCCCCEEEccCCCCccccH-hhc-----CCCCCCEEECCCC-CCcChH-HhccCCCCCEEEee
Confidence            999999984 66 89999999999999998 87765 333     8999999999997 467787 79999999999999


Q ss_pred             cccCCC
Q 042541          684 NCHRLS  689 (695)
Q Consensus       684 ~~~~l~  689 (695)
                      +|+ ++
T Consensus       190 ~N~-i~  194 (197)
T 4ezg_A          190 SQT-IG  194 (197)
T ss_dssp             BC----
T ss_pred             Ccc-cC
Confidence            966 54

>2o6s_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 1.50A {Eptatretus burgeri}

Probab=99.40  E-value=3.8e-12  Score=122.62  Aligned_cols=135  Identities=13%  Similarity=0.175  Sum_probs=82.1

Q ss_pred             CCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--ccccccccc
Q 042541          549 GPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNHLQ  626 (695)
Q Consensus       549 ~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L~  626 (695)
                      .++++.|.++.+......+..+..+++|++|++++|.+..  ++ ...+..+++|++|++++|.+..+|  .++++++|+
T Consensus        27 ~~~l~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~--~~-~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~  103 (208)
T 2o6s_A           27 PAQTTYLDLETNSLKSLPNGVFDELTSLTQLYLGGNKLQS--LP-NGVFNKLTSLTYLNLSTNQLQSLPNGVFDKLTQLK  103 (208)
T ss_dssp             CTTCSEEECCSSCCCCCCTTTTTTCTTCSEEECCSSCCCC--CC-TTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCC
T ss_pred             CCCCcEEEcCCCccCcCChhhhcccccCcEEECCCCccCc--cC-hhhcCCCCCcCEEECCCCcCCccCHhHhcCccCCC
Confidence            3456666666665444444456667777777777665531  11 112456667777777777776666  356677777


Q ss_pred             EEeeccccCCcccccchhhhcccCCCccEEecccccccccCchh-hcCCCCCceeecccccCCCCC
Q 042541          627 KVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDG-LCDIVSMEKLRITNCHRLSAL  691 (695)
Q Consensus       627 ~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~-i~~L~~L~~L~l~~~~~l~~l  691 (695)
                      +|++++|.++.+++..+.    .+++|++|++++| .+..+|.. +..+++|++|++++|+..+..
T Consensus       104 ~L~L~~N~l~~~~~~~~~----~l~~L~~L~l~~N-~l~~~~~~~~~~l~~L~~L~l~~N~~~~~~  164 (208)
T 2o6s_A          104 ELALNTNQLQSLPDGVFD----KLTQLKDLRLYQN-QLKSVPDGVFDRLTSLQYIWLHDNPWDCTC  164 (208)
T ss_dssp             EEECCSSCCCCCCTTTTT----TCTTCCEEECCSS-CCSCCCTTTTTTCTTCCEEECCSCCBCCCT
T ss_pred             EEEcCCCcCcccCHhHhc----cCCcCCEEECCCC-ccceeCHHHhccCCCccEEEecCCCeecCC
Confidence            777777777766665544    6677777777764 34555544 566777777777766544333

>1p9a_G Platelet glycoprotein IB alpha chain precursor; platelet receptors, glycocalicin, leucine rich repeats, BLOO clotting; HET: NAG BMA; 1.70A {Homo sapiens} SCOP: c.10.2.7 PDB: 1ook_G* 1qyy_A* 3pmh_G* 1m0z_A 1m10_B 1sq0_B 1gwb_A* 1p8v_A* 1u0n_D 3p72_A

Probab=99.39  E-value=3.2e-12  Score=129.89  Aligned_cols=131  Identities=18%  Similarity=0.152  Sum_probs=81.2

Q ss_pred             CCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--ccccccc
Q 042541          547 MQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNH  624 (695)
Q Consensus       547 ~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~  624 (695)
                      ..+++|+.|.++.+... .+|..+..+++|++|++++|.+...  + ...+..+++|++|+|++|.+..+|  .+..+++
T Consensus        74 ~~l~~L~~L~Ls~N~l~-~l~~~~~~l~~L~~L~l~~N~l~~l--~-~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~  149 (290)
T 1p9a_G           74 GTLPVLGTLDLSHNQLQ-SLPLLGQTLPALTVLDVSFNRLTSL--P-LGALRGLGELQELYLKGNELKTLPPGLLTPTPK  149 (290)
T ss_dssp             SCCTTCCEEECCSSCCS-SCCCCTTTCTTCCEEECCSSCCCCC--C-SSTTTTCTTCCEEECTTSCCCCCCTTTTTTCTT
T ss_pred             CCCCcCCEEECCCCcCC-cCchhhccCCCCCEEECCCCcCccc--C-HHHHcCCCCCCEEECCCCCCCccChhhcccccC
Confidence            35566666666655332 4555666666677777766655311  1 122556666777777777666666  4556667


Q ss_pred             ccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeeccccc
Q 042541          625 LQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCH  686 (695)
Q Consensus       625 L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~  686 (695)
                      |++|+|++|.++.+|+..+.    .+++|++|++++| .+..+|.++..+.+|++|+|++|+
T Consensus       150 L~~L~L~~N~l~~l~~~~~~----~l~~L~~L~L~~N-~l~~ip~~~~~~~~L~~l~L~~Np  206 (290)
T 1p9a_G          150 LEKLSLANNNLTELPAGLLN----GLENLDTLLLQEN-SLYTIPKGFFGSHLLPFAFLHGNP  206 (290)
T ss_dssp             CCEEECTTSCCSCCCTTTTT----TCTTCCEEECCSS-CCCCCCTTTTTTCCCSEEECCSCC
T ss_pred             CCEEECCCCcCCccCHHHhc----CcCCCCEEECCCC-cCCccChhhcccccCCeEEeCCCC
Confidence            77777777776666666554    5667777777664 456667666666677777776655

>2v9t_B SLIT homolog 2 protein N-product; structural protein-receptor complex, developmental protein, domain, roundabout, chemotaxis, LRR domain; 1.70A {Homo sapiens} PDB: 2v9s_A

Probab=99.39  E-value=2.6e-12  Score=124.87  Aligned_cols=129  Identities=12%  Similarity=0.117  Sum_probs=109.8

Q ss_pred             CceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--cccccccccE
Q 042541          550 PEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNHLQK  627 (695)
Q Consensus       550 ~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L~~  627 (695)
                      ++++.|.++.+......+..|..+++|++|+|++|.+...   .+..+..+++|++|+|++|.++.+|  .+..+++|++
T Consensus        32 ~~l~~L~l~~n~i~~i~~~~~~~l~~L~~L~Ls~N~i~~~---~~~~~~~l~~L~~L~Ls~N~l~~l~~~~f~~l~~L~~  108 (220)
T 2v9t_B           32 ETITEIRLEQNTIKVIPPGAFSPYKKLRRIDLSNNQISEL---APDAFQGLRSLNSLVLYGNKITELPKSLFEGLFSLQL  108 (220)
T ss_dssp             TTCCEEECCSSCCCEECTTSSTTCTTCCEEECCSSCCCEE---CTTTTTTCSSCCEEECCSSCCCCCCTTTTTTCTTCCE
T ss_pred             cCCCEEECCCCcCCCcCHhHhhCCCCCCEEECCCCcCCCc---CHHHhhCCcCCCEEECCCCcCCccCHhHccCCCCCCE
Confidence            6788999988876666666899999999999999877421   1234788999999999999999999  5688999999


Q ss_pred             EeeccccCCcccccchhhhcccCCCccEEecccccccccCch-hhcCCCCCceeeccccc
Q 042541          628 VSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPD-GLCDIVSMEKLRITNCH  686 (695)
Q Consensus       628 L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~-~i~~L~~L~~L~l~~~~  686 (695)
                      |+|++|.++.+++..+.    .+++|++|+|++| .+..+|. .+..+++|++|++++|+
T Consensus       109 L~L~~N~l~~~~~~~~~----~l~~L~~L~L~~N-~l~~~~~~~~~~l~~L~~L~L~~N~  163 (220)
T 2v9t_B          109 LLLNANKINCLRVDAFQ----DLHNLNLLSLYDN-KLQTIAKGTFSPLRAIQTMHLAQNP  163 (220)
T ss_dssp             EECCSSCCCCCCTTTTT----TCTTCCEEECCSS-CCSCCCTTTTTTCTTCCEEECCSSC
T ss_pred             EECCCCCCCEeCHHHcC----CCCCCCEEECCCC-cCCEECHHHHhCCCCCCEEEeCCCC
Confidence            99999999999888776    8999999999996 4666765 48899999999999976

>1p9a_G Platelet glycoprotein IB alpha chain precursor; platelet receptors, glycocalicin, leucine rich repeats, BLOO clotting; HET: NAG BMA; 1.70A {Homo sapiens} SCOP: c.10.2.7 PDB: 1ook_G* 1qyy_A* 3pmh_G* 1m0z_A 1m10_B 1sq0_B 1gwb_A* 1p8v_A* 1u0n_D 3p72_A

Probab=99.39  E-value=2.7e-12  Score=130.45  Aligned_cols=158  Identities=18%  Similarity=0.228  Sum_probs=119.6

Q ss_pred             CccceEEeeecCCcccCCC-CCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCc
Q 042541          526 PNNASLLSISTDETFSSNW-PDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLK  604 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~~~~-~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~  604 (695)
                      +...+.|.+..+....... ....+++|+.|.++.+.... +|.. ..+++|++|++++|.+.  .++  ..+..+++|+
T Consensus        30 ~~~l~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~n~l~~-~~~~-~~l~~L~~L~Ls~N~l~--~l~--~~~~~l~~L~  103 (290)
T 1p9a_G           30 PKDTTILHLSENLLYTFSLATLMPYTRLTQLNLDRAELTK-LQVD-GTLPVLGTLDLSHNQLQ--SLP--LLGQTLPALT  103 (290)
T ss_dssp             CTTCCEEECTTSCCSEEEGGGGTTCTTCCEEECTTSCCCE-EECC-SCCTTCCEEECCSSCCS--SCC--CCTTTCTTCC
T ss_pred             CCCCCEEEcCCCcCCccCHHHhhcCCCCCEEECCCCccCc-ccCC-CCCCcCCEEECCCCcCC--cCc--hhhccCCCCC
Confidence            3567777776554322111 12367888888887775443 2322 67888999999888763  222  2367888999


Q ss_pred             EEEeccCCCCCcc--cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchh-hcCCCCCceee
Q 042541          605 KIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDG-LCDIVSMEKLR  681 (695)
Q Consensus       605 ~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~-i~~L~~L~~L~  681 (695)
                      +|++++|.++.+|  .++++++|++|+|++|.++.+++..+.    .+++|+.|++++| .+..+|.+ +..+++|++|+
T Consensus       104 ~L~l~~N~l~~l~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~----~l~~L~~L~L~~N-~l~~l~~~~~~~l~~L~~L~  178 (290)
T 1p9a_G          104 VLDVSFNRLTSLPLGALRGLGELQELYLKGNELKTLPPGLLT----PTPKLEKLSLANN-NLTELPAGLLNGLENLDTLL  178 (290)
T ss_dssp             EEECCSSCCCCCCSSTTTTCTTCCEEECTTSCCCCCCTTTTT----TCTTCCEEECTTS-CCSCCCTTTTTTCTTCCEEE
T ss_pred             EEECCCCcCcccCHHHHcCCCCCCEEECCCCCCCccChhhcc----cccCCCEEECCCC-cCCccCHHHhcCcCCCCEEE
Confidence            9999999999887  688999999999999999999888776    8999999999986 57788876 57899999999


Q ss_pred             cccccCCCCCCCCC
Q 042541          682 ITNCHRLSALPEGI  695 (695)
Q Consensus       682 l~~~~~l~~lP~~i  695 (695)
                      +++|. +..+|.++
T Consensus       179 L~~N~-l~~ip~~~  191 (290)
T 1p9a_G          179 LQENS-LYTIPKGF  191 (290)
T ss_dssp             CCSSC-CCCCCTTT
T ss_pred             CCCCc-CCccChhh
Confidence            99965 88888764

>3rfs_A Internalin B, repeat modules, variable lymphocyte B; LRR, protein binding, plasma; 1.70A {Listeria monocytogenes} PDB: 3rfj_A

Probab=99.38  E-value=3.8e-12  Score=128.16  Aligned_cols=155  Identities=20%  Similarity=0.291  Sum_probs=120.5

Q ss_pred             cceEEeeecCCcccCCCCCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEE
Q 042541          528 NASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIR  607 (695)
Q Consensus       528 ~~r~l~~~~~~~~~~~~~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~  607 (695)
                      ..+.+.+...... .......+++|+.|.++.+.... + +.+..+++|++|++++|.+...  . ...++.+++|++|+
T Consensus        42 ~L~~L~l~~~~i~-~~~~l~~l~~L~~L~l~~n~l~~-~-~~l~~l~~L~~L~L~~n~l~~~--~-~~~~~~l~~L~~L~  115 (272)
T 3rfs_A           42 SIDQIIANNSDIK-SVQGIQYLPNVRYLALGGNKLHD-I-SALKELTNLTYLILTGNQLQSL--P-NGVFDKLTNLKELV  115 (272)
T ss_dssp             TCCEEECTTSCCC-CCTTGGGCTTCCEEECTTSCCCC-C-GGGTTCTTCCEEECTTSCCCCC--C-TTTTTTCTTCCEEE
T ss_pred             ceeeeeeCCCCcc-cccccccCCCCcEEECCCCCCCC-c-hhhcCCCCCCEEECCCCccCcc--C-hhHhcCCcCCCEEE
Confidence            4555655544321 11122368999999998886543 3 4788999999999999877421  1 12268899999999


Q ss_pred             eccCCCCCcc--cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchh-hcCCCCCceeeccc
Q 042541          608 LEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDG-LCDIVSMEKLRITN  684 (695)
Q Consensus       608 L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~-i~~L~~L~~L~l~~  684 (695)
                      +++|.+..+|  .++++++|++|++++|.++.+++..+.    .+++|++|++++|. +..+|.. ++.+++|++|++++
T Consensus       116 L~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~----~l~~L~~L~l~~n~-l~~~~~~~~~~l~~L~~L~L~~  190 (272)
T 3rfs_A          116 LVENQLQSLPDGVFDKLTNLTYLNLAHNQLQSLPKGVFD----KLTNLTELDLSYNQ-LQSLPEGVFDKLTQLKDLRLYQ  190 (272)
T ss_dssp             CTTSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTT----TCTTCCEEECCSSC-CCCCCTTTTTTCTTCCEEECCS
T ss_pred             CCCCcCCccCHHHhccCCCCCEEECCCCccCccCHHHhc----cCccCCEEECCCCC-cCccCHHHhcCCccCCEEECCC
Confidence            9999999887  588999999999999999999988766    89999999999974 5666655 68999999999999


Q ss_pred             ccCCCCCCCC
Q 042541          685 CHRLSALPEG  694 (695)
Q Consensus       685 ~~~l~~lP~~  694 (695)
                      |. +..+|+.
T Consensus       191 N~-l~~~~~~  199 (272)
T 3rfs_A          191 NQ-LKSVPDG  199 (272)
T ss_dssp             SC-CSCCCTT
T ss_pred             Cc-CCccCHH
Confidence            76 6666653

>1ozn_A Reticulon 4 receptor; NOGO receptor, MAD, myelination inhibition, OMGP, MAG, NOGO- signal transduction, neuronal regeneration, ligand binding; HET: NDG MAN NAG BMA; 1.52A {Homo sapiens} SCOP: c.10.2.7 PDB: 1p8t_A* 3kj4_A*

Probab=99.38  E-value=3.6e-12  Score=129.37  Aligned_cols=158  Identities=10%  Similarity=0.114  Sum_probs=127.0

Q ss_pred             CCccceEEeeecCCcccCCCC-CCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccC-CCCcccCcccccccCCC
Q 042541          525 HPNNASLLSISTDETFSSNWP-DMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYG-FSPAELNNFRVLSALSK  602 (695)
Q Consensus       525 ~~~~~r~l~~~~~~~~~~~~~-~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~-~~~~~~~~~~~l~~l~~  602 (695)
                      .+...+++.+..+........ ...+++|+.|.++.+......|..+.++++|++|++++|. +..  + ....+..+++
T Consensus        30 ~~~~l~~L~l~~n~i~~~~~~~~~~~~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~~l~~--~-~~~~~~~l~~  106 (285)
T 1ozn_A           30 IPAASQRIFLHGNRISHVPAASFRACRNLTILWLHSNVLARIDAAAFTGLALLEQLDLSDNAQLRS--V-DPATFHGLGR  106 (285)
T ss_dssp             CCTTCSEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSCTTCCC--C-CTTTTTTCTT
T ss_pred             CCCCceEEEeeCCcCCccCHHHcccCCCCCEEECCCCccceeCHhhcCCccCCCEEeCCCCCCccc--c-CHHHhcCCcC
Confidence            355788888876654332222 2368899999999887777778899999999999999986 421  1 1233788999


Q ss_pred             CcEEEeccCCCCCcc--cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchh-hcCCCCCce
Q 042541          603 LKKIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDG-LCDIVSMEK  679 (695)
Q Consensus       603 L~~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~-i~~L~~L~~  679 (695)
                      |++|++++|.+..++  .++++++|++|++++|.++.+++..+.    .+++|++|++++| .+..+|.. +..+++|++
T Consensus       107 L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~----~l~~L~~L~l~~n-~l~~~~~~~~~~l~~L~~  181 (285)
T 1ozn_A          107 LHTLHLDRCGLQELGPGLFRGLAALQYLYLQDNALQALPDDTFR----DLGNLTHLFLHGN-RISSVPERAFRGLHSLDR  181 (285)
T ss_dssp             CCEEECTTSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTT----TCTTCCEEECCSS-CCCEECTTTTTTCTTCCE
T ss_pred             CCEEECCCCcCCEECHhHhhCCcCCCEEECCCCcccccCHhHhc----cCCCccEEECCCC-cccccCHHHhcCccccCE
Confidence            999999999999775  789999999999999999999887666    8999999999996 56777764 899999999


Q ss_pred             eecccccCCCCC
Q 042541          680 LRITNCHRLSAL  691 (695)
Q Consensus       680 L~l~~~~~l~~l  691 (695)
                      |++++|. +..+
T Consensus       182 L~l~~n~-l~~~  192 (285)
T 1ozn_A          182 LLLHQNR-VAHV  192 (285)
T ss_dssp             EECCSSC-CCEE
T ss_pred             EECCCCc-cccc
Confidence            9999987 4444

>3e6j_A Variable lymphocyte receptor diversity region; variable lymphocyte receptors, VLR, leucine-rich repeat, LRR adaptive immunity, immune system; HET: DR2; 1.67A {Petromyzon marinus}

Probab=99.38  E-value=4.3e-12  Score=124.16  Aligned_cols=130  Identities=15%  Similarity=0.218  Sum_probs=111.1

Q ss_pred             CCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--ccccccccc
Q 042541          549 GPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNHLQ  626 (695)
Q Consensus       549 ~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L~  626 (695)
                      .++++.|.++.+......|..|..+++|++|+|++|.+..  ++ ...+..+++|++|+|++|.++.+|  .++.+++|+
T Consensus        39 ~~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~L~~N~l~~--i~-~~~~~~l~~L~~L~Ls~N~l~~l~~~~~~~l~~L~  115 (229)
T 3e6j_A           39 PTNAQILYLHDNQITKLEPGVFDSLINLKELYLGSNQLGA--LP-VGVFDSLTQLTVLDLGTNQLTVLPSAVFDRLVHLK  115 (229)
T ss_dssp             CTTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCC--CC-TTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCC
T ss_pred             CCCCCEEEcCCCccCccCHHHhhCccCCcEEECCCCCCCC--cC-hhhcccCCCcCEEECCCCcCCccChhHhCcchhhC
Confidence            4789999999988877778889999999999999988732  21 123678999999999999999888  578999999


Q ss_pred             EEeeccccCCcccccchhhhcccCCCccEEecccccccccCch-hhcCCCCCceeecccccC
Q 042541          627 KVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPD-GLCDIVSMEKLRITNCHR  687 (695)
Q Consensus       627 ~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~-~i~~L~~L~~L~l~~~~~  687 (695)
                      +|+|++|.++.+|....     .+++|++|+|++| .+..+|. .+..+++|+.|++++|+.
T Consensus       116 ~L~Ls~N~l~~lp~~~~-----~l~~L~~L~L~~N-~l~~~~~~~~~~l~~L~~L~l~~N~~  171 (229)
T 3e6j_A          116 ELFMCCNKLTELPRGIE-----RLTHLTHLALDQN-QLKSIPHGAFDRLSSLTHAYLFGNPW  171 (229)
T ss_dssp             EEECCSSCCCSCCTTGG-----GCTTCSEEECCSS-CCCCCCTTTTTTCTTCCEEECTTSCB
T ss_pred             eEeccCCcccccCcccc-----cCCCCCEEECCCC-cCCccCHHHHhCCCCCCEEEeeCCCc
Confidence            99999999998887765     8999999999996 5777775 488999999999999873

>2o6q_A Variable lymphocyte receptor A; leucine-rich repeat protein, LRR, immune system; 2.50A {Eptatretus burgeri}

Probab=99.38  E-value=6.8e-12  Score=126.18  Aligned_cols=153  Identities=13%  Similarity=0.146  Sum_probs=123.9

Q ss_pred             CccceEEeeecCCcccCCCCC-CCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCc
Q 042541          526 PNNASLLSISTDETFSSNWPD-MQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLK  604 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~~~~~~-~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~  604 (695)
                      ....++|.+..+......... ..+++|+.|.++.+......+..+..+++|++|++++|.+....   ...++.+++|+
T Consensus        60 l~~L~~L~l~~n~l~~i~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~---~~~~~~l~~L~  136 (270)
T 2o6q_A           60 LTKLRLLYLNDNKLQTLPAGIFKELKNLETLWVTDNKLQALPIGVFDQLVNLAELRLDRNQLKSLP---PRVFDSLTKLT  136 (270)
T ss_dssp             CTTCCEEECCSSCCSCCCTTTTSSCTTCCEEECCSSCCCCCCTTTTTTCSSCCEEECCSSCCCCCC---TTTTTTCTTCC
T ss_pred             CCCCCEEECCCCccCeeChhhhcCCCCCCEEECCCCcCCcCCHhHcccccCCCEEECCCCccCeeC---HHHhCcCcCCC
Confidence            457788888765432221111 36899999999988766655667899999999999998774221   22368899999


Q ss_pred             EEEeccCCCCCcc--cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchh-hcCCCCCceee
Q 042541          605 KIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDG-LCDIVSMEKLR  681 (695)
Q Consensus       605 ~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~-i~~L~~L~~L~  681 (695)
                      +|+|++|.+..+|  .++.+++|++|+|++|.++.+++..+.    .+++|++|++++| .+..+|.. +..+++|++|+
T Consensus       137 ~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~----~l~~L~~L~L~~N-~l~~~~~~~~~~l~~L~~L~  211 (270)
T 2o6q_A          137 YLSLGYNELQSLPKGVFDKLTSLKELRLYNNQLKRVPEGAFD----KLTELKTLKLDNN-QLKRVPEGAFDSLEKLKMLQ  211 (270)
T ss_dssp             EEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCSCCCTTTTT----TCTTCCEEECCSS-CCSCCCTTTTTTCTTCCEEE
T ss_pred             EEECCCCcCCccCHhHccCCcccceeEecCCcCcEeChhHhc----cCCCcCEEECCCC-cCCcCCHHHhccccCCCEEE
Confidence            9999999999888  588999999999999999999987766    8999999999997 56778765 88999999999


Q ss_pred             ccccc
Q 042541          682 ITNCH  686 (695)
Q Consensus       682 l~~~~  686 (695)
                      +++|+
T Consensus       212 l~~N~  216 (270)
T 2o6q_A          212 LQENP  216 (270)
T ss_dssp             CCSSC
T ss_pred             ecCCC
Confidence            99987

>1ogq_A PGIP-2, polygalacturonase inhibiting protein; inhibitor; HET: NAG; 1.7A {Phaseolus vulgaris} SCOP: c.10.2.8

Probab=99.38  E-value=1.1e-12  Score=135.17  Aligned_cols=131  Identities=11%  Similarity=0.077  Sum_probs=64.5

Q ss_pred             CCCceEEEEEEc-cCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCC-Ccc-ccccccc
Q 042541          548 QGPEVKVVVLNI-RTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLP-NSL-ATVRMNH  624 (695)
Q Consensus       548 ~~~~l~~L~l~~-~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~-~lp-~i~~l~~  624 (695)
                      .+++|++|.++. +...+.+|..+.++++|++|++++|.+.. .+  +..++.+++|++|++++|.+. .+| .++++++
T Consensus        74 ~l~~L~~L~L~~~n~l~~~~p~~l~~l~~L~~L~Ls~n~l~~-~~--p~~~~~l~~L~~L~Ls~N~l~~~~p~~~~~l~~  150 (313)
T 1ogq_A           74 NLPYLNFLYIGGINNLVGPIPPAIAKLTQLHYLYITHTNVSG-AI--PDFLSQIKTLVTLDFSYNALSGTLPPSISSLPN  150 (313)
T ss_dssp             GCTTCSEEEEEEETTEESCCCGGGGGCTTCSEEEEEEECCEE-EC--CGGGGGCTTCCEEECCSSEEESCCCGGGGGCTT
T ss_pred             CCCCCCeeeCCCCCcccccCChhHhcCCCCCEEECcCCeeCC-cC--CHHHhCCCCCCEEeCCCCccCCcCChHHhcCCC
Confidence            455555555553 44444555555555555555555554421 11  112444455555555555444 444 4445555


Q ss_pred             ccEEeeccccCC-------------------------cccccchhhhcccCCCccEEecccccccccCchhhcCCCCCce
Q 042541          625 LQKVSLVMCNVG-------------------------QVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEK  679 (695)
Q Consensus       625 L~~L~l~~~~i~-------------------------~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~  679 (695)
                      |++|++++|.++                         +..|..+.    .++ |+.|++++|......|..++.+++|+.
T Consensus       151 L~~L~L~~N~l~~~~p~~l~~l~~~L~~L~L~~N~l~~~~~~~~~----~l~-L~~L~Ls~N~l~~~~~~~~~~l~~L~~  225 (313)
T 1ogq_A          151 LVGITFDGNRISGAIPDSYGSFSKLFTSMTISRNRLTGKIPPTFA----NLN-LAFVDLSRNMLEGDASVLFGSDKNTQK  225 (313)
T ss_dssp             CCEEECCSSCCEEECCGGGGCCCTTCCEEECCSSEEEEECCGGGG----GCC-CSEEECCSSEEEECCGGGCCTTSCCSE
T ss_pred             CCeEECcCCcccCcCCHHHhhhhhcCcEEECcCCeeeccCChHHh----CCc-ccEEECcCCcccCcCCHHHhcCCCCCE
Confidence            555555555444                         33333222    333 555555554433345555566666666


Q ss_pred             eeccccc
Q 042541          680 LRITNCH  686 (695)
Q Consensus       680 L~l~~~~  686 (695)
                      |++++|.
T Consensus       226 L~L~~N~  232 (313)
T 1ogq_A          226 IHLAKNS  232 (313)
T ss_dssp             EECCSSE
T ss_pred             EECCCCc
Confidence            6666654

>1ogq_A PGIP-2, polygalacturonase inhibiting protein; inhibitor; HET: NAG; 1.7A {Phaseolus vulgaris} SCOP: c.10.2.8

Probab=99.37  E-value=9.6e-13  Score=135.47  Aligned_cols=138  Identities=14%  Similarity=0.176  Sum_probs=116.5

Q ss_pred             CceEEEEEEccCccc--cCChhhcCCCCCcEEEEcc-cCCCCcccCcccccccCCCCcEEEeccCCCC-Ccc-ccccccc
Q 042541          550 PEVKVVVLNIRTKKY--VLPDFLQKMDELKVLIVTN-YGFSPAELNNFRVLSALSKLKKIRLEHVSLP-NSL-ATVRMNH  624 (695)
Q Consensus       550 ~~l~~L~l~~~~~~~--~~p~~~~~l~~Lr~L~l~~-~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~-~lp-~i~~l~~  624 (695)
                      .+++.|.++++...+  .+|..+.++++|++|++++ |.+.. .+  +..++.+++|++|+|++|.+. .+| .++++++
T Consensus        50 ~~l~~L~L~~~~l~~~~~~~~~l~~l~~L~~L~L~~~n~l~~-~~--p~~l~~l~~L~~L~Ls~n~l~~~~p~~~~~l~~  126 (313)
T 1ogq_A           50 YRVNNLDLSGLNLPKPYPIPSSLANLPYLNFLYIGGINNLVG-PI--PPAIAKLTQLHYLYITHTNVSGAIPDFLSQIKT  126 (313)
T ss_dssp             CCEEEEEEECCCCSSCEECCGGGGGCTTCSEEEEEEETTEES-CC--CGGGGGCTTCSEEEEEEECCEEECCGGGGGCTT
T ss_pred             ceEEEEECCCCCccCCcccChhHhCCCCCCeeeCCCCCcccc-cC--ChhHhcCCCCCEEECcCCeeCCcCCHHHhCCCC
Confidence            578999999987777  8999999999999999995 65532 22  234889999999999999998 888 9999999


Q ss_pred             ccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCC-CCceeecccccCCCCCCCC
Q 042541          625 LQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIV-SMEKLRITNCHRLSALPEG  694 (695)
Q Consensus       625 L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~-~L~~L~l~~~~~l~~lP~~  694 (695)
                      |++|++++|.+++..|..+.    .+++|++|++++|...+.+|..++.++ +|++|++++|...+.+|..
T Consensus       127 L~~L~Ls~N~l~~~~p~~~~----~l~~L~~L~L~~N~l~~~~p~~l~~l~~~L~~L~L~~N~l~~~~~~~  193 (313)
T 1ogq_A          127 LVTLDFSYNALSGTLPPSIS----SLPNLVGITFDGNRISGAIPDSYGSFSKLFTSMTISRNRLTGKIPPT  193 (313)
T ss_dssp             CCEEECCSSEEESCCCGGGG----GCTTCCEEECCSSCCEEECCGGGGCCCTTCCEEECCSSEEEEECCGG
T ss_pred             CCEEeCCCCccCCcCChHHh----cCCCCCeEECcCCcccCcCCHHHhhhhhcCcEEECcCCeeeccCChH
Confidence            99999999999966665555    899999999999866558999999998 9999999998755466643

>2xwt_C Thyrotropin receptor; signaling protein-immune system complex, GPCR, graves' disea autoimmunity, receptor-autoantibody complex; HET: NAG BMA MAN; 1.90A {Homo sapiens} PDB: 3g04_C*

Probab=99.37  E-value=5.5e-12  Score=124.39  Aligned_cols=158  Identities=16%  Similarity=0.132  Sum_probs=115.7

Q ss_pred             CccceEEeeecCC-cccCCC-CCCCCCceEEEEEEc-cCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCC
Q 042541          526 PNNASLLSISTDE-TFSSNW-PDMQGPEVKVVVLNI-RTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSK  602 (695)
Q Consensus       526 ~~~~r~l~~~~~~-~~~~~~-~~~~~~~l~~L~l~~-~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~  602 (695)
                      ....+.+.+..+. ...... ....+++|+.|.++. +......+..|.++++|++|++++|.+..  ++.   ++.+++
T Consensus        54 l~~L~~L~l~~n~~l~~i~~~~f~~l~~L~~L~l~~~n~l~~i~~~~f~~l~~L~~L~l~~n~l~~--lp~---~~~l~~  128 (239)
T 2xwt_C           54 LPNISRIYVSIDVTLQQLESHSFYNLSKVTHIEIRNTRNLTYIDPDALKELPLLKFLGIFNTGLKM--FPD---LTKVYS  128 (239)
T ss_dssp             CTTCCEEEEECCSSCCEECTTTEESCTTCCEEEEEEETTCCEECTTSEECCTTCCEEEEEEECCCS--CCC---CTTCCB
T ss_pred             CCCCcEEeCCCCCCcceeCHhHcCCCcCCcEEECCCCCCeeEcCHHHhCCCCCCCEEeCCCCCCcc--ccc---cccccc
Confidence            3466777776654 211111 123677888888887 55544444577888888888888876632  332   555666


Q ss_pred             Cc---EEEeccC-CCCCcc--ccccccccc-EEeeccccCCcccccchhhhcccCCCccEEecccccccccCch-hhcCC
Q 042541          603 LK---KIRLEHV-SLPNSL--ATVRMNHLQ-KVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPD-GLCDI  674 (695)
Q Consensus       603 L~---~L~L~~~-~l~~lp--~i~~l~~L~-~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~-~i~~L  674 (695)
                      |+   +|++++| .+..+|  .+.++++|+ +|++++|.++.+|+..+     ..++|+.|++++|..+..+|. .+..+
T Consensus       129 L~~L~~L~l~~N~~l~~i~~~~~~~l~~L~~~L~l~~n~l~~i~~~~~-----~~~~L~~L~L~~n~~l~~i~~~~~~~l  203 (239)
T 2xwt_C          129 TDIFFILEITDNPYMTSIPVNAFQGLCNETLTLKLYNNGFTSVQGYAF-----NGTKLDAVYLNKNKYLTVIDKDAFGGV  203 (239)
T ss_dssp             CCSEEEEEEESCTTCCEECTTTTTTTBSSEEEEECCSCCCCEECTTTT-----TTCEEEEEECTTCTTCCEECTTTTTTC
T ss_pred             cccccEEECCCCcchhhcCcccccchhcceeEEEcCCCCCcccCHhhc-----CCCCCCEEEcCCCCCcccCCHHHhhcc
Confidence            66   9999999 888887  588899999 99999999998888777     448999999999766778865 47888


Q ss_pred             -CCCceeecccccCCCCCCCC
Q 042541          675 -VSMEKLRITNCHRLSALPEG  694 (695)
Q Consensus       675 -~~L~~L~l~~~~~l~~lP~~  694 (695)
                       ++|+.|++++|+ +..+|..
T Consensus       204 ~~~L~~L~l~~N~-l~~l~~~  223 (239)
T 2xwt_C          204 YSGPSLLDVSQTS-VTALPSK  223 (239)
T ss_dssp             SBCCSEEECTTCC-CCCCCCT
T ss_pred             ccCCcEEECCCCc-cccCChh
Confidence             999999999965 7888864

>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse; HET: NAG BMA MAN; 3.25A {Homo sapiens}

Probab=99.36  E-value=5.6e-12  Score=136.40  Aligned_cols=139  Identities=12%  Similarity=0.115  Sum_probs=76.5

Q ss_pred             CCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcccccccccccE
Q 042541          548 QGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSLATVRMNHLQK  627 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp~i~~l~~L~~  627 (695)
                      .+++|+.|.++.+......+..|.++++|++|++.+|..... ++ ...+..+++|++|+|++|.++.+|.+..+++|++
T Consensus       134 ~l~~L~~L~L~~N~i~~~~~~~~~~l~~L~~L~l~~~~~l~~-i~-~~~~~~l~~L~~L~L~~n~l~~~~~~~~l~~L~~  211 (440)
T 3zyj_A          134 YLSKLKELWLRNNPIESIPSYAFNRIPSLRRLDLGELKRLSY-IS-EGAFEGLSNLRYLNLAMCNLREIPNLTPLIKLDE  211 (440)
T ss_dssp             SCSSCCEEECCSCCCCEECTTTTTTCTTCCEEECCCCTTCCE-EC-TTTTTTCSSCCEEECTTSCCSSCCCCTTCSSCCE
T ss_pred             ccccCceeeCCCCcccccCHHHhhhCcccCEeCCCCCCCcce-eC-cchhhcccccCeecCCCCcCccccccCCCcccCE
Confidence            445555555555544333333455555555555554322111 10 1124556666666666666666665566666666


Q ss_pred             EeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccccCCCCCCC
Q 042541          628 VSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPE  693 (695)
Q Consensus       628 L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~~l~~lP~  693 (695)
                      |+|++|.++.+++..+.    .+++|+.|++++|......|..+.++++|++|+|++|. +..+|.
T Consensus       212 L~Ls~N~l~~~~~~~~~----~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~N~-l~~~~~  272 (440)
T 3zyj_A          212 LDLSGNHLSAIRPGSFQ----GLMHLQKLWMIQSQIQVIERNAFDNLQSLVEINLAHNN-LTLLPH  272 (440)
T ss_dssp             EECTTSCCCEECTTTTT----TCTTCCEEECTTCCCCEECTTSSTTCTTCCEEECTTSC-CCCCCT
T ss_pred             EECCCCccCccChhhhc----cCccCCEEECCCCceeEEChhhhcCCCCCCEEECCCCC-CCccCh
Confidence            66666666666555554    56666666666654333334446666666666666643 555554

>3zyi_A Leucine-rich repeat-containing protein 4; cell adhesion, LRRC4 complex, synapse; HET: NAG; 2.60A {Homo sapiens} PDB: 3zyo_A* 3zyn_A* 2dl9_A

Probab=99.35  E-value=7.5e-12  Score=135.93  Aligned_cols=138  Identities=12%  Similarity=0.107  Sum_probs=80.7

Q ss_pred             CCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcccccccccccEE
Q 042541          549 GPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSLATVRMNHLQKV  628 (695)
Q Consensus       549 ~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp~i~~l~~L~~L  628 (695)
                      +++|+.|.++.|......+..|.++++|+.|++++|.... .++ ...+..+++|++|+|++|.+..+|.+..+++|++|
T Consensus       146 l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~l~~~~~l~-~i~-~~~~~~l~~L~~L~L~~n~l~~~~~~~~l~~L~~L  223 (452)
T 3zyi_A          146 LSKLRELWLRNNPIESIPSYAFNRVPSLMRLDLGELKKLE-YIS-EGAFEGLFNLKYLNLGMCNIKDMPNLTPLVGLEEL  223 (452)
T ss_dssp             CTTCCEEECCSCCCCEECTTTTTTCTTCCEEECCCCTTCC-EEC-TTTTTTCTTCCEEECTTSCCSSCCCCTTCTTCCEE
T ss_pred             cCCCCEEECCCCCcceeCHhHHhcCCcccEEeCCCCCCcc-ccC-hhhccCCCCCCEEECCCCcccccccccccccccEE
Confidence            4455555554443332223344444555555554432211 000 11255667777777777777776666677777777


Q ss_pred             eeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccccCCCCCCC
Q 042541          629 SLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPE  693 (695)
Q Consensus       629 ~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~~l~~lP~  693 (695)
                      +|++|.++.+++..+.    .+++|+.|++++|......|..+..+++|+.|+|++|. +..+|.
T Consensus       224 ~Ls~N~l~~~~~~~~~----~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~N~-l~~~~~  283 (452)
T 3zyi_A          224 EMSGNHFPEIRPGSFH----GLSSLKKLWVMNSQVSLIERNAFDGLASLVELNLAHNN-LSSLPH  283 (452)
T ss_dssp             ECTTSCCSEECGGGGT----TCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECCSSC-CSCCCT
T ss_pred             ECcCCcCcccCccccc----CccCCCEEEeCCCcCceECHHHhcCCCCCCEEECCCCc-CCccCh
Confidence            7777777777666555    67777777777765433445557777777777777754 666664

>2v70_A SLIT-2, SLIT homolog 2 protein N-product; neurogenesis, glycoprotein, secreted, chemotaxis, LRR structural protein, differentiation; HET: NAG; 3.01A {Homo sapiens}

Probab=99.35  E-value=5.8e-12  Score=122.42  Aligned_cols=131  Identities=13%  Similarity=0.125  Sum_probs=108.6

Q ss_pred             CCceEEEEEEccCccccCC-hhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--cccccccc
Q 042541          549 GPEVKVVVLNIRTKKYVLP-DFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNHL  625 (695)
Q Consensus       549 ~~~l~~L~l~~~~~~~~~p-~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L  625 (695)
                      .+.++.|.++.+......| ..|..+++|++|++++|.+..  +. ...+..+++|++|+|++|.+..+|  .++.+++|
T Consensus        31 ~~~~~~L~L~~N~l~~~~~~~~~~~l~~L~~L~L~~N~i~~--i~-~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L  107 (220)
T 2v70_A           31 PQYTAELRLNNNEFTVLEATGIFKKLPQLRKINFSNNKITD--IE-EGAFEGASGVNEILLTSNRLENVQHKMFKGLESL  107 (220)
T ss_dssp             CTTCSEEECCSSCCCEECCCCCGGGCTTCCEEECCSSCCCE--EC-TTTTTTCTTCCEEECCSSCCCCCCGGGGTTCSSC
T ss_pred             CCCCCEEEcCCCcCCccCchhhhccCCCCCEEECCCCcCCE--EC-HHHhCCCCCCCEEECCCCccCccCHhHhcCCcCC
Confidence            3456788888887665544 468999999999999987742  11 123788999999999999999877  68999999


Q ss_pred             cEEeeccccCCcccccchhhhcccCCCccEEecccccccccC-chhhcCCCCCceeecccccC
Q 042541          626 QKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIEL-PDGLCDIVSMEKLRITNCHR  687 (695)
Q Consensus       626 ~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~l-P~~i~~L~~L~~L~l~~~~~  687 (695)
                      ++|+|++|.++.+++..+.    .+++|++|+|++|. +..+ |..+..+++|+.|++++|+.
T Consensus       108 ~~L~Ls~N~l~~~~~~~~~----~l~~L~~L~L~~N~-l~~~~~~~~~~l~~L~~L~L~~N~l  165 (220)
T 2v70_A          108 KTLMLRSNRITCVGNDSFI----GLSSVRLLSLYDNQ-ITTVAPGAFDTLHSLSTLNLLANPF  165 (220)
T ss_dssp             CEEECTTSCCCCBCTTSST----TCTTCSEEECTTSC-CCCBCTTTTTTCTTCCEEECCSCCE
T ss_pred             CEEECCCCcCCeECHhHcC----CCccCCEEECCCCc-CCEECHHHhcCCCCCCEEEecCcCC
Confidence            9999999999999887776    89999999999975 5555 77899999999999999873

>2je0_A Acidic leucine-rich nuclear phosphoprotein 32 FAM member A; nuclear protein; 2.40A {Homo sapiens} PDB: 2je1_A

Probab=99.35  E-value=1.3e-12  Score=118.62  Aligned_cols=126  Identities=21%  Similarity=0.256  Sum_probs=104.9

Q ss_pred             CCceEEEEEEccCcc-ccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCC-cc-cccccccc
Q 042541          549 GPEVKVVVLNIRTKK-YVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPN-SL-ATVRMNHL  625 (695)
Q Consensus       549 ~~~l~~L~l~~~~~~-~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~-lp-~i~~l~~L  625 (695)
                      +++++.|.++.+... +.+|..+..+++|++|++++|.+...     +.++.+++|++|++++|.+.. +| .++++++|
T Consensus        16 ~~~l~~L~l~~n~l~~~~~~~~~~~l~~L~~L~l~~n~l~~~-----~~~~~l~~L~~L~Ls~n~i~~~~~~~~~~l~~L   90 (149)
T 2je0_A           16 PSDVKELVLDNSRSNEGKLEGLTDEFEELEFLSTINVGLTSI-----ANLPKLNKLKKLELSDNRVSGGLEVLAEKCPNL   90 (149)
T ss_dssp             GGGCSEEECTTCBCBTTBCCSCCTTCTTCCEEECTTSCCCCC-----TTCCCCTTCCEEECCSSCCCSCTHHHHHHCTTC
T ss_pred             CccCeEEEccCCcCChhHHHHHHhhcCCCcEEECcCCCCCCc-----hhhhcCCCCCEEECCCCcccchHHHHhhhCCCC
Confidence            356777877777655 57888889999999999999877432     448899999999999999996 88 88889999


Q ss_pred             cEEeeccccCCccc-ccchhhhcccCCCccEEecccccccccCch----hhcCCCCCceeeccc
Q 042541          626 QKVSLVMCNVGQVF-RNSTFRISDAFPNLLEMDIDYCNDLIELPD----GLCDIVSMEKLRITN  684 (695)
Q Consensus       626 ~~L~l~~~~i~~~~-~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~----~i~~L~~L~~L~l~~  684 (695)
                      ++|++++|.++.++ +..+.    .+++|++|++++| .+..+|.    .++.+++|++|++++
T Consensus        91 ~~L~ls~N~i~~~~~~~~~~----~l~~L~~L~l~~N-~l~~~~~~~~~~~~~l~~L~~L~l~d  149 (149)
T 2je0_A           91 THLNLSGNKIKDLSTIEPLK----KLENLKSLDLFNC-EVTNLNDYRENVFKLLPQLTYLDGYD  149 (149)
T ss_dssp             CEEECTTSCCCSHHHHGGGG----GCTTCCEEECTTC-GGGGSTTHHHHHHHHCTTCCEETTBC
T ss_pred             CEEECCCCcCCChHHHHHHh----hCCCCCEEeCcCC-cccchHHHHHHHHHHCCCcccccCCC
Confidence            99999999999865 23444    8999999999997 5677775    689999999999874

>4ezg_A Putative uncharacterized protein; internalin-A, leucine-rich repeat protein, structural genomi center for structural genomics, JCSG; HET: MSE; 1.50A {Listeria monocytogenes}

Probab=99.34  E-value=8e-12  Score=119.20  Aligned_cols=132  Identities=14%  Similarity=0.213  Sum_probs=110.9

Q ss_pred             CCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCC-cc-cccccccc
Q 042541          548 QGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPN-SL-ATVRMNHL  625 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~-lp-~i~~l~~L  625 (695)
                      .+++++.|.++.+... .+| .+..+++|++|++++|..     ..++.+..+++|++|++++|.++. .| .++++++|
T Consensus        42 ~l~~L~~L~l~~n~i~-~l~-~l~~l~~L~~L~l~~n~~-----~~~~~l~~l~~L~~L~l~~n~l~~~~~~~l~~l~~L  114 (197)
T 4ezg_A           42 QMNSLTYITLANINVT-DLT-GIEYAHNIKDLTINNIHA-----TNYNPISGLSNLERLRIMGKDVTSDKIPNLSGLTSL  114 (197)
T ss_dssp             HHHTCCEEEEESSCCS-CCT-TGGGCTTCSEEEEESCCC-----SCCGGGTTCTTCCEEEEECTTCBGGGSCCCTTCTTC
T ss_pred             hcCCccEEeccCCCcc-ChH-HHhcCCCCCEEEccCCCC-----CcchhhhcCCCCCEEEeECCccCcccChhhcCCCCC
Confidence            4678899999887554 566 688999999999999854     233458899999999999999984 66 99999999


Q ss_pred             cEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccccCCCCCC
Q 042541          626 QKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALP  692 (695)
Q Consensus       626 ~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~~l~~lP  692 (695)
                      ++|++++|.++...+..+.    .+++|++|++++|..+..+| .++.+++|++|++++|. +..+|
T Consensus       115 ~~L~Ls~n~i~~~~~~~l~----~l~~L~~L~L~~n~~i~~~~-~l~~l~~L~~L~l~~n~-i~~~~  175 (197)
T 4ezg_A          115 TLLDISHSAHDDSILTKIN----TLPKVNSIDLSYNGAITDIM-PLKTLPELKSLNIQFDG-VHDYR  175 (197)
T ss_dssp             CEEECCSSBCBGGGHHHHT----TCSSCCEEECCSCTBCCCCG-GGGGCSSCCEEECTTBC-CCCCT
T ss_pred             CEEEecCCccCcHhHHHHh----hCCCCCEEEccCCCCccccH-hhcCCCCCCEEECCCCC-CcChH
Confidence            9999999999875555554    89999999999987688898 69999999999999976 66665

>3rgz_A Protein brassinosteroid insensitive 1; phytohormone, leucine-rich RE receptor-like kinases, leucine-rich repeat; HET: NAG BLD; 2.28A {Arabidopsis thaliana} PDB: 3rgx_A* 3riz_A* 3rj0_A*

Probab=99.33  E-value=3.3e-12  Score=148.20  Aligned_cols=161  Identities=15%  Similarity=0.088  Sum_probs=128.2

Q ss_pred             ccceEEeeecCCcccCCCCC-CCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcE
Q 042541          527 NNASLLSISTDETFSSNWPD-MQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKK  605 (695)
Q Consensus       527 ~~~r~l~~~~~~~~~~~~~~-~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~  605 (695)
                      ...+.+.+..+......+.. ..+++|+.|.++.+...+.+|..+..+++|++|++++|.+... +  +..++.+++|++
T Consensus       394 ~~L~~L~L~~n~l~~~~p~~l~~l~~L~~L~Ls~N~l~~~~p~~l~~l~~L~~L~L~~n~l~~~-~--p~~~~~l~~L~~  470 (768)
T 3rgz_A          394 NTLQELYLQNNGFTGKIPPTLSNCSELVSLHLSFNYLSGTIPSSLGSLSKLRDLKLWLNMLEGE-I--PQELMYVKTLET  470 (768)
T ss_dssp             CCCCEEECCSSEEEEECCGGGGGCTTCCEEECCSSEEESCCCGGGGGCTTCCEEECCSSCCCSC-C--CGGGGGCTTCCE
T ss_pred             CCccEEECCCCccccccCHHHhcCCCCCEEECcCCcccCcccHHHhcCCCCCEEECCCCcccCc-C--CHHHcCCCCceE
Confidence            35666666554332222222 2678888888888877778888888899999999988876422 2  234788899999


Q ss_pred             EEeccCCCC-Ccc-cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecc
Q 042541          606 IRLEHVSLP-NSL-ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRIT  683 (695)
Q Consensus       606 L~L~~~~l~-~lp-~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~  683 (695)
                      |++++|.+. .+| .++++++|++|+|++|.+++..|..+.    .+++|++|++++|...+.+|..++++++|+.|+++
T Consensus       471 L~L~~N~l~~~~p~~l~~l~~L~~L~L~~N~l~~~~p~~~~----~l~~L~~L~L~~N~l~~~~p~~l~~l~~L~~L~Ls  546 (768)
T 3rgz_A          471 LILDFNDLTGEIPSGLSNCTNLNWISLSNNRLTGEIPKWIG----RLENLAILKLSNNSFSGNIPAELGDCRSLIWLDLN  546 (768)
T ss_dssp             EECCSSCCCSCCCGGGGGCTTCCEEECCSSCCCSCCCGGGG----GCTTCCEEECCSSCCEEECCGGGGGCTTCCEEECC
T ss_pred             EEecCCcccCcCCHHHhcCCCCCEEEccCCccCCcCChHHh----cCCCCCEEECCCCcccCcCCHHHcCCCCCCEEECC
Confidence            999999998 778 899999999999999999877776665    89999999999988777999999999999999999


Q ss_pred             cccCCCCCCCC
Q 042541          684 NCHRLSALPEG  694 (695)
Q Consensus       684 ~~~~l~~lP~~  694 (695)
                      +|+..+.+|.+
T Consensus       547 ~N~l~g~ip~~  557 (768)
T 3rgz_A          547 TNLFNGTIPAA  557 (768)
T ss_dssp             SSEEESBCCGG
T ss_pred             CCccCCcCChH
Confidence            99888888864

>2o6s_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 1.50A {Eptatretus burgeri}

Probab=99.32  E-value=7.3e-12  Score=120.61  Aligned_cols=156  Identities=13%  Similarity=0.081  Sum_probs=122.3

Q ss_pred             CccceEEeeecCCcccCCCC-CCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCc
Q 042541          526 PNNASLLSISTDETFSSNWP-DMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLK  604 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~~~~~-~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~  604 (695)
                      ....+++.+..+........ ...+++|+.|.++.+......+..+..+++|++|++++|.+..  ++ ...+..+++|+
T Consensus        27 ~~~l~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~--~~-~~~~~~l~~L~  103 (208)
T 2o6s_A           27 PAQTTYLDLETNSLKSLPNGVFDELTSLTQLYLGGNKLQSLPNGVFNKLTSLTYLNLSTNQLQS--LP-NGVFDKLTQLK  103 (208)
T ss_dssp             CTTCSEEECCSSCCCCCCTTTTTTCTTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCC--CC-TTTTTTCTTCC
T ss_pred             CCCCcEEEcCCCccCcCChhhhcccccCcEEECCCCccCccChhhcCCCCCcCEEECCCCcCCc--cC-HhHhcCccCCC
Confidence            45678888876644322221 1368999999999886665555578999999999999987742  11 12267899999


Q ss_pred             EEEeccCCCCCcc--cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeec
Q 042541          605 KIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRI  682 (695)
Q Consensus       605 ~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l  682 (695)
                      +|++++|.+..+|  .++++++|++|++++|.++.+++..+.    .+++|+.|++++|..       .+.+++|++|++
T Consensus       104 ~L~L~~N~l~~~~~~~~~~l~~L~~L~l~~N~l~~~~~~~~~----~l~~L~~L~l~~N~~-------~~~~~~l~~L~~  172 (208)
T 2o6s_A          104 ELALNTNQLQSLPDGVFDKLTQLKDLRLYQNQLKSVPDGVFD----RLTSLQYIWLHDNPW-------DCTCPGIRYLSE  172 (208)
T ss_dssp             EEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCSCCCTTTTT----TCTTCCEEECCSCCB-------CCCTTTTHHHHH
T ss_pred             EEEcCCCcCcccCHhHhccCCcCCEEECCCCccceeCHHHhc----cCCCccEEEecCCCe-------ecCCCCHHHHHH
Confidence            9999999999888  578999999999999999999887765    899999999999743       345668889999


Q ss_pred             ccccCCCCCCCCC
Q 042541          683 TNCHRLSALPEGI  695 (695)
Q Consensus       683 ~~~~~l~~lP~~i  695 (695)
                      +.|...+.+|.++
T Consensus       173 ~~n~~~g~ip~~~  185 (208)
T 2o6s_A          173 WINKHSGVVRNSA  185 (208)
T ss_dssp             HHHHCTTTBBCTT
T ss_pred             HHHhCCceeeccC
Confidence            9888777888653

>3e6j_A Variable lymphocyte receptor diversity region; variable lymphocyte receptors, VLR, leucine-rich repeat, LRR adaptive immunity, immune system; HET: DR2; 1.67A {Petromyzon marinus}

Probab=99.31  E-value=1.2e-11  Score=121.02  Aligned_cols=121  Identities=18%  Similarity=0.226  Sum_probs=102.4

Q ss_pred             cccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--cccccccccEEeeccccCCcccc
Q 042541          563 KYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFR  640 (695)
Q Consensus       563 ~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~  640 (695)
                      ...+|..+  .++|++|++++|.+....   ...+..+++|++|+|++|.+..+|  .++.+++|++|+|++|.++.+++
T Consensus        31 l~~ip~~~--~~~L~~L~Ls~n~i~~~~---~~~~~~l~~L~~L~L~~N~l~~i~~~~~~~l~~L~~L~Ls~N~l~~l~~  105 (229)
T 3e6j_A           31 HASVPAGI--PTNAQILYLHDNQITKLE---PGVFDSLINLKELYLGSNQLGALPVGVFDSLTQLTVLDLGTNQLTVLPS  105 (229)
T ss_dssp             CSSCCSCC--CTTCSEEECCSSCCCCCC---TTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCT
T ss_pred             cCccCCCC--CCCCCEEEcCCCccCccC---HHHhhCccCCcEEECCCCCCCCcChhhcccCCCcCEEECCCCcCCccCh
Confidence            34566544  388999999999874321   233788999999999999999888  57899999999999999999998


Q ss_pred             cchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccccCCCCCCCC
Q 042541          641 NSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPEG  694 (695)
Q Consensus       641 ~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~~l~~lP~~  694 (695)
                      ..+.    .+++|++|+|++| .+..+|.++..+++|++|+|++|. +..+|.+
T Consensus       106 ~~~~----~l~~L~~L~Ls~N-~l~~lp~~~~~l~~L~~L~L~~N~-l~~~~~~  153 (229)
T 3e6j_A          106 AVFD----RLVHLKELFMCCN-KLTELPRGIERLTHLTHLALDQNQ-LKSIPHG  153 (229)
T ss_dssp             TTTT----TCTTCCEEECCSS-CCCSCCTTGGGCTTCSEEECCSSC-CCCCCTT
T ss_pred             hHhC----cchhhCeEeccCC-cccccCcccccCCCCCEEECCCCc-CCccCHH
Confidence            8776    8999999999996 578999999999999999999965 8888753

>3zyi_A Leucine-rich repeat-containing protein 4; cell adhesion, LRRC4 complex, synapse; HET: NAG; 2.60A {Homo sapiens} PDB: 3zyo_A* 3zyn_A* 2dl9_A

Probab=99.31  E-value=9.2e-12  Score=135.22  Aligned_cols=156  Identities=16%  Similarity=0.247  Sum_probs=106.9

Q ss_pred             CccceEEeeecCCcccCCCC-CCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCc
Q 042541          526 PNNASLLSISTDETFSSNWP-DMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLK  604 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~~~~~-~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~  604 (695)
                      +...++|.+..+........ ...+++|+.|.|+.+......|..|.++++|++|+|++|.+..  ++ ...+..+++|+
T Consensus        74 ~~~l~~L~L~~n~i~~~~~~~~~~l~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~L~~n~l~~--~~-~~~~~~l~~L~  150 (452)
T 3zyi_A           74 PSNTRYLNLMENNIQMIQADTFRHLHHLEVLQLGRNSIRQIEVGAFNGLASLNTLELFDNWLTV--IP-SGAFEYLSKLR  150 (452)
T ss_dssp             CTTCSEEECCSSCCCEECTTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSCCSB--CC-TTTSSSCTTCC
T ss_pred             CCCccEEECcCCcCceECHHHcCCCCCCCEEECCCCccCCcChhhccCcccCCEEECCCCcCCc--cC-hhhhcccCCCC
Confidence            45667777766543322222 2367778888887776666666777788888888888776531  11 12266777888


Q ss_pred             EEEeccCCCCCcc--cccccccccEEeeccc-cCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceee
Q 042541          605 KIRLEHVSLPNSL--ATVRMNHLQKVSLVMC-NVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLR  681 (695)
Q Consensus       605 ~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~-~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~  681 (695)
                      +|+|++|.+..+|  .+.++++|++|++++| .+..+++..+.    .+++|++|++++| .+..+|. +..+++|+.|+
T Consensus       151 ~L~L~~N~l~~~~~~~~~~l~~L~~L~l~~~~~l~~i~~~~~~----~l~~L~~L~L~~n-~l~~~~~-~~~l~~L~~L~  224 (452)
T 3zyi_A          151 ELWLRNNPIESIPSYAFNRVPSLMRLDLGELKKLEYISEGAFE----GLFNLKYLNLGMC-NIKDMPN-LTPLVGLEELE  224 (452)
T ss_dssp             EEECCSCCCCEECTTTTTTCTTCCEEECCCCTTCCEECTTTTT----TCTTCCEEECTTS-CCSSCCC-CTTCTTCCEEE
T ss_pred             EEECCCCCcceeCHhHHhcCCcccEEeCCCCCCccccChhhcc----CCCCCCEEECCCC-ccccccc-ccccccccEEE
Confidence            8888888887776  6777888888888874 56666666555    7888888888875 4667764 77888888888


Q ss_pred             cccccCCCCC
Q 042541          682 ITNCHRLSAL  691 (695)
Q Consensus       682 l~~~~~l~~l  691 (695)
                      |++|. +..+
T Consensus       225 Ls~N~-l~~~  233 (452)
T 3zyi_A          225 MSGNH-FPEI  233 (452)
T ss_dssp             CTTSC-CSEE
T ss_pred             CcCCc-Cccc
Confidence            88865 4444

>2xwt_C Thyrotropin receptor; signaling protein-immune system complex, GPCR, graves' disea autoimmunity, receptor-autoantibody complex; HET: NAG BMA MAN; 1.90A {Homo sapiens} PDB: 3g04_C*

Probab=99.31  E-value=1.2e-11  Score=121.86  Aligned_cols=161  Identities=8%  Similarity=0.070  Sum_probs=123.8

Q ss_pred             CccceEEeeecCCcccCCC-CCCCCCceEEEEEEccC-ccccCChhhcCCCCCcEEEEcc-cCCCCcccCcccccccCCC
Q 042541          526 PNNASLLSISTDETFSSNW-PDMQGPEVKVVVLNIRT-KKYVLPDFLQKMDELKVLIVTN-YGFSPAELNNFRVLSALSK  602 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~~~~-~~~~~~~l~~L~l~~~~-~~~~~p~~~~~l~~Lr~L~l~~-~~~~~~~~~~~~~l~~l~~  602 (695)
                      +...+++.+..+....... ....+++|+.|.++.+. .....+..|.++++|++|++++ |.+..  ++ ...+..+++
T Consensus        30 ~~~l~~L~l~~n~l~~i~~~~~~~l~~L~~L~l~~n~~l~~i~~~~f~~l~~L~~L~l~~~n~l~~--i~-~~~f~~l~~  106 (239)
T 2xwt_C           30 PPSTQTLKLIETHLRTIPSHAFSNLPNISRIYVSIDVTLQQLESHSFYNLSKVTHIEIRNTRNLTY--ID-PDALKELPL  106 (239)
T ss_dssp             CTTCCEEEEESCCCSEECTTTTTTCTTCCEEEEECCSSCCEECTTTEESCTTCCEEEEEEETTCCE--EC-TTSEECCTT
T ss_pred             CCcccEEEEeCCcceEECHHHccCCCCCcEEeCCCCCCcceeCHhHcCCCcCCcEEECCCCCCeeE--cC-HHHhCCCCC
Confidence            4467888887665432222 12368999999999886 4444445789999999999998 76632  11 123778999


Q ss_pred             CcEEEeccCCCCCccccccccccc---EEeeccc-cCCcccccchhhhcccCCCcc-EEecccccccccCchhhcCCCCC
Q 042541          603 LKKIRLEHVSLPNSLATVRMNHLQ---KVSLVMC-NVGQVFRNSTFRISDAFPNLL-EMDIDYCNDLIELPDGLCDIVSM  677 (695)
Q Consensus       603 L~~L~L~~~~l~~lp~i~~l~~L~---~L~l~~~-~i~~~~~~~~~~l~~~l~~L~-~L~l~~c~~l~~lP~~i~~L~~L  677 (695)
                      |++|++++|.+..+|.++.+++|+   +|++++| .++.+++..+.    .+++|+ .|++++| .+..+|......++|
T Consensus       107 L~~L~l~~n~l~~lp~~~~l~~L~~L~~L~l~~N~~l~~i~~~~~~----~l~~L~~~L~l~~n-~l~~i~~~~~~~~~L  181 (239)
T 2xwt_C          107 LKFLGIFNTGLKMFPDLTKVYSTDIFFILEITDNPYMTSIPVNAFQ----GLCNETLTLKLYNN-GFTSVQGYAFNGTKL  181 (239)
T ss_dssp             CCEEEEEEECCCSCCCCTTCCBCCSEEEEEEESCTTCCEECTTTTT----TTBSSEEEEECCSC-CCCEECTTTTTTCEE
T ss_pred             CCEEeCCCCCCccccccccccccccccEEECCCCcchhhcCccccc----chhcceeEEEcCCC-CCcccCHhhcCCCCC
Confidence            999999999999888777777777   9999999 89999888776    899999 9999986 567899876666899


Q ss_pred             ceeecccccCCCCCCCC
Q 042541          678 EKLRITNCHRLSALPEG  694 (695)
Q Consensus       678 ~~L~l~~~~~l~~lP~~  694 (695)
                      +.|++++|..++.+|..
T Consensus       182 ~~L~L~~n~~l~~i~~~  198 (239)
T 2xwt_C          182 DAVYLNKNKYLTVIDKD  198 (239)
T ss_dssp             EEEECTTCTTCCEECTT
T ss_pred             CEEEcCCCCCcccCCHH
Confidence            99999997557777653

>2z62_A TOLL-like receptor 4, variable lymphocyte recepto; TLR, VLR hybrid, MD-2, LPS, glycoprotein response, inflammatory response, innate immunity; HET: NAG FUL BMA; 1.70A {Homo sapiens} PDB: 2z65_A* 3ul8_A* 3ula_A* 3ul7_A*

Probab=99.30  E-value=1.3e-11  Score=124.60  Aligned_cols=157  Identities=15%  Similarity=0.201  Sum_probs=91.3

Q ss_pred             ccceEEeeecCCcccCCC-CCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcE
Q 042541          527 NNASLLSISTDETFSSNW-PDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKK  605 (695)
Q Consensus       527 ~~~r~l~~~~~~~~~~~~-~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~  605 (695)
                      ...+++.+..+....... ....+++|+.|.++.+......|..+.++++|++|++.+|.+..  +.. ..++.+++|++
T Consensus        52 ~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~--~~~-~~~~~l~~L~~  128 (276)
T 2z62_A           52 PELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQKLVAVETNLAS--LEN-FPIGHLKTLKE  128 (276)
T ss_dssp             TTCSEEECTTCCCCEECTTTTTTCTTCCEEECTTCCCCEECTTTTTTCTTCCEEECTTSCCCC--STT-CCCTTCTTCCE
T ss_pred             cCCcEEECCCCcCCccCHHHccCCcCCCEEECCCCccCccChhhhcCCccccEEECCCCCccc--cCc-hhcccCCCCCE
Confidence            345566655443221111 11245667777776665555555566677777777777665432  111 12566777777


Q ss_pred             EEeccCCCCC--cc-cccccccccEEeeccccCCcccccchhhhcc-----------------------cCCCccEEecc
Q 042541          606 IRLEHVSLPN--SL-ATVRMNHLQKVSLVMCNVGQVFRNSTFRISD-----------------------AFPNLLEMDID  659 (695)
Q Consensus       606 L~L~~~~l~~--lp-~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~-----------------------~l~~L~~L~l~  659 (695)
                      |++++|.+..  +| .++++++|++|++++|.++.+++..+..++.                       ...+|+.|+++
T Consensus       129 L~l~~n~l~~~~l~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~l~l~L~ls~n~l~~~~~~~~~~~~L~~L~L~  208 (276)
T 2z62_A          129 LNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQMPLLNLSLDLSLNPMNFIQPGAFKEIRLKELALD  208 (276)
T ss_dssp             EECCSSCCCCCCCCGGGGGCTTCCEEECCSSCCCEECGGGGHHHHTCTTCCEEEECCSSCCCEECTTSSCSCCEEEEECC
T ss_pred             EECcCCccceecCchhhccCCCCCEEECCCCCCCcCCHHHhhhhhhccccceeeecCCCcccccCccccCCCcccEEECC
Confidence            7777777764  56 7777777777777777777666544432220                       22356666666


Q ss_pred             cccccccCchh-hcCCCCCceeecccccC
Q 042541          660 YCNDLIELPDG-LCDIVSMEKLRITNCHR  687 (695)
Q Consensus       660 ~c~~l~~lP~~-i~~L~~L~~L~l~~~~~  687 (695)
                      +|. +..+|.. +.++++|+.|++++|+.
T Consensus       209 ~n~-l~~~~~~~~~~l~~L~~L~l~~N~~  236 (276)
T 2z62_A          209 TNQ-LKSVPDGIFDRLTSLQKIWLHTNPW  236 (276)
T ss_dssp             SSC-CSCCCTTTTTTCCSCCEEECCSSCB
T ss_pred             CCc-eeecCHhHhcccccccEEEccCCcc
Confidence            643 5555554 46677777777776553

>2xot_A Amphoterin-induced protein 1; cell adhesion, neuronal protein, neurite growth regulation; HET: NAG BMA; 2.00A {Mus musculus}

Probab=99.30  E-value=1.2e-11  Score=129.96  Aligned_cols=132  Identities=14%  Similarity=0.184  Sum_probs=63.2

Q ss_pred             eEEEEEEccCccccCChhhc-CCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--cccccccccEE
Q 042541          552 VKVVVLNIRTKKYVLPDFLQ-KMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNHLQKV  628 (695)
Q Consensus       552 l~~L~l~~~~~~~~~p~~~~-~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L~~L  628 (695)
                      ++.|.|+.+......+..+. ++++|++|+|++|.+...  . ...+..+++|++|+|++|.++.+|  .+.++++|++|
T Consensus        41 l~~L~Ls~N~l~~l~~~~~~~~l~~L~~L~L~~N~i~~i--~-~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L  117 (361)
T 2xot_A           41 TALLDLSHNNLSRLRAEWTPTRLTNLHSLLLSHNHLNFI--S-SEAFVPVPNLRYLDLSSNHLHTLDEFLFSDLQALEVL  117 (361)
T ss_dssp             CSEEECCSSCCCEECTTSSSSCCTTCCEEECCSSCCCEE--C-TTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTCCEE
T ss_pred             CCEEECCCCCCCccChhhhhhcccccCEEECCCCcCCcc--C-hhhccCCCCCCEEECCCCcCCcCCHHHhCCCcCCCEE
Confidence            44555554444333333444 555555555555544211  0 012445555555555555555444  34555555555


Q ss_pred             eeccccCCcccccchhhhcccCCCccEEecccccccccCchhh----cCCCCCceeecccccCCCCCC
Q 042541          629 SLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGL----CDIVSMEKLRITNCHRLSALP  692 (695)
Q Consensus       629 ~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i----~~L~~L~~L~l~~~~~l~~lP  692 (695)
                      +|++|.++.+++..+.    .+++|+.|+|++| .+..+|..+    ..+++|++|+|++|. +..+|
T Consensus       118 ~L~~N~i~~~~~~~~~----~l~~L~~L~L~~N-~l~~l~~~~~~~~~~l~~L~~L~L~~N~-l~~l~  179 (361)
T 2xot_A          118 LLYNNHIVVVDRNAFE----DMAQLQKLYLSQN-QISRFPVELIKDGNKLPKLMLLDLSSNK-LKKLP  179 (361)
T ss_dssp             ECCSSCCCEECTTTTT----TCTTCCEEECCSS-CCCSCCGGGTC----CTTCCEEECCSSC-CCCCC
T ss_pred             ECCCCcccEECHHHhC----CcccCCEEECCCC-cCCeeCHHHhcCcccCCcCCEEECCCCC-CCccC
Confidence            5555555555444443    4555555555553 344455443    345555555555533 44444

>3zyj_A Leucine-rich repeat-containing protein 4C; cell adhesion, synapse; HET: NAG BMA MAN; 3.25A {Homo sapiens}

Probab=99.30  E-value=1.2e-11  Score=133.69  Aligned_cols=158  Identities=18%  Similarity=0.269  Sum_probs=117.0

Q ss_pred             CCccceEEeeecCCcccCCCC-CCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCC
Q 042541          525 HPNNASLLSISTDETFSSNWP-DMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKL  603 (695)
Q Consensus       525 ~~~~~r~l~~~~~~~~~~~~~-~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L  603 (695)
                      .+...++|.+..+........ ...+++|+.|.|+.+......+..|.++++|++|+|++|.+..  ++ ...+..+++|
T Consensus        62 ~~~~l~~L~L~~n~i~~~~~~~~~~l~~L~~L~Ls~n~i~~i~~~~~~~l~~L~~L~L~~n~l~~--~~-~~~~~~l~~L  138 (440)
T 3zyj_A           62 ISTNTRLLNLHENQIQIIKVNSFKHLRHLEILQLSRNHIRTIEIGAFNGLANLNTLELFDNRLTT--IP-NGAFVYLSKL  138 (440)
T ss_dssp             CCTTCSEEECCSCCCCEECTTTTSSCSSCCEEECCSSCCCEECGGGGTTCSSCCEEECCSSCCSS--CC-TTTSCSCSSC
T ss_pred             CCCCCcEEEccCCcCCeeCHHHhhCCCCCCEEECCCCcCCccChhhccCCccCCEEECCCCcCCe--eC-HhHhhccccC
Confidence            345677787776544332222 2367888888888887666666788888999999998886632  11 1236788889


Q ss_pred             cEEEeccCCCCCcc--cccccccccEEeeccc-cCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCcee
Q 042541          604 KKIRLEHVSLPNSL--ATVRMNHLQKVSLVMC-NVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKL  680 (695)
Q Consensus       604 ~~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~-~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L  680 (695)
                      ++|+|++|.+..+|  .+.++++|++|+|++| .+..+++..+.    .+++|++|++++| .+..+|. +..+++|+.|
T Consensus       139 ~~L~L~~N~i~~~~~~~~~~l~~L~~L~l~~~~~l~~i~~~~~~----~l~~L~~L~L~~n-~l~~~~~-~~~l~~L~~L  212 (440)
T 3zyj_A          139 KELWLRNNPIESIPSYAFNRIPSLRRLDLGELKRLSYISEGAFE----GLSNLRYLNLAMC-NLREIPN-LTPLIKLDEL  212 (440)
T ss_dssp             CEEECCSCCCCEECTTTTTTCTTCCEEECCCCTTCCEECTTTTT----TCSSCCEEECTTS-CCSSCCC-CTTCSSCCEE
T ss_pred             ceeeCCCCcccccCHHHhhhCcccCEeCCCCCCCcceeCcchhh----cccccCeecCCCC-cCccccc-cCCCcccCEE
Confidence            99999999888777  7888899999999885 56777776665    7889999999986 5778884 8889999999


Q ss_pred             ecccccCCCCCC
Q 042541          681 RITNCHRLSALP  692 (695)
Q Consensus       681 ~l~~~~~l~~lP  692 (695)
                      +|++|. +..++
T Consensus       213 ~Ls~N~-l~~~~  223 (440)
T 3zyj_A          213 DLSGNH-LSAIR  223 (440)
T ss_dssp             ECTTSC-CCEEC
T ss_pred             ECCCCc-cCccC
Confidence            999875 55553

>1h6u_A Internalin H; cell adhesion, leucine rich repeat, IG-like domain, EF-hand domain; 1.8A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1

Probab=99.29  E-value=1.9e-11  Score=125.47  Aligned_cols=150  Identities=16%  Similarity=0.193  Sum_probs=112.1

Q ss_pred             CccceEEeeecCCcccCCCCCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcE
Q 042541          526 PNNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKK  605 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~~~~~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~  605 (695)
                      ....+.|.+..+.... ......+++|+.|.++.+.... +| .+..+++|++|++++|.+..     .+.+..+++|++
T Consensus        62 l~~L~~L~L~~n~i~~-~~~~~~l~~L~~L~L~~n~l~~-~~-~~~~l~~L~~L~l~~n~l~~-----~~~l~~l~~L~~  133 (308)
T 1h6u_A           62 LNNLIGLELKDNQITD-LAPLKNLTKITELELSGNPLKN-VS-AIAGLQSIKTLDLTSTQITD-----VTPLAGLSNLQV  133 (308)
T ss_dssp             CTTCCEEECCSSCCCC-CGGGTTCCSCCEEECCSCCCSC-CG-GGTTCTTCCEEECTTSCCCC-----CGGGTTCTTCCE
T ss_pred             cCCCCEEEccCCcCCC-ChhHccCCCCCEEEccCCcCCC-ch-hhcCCCCCCEEECCCCCCCC-----chhhcCCCCCCE
Confidence            3567777776654322 1223467888888888775433 33 57888889999998887632     233788889999


Q ss_pred             EEeccCCCCCcccccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccc
Q 042541          606 IRLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNC  685 (695)
Q Consensus       606 L~L~~~~l~~lp~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~  685 (695)
                      |++++|.+..+|.++.+++|++|++++|.++.+++  +.    .+++|+.|++++| .+..+|. +..+++|++|++++|
T Consensus       134 L~l~~n~l~~~~~l~~l~~L~~L~l~~n~l~~~~~--l~----~l~~L~~L~l~~n-~l~~~~~-l~~l~~L~~L~L~~N  205 (308)
T 1h6u_A          134 LYLDLNQITNISPLAGLTNLQYLSIGNAQVSDLTP--LA----NLSKLTTLKADDN-KISDISP-LASLPNLIEVHLKNN  205 (308)
T ss_dssp             EECCSSCCCCCGGGGGCTTCCEEECCSSCCCCCGG--GT----TCTTCCEEECCSS-CCCCCGG-GGGCTTCCEEECTTS
T ss_pred             EECCCCccCcCccccCCCCccEEEccCCcCCCChh--hc----CCCCCCEEECCCC-ccCcChh-hcCCCCCCEEEccCC
Confidence            99999988877777788999999999998888766  33    7899999999986 5677775 888999999999987


Q ss_pred             cCCCCCC
Q 042541          686 HRLSALP  692 (695)
Q Consensus       686 ~~l~~lP  692 (695)
                      . +..+|
T Consensus       206 ~-l~~~~  211 (308)
T 1h6u_A          206 Q-ISDVS  211 (308)
T ss_dssp             C-CCBCG
T ss_pred             c-cCccc
Confidence            6 55554

>1h6t_A Internalin B; cell adhesion, leucine rich repeat, IG-like domain, EF-hand domain; 1.6A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 2wqu_A 2uzy_A 2uzx_A 2wqv_A* 2wqw_A 2wqx_A 1d0b_A 1otn_A 1oto_A 1otm_A

Probab=99.29  E-value=2.2e-11  Score=123.82  Aligned_cols=150  Identities=17%  Similarity=0.209  Sum_probs=114.2

Q ss_pred             CccceEEeeecCCcccCCCCCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcE
Q 042541          526 PNNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKK  605 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~~~~~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~  605 (695)
                      ....+.|.+..+.... ......+++|+.|.++.+.... +| .+..+++|++|++++|.+..     ++.+..+++|++
T Consensus        67 l~~L~~L~L~~n~l~~-~~~l~~l~~L~~L~l~~n~l~~-~~-~l~~l~~L~~L~L~~n~i~~-----~~~l~~l~~L~~  138 (291)
T 1h6t_A           67 LPNVTKLFLNGNKLTD-IKPLANLKNLGWLFLDENKVKD-LS-SLKDLKKLKSLSLEHNGISD-----INGLVHLPQLES  138 (291)
T ss_dssp             CTTCCEEECCSSCCCC-CGGGTTCTTCCEEECCSSCCCC-GG-GGTTCTTCCEEECTTSCCCC-----CGGGGGCTTCCE
T ss_pred             CCCCCEEEccCCccCC-CcccccCCCCCEEECCCCcCCC-Ch-hhccCCCCCEEECCCCcCCC-----ChhhcCCCCCCE
Confidence            3567777776654322 1223467888999888775433 33 48888999999999887632     244788899999


Q ss_pred             EEeccCCCCCcccccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccc
Q 042541          606 IRLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNC  685 (695)
Q Consensus       606 L~L~~~~l~~lp~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~  685 (695)
                      |++++|.+..++.++.+++|++|++++|.++.+++  +.    .+++|+.|++++| .+..+|. +..+++|+.|++++|
T Consensus       139 L~l~~n~l~~~~~l~~l~~L~~L~L~~N~l~~~~~--l~----~l~~L~~L~L~~N-~i~~l~~-l~~l~~L~~L~l~~n  210 (291)
T 1h6t_A          139 LYLGNNKITDITVLSRLTKLDTLSLEDNQISDIVP--LA----GLTKLQNLYLSKN-HISDLRA-LAGLKNLDVLELFSQ  210 (291)
T ss_dssp             EECCSSCCCCCGGGGGCTTCSEEECCSSCCCCCGG--GT----TCTTCCEEECCSS-CCCBCGG-GTTCTTCSEEEEEEE
T ss_pred             EEccCCcCCcchhhccCCCCCEEEccCCccccchh--hc----CCCccCEEECCCC-cCCCChh-hccCCCCCEEECcCC
Confidence            99999998887878889999999999999988776  33    7899999999986 5777875 899999999999987


Q ss_pred             cCCCCCC
Q 042541          686 HRLSALP  692 (695)
Q Consensus       686 ~~l~~lP  692 (695)
                      + +...|
T Consensus       211 ~-i~~~~  216 (291)
T 1h6t_A          211 E-CLNKP  216 (291)
T ss_dssp             E-EECCC
T ss_pred             c-ccCCc
Confidence            6 44443

>3oja_B Anopheles plasmodium-responsive leucine-rich REPE 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=99.28  E-value=1.9e-11  Score=137.53  Aligned_cols=159  Identities=14%  Similarity=0.173  Sum_probs=108.8

Q ss_pred             CccceEEeeecCCcccCCCCC--CCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccC-----------
Q 042541          526 PNNASLLSISTDETFSSNWPD--MQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELN-----------  592 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~~~~~~--~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~-----------  592 (695)
                      ....++|.+.++... ..+..  ..+++|+.|.++.+......|..|.++++|++|++++|.+....+.           
T Consensus       122 l~~L~~L~L~~n~l~-~l~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~l~~L~~L~l~  200 (597)
T 3oja_B          122 VPLLTVLVLERNDLS-SLPRGIFHNTPKLTTLSMSNNNLERIEDDTFQATTSLQNLQLSSNRLTHVDLSLIPSLFHANVS  200 (597)
T ss_dssp             CTTCCEEECCSSCCC-CCCTTTTTTCTTCCEEECCSSCCCBCCTTTTTTCTTCCEEECTTSCCSBCCGGGCTTCSEEECC
T ss_pred             CCCCCEEEeeCCCCC-CCCHHHhccCCCCCEEEeeCCcCCCCChhhhhcCCcCcEEECcCCCCCCcChhhhhhhhhhhcc
Confidence            346677777655432 22222  3677888888888777666677788888888888887755321110           


Q ss_pred             ---------------------------------------------cccccccCCCCcEEEeccCCCCCc-c-cccccccc
Q 042541          593 ---------------------------------------------NFRVLSALSKLKKIRLEHVSLPNS-L-ATVRMNHL  625 (695)
Q Consensus       593 ---------------------------------------------~~~~l~~l~~L~~L~L~~~~l~~l-p-~i~~l~~L  625 (695)
                                                                   .++.++.+++|++|+|++|.+..+ | .++.+++|
T Consensus       201 ~n~l~~l~~~~~L~~L~ls~n~l~~~~~~~~~~L~~L~L~~n~l~~~~~l~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L  280 (597)
T 3oja_B          201 YNLLSTLAIPIAVEELDASHNSINVVRGPVNVELTILKLQHNNLTDTAWLLNYPGLVEVDLSYNELEKIMYHPFVKMQRL  280 (597)
T ss_dssp             SSCCSEEECCTTCSEEECCSSCCCEEECSCCSCCCEEECCSSCCCCCGGGGGCTTCSEEECCSSCCCEEESGGGTTCSSC
T ss_pred             cCccccccCCchhheeeccCCcccccccccCCCCCEEECCCCCCCCChhhccCCCCCEEECCCCccCCCCHHHhcCccCC
Confidence                                                         112355667777777777777744 4 77778888


Q ss_pred             cEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccccCCCCCC
Q 042541          626 QKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALP  692 (695)
Q Consensus       626 ~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~~l~~lP  692 (695)
                      ++|+|++|.++.+|....     .+++|+.|+|++| .+..+|..++.+++|++|+|++|+ +..+|
T Consensus       281 ~~L~Ls~N~l~~l~~~~~-----~l~~L~~L~Ls~N-~l~~i~~~~~~l~~L~~L~L~~N~-l~~~~  340 (597)
T 3oja_B          281 ERLYISNNRLVALNLYGQ-----PIPTLKVLDLSHN-HLLHVERNQPQFDRLENLYLDHNS-IVTLK  340 (597)
T ss_dssp             CEEECTTSCCCEEECSSS-----CCTTCCEEECCSS-CCCCCGGGHHHHTTCSEEECCSSC-CCCCC
T ss_pred             CEEECCCCCCCCCCcccc-----cCCCCcEEECCCC-CCCccCcccccCCCCCEEECCCCC-CCCcC
Confidence            888888887777665544     6788888888886 466788888888888888888866 55554

>4g8a_A TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, immune system; HET: NAG LP4 LP5 DAO MYR KDO; 2.40A {Homo sapiens} PDB: 3fxi_A*

Probab=99.28  E-value=5.8e-12  Score=142.96  Aligned_cols=135  Identities=16%  Similarity=0.170  Sum_probs=104.4

Q ss_pred             CceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--cccccccccE
Q 042541          550 PEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNHLQK  627 (695)
Q Consensus       550 ~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L~~  627 (695)
                      +.++.|+|+.|......|..|.++++|++|+|++|.+..  ++ ...+.+|++|++|+|++|.++.+|  .+++|++|++
T Consensus        52 ~~~~~LdLs~N~i~~l~~~~f~~l~~L~~L~Ls~N~i~~--i~-~~~f~~L~~L~~L~Ls~N~l~~l~~~~f~~L~~L~~  128 (635)
T 4g8a_A           52 FSTKNLDLSFNPLRHLGSYSFFSFPELQVLDLSRCEIQT--IE-DGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQK  128 (635)
T ss_dssp             TTCCEEECTTSCCCEECTTTTTTCTTCCEEECTTCCCCE--EC-TTTTTTCTTCCEEECTTCCCCEECGGGGTTCTTCCE
T ss_pred             cCCCEEEeeCCCCCCCCHHHHhCCCCCCEEECCCCcCCC--cC-hhHhcCCCCCCEEEccCCcCCCCCHHHhcCCCCCCE
Confidence            468888888876665556688889999999999887631  11 123778889999999999988887  6788999999


Q ss_pred             EeeccccCCcccccchhhhcccCCCccEEecccccccc-cCchhhcCCCCCceeecccccCCCCCC
Q 042541          628 VSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLI-ELPDGLCDIVSMEKLRITNCHRLSALP  692 (695)
Q Consensus       628 L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~-~lP~~i~~L~~L~~L~l~~~~~l~~lP  692 (695)
                      |+|++|.++.+++..+.    .|++|++|++++|.... .+|..++.+++|++|++++|. +..++
T Consensus       129 L~Ls~N~l~~l~~~~~~----~L~~L~~L~Ls~N~l~~~~~~~~~~~l~~L~~L~L~~N~-l~~~~  189 (635)
T 4g8a_A          129 LVAVETNLASLENFPIG----HLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNK-IQSIY  189 (635)
T ss_dssp             EECTTSCCCCSTTCCCT----TCTTCCEEECCSSCCCCCCCCGGGGGCTTCCEEECCSSC-CCEEC
T ss_pred             EECCCCcCCCCChhhhh----cCcccCeeccccCccccCCCchhhccchhhhhhcccCcc-ccccc
Confidence            99999998888887666    88899999998864322 467778889999999998865 54443

>2z66_A Variable lymphocyte receptor B, TOLL-like recepto; TLR4, TOLL-like receptor, MD-2, LPS, leucine-rich repeat, glycoprotein, immune response; HET: NAG BMA FUL; 1.90A {Eptatretus burgeri}

Probab=99.28  E-value=1e-11  Score=127.44  Aligned_cols=154  Identities=13%  Similarity=0.097  Sum_probs=112.5

Q ss_pred             ccceEEeeecCCcccCCC--CCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCc
Q 042541          527 NNASLLSISTDETFSSNW--PDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLK  604 (695)
Q Consensus       527 ~~~r~l~~~~~~~~~~~~--~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~  604 (695)
                      ...+++.+..+.......  ....+++|+.|.++.+......|..+..+++|++|++++|.+.....  +..+..+++|+
T Consensus       101 ~~L~~L~l~~n~l~~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~--~~~~~~l~~L~  178 (306)
T 2z66_A          101 EQLEHLDFQHSNLKQMSEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFL--PDIFTELRNLT  178 (306)
T ss_dssp             TTCCEEECTTSEEESSTTTTTTTTCTTCCEEECTTSCCEECSTTTTTTCTTCCEEECTTCEEGGGEE--CSCCTTCTTCC
T ss_pred             CCCCEEECCCCcccccccchhhhhccCCCEEECCCCcCCccchhhcccCcCCCEEECCCCccccccc--hhHHhhCcCCC
Confidence            456666665543222111  22367788888888777666777778888888888888876532111  22367888899


Q ss_pred             EEEeccCCCCCc-c-cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCC-CCceee
Q 042541          605 KIRLEHVSLPNS-L-ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIV-SMEKLR  681 (695)
Q Consensus       605 ~L~L~~~~l~~l-p-~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~-~L~~L~  681 (695)
                      +|++++|.+..+ | .++++++|++|++++|.++.+++..+.    .+++|+.|++++|......|..+..++ +|++|+
T Consensus       179 ~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~----~l~~L~~L~L~~N~l~~~~~~~~~~~~~~L~~L~  254 (306)
T 2z66_A          179 FLDLSQCQLEQLSPTAFNSLSSLQVLNMSHNNFFSLDTFPYK----CLNSLQVLDYSLNHIMTSKKQELQHFPSSLAFLN  254 (306)
T ss_dssp             EEECTTSCCCEECTTTTTTCTTCCEEECTTSCCSBCCSGGGT----TCTTCCEEECTTSCCCBCSSSSCCCCCTTCCEEE
T ss_pred             EEECCCCCcCCcCHHHhcCCCCCCEEECCCCccCccChhhcc----CcccCCEeECCCCCCcccCHHHHHhhhccCCEEE
Confidence            999999888866 4 788888999999999988888776555    788899999998866666777788884 899999


Q ss_pred             ccccc
Q 042541          682 ITNCH  686 (695)
Q Consensus       682 l~~~~  686 (695)
                      +++|+
T Consensus       255 L~~N~  259 (306)
T 2z66_A          255 LTQND  259 (306)
T ss_dssp             CTTCC
T ss_pred             ccCCC
Confidence            98876

>2z62_A TOLL-like receptor 4, variable lymphocyte recepto; TLR, VLR hybrid, MD-2, LPS, glycoprotein response, inflammatory response, innate immunity; HET: NAG FUL BMA; 1.70A {Homo sapiens} PDB: 2z65_A* 3ul8_A* 3ula_A* 3ul7_A*

Probab=99.28  E-value=1.3e-11  Score=124.51  Aligned_cols=135  Identities=16%  Similarity=0.153  Sum_probs=100.0

Q ss_pred             CccceEEeeecCCcccCCC-CCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCc
Q 042541          526 PNNASLLSISTDETFSSNW-PDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLK  604 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~~~~-~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~  604 (695)
                      +...+++.+..+....... ....+++|+.|.++.+......+..+.++++|++|++++|.+....   ...+..+++|+
T Consensus        27 ~~~l~~L~ls~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~---~~~~~~l~~L~  103 (276)
T 2z62_A           27 PFSTKNLDLSFNPLRHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLA---LGAFSGLSSLQ  103 (276)
T ss_dssp             CTTCCEEECTTCCCCEECTTTTTTCTTCSEEECTTCCCCEECTTTTTTCTTCCEEECTTCCCCEEC---TTTTTTCTTCC
T ss_pred             CCCccEEECCCCcccccCHhHhccccCCcEEECCCCcCCccCHHHccCCcCCCEEECCCCccCccC---hhhhcCCcccc
Confidence            4567888887654332222 2236789999999888666666668899999999999998764211   12377889999


Q ss_pred             EEEeccCCCCCcc--cccccccccEEeeccccCCccc-ccchhhhcccCCCccEEecccccccccCc
Q 042541          605 KIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVF-RNSTFRISDAFPNLLEMDIDYCNDLIELP  668 (695)
Q Consensus       605 ~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~-~~~~~~l~~~l~~L~~L~l~~c~~l~~lP  668 (695)
                      +|++++|.+..++  .++++++|++|++++|.++... |..+.    .+++|++|++++|. +..+|
T Consensus       104 ~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~l~~~~~----~l~~L~~L~Ls~N~-l~~~~  165 (276)
T 2z62_A          104 KLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFS----NLTNLEHLDLSSNK-IQSIY  165 (276)
T ss_dssp             EEECTTSCCCCSTTCCCTTCTTCCEEECCSSCCCCCCCCGGGG----GCTTCCEEECCSSC-CCEEC
T ss_pred             EEECCCCCccccCchhcccCCCCCEEECcCCccceecCchhhc----cCCCCCEEECCCCC-CCcCC
Confidence            9999999998776  7889999999999999988743 44444    78999999999864 44443

>2z66_A Variable lymphocyte receptor B, TOLL-like recepto; TLR4, TOLL-like receptor, MD-2, LPS, leucine-rich repeat, glycoprotein, immune response; HET: NAG BMA FUL; 1.90A {Eptatretus burgeri}

Probab=99.27  E-value=7.3e-12  Score=128.45  Aligned_cols=137  Identities=13%  Similarity=0.137  Sum_probs=102.5

Q ss_pred             CCCceEEEEEEccCccccCC-hhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCC--cc-cccccc
Q 042541          548 QGPEVKVVVLNIRTKKYVLP-DFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPN--SL-ATVRMN  623 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p-~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~--lp-~i~~l~  623 (695)
                      .+++|+.|.++.+......+ ..+..+++|++|++++|.+...   ....+..+++|++|++++|.+..  +| .++.++
T Consensus        99 ~l~~L~~L~l~~n~l~~~~~~~~~~~l~~L~~L~l~~n~l~~~---~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~l~  175 (306)
T 2z66_A           99 GLEQLEHLDFQHSNLKQMSEFSVFLSLRNLIYLDISHTHTRVA---FNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELR  175 (306)
T ss_dssp             TCTTCCEEECTTSEEESSTTTTTTTTCTTCCEEECTTSCCEEC---STTTTTTCTTCCEEECTTCEEGGGEECSCCTTCT
T ss_pred             CCCCCCEEECCCCcccccccchhhhhccCCCEEECCCCcCCcc---chhhcccCcCCCEEECCCCccccccchhHHhhCc
Confidence            56777777777664433333 4677888888888887765311   11236778899999999998874  67 888999


Q ss_pred             cccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCch-hhcCCCCCceeecccccCCCCCC
Q 042541          624 HLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPD-GLCDIVSMEKLRITNCHRLSALP  692 (695)
Q Consensus       624 ~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~-~i~~L~~L~~L~l~~~~~l~~lP  692 (695)
                      +|++|++++|.++.+++..+.    .+++|++|++++|. +..+|. .+..+++|++|++++|...+..|
T Consensus       176 ~L~~L~Ls~n~l~~~~~~~~~----~l~~L~~L~L~~N~-l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~  240 (306)
T 2z66_A          176 NLTFLDLSQCQLEQLSPTAFN----SLSSLQVLNMSHNN-FFSLDTFPYKCLNSLQVLDYSLNHIMTSKK  240 (306)
T ss_dssp             TCCEEECTTSCCCEECTTTTT----TCTTCCEEECTTSC-CSBCCSGGGTTCTTCCEEECTTSCCCBCSS
T ss_pred             CCCEEECCCCCcCCcCHHHhc----CCCCCCEEECCCCc-cCccChhhccCcccCCEeECCCCCCcccCH
Confidence            999999999999988777665    78999999999875 555554 68899999999999987444444

>3vq2_A TLR4, TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, secreted, immune SY; HET: NAG LP4 LP5 DAO MYR; 2.48A {Mus musculus} PDB: 3vq1_A* 2z64_A*

Probab=99.27  E-value=2e-11  Score=137.89  Aligned_cols=130  Identities=11%  Similarity=0.112  Sum_probs=61.9

Q ss_pred             CceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCc-c-cccccccccE
Q 042541          550 PEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNS-L-ATVRMNHLQK  627 (695)
Q Consensus       550 ~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~l-p-~i~~l~~L~~  627 (695)
                      ++++.|.++.+......|..|.++++|++|++++|.+..  + .+..++.+++|++|+|++|.+..+ | .++++++|++
T Consensus        32 ~~l~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~--i-~~~~~~~l~~L~~L~Ls~n~l~~~~p~~~~~l~~L~~  108 (606)
T 3vq2_A           32 SSTKNIDLSFNPLKILKSYSFSNFSELQWLDLSRCEIET--I-EDKAWHGLHHLSNLILTGNPIQSFSPGSFSGLTSLEN  108 (606)
T ss_dssp             TTCCEEECTTSCCCEECTTTTTTCTTCCEEECTTCCCCE--E-CTTTTTTCTTCCEEECTTCCCCCCCTTSSTTCTTCCE
T ss_pred             CCcCEEECCCCCcCEeChhhccCCccCcEEeCCCCcccc--c-CHHHhhchhhcCEeECCCCcccccChhhcCCcccCCE
Confidence            344455554444433334445555555555555544321  0 011244555555555555555543 3 5555555555


Q ss_pred             EeeccccCCcccccchhhhcccCCCccEEecccccccc-cCchhhcCCCCCceeeccccc
Q 042541          628 VSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLI-ELPDGLCDIVSMEKLRITNCH  686 (695)
Q Consensus       628 L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~-~lP~~i~~L~~L~~L~l~~~~  686 (695)
                      |++++|.++.+++..+.    .+++|++|++++|.... .+|..++++++|++|++++|.
T Consensus       109 L~L~~n~l~~~~~~~~~----~l~~L~~L~L~~n~l~~~~lp~~~~~l~~L~~L~Ls~n~  164 (606)
T 3vq2_A          109 LVAVETKLASLESFPIG----QLITLKKLNVAHNFIHSCKLPAYFSNLTNLVHVDLSYNY  164 (606)
T ss_dssp             EECTTSCCCCSSSSCCT----TCTTCCEEECCSSCCCCCCCCGGGGTCTTCCEEECCSSC
T ss_pred             EEccCCccccccccccC----CCCCCCEEeCCCCcccceechHhHhhcCCCCEEEccCCc
Confidence            55555555554443333    45555555555543222 345555555555555555543

>1h6t_A Internalin B; cell adhesion, leucine rich repeat, IG-like domain, EF-hand domain; 1.6A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 2wqu_A 2uzy_A 2uzx_A 2wqv_A* 2wqw_A 2wqx_A 1d0b_A 1otn_A 1oto_A 1otm_A

Probab=99.27  E-value=2.4e-11  Score=123.53  Aligned_cols=148  Identities=17%  Similarity=0.237  Sum_probs=116.1

Q ss_pred             cceEEeeecCCcccCCCCCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEE
Q 042541          528 NASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIR  607 (695)
Q Consensus       528 ~~r~l~~~~~~~~~~~~~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~  607 (695)
                      ..+.+.+...... .......+++|+.|.++.+..... +. +.++++|++|++++|.+.     .++.+..+++|++|+
T Consensus        47 ~L~~L~l~~~~i~-~~~~~~~l~~L~~L~L~~n~l~~~-~~-l~~l~~L~~L~l~~n~l~-----~~~~l~~l~~L~~L~  118 (291)
T 1h6t_A           47 SIDQIIANNSDIK-SVQGIQYLPNVTKLFLNGNKLTDI-KP-LANLKNLGWLFLDENKVK-----DLSSLKDLKKLKSLS  118 (291)
T ss_dssp             TCCEEECTTSCCC-CCTTGGGCTTCCEEECCSSCCCCC-GG-GTTCTTCCEEECCSSCCC-----CGGGGTTCTTCCEEE
T ss_pred             cccEEEccCCCcc-cChhHhcCCCCCEEEccCCccCCC-cc-cccCCCCCEEECCCCcCC-----CChhhccCCCCCEEE
Confidence            4555655543321 111223678999999988865543 33 899999999999998763     234488999999999


Q ss_pred             eccCCCCCcccccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccccC
Q 042541          608 LEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHR  687 (695)
Q Consensus       608 L~~~~l~~lp~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~~  687 (695)
                      +++|.+..++.++.+++|++|++++|.++.+ +...     .+++|++|++++| .+..+|. +..+++|++|++++|. 
T Consensus       119 L~~n~i~~~~~l~~l~~L~~L~l~~n~l~~~-~~l~-----~l~~L~~L~L~~N-~l~~~~~-l~~l~~L~~L~L~~N~-  189 (291)
T 1h6t_A          119 LEHNGISDINGLVHLPQLESLYLGNNKITDI-TVLS-----RLTKLDTLSLEDN-QISDIVP-LAGLTKLQNLYLSKNH-  189 (291)
T ss_dssp             CTTSCCCCCGGGGGCTTCCEEECCSSCCCCC-GGGG-----GCTTCSEEECCSS-CCCCCGG-GTTCTTCCEEECCSSC-
T ss_pred             CCCCcCCCChhhcCCCCCCEEEccCCcCCcc-hhhc-----cCCCCCEEEccCC-ccccchh-hcCCCccCEEECCCCc-
Confidence            9999999888888999999999999999887 3333     8999999999997 5677776 9999999999999975 


Q ss_pred             CCCCC
Q 042541          688 LSALP  692 (695)
Q Consensus       688 l~~lP  692 (695)
                      ++.+|
T Consensus       190 i~~l~  194 (291)
T 1h6t_A          190 ISDLR  194 (291)
T ss_dssp             CCBCG
T ss_pred             CCCCh
Confidence            66665

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=99.27  E-value=1.1e-10  Score=115.13  Aligned_cols=192  Identities=17%  Similarity=0.117  Sum_probs=115.7

Q ss_pred             CCCCCCCcchHHHHHHHHHcCC-ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhc
Q 042541          165 PVISPGLDVPLKELKMELFKDG-RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHK  243 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~-~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l  243 (695)
                      ...++||+..++.+..++..+. .+.+.|+|++|+||||||+.+++.  ....+.. . ...+...   .. ...+....
T Consensus        22 ~~~~~g~~~~~~~l~~~l~~~~~~~~~ll~G~~G~GKT~l~~~~~~~--~~~~~~~-~-~~~~~~~---~~-~~~~~~~~   93 (250)
T 1njg_A           22 FADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKG--LNCETGI-T-ATPCGVC---DN-CREIEQGR   93 (250)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHTCCCSEEEEECSTTSCHHHHHHHHHHH--HHCTTCS-C-SSCCSCS---HH-HHHHHTTC
T ss_pred             HHHHhCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHH--hcCCCCC-C-CCCCccc---HH-HHHHhccC
Confidence            3468999999999999998554 468999999999999999999873  2221110 0 0000000   00 00111000


Q ss_pred             CCCCCC-CCChHHHHHHHHHHHHhc-----CCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCC-----
Q 042541          244 GYPVPE-FQTDEAAINDLERFFKQM-----RIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFP-----  308 (695)
Q Consensus       244 ~~~~~~-~~~~~~~~~~l~~~~~~l-----~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~-----  308 (695)
                      ...... ..........+..+++.+     .+++.+||+||++.....    ++..+.....+..+|+||+....     
T Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlviDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~t~~~~~~~~~l  173 (250)
T 1njg_A           94 FVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTI  173 (250)
T ss_dssp             CSSEEEEETTCGGGHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCGGGSCHHH
T ss_pred             CcceEEecCcccccHHHHHHHHHHhhhchhcCCceEEEEECcccccHHHHHHHHHHHhcCCCceEEEEEeCChHhCCHHH
Confidence            000000 000001122233333332     457899999999776543    33333334457788888876521     


Q ss_pred             -CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHHHh
Q 042541          309 -QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGGS  367 (695)
Q Consensus       309 -~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~~~  367 (695)
                       .....+.+++++.++..+++...+.....   .-..+....|++.|+|+|..+..+...
T Consensus       174 ~~r~~~i~l~~l~~~e~~~~l~~~~~~~~~---~~~~~~~~~l~~~~~G~~~~~~~~~~~  230 (250)
T 1njg_A          174 LSRCLQFHLKALDVEQIRHQLEHILNEEHI---AHEPRALQLLARAAEGSLRDALSLTDQ  230 (250)
T ss_dssp             HTTSEEEECCCCCHHHHHHHHHHHHHHTTC---CBCHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHhhhccCCCCCHHHHHHHHHHHHHhcCC---CCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence             11247999999999999999987654322   123567889999999999988876543

>4b8c_D Glucose-repressible alcohol dehydrogenase transcr effector; hydrolase-cell cycle complex; 3.41A {Saccharomyces cerevisiae S288C}

Probab=99.27  E-value=3.9e-12  Score=145.75  Aligned_cols=118  Identities=11%  Similarity=0.027  Sum_probs=93.4

Q ss_pred             cCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc-cccccccccEEeeccccCCcccccch
Q 042541          565 VLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL-ATVRMNHLQKVSLVMCNVGQVFRNST  643 (695)
Q Consensus       565 ~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp-~i~~l~~L~~L~l~~~~i~~~~~~~~  643 (695)
                      ..|..+..+++|++|+|++|.+.  .++  +.+..+++|++|+|++|.++.+| .+++|++|++|+|++|.|+.+|..+.
T Consensus       215 ~~~~~~~~l~~L~~L~Ls~n~l~--~l~--~~~~~l~~L~~L~Ls~N~l~~lp~~~~~l~~L~~L~Ls~N~l~~lp~~~~  290 (727)
T 4b8c_D          215 MPKDSKYDDQLWHALDLSNLQIF--NIS--ANIFKYDFLTRLYLNGNSLTELPAEIKNLSNLRVLDLSHNRLTSLPAELG  290 (727)
T ss_dssp             -------CCCCCCEEECTTSCCS--CCC--GGGGGCCSCSCCBCTTSCCSCCCGGGGGGTTCCEEECTTSCCSSCCSSGG
T ss_pred             cChhhhccCCCCcEEECCCCCCC--CCC--hhhcCCCCCCEEEeeCCcCcccChhhhCCCCCCEEeCcCCcCCccChhhc
Confidence            45678889999999999998764  222  23668999999999999999999 99999999999999999998766655


Q ss_pred             hhhcccCCCccEEecccccccccCchhhcCCCCCceeecccccCCCCCC
Q 042541          644 FRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALP  692 (695)
Q Consensus       644 ~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~~l~~lP  692 (695)
                           .|++|++|+|++| .+..+|.+|++|++|++|+|++|+..+.+|
T Consensus       291 -----~l~~L~~L~L~~N-~l~~lp~~~~~l~~L~~L~L~~N~l~~~~p  333 (727)
T 4b8c_D          291 -----SCFQLKYFYFFDN-MVTTLPWEFGNLCNLQFLGVEGNPLEKQFL  333 (727)
T ss_dssp             -----GGTTCSEEECCSS-CCCCCCSSTTSCTTCCCEECTTSCCCSHHH
T ss_pred             -----CCCCCCEEECCCC-CCCccChhhhcCCCccEEeCCCCccCCCCh
Confidence                 8999999999986 578999999999999999999987444433

>1xku_A Decorin; proteoglycan, leucine-rich repeat, structural protein; HET: NAG; 2.15A {Bos taurus} SCOP: c.10.2.7 PDB: 1xec_A* 1xcd_A*

Probab=99.26  E-value=5.6e-11  Score=123.25  Aligned_cols=88  Identities=22%  Similarity=0.363  Sum_probs=71.3

Q ss_pred             CCCcEEEeccCCCCCc-c-cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCc
Q 042541          601 SKLKKIRLEHVSLPNS-L-ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSME  678 (695)
Q Consensus       601 ~~L~~L~L~~~~l~~l-p-~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~  678 (695)
                      ++|++|++++|.+..+ | .++++++|++|++++|.++..++..+.    .+++|+.|++++| .+..+|.++..+++|+
T Consensus       192 ~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~----~l~~L~~L~L~~N-~l~~lp~~l~~l~~L~  266 (330)
T 1xku_A          192 PSLTELHLDGNKITKVDAASLKGLNNLAKLGLSFNSISAVDNGSLA----NTPHLRELHLNNN-KLVKVPGGLADHKYIQ  266 (330)
T ss_dssp             TTCSEEECTTSCCCEECTGGGTTCTTCCEEECCSSCCCEECTTTGG----GSTTCCEEECCSS-CCSSCCTTTTTCSSCC
T ss_pred             ccCCEEECCCCcCCccCHHHhcCCCCCCEEECCCCcCceeChhhcc----CCCCCCEEECCCC-cCccCChhhccCCCcC
Confidence            5677777777777755 4 788888899999999988888776665    7889999999986 5778999999999999


Q ss_pred             eeecccccCCCCCCCC
Q 042541          679 KLRITNCHRLSALPEG  694 (695)
Q Consensus       679 ~L~l~~~~~l~~lP~~  694 (695)
                      +|++++|+ ++.+|..
T Consensus       267 ~L~l~~N~-i~~~~~~  281 (330)
T 1xku_A          267 VVYLHNNN-ISAIGSN  281 (330)
T ss_dssp             EEECCSSC-CCCCCTT
T ss_pred             EEECCCCc-CCccChh
Confidence            99999866 7777653

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae}

Probab=99.26  E-value=3.6e-11  Score=127.85  Aligned_cols=158  Identities=14%  Similarity=0.177  Sum_probs=99.5

Q ss_pred             ccceEEeeecCCcccCCCCC--CCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCccc-------------
Q 042541          527 NNASLLSISTDETFSSNWPD--MQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAEL-------------  591 (695)
Q Consensus       527 ~~~r~l~~~~~~~~~~~~~~--~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~-------------  591 (695)
                      ...++|.+..+... ..+..  ..+++|+.|.++.+......|..+.++++|++|++++|.+....+             
T Consensus       117 ~~L~~L~L~~n~l~-~l~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~l~~L~~L~l~~  195 (390)
T 3o6n_A          117 PLLTVLVLERNDLS-SLPRGIFHNTPKLTTLSMSNNNLERIEDDTFQATTSLQNLQLSSNRLTHVDLSLIPSLFHANVSY  195 (390)
T ss_dssp             TTCCEEECCSSCCC-CCCTTTTTTCTTCCEEECCSSCCCBCCTTTTSSCTTCCEEECCSSCCSBCCGGGCTTCSEEECCS
T ss_pred             CCCCEEECCCCccC-cCCHHHhcCCCCCcEEECCCCccCccChhhccCCCCCCEEECCCCcCCccccccccccceeeccc
Confidence            45666666554332 11211  256777777777766555555667777777777777765432111             


Q ss_pred             -------------------------------------------CcccccccCCCCcEEEeccCCCCCc-c-ccccccccc
Q 042541          592 -------------------------------------------NNFRVLSALSKLKKIRLEHVSLPNS-L-ATVRMNHLQ  626 (695)
Q Consensus       592 -------------------------------------------~~~~~l~~l~~L~~L~L~~~~l~~l-p-~i~~l~~L~  626 (695)
                                                                 ...+.++.+++|++|++++|.+..+ | .++.+++|+
T Consensus       196 n~l~~~~~~~~L~~L~l~~n~l~~~~~~~~~~L~~L~l~~n~l~~~~~l~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~  275 (390)
T 3o6n_A          196 NLLSTLAIPIAVEELDASHNSINVVRGPVNVELTILKLQHNNLTDTAWLLNYPGLVEVDLSYNELEKIMYHPFVKMQRLE  275 (390)
T ss_dssp             SCCSEEECCSSCSEEECCSSCCCEEECCCCSSCCEEECCSSCCCCCGGGGGCTTCSEEECCSSCCCEEESGGGTTCSSCC
T ss_pred             ccccccCCCCcceEEECCCCeeeeccccccccccEEECCCCCCcccHHHcCCCCccEEECCCCcCCCcChhHccccccCC
Confidence                                                       0112245566777777777777644 4 677777777


Q ss_pred             EEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccccCCCCCC
Q 042541          627 KVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALP  692 (695)
Q Consensus       627 ~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~~l~~lP  692 (695)
                      +|++++|.++.++....     .+++|++|++++| .+..+|..++.+++|+.|++++|+ +..+|
T Consensus       276 ~L~L~~n~l~~~~~~~~-----~l~~L~~L~L~~n-~l~~~~~~~~~l~~L~~L~L~~N~-i~~~~  334 (390)
T 3o6n_A          276 RLYISNNRLVALNLYGQ-----PIPTLKVLDLSHN-HLLHVERNQPQFDRLENLYLDHNS-IVTLK  334 (390)
T ss_dssp             EEECCSSCCCEEECSSS-----CCTTCCEEECCSS-CCCCCGGGHHHHTTCSEEECCSSC-CCCCC
T ss_pred             EEECCCCcCcccCcccC-----CCCCCCEEECCCC-cceecCccccccCcCCEEECCCCc-cceeC
Confidence            77777777776655443     6777888888876 466777777778888888888765 55554

>1w8a_A SLIT protein; signaling protein, secreted protein, AXON guidance, leucine-rich repeat glycoprotein, EGF-like domain, signal protein; 2.8A {Drosophila melanogaster} SCOP: c.10.2.7

Probab=99.26  E-value=1.5e-11  Score=116.78  Aligned_cols=117  Identities=13%  Similarity=0.155  Sum_probs=84.5

Q ss_pred             ccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCc-c-cccccccccEEeeccccCCccccc
Q 042541          564 YVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNS-L-ATVRMNHLQKVSLVMCNVGQVFRN  641 (695)
Q Consensus       564 ~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~l-p-~i~~l~~L~~L~l~~~~i~~~~~~  641 (695)
                      ..+|..+.  .+|++|++++|.+..  +.....++.+++|++|+|++|.++.+ | .++++++|++|+|++|.++.+++.
T Consensus        21 ~~ip~~~~--~~l~~L~l~~n~i~~--~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~   96 (192)
T 1w8a_A           21 KEIPRDIP--LHTTELLLNDNELGR--ISSDGLFGRLPHLVKLELKRNQLTGIEPNAFEGASHIQELQLGENKIKEISNK   96 (192)
T ss_dssp             SSCCSCCC--TTCSEEECCSCCCCS--BCCSCSGGGCTTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSCCCCEECSS
T ss_pred             CcCccCCC--CCCCEEECCCCcCCc--cCCccccccCCCCCEEECCCCCCCCcCHhHcCCcccCCEEECCCCcCCccCHH
Confidence            44555443  278888888876632  11111267788888888888888866 5 788888888888888888888877


Q ss_pred             chhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccccCC
Q 042541          642 STFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRL  688 (695)
Q Consensus       642 ~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~~l  688 (695)
                      .+.    .+++|++|+|++|......|..++.+++|++|++++|+..
T Consensus        97 ~~~----~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~N~l~  139 (192)
T 1w8a_A           97 MFL----GLHQLKTLNLYDNQISCVMPGSFEHLNSLTSLNLASNPFN  139 (192)
T ss_dssp             SST----TCTTCCEEECCSSCCCEECTTSSTTCTTCCEEECTTCCBC
T ss_pred             Hhc----CCCCCCEEECCCCcCCeeCHHHhhcCCCCCEEEeCCCCcc
Confidence            665    7888888888886554455777888888888888887643

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=99.26  E-value=8.8e-11  Score=114.06  Aligned_cols=179  Identities=15%  Similarity=0.128  Sum_probs=115.7

Q ss_pred             CCCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcC
Q 042541          165 PVISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKG  244 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~  244 (695)
                      -..++|++..++.+.+++.....+.+.|+|++|+|||++|+.+++.. ....+....+.++.+.......+...+.....
T Consensus        16 ~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l~~~l~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   94 (226)
T 2chg_A           16 LDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDL-FGENWRDNFIEMNASDERGIDVVRHKIKEFAR   94 (226)
T ss_dssp             GGGCCSCHHHHHHHHHHHHTTCCCCEEEECSTTSSHHHHHHHHHHHH-HGGGGGGGEEEEETTCTTCHHHHHHHHHHHHT
T ss_pred             HHHHcCcHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHH-hccccccceEEeccccccChHHHHHHHHHHhc
Confidence            34689999999999999987665569999999999999999998731 12223332344444443333322222111111


Q ss_pred             CCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCC------CCCCeE
Q 042541          245 YPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFP------QFGSVH  314 (695)
Q Consensus       245 ~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~------~~~~~~  314 (695)
                      ..                  ....+++.+||+||++.....    +...+.....++.+|+||+....      .....+
T Consensus        95 ~~------------------~~~~~~~~vliiDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~~~~~~~~~~~l~~r~~~i  156 (226)
T 2chg_A           95 TA------------------PIGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSRCAVF  156 (226)
T ss_dssp             SC------------------CSTTCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSEEE
T ss_pred             cc------------------CCCccCceEEEEeChhhcCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcCHHHHHhCcee
Confidence            00                  001367899999999876543    22333334456788888876521      112278


Q ss_pred             ecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHH
Q 042541          315 YLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVG  365 (695)
Q Consensus       315 ~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~  365 (695)
                      .+.+++.++..+++...+.....   .-..+....|++.++|.|..+..+.
T Consensus       157 ~~~~~~~~~~~~~l~~~~~~~~~---~~~~~~~~~l~~~~~g~~r~l~~~l  204 (226)
T 2chg_A          157 RFKPVPKEAMKKRLLEICEKEGV---KITEDGLEALIYISGGDFRKAINAL  204 (226)
T ss_dssp             ECCCCCHHHHHHHHHHHHHHHTC---CBCHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             ecCCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHcCCCHHHHHHHH
Confidence            99999999999999887643222   1235678889999999998655443

>1a9n_A U2A', U2A'; complex (nuclear protein/RNA), RNA, snRNP, ribonucleoprotein, RNA binding protein/RNA complex; 2.38A {Homo sapiens} SCOP: c.10.2.4

Probab=99.26  E-value=1.1e-11  Score=115.79  Aligned_cols=128  Identities=9%  Similarity=0.074  Sum_probs=104.1

Q ss_pred             CCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc-cc-cccccc
Q 042541          548 QGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL-AT-VRMNHL  625 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp-~i-~~l~~L  625 (695)
                      .+++++.|.++++... .+|......++|++|++++|.+..  +   +.++.+++|++|++++|.+..+| .+ +.+++|
T Consensus        17 ~~~~L~~L~l~~n~l~-~i~~~~~~~~~L~~L~Ls~N~l~~--~---~~l~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L   90 (176)
T 1a9n_A           17 NAVRDRELDLRGYKIP-VIENLGATLDQFDAIDFSDNEIRK--L---DGFPLLRRLKTLLVNNNRICRIGEGLDQALPDL   90 (176)
T ss_dssp             CTTSCEEEECTTSCCC-SCCCGGGGTTCCSEEECCSSCCCE--E---CCCCCCSSCCEEECCSSCCCEECSCHHHHCTTC
T ss_pred             CcCCceEEEeeCCCCc-hhHHhhhcCCCCCEEECCCCCCCc--c---cccccCCCCCEEECCCCcccccCcchhhcCCCC
Confidence            5678888888887544 445533334499999999987742  2   45889999999999999999888 55 899999


Q ss_pred             cEEeeccccCCcccc-cchhhhcccCCCccEEecccccccccCchh----hcCCCCCceeeccccc
Q 042541          626 QKVSLVMCNVGQVFR-NSTFRISDAFPNLLEMDIDYCNDLIELPDG----LCDIVSMEKLRITNCH  686 (695)
Q Consensus       626 ~~L~l~~~~i~~~~~-~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~----i~~L~~L~~L~l~~~~  686 (695)
                      ++|++++|.++.+|+ ..+.    .+++|++|++++| .+..+|..    ++.+++|+.|++++|.
T Consensus        91 ~~L~L~~N~i~~~~~~~~l~----~l~~L~~L~l~~N-~i~~~~~~~~~~~~~l~~L~~Ld~~~n~  151 (176)
T 1a9n_A           91 TELILTNNSLVELGDLDPLA----SLKSLTYLCILRN-PVTNKKHYRLYVIYKVPQVRVLDFQKVK  151 (176)
T ss_dssp             CEEECCSCCCCCGGGGGGGG----GCTTCCEEECCSS-GGGGSTTHHHHHHHHCTTCSEETTEECC
T ss_pred             CEEECCCCcCCcchhhHhhh----cCCCCCEEEecCC-CCCCcHhHHHHHHHHCCccceeCCCcCC
Confidence            999999999988776 2333    8999999999996 46788885    8999999999999875

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron}

Probab=99.26  E-value=1.1e-11  Score=143.56  Aligned_cols=161  Identities=19%  Similarity=0.222  Sum_probs=120.7

Q ss_pred             CccceEEeeecCCccc-----------------CCCCCC---CCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccC
Q 042541          526 PNNASLLSISTDETFS-----------------SNWPDM---QGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYG  585 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~-----------------~~~~~~---~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~  585 (695)
                      ....+.|.+..+....                 ..+..+   .+++|+.|.|+.|...+.+|..+.++++|++|++++|.
T Consensus       447 L~~L~~L~Ls~N~Lsg~~i~~~~~~~s~n~~~g~iP~~l~f~~L~~L~~L~Ls~N~l~~~iP~~l~~L~~L~~L~Ls~N~  526 (876)
T 4ecn_A          447 LTKLQIIYFANSPFTYDNIAVDWEDANSDYAKQYENEELSWSNLKDLTDVELYNCPNMTQLPDFLYDLPELQSLNIACNR  526 (876)
T ss_dssp             CTTCCEEEEESCCCCGGGBSSSCSCTTSHHHHHHTTSCCCGGGCTTCCEEEEESCTTCCSCCGGGGGCSSCCEEECTTCT
T ss_pred             CCCCCEEECcCCcCCCCcccccccccccccccccCChhhhhccCCCCCEEECcCCCCCccChHHHhCCCCCCEEECcCCC
Confidence            3467888887665333                 133333   58999999999998889999999999999999999987


Q ss_pred             -CCCcccC----ccc-ccccCCCCcEEEeccCCCCCccc---ccccccccEEeeccccCCcccccchhhhcccCCCccEE
Q 042541          586 -FSPAELN----NFR-VLSALSKLKKIRLEHVSLPNSLA---TVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEM  656 (695)
Q Consensus       586 -~~~~~~~----~~~-~l~~l~~L~~L~L~~~~l~~lp~---i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L  656 (695)
                       +....++    .++ .+..+++|++|+|++|.+..+|.   ++++++|++|+|++|.++.+| .+ .    .+++|+.|
T Consensus       527 ~lsg~~iP~~i~~L~~~~~~l~~L~~L~Ls~N~L~~ip~~~~l~~L~~L~~L~Ls~N~l~~lp-~~-~----~L~~L~~L  600 (876)
T 4ecn_A          527 GISAAQLKADWTRLADDEDTGPKIQIFYMGYNNLEEFPASASLQKMVKLGLLDCVHNKVRHLE-AF-G----TNVKLTDL  600 (876)
T ss_dssp             TSCHHHHHHHHHHHHHCTTTTTTCCEEECCSSCCCBCCCHHHHTTCTTCCEEECTTSCCCBCC-CC-C----TTSEESEE
T ss_pred             CcccccchHHHHhhhhcccccCCccEEEeeCCcCCccCChhhhhcCCCCCEEECCCCCcccch-hh-c----CCCcceEE
Confidence             5320121    111 23445589999999998888874   788889999999999888665 33 3    78888888


Q ss_pred             ecccccccccCchhhcCCCC-CceeecccccCCCCCCCC
Q 042541          657 DIDYCNDLIELPDGLCDIVS-MEKLRITNCHRLSALPEG  694 (695)
Q Consensus       657 ~l~~c~~l~~lP~~i~~L~~-L~~L~l~~~~~l~~lP~~  694 (695)
                      ++++|. +..+|.+++++++ |++|+|++|. +..+|..
T Consensus       601 ~Ls~N~-l~~lp~~l~~l~~~L~~L~Ls~N~-L~~lp~~  637 (876)
T 4ecn_A          601 KLDYNQ-IEEIPEDFCAFTDQVEGLGFSHNK-LKYIPNI  637 (876)
T ss_dssp             ECCSSC-CSCCCTTSCEECTTCCEEECCSSC-CCSCCSC
T ss_pred             ECcCCc-cccchHHHhhccccCCEEECcCCC-CCcCchh
Confidence            888864 5588888888888 8888888866 6677754

>2id5_A Lingo-1, leucine rich repeat neuronal 6A; CNS-specific LRR-IG containing, ligand binding protein,membr protein; HET: NAG MAN; 2.70A {Homo sapiens}

Probab=99.26  E-value=2.5e-11  Score=132.81  Aligned_cols=88  Identities=23%  Similarity=0.274  Sum_probs=36.5

Q ss_pred             CCCCcEEEeccCCCCCcc--cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCC
Q 042541          600 LSKLKKIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSM  677 (695)
Q Consensus       600 l~~L~~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L  677 (695)
                      +++|+.|++++|.++.+|  .+.++++|++|++++|.+..+++..+.    .+++|+.|++++|..+..+|..+....+|
T Consensus       151 l~~L~~L~l~~n~l~~~~~~~l~~l~~L~~L~l~~n~i~~~~~~~~~----~l~~L~~L~l~~~~~~~~~~~~~~~~~~L  226 (477)
T 2id5_A          151 LNSLEQLTLEKCNLTSIPTEALSHLHGLIVLRLRHLNINAIRDYSFK----RLYRLKVLEISHWPYLDTMTPNCLYGLNL  226 (477)
T ss_dssp             CTTCCEEEEESCCCSSCCHHHHTTCTTCCEEEEESCCCCEECTTCSC----SCTTCCEEEEECCTTCCEECTTTTTTCCC
T ss_pred             CCCCCEEECCCCcCcccChhHhcccCCCcEEeCCCCcCcEeChhhcc----cCcccceeeCCCCccccccCcccccCccc
Confidence            333344444443333333  233344444444444443333333332    34444444444444444444444444444


Q ss_pred             ceeecccccCCCCCC
Q 042541          678 EKLRITNCHRLSALP  692 (695)
Q Consensus       678 ~~L~l~~~~~l~~lP  692 (695)
                      +.|++++|. +..+|
T Consensus       227 ~~L~l~~n~-l~~~~  240 (477)
T 2id5_A          227 TSLSITHCN-LTAVP  240 (477)
T ss_dssp             SEEEEESSC-CCSCC
T ss_pred             cEEECcCCc-ccccC
Confidence            445554433 43443

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697}

Probab=99.25  E-value=7.4e-12  Score=141.85  Aligned_cols=125  Identities=13%  Similarity=0.161  Sum_probs=73.0

Q ss_pred             CChhhcCCCCCcEEEEcccCCCCcccC--------------cccccc--cCCCCcEEEeccCCCC-Ccc-cccccccccE
Q 042541          566 LPDFLQKMDELKVLIVTNYGFSPAELN--------------NFRVLS--ALSKLKKIRLEHVSLP-NSL-ATVRMNHLQK  627 (695)
Q Consensus       566 ~p~~~~~l~~Lr~L~l~~~~~~~~~~~--------------~~~~l~--~l~~L~~L~L~~~~l~-~lp-~i~~l~~L~~  627 (695)
                      +|..++++++|++|+|++|.+......              -++.++  ++++|++|+|++|.+. .+| .++++++|++
T Consensus       198 ip~~l~~l~~L~~L~Ls~n~l~~~~~~~~~~~~~~~~~~~~ip~~l~~~~l~~L~~L~L~~n~l~~~~p~~l~~l~~L~~  277 (636)
T 4eco_A          198 VSKAVMRLTKLRQFYMGNSPFVAENICEAWENENSEYAQQYKTEDLKWDNLKDLTDVEVYNCPNLTKLPTFLKALPEMQL  277 (636)
T ss_dssp             ECGGGGGCTTCCEEEEESCCCCGGGBSSSCSCTTSHHHHHHTTSCCCGGGCTTCCEEEEECCTTCSSCCTTTTTCSSCCE
T ss_pred             CCHHHhcccCCCEEECcCCccccccccccccccccchhcccCchhhhhcccCCCCEEEecCCcCCccChHHHhcCCCCCE
Confidence            566667777777777777665331000              122355  6777777777777655 666 6777777777


Q ss_pred             Eeecccc-CCc--ccccchhhhc--ccCCCccEEecccccccccCch--hhcCCCCCceeecccccCCCCCC
Q 042541          628 VSLVMCN-VGQ--VFRNSTFRIS--DAFPNLLEMDIDYCNDLIELPD--GLCDIVSMEKLRITNCHRLSALP  692 (695)
Q Consensus       628 L~l~~~~-i~~--~~~~~~~~l~--~~l~~L~~L~l~~c~~l~~lP~--~i~~L~~L~~L~l~~~~~l~~lP  692 (695)
                      |++++|. +++  +|+.+. .++  ..+++|++|++++|. +..+|.  .++++++|++|++++|...+.+|
T Consensus       278 L~Ls~n~~l~~~~lp~~~~-~L~~~~~l~~L~~L~L~~n~-l~~ip~~~~l~~l~~L~~L~L~~N~l~g~ip  347 (636)
T 4eco_A          278 INVACNRGISGEQLKDDWQ-ALADAPVGEKIQIIYIGYNN-LKTFPVETSLQKMKKLGMLECLYNQLEGKLP  347 (636)
T ss_dssp             EECTTCTTSCHHHHHHHHH-HHHHSGGGGTCCEEECCSSC-CSSCCCHHHHTTCTTCCEEECCSCCCEEECC
T ss_pred             EECcCCCCCccccchHHHH-hhhccccCCCCCEEECCCCc-CCccCchhhhccCCCCCEEeCcCCcCccchh
Confidence            7777776 664  333332 000  012667777776653 446666  66677777777776655333555

>1wwl_A Monocyte differentiation antigen CD14; LPS, immune system; HET: NAG; 2.50A {Mus musculus}

Probab=99.25  E-value=2.1e-11  Score=125.42  Aligned_cols=159  Identities=13%  Similarity=0.133  Sum_probs=112.8

Q ss_pred             CCccceEEeeecCCcccCCCCCC-C-----CCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCccccc-
Q 042541          525 HPNNASLLSISTDETFSSNWPDM-Q-----GPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVL-  597 (695)
Q Consensus       525 ~~~~~r~l~~~~~~~~~~~~~~~-~-----~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l-  597 (695)
                      .....++|.+..+..... +..+ .     +++|+.|.++.+......|..+..+++|++|++++|.+... ...++.+ 
T Consensus       119 ~l~~L~~L~Ls~N~l~~~-~~~~~~l~~~~~~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~-~~~~~~~~  196 (312)
T 1wwl_A          119 TGPDLNILNLRNVSWATR-DAWLAELQQWLKPGLKVLSIAQAHSLNFSCEQVRVFPALSTLDLSDNPELGE-RGLISALC  196 (312)
T ss_dssp             CSCCCSEEEEESCBCSSS-SSHHHHHHTTCCTTCCEEEEESCSCCCCCTTTCCCCSSCCEEECCSCTTCHH-HHHHHHSC
T ss_pred             cCCCccEEEccCCCCcch-hHHHHHHHHhhcCCCcEEEeeCCCCccchHHHhccCCCCCEEECCCCCcCcc-hHHHHHHH
Confidence            345677777776543222 1111 1     37888888888877776777888899999999988875321 1111123 


Q ss_pred             -ccCCCCcEEEeccCCCCCcc-----cccccccccEEeeccccCCcccc-cchhhhcccCCCccEEecccccccccCchh
Q 042541          598 -SALSKLKKIRLEHVSLPNSL-----ATVRMNHLQKVSLVMCNVGQVFR-NSTFRISDAFPNLLEMDIDYCNDLIELPDG  670 (695)
Q Consensus       598 -~~l~~L~~L~L~~~~l~~lp-----~i~~l~~L~~L~l~~~~i~~~~~-~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~  670 (695)
                       +.+++|++|++++|.++.+|     .+.++++|++|++++|.++..+| ..+.    .+++|++|++++| .+..+|..
T Consensus       197 ~~~l~~L~~L~L~~N~l~~~~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~----~l~~L~~L~Ls~N-~l~~ip~~  271 (312)
T 1wwl_A          197 PLKFPTLQVLALRNAGMETPSGVCSALAAARVQLQGLDLSHNSLRDAAGAPSCD----WPSQLNSLNLSFT-GLKQVPKG  271 (312)
T ss_dssp             TTSCTTCCEEECTTSCCCCHHHHHHHHHHTTCCCSEEECTTSCCCSSCCCSCCC----CCTTCCEEECTTS-CCSSCCSS
T ss_pred             hccCCCCCEEECCCCcCcchHHHHHHHHhcCCCCCEEECCCCcCCcccchhhhh----hcCCCCEEECCCC-ccChhhhh
Confidence             77888999999999888444     23467899999999998888664 3333    6789999999986 46788887


Q ss_pred             hcCCCCCceeecccccCCCCCCC
Q 042541          671 LCDIVSMEKLRITNCHRLSALPE  693 (695)
Q Consensus       671 i~~L~~L~~L~l~~~~~l~~lP~  693 (695)
                      +.  ++|++|++++|. +..+|.
T Consensus       272 ~~--~~L~~L~Ls~N~-l~~~p~  291 (312)
T 1wwl_A          272 LP--AKLSVLDLSYNR-LDRNPS  291 (312)
T ss_dssp             CC--SEEEEEECCSSC-CCSCCC
T ss_pred             cc--CCceEEECCCCC-CCCChh
Confidence            77  889999999865 777764

>3vq2_A TLR4, TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, secreted, immune SY; HET: NAG LP4 LP5 DAO MYR; 2.48A {Mus musculus} PDB: 3vq1_A* 2z64_A*

Probab=99.25  E-value=1.1e-11  Score=140.03  Aligned_cols=132  Identities=14%  Similarity=0.121  Sum_probs=73.6

Q ss_pred             CCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--cccccccc
Q 042541          548 QGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNHL  625 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L  625 (695)
                      .+++|+.|.++.+......|..+..+++|++|++++|.+....+  +..++.+++|++|++++|.+..++  .++++++|
T Consensus       422 ~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~--~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L  499 (606)
T 3vq2_A          422 SLEKLLYLDISYTNTKIDFDGIFLGLTSLNTLKMAGNSFKDNTL--SNVFANTTNLTFLDLSKCQLEQISWGVFDTLHRL  499 (606)
T ss_dssp             TCTTCCEEECTTSCCEECCTTTTTTCTTCCEEECTTCEEGGGEE--CSCCTTCTTCCEEECTTSCCCEECTTTTTTCTTC
T ss_pred             ccccCCEEECcCCCCCccchhhhcCCCCCCEEECCCCcCCCcch--HHhhccCCCCCEEECCCCcCCccChhhhcccccC
Confidence            44555555555554444455555555556666655554421111  112455666666666666665433  55666666


Q ss_pred             cEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCC-CCceeeccccc
Q 042541          626 QKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIV-SMEKLRITNCH  686 (695)
Q Consensus       626 ~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~-~L~~L~l~~~~  686 (695)
                      ++|++++|.++..+|..+.    .+++|++|++++|. +..+|..+..++ +|++|++++|+
T Consensus       500 ~~L~Ls~N~l~~~~~~~~~----~l~~L~~L~l~~N~-l~~~p~~~~~l~~~L~~l~l~~N~  556 (606)
T 3vq2_A          500 QLLNMSHNNLLFLDSSHYN----QLYSLSTLDCSFNR-IETSKGILQHFPKSLAFFNLTNNS  556 (606)
T ss_dssp             CEEECCSSCCSCEEGGGTT----TCTTCCEEECTTSC-CCCEESCGGGSCTTCCEEECCSCC
T ss_pred             CEEECCCCcCCCcCHHHcc----CCCcCCEEECCCCc-CcccCHhHhhhcccCcEEEccCCC
Confidence            6666666666665554444    56666666666643 556666666664 46666666655

>4glp_A Monocyte differentiation antigen CD14; alpha beta BENT solenoid, LRR, lipopolysaccharide, serum, CD leucine-rich repeat, pattern recognition; 4.00A {Homo sapiens}

Probab=99.24  E-value=1.7e-11  Score=125.92  Aligned_cols=162  Identities=12%  Similarity=0.117  Sum_probs=116.8

Q ss_pred             CccceEEeeecCCcccCCC-----CCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCc-ccCccccccc
Q 042541          526 PNNASLLSISTDETFSSNW-----PDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPA-ELNNFRVLSA  599 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~~~~-----~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~-~~~~~~~l~~  599 (695)
                      ....+.+.+..+.......     ....+++|+.|.++.+......|..+..+++|++|++++|.+... .++....++.
T Consensus       116 ~~~L~~L~Ls~n~i~~~~~~~~~~~~~~~~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~~~~~  195 (310)
T 4glp_A          116 GLALSSLRLRNVSWATGRSWLAELQQWLKPGLKVLSIAQAHSPAFSCEQVRAFPALTSLDLSDNPGLGERGLMAALCPHK  195 (310)
T ss_dssp             CBCCSSCEEESCCCSSTTSSHHHHHTTBCSCCCEEEEECCSSCCCCTTSCCCCTTCCEEECCSCTTCHHHHHHTTSCTTS
T ss_pred             CCCCCEEEeecccccchhhhhHHHHhhhccCCCEEEeeCCCcchhhHHHhccCCCCCEEECCCCCCccchhhhHHHhhhc
Confidence            4566777776654322111     012578999999999887777778899999999999999876321 1111222468


Q ss_pred             CCCCcEEEeccCCCCCcc-c----ccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCC
Q 042541          600 LSKLKKIRLEHVSLPNSL-A----TVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDI  674 (695)
Q Consensus       600 l~~L~~L~L~~~~l~~lp-~----i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L  674 (695)
                      +++|++|+|++|.++.+| .    ++.+++|++|+|++|.++...|..+..+. .+++|++|++++| .+..+|..+.  
T Consensus       196 l~~L~~L~Ls~N~l~~l~~~~~~l~~~l~~L~~L~Ls~N~l~~~~p~~~~~~~-~~~~L~~L~Ls~N-~l~~lp~~~~--  271 (310)
T 4glp_A          196 FPAIQNLALRNTGMETPTGVCAALAAAGVQPHSLDLSHNSLRATVNPSAPRCM-WSSALNSLNLSFA-GLEQVPKGLP--  271 (310)
T ss_dssp             SCCCCSCBCCSSCCCCHHHHHHHHHHHTCCCSSEECTTSCCCCCCCSCCSSCC-CCTTCCCEECCSS-CCCSCCSCCC--
T ss_pred             CCCCCEEECCCCCCCchHHHHHHHHhcCCCCCEEECCCCCCCccchhhHHhcc-CcCcCCEEECCCC-CCCchhhhhc--
Confidence            889999999999998766 3    46789999999999999988443332111 2379999999986 5678998775  


Q ss_pred             CCCceeecccccCCCCCC
Q 042541          675 VSMEKLRITNCHRLSALP  692 (695)
Q Consensus       675 ~~L~~L~l~~~~~l~~lP  692 (695)
                      ++|++|++++|. +..+|
T Consensus       272 ~~L~~L~Ls~N~-l~~~~  288 (310)
T 4glp_A          272 AKLRVLDLSSNR-LNRAP  288 (310)
T ss_dssp             SCCSCEECCSCC-CCSCC
T ss_pred             CCCCEEECCCCc-CCCCc
Confidence            899999999976 66655

>2id5_A Lingo-1, leucine rich repeat neuronal 6A; CNS-specific LRR-IG containing, ligand binding protein,membr protein; HET: NAG MAN; 2.70A {Homo sapiens}

Probab=99.24  E-value=2.8e-11  Score=132.36  Aligned_cols=151  Identities=17%  Similarity=0.255  Sum_probs=82.4

Q ss_pred             CccceEEeeecCCcccCCCC-CCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCc
Q 042541          526 PNNASLLSISTDETFSSNWP-DMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLK  604 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~~~~~-~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~  604 (695)
                      +...++|.+..+........ ...+++|+.|.|+.+......|..|.++++|++|+|++|.+..  ++ ...+..+++|+
T Consensus        31 ~~~l~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~n~i~~~~~~~~~~l~~L~~L~L~~n~l~~--~~-~~~~~~l~~L~  107 (477)
T 2id5_A           31 PTETRLLDLGKNRIKTLNQDEFASFPHLEELELNENIVSAVEPGAFNNLFNLRTLGLRSNRLKL--IP-LGVFTGLSNLT  107 (477)
T ss_dssp             CTTCSEEECCSSCCCEECTTTTTTCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCCS--CC-TTSSTTCTTCC
T ss_pred             CCCCcEEECCCCccceECHhHccCCCCCCEEECCCCccCEeChhhhhCCccCCEEECCCCcCCc--cC-cccccCCCCCC
Confidence            44667777665543222211 2256777777777766555566677777777777777765531  11 11245566666


Q ss_pred             EEEeccCCCCCcc--cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCch-hhcCCCCCceee
Q 042541          605 KIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPD-GLCDIVSMEKLR  681 (695)
Q Consensus       605 ~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~-~i~~L~~L~~L~  681 (695)
                      +|+|++|.+..++  .+.++++|++|++++|.+..+++..+.    .+++|+.|++++| .+..+|. .+.++++|+.|+
T Consensus       108 ~L~Ls~n~i~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~----~l~~L~~L~l~~n-~l~~~~~~~l~~l~~L~~L~  182 (477)
T 2id5_A          108 KLDISENKIVILLDYMFQDLYNLKSLEVGDNDLVYISHRAFS----GLNSLEQLTLEKC-NLTSIPTEALSHLHGLIVLR  182 (477)
T ss_dssp             EEECTTSCCCEECTTTTTTCTTCCEEEECCTTCCEECTTSST----TCTTCCEEEEESC-CCSSCCHHHHTTCTTCCEEE
T ss_pred             EEECCCCccccCChhHccccccCCEEECCCCccceeChhhcc----CCCCCCEEECCCC-cCcccChhHhcccCCCcEEe
Confidence            6666666665433  555666666666666666555554443    4555555555554 2333332 234444444444


Q ss_pred             ccc
Q 042541          682 ITN  684 (695)
Q Consensus       682 l~~  684 (695)
                      +++
T Consensus       183 l~~  185 (477)
T 2id5_A          183 LRH  185 (477)
T ss_dssp             EES
T ss_pred             CCC
Confidence            443

>2z80_A TOLL-like receptor 2, variable lymphocyte recepto; TLR2, lipopeptide, innate immunity, glycoprotein, immune RES inflammatory response; HET: NAG; 1.80A {Homo sapiens}

Probab=99.24  E-value=1.6e-11  Score=128.71  Aligned_cols=158  Identities=16%  Similarity=0.085  Sum_probs=111.3

Q ss_pred             ccceEEeeecCCcccCCC-CCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcE
Q 042541          527 NNASLLSISTDETFSSNW-PDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKK  605 (695)
Q Consensus       527 ~~~r~l~~~~~~~~~~~~-~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~  605 (695)
                      ...+++.+..+....... ....+++|+.|.++.+......|..+.++++|++|++++|.+..  ++ ...++.+++|++
T Consensus        52 ~~L~~L~l~~n~i~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~--~~-~~~~~~l~~L~~  128 (353)
T 2z80_A           52 EAVKSLDLSNNRITYISNSDLQRCVNLQALVLTSNGINTIEEDSFSSLGSLEHLDLSYNYLSN--LS-SSWFKPLSSLTF  128 (353)
T ss_dssp             TTCCEEECTTSCCCEECTTTTTTCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCSS--CC-HHHHTTCTTCSE
T ss_pred             ccCcEEECCCCcCcccCHHHhccCCCCCEEECCCCccCccCHhhcCCCCCCCEEECCCCcCCc--CC-HhHhCCCccCCE
Confidence            467777776654322222 12367888888887776666666678888888888888876632  11 122677888888


Q ss_pred             EEeccCCCCCcc---cccccccccEEeeccc-cCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceee
Q 042541          606 IRLEHVSLPNSL---ATVRMNHLQKVSLVMC-NVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLR  681 (695)
Q Consensus       606 L~L~~~~l~~lp---~i~~l~~L~~L~l~~~-~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~  681 (695)
                      |++++|.+..+|   .++++++|++|++++| .+..+++..+.    .+++|++|++++|......|..++++++|++|+
T Consensus       129 L~L~~n~l~~l~~~~~~~~l~~L~~L~l~~n~~~~~~~~~~~~----~l~~L~~L~l~~n~l~~~~~~~l~~l~~L~~L~  204 (353)
T 2z80_A          129 LNLLGNPYKTLGETSLFSHLTKLQILRVGNMDTFTKIQRKDFA----GLTFLEELEIDASDLQSYEPKSLKSIQNVSHLI  204 (353)
T ss_dssp             EECTTCCCSSSCSSCSCTTCTTCCEEEEEESSSCCEECTTTTT----TCCEEEEEEEEETTCCEECTTTTTTCSEEEEEE
T ss_pred             EECCCCCCcccCchhhhccCCCCcEEECCCCccccccCHHHcc----CCCCCCEEECCCCCcCccCHHHHhccccCCeec
Confidence            888888888776   3677888888888888 47777666655    788888888888765445577788888888888


Q ss_pred             cccccCCCCCC
Q 042541          682 ITNCHRLSALP  692 (695)
Q Consensus       682 l~~~~~l~~lP  692 (695)
                      +++|. ++.+|
T Consensus       205 l~~n~-l~~~~  214 (353)
T 2z80_A          205 LHMKQ-HILLL  214 (353)
T ss_dssp             EECSC-STTHH
T ss_pred             CCCCc-cccch
Confidence            88865 55544

>3oja_B Anopheles plasmodium-responsive leucine-rich REPE 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=99.24  E-value=1.7e-11  Score=137.90  Aligned_cols=126  Identities=14%  Similarity=0.077  Sum_probs=61.3

Q ss_pred             CCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc-c-cccccccc
Q 042541          549 GPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL-A-TVRMNHLQ  626 (695)
Q Consensus       549 ~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp-~-i~~l~~L~  626 (695)
                      +++|++|.++.+......|..|..+++|++|+|++|.+...   .+..++.+++|++|+|++|.+..+| . ++++++|+
T Consensus        74 l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~---~~~~~~~l~~L~~L~L~~n~l~~l~~~~~~~l~~L~  150 (597)
T 3oja_B           74 FRQVELLNLNDLQIEEIDTYAFAYAHTIQKLYMGFNAIRYL---PPHVFQNVPLLTVLVLERNDLSSLPRGIFHNTPKLT  150 (597)
T ss_dssp             CCCCSEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCCCC---CTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCC
T ss_pred             CCCCcEEECCCCCCCCCChHHhcCCCCCCEEECCCCcCCCC---CHHHHcCCCCCCEEEeeCCCCCCCCHHHhccCCCCC
Confidence            44555555555444444444555555555555555544211   0112445555555555555555555 2 35555555


Q ss_pred             EEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeeccc
Q 042541          627 KVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITN  684 (695)
Q Consensus       627 ~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~  684 (695)
                      +|+|++|.++.+++..+.    .+++|++|++++| .+..+|  ++.+++|++|++++
T Consensus       151 ~L~Ls~N~l~~~~~~~~~----~l~~L~~L~L~~N-~l~~~~--~~~l~~L~~L~l~~  201 (597)
T 3oja_B          151 TLSMSNNNLERIEDDTFQ----ATTSLQNLQLSSN-RLTHVD--LSLIPSLFHANVSY  201 (597)
T ss_dssp             EEECCSSCCCBCCTTTTT----TCTTCCEEECTTS-CCSBCC--GGGCTTCSEEECCS
T ss_pred             EEEeeCCcCCCCChhhhh----cCCcCcEEECcCC-CCCCcC--hhhhhhhhhhhccc
Confidence            555555555555554443    4555555555554 233333  33344444444444

>2z80_A TOLL-like receptor 2, variable lymphocyte recepto; TLR2, lipopeptide, innate immunity, glycoprotein, immune RES inflammatory response; HET: NAG; 1.80A {Homo sapiens}

Probab=99.24  E-value=1.4e-11  Score=129.15  Aligned_cols=159  Identities=13%  Similarity=0.128  Sum_probs=110.7

Q ss_pred             CccceEEeeecCCcccCCCC-CCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCc
Q 042541          526 PNNASLLSISTDETFSSNWP-DMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLK  604 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~~~~~-~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~  604 (695)
                      ....+++.+..+......+. ...+++|+.|.++.+......+..+.++++|++|++++|.+.  .++....+..+++|+
T Consensus        75 l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~n~l~--~l~~~~~~~~l~~L~  152 (353)
T 2z80_A           75 CVNLQALVLTSNGINTIEEDSFSSLGSLEHLDLSYNYLSNLSSSWFKPLSSLTFLNLLGNPYK--TLGETSLFSHLTKLQ  152 (353)
T ss_dssp             CTTCCEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCSSCCHHHHTTCTTCSEEECTTCCCS--SSCSSCSCTTCTTCC
T ss_pred             CCCCCEEECCCCccCccCHhhcCCCCCCCEEECCCCcCCcCCHhHhCCCccCCEEECCCCCCc--ccCchhhhccCCCCc
Confidence            45677777765543222221 236788888888877555433345788888888888887663  222212367788888


Q ss_pred             EEEeccC-CCCCcc--cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhh-cCCCCCcee
Q 042541          605 KIRLEHV-SLPNSL--ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGL-CDIVSMEKL  680 (695)
Q Consensus       605 ~L~L~~~-~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i-~~L~~L~~L  680 (695)
                      +|++++| .+..++  .++++++|++|++++|.++..++..+.    .+++|++|++++|. +..+|..+ ..+++|+.|
T Consensus       153 ~L~l~~n~~~~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~l~----~l~~L~~L~l~~n~-l~~~~~~~~~~~~~L~~L  227 (353)
T 2z80_A          153 ILRVGNMDTFTKIQRKDFAGLTFLEELEIDASDLQSYEPKSLK----SIQNVSHLILHMKQ-HILLLEIFVDVTSSVECL  227 (353)
T ss_dssp             EEEEEESSSCCEECTTTTTTCCEEEEEEEEETTCCEECTTTTT----TCSEEEEEEEECSC-STTHHHHHHHHTTTEEEE
T ss_pred             EEECCCCccccccCHHHccCCCCCCEEECCCCCcCccCHHHHh----ccccCCeecCCCCc-cccchhhhhhhcccccEE
Confidence            8888888 466664  778888888888888888887666665    78888888888864 57777653 458888888


Q ss_pred             ecccccCCCCCC
Q 042541          681 RITNCHRLSALP  692 (695)
Q Consensus       681 ~l~~~~~l~~lP  692 (695)
                      ++++|. +..+|
T Consensus       228 ~L~~n~-l~~~~  238 (353)
T 2z80_A          228 ELRDTD-LDTFH  238 (353)
T ss_dssp             EEESCB-CTTCC
T ss_pred             ECCCCc-ccccc
Confidence            888865 55443

>4eco_A Uncharacterized protein; leucine-rich repeats, protein binding, structural genomics, center for structural genomics, JCSG; 2.70A {Bacteroides eggerthii dsm 20697}

Probab=99.24  E-value=7.5e-11  Score=133.60  Aligned_cols=159  Identities=17%  Similarity=0.155  Sum_probs=120.1

Q ss_pred             cceEEeeecCCcccCCCC--------CCCCCceEEEEEEccCccccCCh-hhcCCCCCcEEEEcccCCCCcccCcc----
Q 042541          528 NASLLSISTDETFSSNWP--------DMQGPEVKVVVLNIRTKKYVLPD-FLQKMDELKVLIVTNYGFSPAELNNF----  594 (695)
Q Consensus       528 ~~r~l~~~~~~~~~~~~~--------~~~~~~l~~L~l~~~~~~~~~p~-~~~~l~~Lr~L~l~~~~~~~~~~~~~----  594 (695)
                      ..+.+.+..+......+.        ...+++|+.|.++.+... .+|. .+..+++|++|++++|.+.  .++..    
T Consensus       403 ~L~~L~Ls~N~l~~~~p~~l~~~~~~~~~~~~L~~L~Ls~N~l~-~lp~~~~~~l~~L~~L~Ls~N~l~--~i~~~~~~~  479 (636)
T 4eco_A          403 VMSAIDFSYNEIGSVDGKNFDPLDPTPFKGINVSSINLSNNQIS-KFPKELFSTGSPLSSINLMGNMLT--EIPKNSLKD  479 (636)
T ss_dssp             CEEEEECCSSCTTTTTTCSSCTTCSSCCCCCCEEEEECCSSCCC-SCCTHHHHTTCCCSEEECCSSCCS--BCCSSSSEE
T ss_pred             ccCEEECcCCcCCCcchhhhcccccccccCCCCCEEECcCCccC-cCCHHHHccCCCCCEEECCCCCCC--CcCHHHhcc
Confidence            466777665543221111        125668999999888665 4555 5667899999999998774  22211    


Q ss_pred             --cccccCCCCcEEEeccCCCCCcc-ccc--ccccccEEeeccccCCcccccchhhhcccCCCccEEecc------cccc
Q 042541          595 --RVLSALSKLKKIRLEHVSLPNSL-ATV--RMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDID------YCND  663 (695)
Q Consensus       595 --~~l~~l~~L~~L~L~~~~l~~lp-~i~--~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~------~c~~  663 (695)
                        +.+.++++|++|+|++|.++.+| .+.  .+++|++|+|++|.++.+|....     .+++|++|+++      +|..
T Consensus       480 ~~~~~~~l~~L~~L~Ls~N~l~~lp~~~~~~~l~~L~~L~Ls~N~l~~ip~~~~-----~l~~L~~L~Ls~N~~ls~N~l  554 (636)
T 4eco_A          480 ENENFKNTYLLTSIDLRFNKLTKLSDDFRATTLPYLVGIDLSYNSFSKFPTQPL-----NSSTLKGFGIRNQRDAQGNRT  554 (636)
T ss_dssp             TTEECTTGGGCCEEECCSSCCCBCCGGGSTTTCTTCCEEECCSSCCSSCCCGGG-----GCSSCCEEECCSCBCTTCCBC
T ss_pred             ccccccccCCccEEECcCCcCCccChhhhhccCCCcCEEECCCCCCCCcChhhh-----cCCCCCEEECCCCcccccCcc
Confidence              01223448999999999999999 887  99999999999999999766665     89999999995      4556


Q ss_pred             cccCchhhcCCCCCceeecccccCCCCCCCCC
Q 042541          664 LIELPDGLCDIVSMEKLRITNCHRLSALPEGI  695 (695)
Q Consensus       664 l~~lP~~i~~L~~L~~L~l~~~~~l~~lP~~i  695 (695)
                      .+.+|.+++++++|+.|+|++|. ++.+|..+
T Consensus       555 ~~~~p~~l~~l~~L~~L~Ls~N~-l~~ip~~~  585 (636)
T 4eco_A          555 LREWPEGITLCPSLTQLQIGSND-IRKVNEKI  585 (636)
T ss_dssp             CCCCCTTGGGCSSCCEEECCSSC-CCBCCSCC
T ss_pred             cccChHHHhcCCCCCEEECCCCc-CCccCHhH
Confidence            77899999999999999999977 69999753

>2v9t_B SLIT homolog 2 protein N-product; structural protein-receptor complex, developmental protein, domain, roundabout, chemotaxis, LRR domain; 1.70A {Homo sapiens} PDB: 2v9s_A

Probab=99.24  E-value=4.5e-11  Score=116.09  Aligned_cols=121  Identities=13%  Similarity=0.147  Sum_probs=99.1

Q ss_pred             ccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCc-c-cccccccccEEeeccccCCccccc
Q 042541          564 YVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNS-L-ATVRMNHLQKVSLVMCNVGQVFRN  641 (695)
Q Consensus       564 ~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~l-p-~i~~l~~L~~L~l~~~~i~~~~~~  641 (695)
                      ..+|..+.  ++|+.|++++|.+..  ++ ...+..+++|++|+|++|.+..+ | .+.++++|++|+|++|.++.+|+.
T Consensus        24 ~~iP~~l~--~~l~~L~l~~n~i~~--i~-~~~~~~l~~L~~L~Ls~N~i~~~~~~~~~~l~~L~~L~Ls~N~l~~l~~~   98 (220)
T 2v9t_B           24 TEIPTNLP--ETITEIRLEQNTIKV--IP-PGAFSPYKKLRRIDLSNNQISELAPDAFQGLRSLNSLVLYGNKITELPKS   98 (220)
T ss_dssp             SSCCSSCC--TTCCEEECCSSCCCE--EC-TTSSTTCTTCCEEECCSSCCCEECTTTTTTCSSCCEEECCSSCCCCCCTT
T ss_pred             CcCCCccC--cCCCEEECCCCcCCC--cC-HhHhhCCCCCCEEECCCCcCCCcCHHHhhCCcCCCEEECCCCcCCccCHh
Confidence            45565443  689999999987742  11 12378899999999999999977 5 899999999999999999999998


Q ss_pred             chhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccccCCCCCCCC
Q 042541          642 STFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPEG  694 (695)
Q Consensus       642 ~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~~l~~lP~~  694 (695)
                      .+.    .+++|++|+|++|......|..+..+++|++|+|++|. +..+|.+
T Consensus        99 ~f~----~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~L~~N~-l~~~~~~  146 (220)
T 2v9t_B           99 LFE----GLFSLQLLLLNANKINCLRVDAFQDLHNLNLLSLYDNK-LQTIAKG  146 (220)
T ss_dssp             TTT----TCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSC-CSCCCTT
T ss_pred             Hcc----CCCCCCEEECCCCCCCEeCHHHcCCCCCCCEEECCCCc-CCEECHH
Confidence            876    89999999999975444446679999999999999976 7777753

>4ecn_A Leucine-rich repeat protein; leucine-rich repeats, DUF4458 domain, protein binding, extra protein, structural genomics; 2.80A {Bacteroides thetaiotaomicron}

Probab=99.23  E-value=6.5e-11  Score=137.05  Aligned_cols=139  Identities=14%  Similarity=0.152  Sum_probs=112.3

Q ss_pred             CCCceEEEEEEccCccccCChh-hcCCCCCcEEEEcccCCCCcccCcc------cccccCCCCcEEEeccCCCCCcc-cc
Q 042541          548 QGPEVKVVVLNIRTKKYVLPDF-LQKMDELKVLIVTNYGFSPAELNNF------RVLSALSKLKKIRLEHVSLPNSL-AT  619 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~~-~~~l~~Lr~L~l~~~~~~~~~~~~~------~~l~~l~~L~~L~L~~~~l~~lp-~i  619 (695)
                      .+++|+.|.++.|... .+|.. +..+++|+.|+|++|.+.  .++..      +.+.+|++|++|+|++|.+..+| .+
T Consensus       671 ~~~~L~~L~Ls~N~L~-~lp~~~~~~l~~L~~L~Ls~N~L~--~ip~~~~~~~~~~l~nl~~L~~L~Ls~N~L~~lp~~l  747 (876)
T 4ecn_A          671 KGINASTVTLSYNEIQ-KFPTELFATGSPISTIILSNNLMT--SIPENSLKPKDGNYKNTYLLTTIDLRFNKLTSLSDDF  747 (876)
T ss_dssp             CCCCEEEEECCSSCCC-SCCHHHHHTTCCCSEEECCSCCCS--CCCTTSSSCTTSCCTTGGGCCEEECCSSCCCCCCGGG
T ss_pred             cCCCcCEEEccCCcCC-ccCHHHHccCCCCCEEECCCCcCC--ccChHHhccccccccccCCccEEECCCCCCccchHHh
Confidence            4457888888877655 56764 458999999999998764  22211      11334559999999999999999 88


Q ss_pred             c--ccccccEEeeccccCCcccccchhhhcccCCCccEEeccc------ccccccCchhhcCCCCCceeecccccCCCCC
Q 042541          620 V--RMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDY------CNDLIELPDGLCDIVSMEKLRITNCHRLSAL  691 (695)
Q Consensus       620 ~--~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~------c~~l~~lP~~i~~L~~L~~L~l~~~~~l~~l  691 (695)
                      .  .+++|+.|+|++|.++.+|....     .+++|+.|+|++      |.....+|..++++++|+.|+|++|. ++.+
T Consensus       748 ~~~~l~~L~~L~Ls~N~L~~lp~~l~-----~L~~L~~L~Ls~N~~ls~N~l~~~ip~~l~~L~~L~~L~Ls~N~-L~~I  821 (876)
T 4ecn_A          748 RATTLPYLSNMDVSYNCFSSFPTQPL-----NSSQLKAFGIRHQRDAEGNRILRQWPTGITTCPSLIQLQIGSND-IRKV  821 (876)
T ss_dssp             STTTCTTCCEEECCSSCCSSCCCGGG-----GCTTCCEEECCCCBCTTCCBCCCCCCTTGGGCSSCCEEECCSSC-CCBC
T ss_pred             hhccCCCcCEEEeCCCCCCccchhhh-----cCCCCCEEECCCCCCcccccccccChHHHhcCCCCCEEECCCCC-CCcc
Confidence            7  99999999999999999776665     899999999976      55677899999999999999999977 6999


Q ss_pred             CCCC
Q 042541          692 PEGI  695 (695)
Q Consensus       692 P~~i  695 (695)
                      |..+
T Consensus       822 p~~l  825 (876)
T 4ecn_A          822 DEKL  825 (876)
T ss_dssp             CSCC
T ss_pred             CHhh
Confidence            9864

>1h6u_A Internalin H; cell adhesion, leucine rich repeat, IG-like domain, EF-hand domain; 1.8A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1

Probab=99.23  E-value=6.6e-11  Score=121.34  Aligned_cols=152  Identities=13%  Similarity=0.189  Sum_probs=119.8

Q ss_pred             CCccceEEeeecCCcccCCCCCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCc
Q 042541          525 HPNNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLK  604 (695)
Q Consensus       525 ~~~~~r~l~~~~~~~~~~~~~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~  604 (695)
                      .....++|.+..+... .......+++|+.|.++.+.... +|. +..+++|++|++++|.+..     .+.++.+++|+
T Consensus        83 ~l~~L~~L~L~~n~l~-~~~~~~~l~~L~~L~l~~n~l~~-~~~-l~~l~~L~~L~l~~n~l~~-----~~~l~~l~~L~  154 (308)
T 1h6u_A           83 NLTKITELELSGNPLK-NVSAIAGLQSIKTLDLTSTQITD-VTP-LAGLSNLQVLYLDLNQITN-----ISPLAGLTNLQ  154 (308)
T ss_dssp             TCCSCCEEECCSCCCS-CCGGGTTCTTCCEEECTTSCCCC-CGG-GTTCTTCCEEECCSSCCCC-----CGGGGGCTTCC
T ss_pred             cCCCCCEEEccCCcCC-CchhhcCCCCCCEEECCCCCCCC-chh-hcCCCCCCEEECCCCccCc-----CccccCCCCcc
Confidence            3457788888766532 22233478899999998885543 343 8899999999999987642     22278899999


Q ss_pred             EEEeccCCCCCcccccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeeccc
Q 042541          605 KIRLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITN  684 (695)
Q Consensus       605 ~L~L~~~~l~~lp~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~  684 (695)
                      +|++++|.+..++.++.+++|++|++++|.++.+++  +.    .+++|+.|++++| .+..+|. +..+++|+.|++++
T Consensus       155 ~L~l~~n~l~~~~~l~~l~~L~~L~l~~n~l~~~~~--l~----~l~~L~~L~L~~N-~l~~~~~-l~~l~~L~~L~l~~  226 (308)
T 1h6u_A          155 YLSIGNAQVSDLTPLANLSKLTTLKADDNKISDISP--LA----SLPNLIEVHLKNN-QISDVSP-LANTSNLFIVTLTN  226 (308)
T ss_dssp             EEECCSSCCCCCGGGTTCTTCCEEECCSSCCCCCGG--GG----GCTTCCEEECTTS-CCCBCGG-GTTCTTCCEEEEEE
T ss_pred             EEEccCCcCCCChhhcCCCCCCEEECCCCccCcChh--hc----CCCCCCEEEccCC-ccCcccc-ccCCCCCCEEEccC
Confidence            999999999988778899999999999999998776  33    8999999999996 5677774 89999999999999


Q ss_pred             ccCCCCCCC
Q 042541          685 CHRLSALPE  693 (695)
Q Consensus       685 ~~~l~~lP~  693 (695)
                      |+ +...|.
T Consensus       227 N~-i~~~~~  234 (308)
T 1h6u_A          227 QT-ITNQPV  234 (308)
T ss_dssp             EE-EECCCE
T ss_pred             Ce-eecCCe
Confidence            76 666553

>3o6n_A APL1; leucine-rich repeat, protein binding; HET: NAG; 1.85A {Anopheles gambiae}

Probab=99.23  E-value=2.9e-11  Score=128.55  Aligned_cols=128  Identities=14%  Similarity=0.072  Sum_probs=69.2

Q ss_pred             CCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc-c-ccccccc
Q 042541          548 QGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL-A-TVRMNHL  625 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp-~-i~~l~~L  625 (695)
                      .+++|+.|.++.+......|..+..+++|++|++++|.+...   .+..++.+++|++|++++|.+..+| . ++++++|
T Consensus        67 ~l~~L~~L~L~~n~i~~~~~~~~~~l~~L~~L~L~~n~l~~~---~~~~~~~l~~L~~L~L~~n~l~~l~~~~~~~l~~L  143 (390)
T 3o6n_A           67 SFRQVELLNLNDLQIEEIDTYAFAYAHTIQKLYMGFNAIRYL---PPHVFQNVPLLTVLVLERNDLSSLPRGIFHNTPKL  143 (390)
T ss_dssp             HCCCCSEEECTTSCCCEECTTTTTTCTTCCEEECCSSCCCCC---CTTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTC
T ss_pred             ccccCcEEECCCCcccccChhhccCCCCcCEEECCCCCCCcC---CHHHhcCCCCCCEEECCCCccCcCCHHHhcCCCCC
Confidence            345566666655544444444566666666666666544211   1112455666666666666666665 3 3566666


Q ss_pred             cEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccc
Q 042541          626 QKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNC  685 (695)
Q Consensus       626 ~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~  685 (695)
                      ++|++++|.++.+++..+.    .+++|++|++++| .+..+|  ++.+++|++|++++|
T Consensus       144 ~~L~L~~n~l~~~~~~~~~----~l~~L~~L~l~~n-~l~~~~--~~~l~~L~~L~l~~n  196 (390)
T 3o6n_A          144 TTLSMSNNNLERIEDDTFQ----ATTSLQNLQLSSN-RLTHVD--LSLIPSLFHANVSYN  196 (390)
T ss_dssp             CEEECCSSCCCBCCTTTTS----SCTTCCEEECCSS-CCSBCC--GGGCTTCSEEECCSS
T ss_pred             cEEECCCCccCccChhhcc----CCCCCCEEECCCC-cCCccc--cccccccceeecccc
Confidence            6666666666665555444    5666666666654 234443  344455555555443

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=99.22  E-value=1.6e-11  Score=134.23  Aligned_cols=151  Identities=10%  Similarity=0.035  Sum_probs=118.1

Q ss_pred             ccceEEeeecCCcccCCCCCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCccccc-ccCCCCcE
Q 042541          527 NNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVL-SALSKLKK  605 (695)
Q Consensus       527 ~~~r~l~~~~~~~~~~~~~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l-~~l~~L~~  605 (695)
                      ...++|.+.++.....  ....+++|+.|.++.|......|..++.+++|++|++++|.+....   +..+ +.+++|++
T Consensus        99 ~~L~~L~L~~N~l~~~--~~~~l~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~---~~~l~~~l~~L~~  173 (487)
T 3oja_A           99 PSIETLHAANNNISRV--SCSRGQGKKNIYLANNKITMLRDLDEGCRSRVQYLDLKLNEIDTVN---FAELAASSDTLEH  173 (487)
T ss_dssp             TTCCEEECCSSCCCCE--EECCCSSCEEEECCSSCCCSGGGBCGGGGSSEEEEECTTSCCCEEE---GGGGGGGTTTCCE
T ss_pred             CCcCEEECcCCcCCCC--CccccCCCCEEECCCCCCCCCCchhhcCCCCCCEEECCCCCCCCcC---hHHHhhhCCcccE
Confidence            3455666654432211  1124688999999888877777888899999999999998775322   2224 37899999


Q ss_pred             EEeccCCCCCcccccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccc
Q 042541          606 IRLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNC  685 (695)
Q Consensus       606 L~L~~~~l~~lp~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~  685 (695)
                      |+|++|.++.+|....+++|++|+|++|.++.+|+.+.     .+++|+.|++++| .+..+|..++.+++|+.|++++|
T Consensus       174 L~Ls~N~l~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~-----~l~~L~~L~Ls~N-~l~~lp~~l~~l~~L~~L~l~~N  247 (487)
T 3oja_A          174 LNLQYNFIYDVKGQVVFAKLKTLDLSSNKLAFMGPEFQ-----SAAGVTWISLRNN-KLVLIEKALRFSQNLEHFDLRGN  247 (487)
T ss_dssp             EECTTSCCCEEECCCCCTTCCEEECCSSCCCEECGGGG-----GGTTCSEEECTTS-CCCEECTTCCCCTTCCEEECTTC
T ss_pred             EecCCCccccccccccCCCCCEEECCCCCCCCCCHhHc-----CCCCccEEEecCC-cCcccchhhccCCCCCEEEcCCC
Confidence            99999999988844569999999999999999888754     7999999999996 56789999999999999999998


Q ss_pred             cCC
Q 042541          686 HRL  688 (695)
Q Consensus       686 ~~l  688 (695)
                      +..
T Consensus       248 ~l~  250 (487)
T 3oja_A          248 GFH  250 (487)
T ss_dssp             CBC
T ss_pred             CCc
Confidence            743

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus}

Probab=99.22  E-value=8.5e-11  Score=121.98  Aligned_cols=160  Identities=14%  Similarity=0.196  Sum_probs=111.5

Q ss_pred             CccceEEeeecCCcccCCCCCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCC-----cccCcc--cc--
Q 042541          526 PNNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSP-----AELNNF--RV--  596 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~~~~~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~-----~~~~~~--~~--  596 (695)
                      ....++|.+..+... ..+. .-.++|+.|.++.+......+..+..+++|++|++++|.+..     ..+..+  ..  
T Consensus       101 l~~L~~L~L~~n~l~-~l~~-~~~~~L~~L~l~~n~i~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~~l~L~~L~  178 (332)
T 2ft3_A          101 LRKLQKLYISKNHLV-EIPP-NLPSSLVELRIHDNRIRKVPKGVFSGLRNMNCIEMGGNPLENSGFEPGAFDGLKLNYLR  178 (332)
T ss_dssp             CTTCCEEECCSSCCC-SCCS-SCCTTCCEEECCSSCCCCCCSGGGSSCSSCCEEECCSCCCBGGGSCTTSSCSCCCSCCB
T ss_pred             cCCCCEEECCCCcCC-ccCc-cccccCCEEECCCCccCccCHhHhCCCccCCEEECCCCccccCCCCcccccCCccCEEE
Confidence            345666666554322 1111 122677777777765554445567788888888888775521     100000  00  


Q ss_pred             -----c-----ccCCCCcEEEeccCCCCCcc--cccccccccEEeeccccCCcccccchhhhcccCCCccEEeccccccc
Q 042541          597 -----L-----SALSKLKKIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDL  664 (695)
Q Consensus       597 -----l-----~~l~~L~~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l  664 (695)
                           +     .-.++|++|++++|.+..++  .+.++++|++|++++|.++.+++..+.    .+++|+.|++++| .+
T Consensus       179 l~~n~l~~l~~~~~~~L~~L~l~~n~i~~~~~~~l~~l~~L~~L~L~~N~l~~~~~~~~~----~l~~L~~L~L~~N-~l  253 (332)
T 2ft3_A          179 ISEAKLTGIPKDLPETLNELHLDHNKIQAIELEDLLRYSKLYRLGLGHNQIRMIENGSLS----FLPTLRELHLDNN-KL  253 (332)
T ss_dssp             CCSSBCSSCCSSSCSSCSCCBCCSSCCCCCCTTSSTTCTTCSCCBCCSSCCCCCCTTGGG----GCTTCCEEECCSS-CC
T ss_pred             CcCCCCCccCccccCCCCEEECCCCcCCccCHHHhcCCCCCCEEECCCCcCCcCChhHhh----CCCCCCEEECCCC-cC
Confidence                 0     01147888888888888665  788899999999999999988887666    8999999999986 57


Q ss_pred             ccCchhhcCCCCCceeecccccCCCCCCC
Q 042541          665 IELPDGLCDIVSMEKLRITNCHRLSALPE  693 (695)
Q Consensus       665 ~~lP~~i~~L~~L~~L~l~~~~~l~~lP~  693 (695)
                      ..+|.+++.+++|++|++++|. ++.+|.
T Consensus       254 ~~lp~~l~~l~~L~~L~l~~N~-l~~~~~  281 (332)
T 2ft3_A          254 SRVPAGLPDLKLLQVVYLHTNN-ITKVGV  281 (332)
T ss_dssp             CBCCTTGGGCTTCCEEECCSSC-CCBCCT
T ss_pred             eecChhhhcCccCCEEECCCCC-CCccCh
Confidence            7999999999999999999965 777765

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae}

Probab=99.22  E-value=1.9e-11  Score=126.07  Aligned_cols=151  Identities=9%  Similarity=0.027  Sum_probs=112.7

Q ss_pred             ccceEEeeecCCcccCCCCCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEE
Q 042541          527 NNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKI  606 (695)
Q Consensus       527 ~~~r~l~~~~~~~~~~~~~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L  606 (695)
                      ...+++.+..+.....  ....+++|+.|.++.+......|..+..+++|++|++++|.+.......  ....+++|++|
T Consensus        99 ~~L~~L~l~~n~l~~~--~~~~~~~L~~L~l~~N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~--~~~~l~~L~~L  174 (317)
T 3o53_A           99 PSIETLHAANNNISRV--SCSRGQGKKNIYLANNKITMLRDLDEGCRSRVQYLDLKLNEIDTVNFAE--LAASSDTLEHL  174 (317)
T ss_dssp             TTCCEEECCSSCCSEE--EECCCSSCEEEECCSSCCCSGGGBCTGGGSSEEEEECTTSCCCEEEGGG--GGGGTTTCCEE
T ss_pred             CCcCEEECCCCccCCc--CccccCCCCEEECCCCCCCCccchhhhccCCCCEEECCCCCCCcccHHH--HhhccCcCCEE
Confidence            3455565554432111  1124678899988888766666667888899999999988764321111  13478899999


Q ss_pred             EeccCCCCCcccccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeeccccc
Q 042541          607 RLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCH  686 (695)
Q Consensus       607 ~L~~~~l~~lp~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~  686 (695)
                      ++++|.++.+|....+++|++|+|++|.++.+++.+.     .+++|+.|++++| .+..+|..+..+++|+.|++++|+
T Consensus       175 ~L~~N~l~~~~~~~~l~~L~~L~Ls~N~l~~l~~~~~-----~l~~L~~L~L~~N-~l~~l~~~~~~l~~L~~L~l~~N~  248 (317)
T 3o53_A          175 NLQYNFIYDVKGQVVFAKLKTLDLSSNKLAFMGPEFQ-----SAAGVTWISLRNN-KLVLIEKALRFSQNLEHFDLRGNG  248 (317)
T ss_dssp             ECTTSCCCEEECCCCCTTCCEEECCSSCCCEECGGGG-----GGTTCSEEECTTS-CCCEECTTCCCCTTCCEEECTTCC
T ss_pred             ECCCCcCcccccccccccCCEEECCCCcCCcchhhhc-----ccCcccEEECcCC-cccchhhHhhcCCCCCEEEccCCC
Confidence            9999999888844458899999999999998888754     7899999999986 577899889999999999999977


Q ss_pred             C
Q 042541          687 R  687 (695)
Q Consensus       687 ~  687 (695)
                      .
T Consensus       249 ~  249 (317)
T 3o53_A          249 F  249 (317)
T ss_dssp             C
T ss_pred             c
Confidence            3

>1m9s_A Internalin B; cell invasion, GW domains, SH3 domains, signaling protein; 2.65A {Listeria monocytogenes} SCOP: b.1.18.15 b.34.11.1 b.34.11.1 b.34.11.1 c.10.2.1 PDB: 2y5q_A

Probab=99.22  E-value=5.3e-11  Score=132.99  Aligned_cols=150  Identities=17%  Similarity=0.210  Sum_probs=119.0

Q ss_pred             CccceEEeeecCCcccCCCCCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcE
Q 042541          526 PNNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKK  605 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~~~~~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~  605 (695)
                      ....+.|.+..+.... ......+++|+.|.|+.|.... +| .+..+++|+.|+|++|.+..     ++.+..|++|+.
T Consensus        64 l~~L~~L~Ls~N~l~~-~~~l~~l~~L~~L~Ls~N~l~~-l~-~l~~l~~L~~L~Ls~N~l~~-----l~~l~~l~~L~~  135 (605)
T 1m9s_A           64 LPNVTKLFLNGNKLTD-IKPLTNLKNLGWLFLDENKIKD-LS-SLKDLKKLKSLSLEHNGISD-----INGLVHLPQLES  135 (605)
T ss_dssp             CTTCCEEECTTSCCCC-CGGGGGCTTCCEEECCSSCCCC-CT-TSTTCTTCCEEECTTSCCCC-----CGGGGGCTTCSE
T ss_pred             CCCCCEEEeeCCCCCC-ChhhccCCCCCEEECcCCCCCC-Ch-hhccCCCCCEEEecCCCCCC-----CccccCCCccCE
Confidence            3567777776554322 2223478899999998885443 33 68899999999999987742     345889999999


Q ss_pred             EEeccCCCCCcccccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccc
Q 042541          606 IRLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNC  685 (695)
Q Consensus       606 L~L~~~~l~~lp~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~  685 (695)
                      |+|++|.+..++.++.|++|+.|+|++|.+..+++  +.    .+++|+.|+|++| .+..+| .+..|++|+.|+|++|
T Consensus       136 L~Ls~N~l~~l~~l~~l~~L~~L~Ls~N~l~~~~~--l~----~l~~L~~L~Ls~N-~i~~l~-~l~~l~~L~~L~L~~N  207 (605)
T 1m9s_A          136 LYLGNNKITDITVLSRLTKLDTLSLEDNQISDIVP--LA----GLTKLQNLYLSKN-HISDLR-ALAGLKNLDVLELFSQ  207 (605)
T ss_dssp             EECCSSCCCCCGGGGSCTTCSEEECCSSCCCCCGG--GT----TCTTCCEEECCSS-CCCBCG-GGTTCTTCSEEECCSE
T ss_pred             EECCCCccCCchhhcccCCCCEEECcCCcCCCchh--hc----cCCCCCEEECcCC-CCCCCh-HHccCCCCCEEEccCC
Confidence            99999999988888899999999999999999877  33    8999999999997 567776 5999999999999998


Q ss_pred             cCCCCCC
Q 042541          686 HRLSALP  692 (695)
Q Consensus       686 ~~l~~lP  692 (695)
                      + +...|
T Consensus       208 ~-l~~~p  213 (605)
T 1m9s_A          208 E-CLNKP  213 (605)
T ss_dssp             E-EECCC
T ss_pred             c-CcCCc
Confidence            7 44444

>1m9s_A Internalin B; cell invasion, GW domains, SH3 domains, signaling protein; 2.65A {Listeria monocytogenes} SCOP: b.1.18.15 b.34.11.1 b.34.11.1 b.34.11.1 c.10.2.1 PDB: 2y5q_A

Probab=99.21  E-value=3.9e-11  Score=134.07  Aligned_cols=130  Identities=19%  Similarity=0.303  Sum_probs=109.1

Q ss_pred             CCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCccccccccccc
Q 042541          547 MQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSLATVRMNHLQ  626 (695)
Q Consensus       547 ~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp~i~~l~~L~  626 (695)
                      ..+++|+.|.|+.+......|  +..+++|+.|+|++|.+..     ++.++.|++|++|+|++|.+..+|.++.|++|+
T Consensus        62 ~~l~~L~~L~Ls~N~l~~~~~--l~~l~~L~~L~Ls~N~l~~-----l~~l~~l~~L~~L~Ls~N~l~~l~~l~~l~~L~  134 (605)
T 1m9s_A           62 QYLPNVTKLFLNGNKLTDIKP--LTNLKNLGWLFLDENKIKD-----LSSLKDLKKLKSLSLEHNGISDINGLVHLPQLE  134 (605)
T ss_dssp             GGCTTCCEEECTTSCCCCCGG--GGGCTTCCEEECCSSCCCC-----CTTSTTCTTCCEEECTTSCCCCCGGGGGCTTCS
T ss_pred             ccCCCCCEEEeeCCCCCCChh--hccCCCCCEEECcCCCCCC-----ChhhccCCCCCEEEecCCCCCCCccccCCCccC
Confidence            368999999998886554333  8899999999999987742     335889999999999999999888888999999


Q ss_pred             EEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccccCCCCCC
Q 042541          627 KVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALP  692 (695)
Q Consensus       627 ~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~~l~~lP  692 (695)
                      .|+|++|.++.+ +.+.     .|++|+.|+|++|. +..+|. +..+++|++|+|++|. +..+|
T Consensus       135 ~L~Ls~N~l~~l-~~l~-----~l~~L~~L~Ls~N~-l~~~~~-l~~l~~L~~L~Ls~N~-i~~l~  191 (605)
T 1m9s_A          135 SLYLGNNKITDI-TVLS-----RLTKLDTLSLEDNQ-ISDIVP-LAGLTKLQNLYLSKNH-ISDLR  191 (605)
T ss_dssp             EEECCSSCCCCC-GGGG-----SCTTCSEEECCSSC-CCCCGG-GTTCTTCCEEECCSSC-CCBCG
T ss_pred             EEECCCCccCCc-hhhc-----ccCCCCEEECcCCc-CCCchh-hccCCCCCEEECcCCC-CCCCh
Confidence            999999999987 3333     89999999999974 666666 9999999999999976 66654

>1a9n_A U2A', U2A'; complex (nuclear protein/RNA), RNA, snRNP, ribonucleoprotein, RNA binding protein/RNA complex; 2.38A {Homo sapiens} SCOP: c.10.2.4

Probab=99.21  E-value=3.1e-11  Score=112.79  Aligned_cols=114  Identities=16%  Similarity=0.155  Sum_probs=97.4

Q ss_pred             hhcCCCCCcEEEEcccCCCCcccCcccccccCC-CCcEEEeccCCCCCcccccccccccEEeeccccCCcccccchhhhc
Q 042541          569 FLQKMDELKVLIVTNYGFSPAELNNFRVLSALS-KLKKIRLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRIS  647 (695)
Q Consensus       569 ~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~-~L~~L~L~~~~l~~lp~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~  647 (695)
                      .+..+.+|+.|++++|.+.  .+   +.+..+. +|++|++++|.++.++.++.+++|++|++++|.++.+|+..+.   
T Consensus        14 ~~~~~~~L~~L~l~~n~l~--~i---~~~~~~~~~L~~L~Ls~N~l~~~~~l~~l~~L~~L~Ls~N~l~~~~~~~~~---   85 (176)
T 1a9n_A           14 QYTNAVRDRELDLRGYKIP--VI---ENLGATLDQFDAIDFSDNEIRKLDGFPLLRRLKTLLVNNNRICRIGEGLDQ---   85 (176)
T ss_dssp             EEECTTSCEEEECTTSCCC--SC---CCGGGGTTCCSEEECCSSCCCEECCCCCCSSCCEEECCSSCCCEECSCHHH---
T ss_pred             hcCCcCCceEEEeeCCCCc--hh---HHhhhcCCCCCEEECCCCCCCcccccccCCCCCEEECCCCcccccCcchhh---
Confidence            3567889999999998774  23   3355655 9999999999999877888999999999999999999888765   


Q ss_pred             ccCCCccEEecccccccccCch--hhcCCCCCceeecccccCCCCCCC
Q 042541          648 DAFPNLLEMDIDYCNDLIELPD--GLCDIVSMEKLRITNCHRLSALPE  693 (695)
Q Consensus       648 ~~l~~L~~L~l~~c~~l~~lP~--~i~~L~~L~~L~l~~~~~l~~lP~  693 (695)
                       .+++|++|++++| .+..+|.  .++.+++|++|++++|+ +..+|.
T Consensus        86 -~l~~L~~L~L~~N-~i~~~~~~~~l~~l~~L~~L~l~~N~-i~~~~~  130 (176)
T 1a9n_A           86 -ALPDLTELILTNN-SLVELGDLDPLASLKSLTYLCILRNP-VTNKKH  130 (176)
T ss_dssp             -HCTTCCEEECCSC-CCCCGGGGGGGGGCTTCCEEECCSSG-GGGSTT
T ss_pred             -cCCCCCEEECCCC-cCCcchhhHhhhcCCCCCEEEecCCC-CCCcHh
Confidence             8999999999996 5788997  89999999999999977 667765

>3oja_A Leucine-rich immune molecule 1; coiled-coil, helix-loop-helix, leucine-rich repeat, protein; HET: NAG MAN; 2.70A {Anopheles gambiae}

Probab=99.21  E-value=2e-11  Score=133.46  Aligned_cols=90  Identities=12%  Similarity=0.164  Sum_probs=65.8

Q ss_pred             cccCCCCcEEEeccCCCCC-cc-ccc-ccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcC
Q 042541          597 LSALSKLKKIRLEHVSLPN-SL-ATV-RMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCD  673 (695)
Q Consensus       597 l~~l~~L~~L~L~~~~l~~-lp-~i~-~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~  673 (695)
                      ++.+++|++|+|++|.++. .| .+. .+++|++|+|++|.++.+++..      .+++|++|+|++| .+..+|..++.
T Consensus       140 ~~~l~~L~~L~Ls~N~l~~~~~~~l~~~l~~L~~L~Ls~N~l~~~~~~~------~l~~L~~L~Ls~N-~l~~~~~~~~~  212 (487)
T 3oja_A          140 EGCRSRVQYLDLKLNEIDTVNFAELAASSDTLEHLNLQYNFIYDVKGQV------VFAKLKTLDLSSN-KLAFMGPEFQS  212 (487)
T ss_dssp             GGGGSSEEEEECTTSCCCEEEGGGGGGGTTTCCEEECTTSCCCEEECCC------CCTTCCEEECCSS-CCCEECGGGGG
T ss_pred             hcCCCCCCEEECCCCCCCCcChHHHhhhCCcccEEecCCCccccccccc------cCCCCCEEECCCC-CCCCCCHhHcC
Confidence            5566677777777777664 33 444 5677777777777766654322      5888999999986 57788888999


Q ss_pred             CCCCceeecccccCCCCCCCC
Q 042541          674 IVSMEKLRITNCHRLSALPEG  694 (695)
Q Consensus       674 L~~L~~L~l~~~~~l~~lP~~  694 (695)
                      +++|+.|++++|. +..+|..
T Consensus       213 l~~L~~L~Ls~N~-l~~lp~~  232 (487)
T 3oja_A          213 AAGVTWISLRNNK-LVLIEKA  232 (487)
T ss_dssp             GTTCSEEECTTSC-CCEECTT
T ss_pred             CCCccEEEecCCc-Ccccchh
Confidence            9999999999966 7777765

>2v70_A SLIT-2, SLIT homolog 2 protein N-product; neurogenesis, glycoprotein, secreted, chemotaxis, LRR structural protein, differentiation; HET: NAG; 3.01A {Homo sapiens}

Probab=99.21  E-value=8.1e-11  Score=114.26  Aligned_cols=120  Identities=13%  Similarity=0.162  Sum_probs=97.6

Q ss_pred             ccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--cccccccccEEeeccccCCccccc
Q 042541          564 YVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFRN  641 (695)
Q Consensus       564 ~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~  641 (695)
                      ..+|..+  ...+++|++++|.+..  +.....+..+++|++|+|++|.++.++  .++++++|++|+|++|.++.+++.
T Consensus        24 ~~iP~~~--~~~~~~L~L~~N~l~~--~~~~~~~~~l~~L~~L~L~~N~i~~i~~~~~~~l~~L~~L~Ls~N~l~~~~~~   99 (220)
T 2v70_A           24 NKIPEHI--PQYTAELRLNNNEFTV--LEATGIFKKLPQLRKINFSNNKITDIEEGAFEGASGVNEILLTSNRLENVQHK   99 (220)
T ss_dssp             SSCCSCC--CTTCSEEECCSSCCCE--ECCCCCGGGCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSCCCCCCGG
T ss_pred             ccCccCC--CCCCCEEEcCCCcCCc--cCchhhhccCCCCCEEECCCCcCCEECHHHhCCCCCCCEEECCCCccCccCHh
Confidence            3466544  3457899999987742  222223789999999999999999777  799999999999999999999998


Q ss_pred             chhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccccCCCCCC
Q 042541          642 STFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALP  692 (695)
Q Consensus       642 ~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~~l~~lP  692 (695)
                      .+.    .+++|++|+|++|......|..+..+++|++|+|++|. +..++
T Consensus       100 ~~~----~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~L~~N~-l~~~~  145 (220)
T 2v70_A          100 MFK----GLESLKTLMLRSNRITCVGNDSFIGLSSVRLLSLYDNQ-ITTVA  145 (220)
T ss_dssp             GGT----TCSSCCEEECTTSCCCCBCTTSSTTCTTCSEEECTTSC-CCCBC
T ss_pred             Hhc----CCcCCCEEECCCCcCCeECHhHcCCCccCCEEECCCCc-CCEEC
Confidence            776    89999999999975444447789999999999999976 66663

>1wwl_A Monocyte differentiation antigen CD14; LPS, immune system; HET: NAG; 2.50A {Mus musculus}

Probab=99.20  E-value=2e-11  Score=125.51  Aligned_cols=151  Identities=19%  Similarity=0.196  Sum_probs=73.3

Q ss_pred             ccceEEeeecCCcccCCCCC-CCCCceEEEEEEccCcccc--CChhh--cCCCCCcEEEEcccCCCCcccCcccccccCC
Q 042541          527 NNASLLSISTDETFSSNWPD-MQGPEVKVVVLNIRTKKYV--LPDFL--QKMDELKVLIVTNYGFSPAELNNFRVLSALS  601 (695)
Q Consensus       527 ~~~r~l~~~~~~~~~~~~~~-~~~~~l~~L~l~~~~~~~~--~p~~~--~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~  601 (695)
                      ...++|.+..+......+.. ..+++|+.|.++.|...+.  +|..+  ..+++|++|++++|.+....-.....+..++
T Consensus       149 ~~L~~L~L~~N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~~~~l~  228 (312)
T 1wwl_A          149 PGLKVLSIAQAHSLNFSCEQVRVFPALSTLDLSDNPELGERGLISALCPLKFPTLQVLALRNAGMETPSGVCSALAAARV  228 (312)
T ss_dssp             TTCCEEEEESCSCCCCCTTTCCCCSSCCEEECCSCTTCHHHHHHHHSCTTSCTTCCEEECTTSCCCCHHHHHHHHHHTTC
T ss_pred             CCCcEEEeeCCCCccchHHHhccCCCCCEEECCCCCcCcchHHHHHHHhccCCCCCEEECCCCcCcchHHHHHHHHhcCC
Confidence            34555555544332222111 2455666666655543322  22222  5556666666666554210000001123455


Q ss_pred             CCcEEEeccCCCCC-cc--cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCc
Q 042541          602 KLKKIRLEHVSLPN-SL--ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSME  678 (695)
Q Consensus       602 ~L~~L~L~~~~l~~-lp--~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~  678 (695)
                      +|++|++++|.+.. .|  .+..+++|++|+|++|.++.+|...      . ++|++|++++| .+..+|. +..+++|+
T Consensus       229 ~L~~L~Ls~N~l~~~~~~~~~~~l~~L~~L~Ls~N~l~~ip~~~------~-~~L~~L~Ls~N-~l~~~p~-~~~l~~L~  299 (312)
T 1wwl_A          229 QLQGLDLSHNSLRDAAGAPSCDWPSQLNSLNLSFTGLKQVPKGL------P-AKLSVLDLSYN-RLDRNPS-PDELPQVG  299 (312)
T ss_dssp             CCSEEECTTSCCCSSCCCSCCCCCTTCCEEECTTSCCSSCCSSC------C-SEEEEEECCSS-CCCSCCC-TTTSCEEE
T ss_pred             CCCEEECCCCcCCcccchhhhhhcCCCCEEECCCCccChhhhhc------c-CCceEEECCCC-CCCCChh-HhhCCCCC
Confidence            66666666666553 22  3344556666666666665444322      2 45666666654 3455554 56666666


Q ss_pred             eeeccccc
Q 042541          679 KLRITNCH  686 (695)
Q Consensus       679 ~L~l~~~~  686 (695)
                      +|++++|+
T Consensus       300 ~L~L~~N~  307 (312)
T 1wwl_A          300 NLSLKGNP  307 (312)
T ss_dssp             EEECTTCT
T ss_pred             EEeccCCC
Confidence            66666644

>3v47_A TOLL-like receptor 5B and variable lymphocyte REC chimeric protein; innate immunity, leucine-rich repeat, innate immune receptor system; HET: NAG; 2.47A {Danio rerio} PDB: 3v44_A*

Probab=99.20  E-value=3.6e-11  Score=130.62  Aligned_cols=159  Identities=14%  Similarity=0.200  Sum_probs=101.2

Q ss_pred             CccceEEeeecCCcccCCCC-CCCCCceEEEEEEccCccccC-ChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCC
Q 042541          526 PNNASLLSISTDETFSSNWP-DMQGPEVKVVVLNIRTKKYVL-PDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKL  603 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~~~~~-~~~~~~l~~L~l~~~~~~~~~-p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L  603 (695)
                      +...++|.+..+......+. ...+++|++|.++.+.....+ |..|.++++|++|++++|.+...   .+..++.+++|
T Consensus        29 ~~~l~~L~Ls~n~i~~~~~~~~~~l~~L~~L~L~~n~~~~~i~~~~~~~l~~L~~L~Ls~n~l~~~---~~~~~~~l~~L  105 (455)
T 3v47_A           29 PAHVNYVDLSLNSIAELNETSFSRLQDLQFLKVEQQTPGLVIRNNTFRGLSSLIILKLDYNQFLQL---ETGAFNGLANL  105 (455)
T ss_dssp             CTTCCEEECCSSCCCEECTTTTSSCTTCCEEECCCCSTTCEECTTTTTTCTTCCEEECTTCTTCEE---CTTTTTTCTTC
T ss_pred             CCccCEEEecCCccCcCChhHhccCccccEEECcCCcccceECcccccccccCCEEeCCCCccCcc---ChhhccCcccC
Confidence            35667777766543322222 235677777777777554444 44677777777777777765321   12236677777


Q ss_pred             cEEEeccCCCCC-cc-c--ccccccccEEeeccccCCcccccc-hhhhcccCCCccEEecccccccccCchhhcCC--CC
Q 042541          604 KKIRLEHVSLPN-SL-A--TVRMNHLQKVSLVMCNVGQVFRNS-TFRISDAFPNLLEMDIDYCNDLIELPDGLCDI--VS  676 (695)
Q Consensus       604 ~~L~L~~~~l~~-lp-~--i~~l~~L~~L~l~~~~i~~~~~~~-~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L--~~  676 (695)
                      ++|++++|.+.. +| .  ++++++|++|+|++|.++..+|.. +.    .+++|++|++++|......|..++.+  .+
T Consensus       106 ~~L~L~~n~l~~~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~----~l~~L~~L~L~~n~l~~~~~~~l~~l~~~~  181 (455)
T 3v47_A          106 EVLTLTQCNLDGAVLSGNFFKPLTSLEMLVLRDNNIKKIQPASFFL----NMRRFHVLDLTFNKVKSICEEDLLNFQGKH  181 (455)
T ss_dssp             CEEECTTSCCBTHHHHSSTTTTCTTCCEEECCSSBCCSCCCCGGGG----GCTTCCEEECTTCCBSCCCTTTSGGGTTCE
T ss_pred             CEEeCCCCCCCccccCcccccCcccCCEEECCCCccCccCcccccC----CCCcccEEeCCCCcccccChhhhhcccccc
Confidence            777777777764 34 3  777777777887777777765543 44    67777777777765544555566655  57


Q ss_pred             CceeecccccCCCCCC
Q 042541          677 MEKLRITNCHRLSALP  692 (695)
Q Consensus       677 L~~L~l~~~~~l~~lP  692 (695)
                      |+.|++++|. +..+|
T Consensus       182 L~~L~l~~n~-l~~~~  196 (455)
T 3v47_A          182 FTLLRLSSIT-LQDMN  196 (455)
T ss_dssp             EEEEECTTCB-CTTCS
T ss_pred             ccccccccCc-ccccc
Confidence            7777777755 55544

>2xot_A Amphoterin-induced protein 1; cell adhesion, neuronal protein, neurite growth regulation; HET: NAG BMA; 2.00A {Mus musculus}

Probab=99.20  E-value=4.4e-11  Score=125.62  Aligned_cols=157  Identities=17%  Similarity=0.173  Sum_probs=122.4

Q ss_pred             CCccceEEeeecCCcccCCCCCC--CCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCC
Q 042541          525 HPNNASLLSISTDETFSSNWPDM--QGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSK  602 (695)
Q Consensus       525 ~~~~~r~l~~~~~~~~~~~~~~~--~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~  602 (695)
                      .+...++|.+..+.........+  .+++|+.|.|+.+......|..|.++++|++|+|++|.+..  +. ...+..+++
T Consensus        37 ~~~~l~~L~Ls~N~l~~l~~~~~~~~l~~L~~L~L~~N~i~~i~~~~~~~l~~L~~L~Ls~N~l~~--~~-~~~~~~l~~  113 (361)
T 2xot_A           37 LPSYTALLDLSHNNLSRLRAEWTPTRLTNLHSLLLSHNHLNFISSEAFVPVPNLRYLDLSSNHLHT--LD-EFLFSDLQA  113 (361)
T ss_dssp             CCTTCSEEECCSSCCCEECTTSSSSCCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSCCCE--EC-TTTTTTCTT
T ss_pred             CCCCCCEEECCCCCCCccChhhhhhcccccCEEECCCCcCCccChhhccCCCCCCEEECCCCcCCc--CC-HHHhCCCcC
Confidence            34467788887765433222222  78999999999887777677789999999999999987742  11 123788999


Q ss_pred             CcEEEeccCCCCCcc--cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCch-hhcCCCC--C
Q 042541          603 LKKIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPD-GLCDIVS--M  677 (695)
Q Consensus       603 L~~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~-~i~~L~~--L  677 (695)
                      |++|+|++|.+..++  .+.++++|++|+|++|.++.+|+..+..+. .+++|+.|+|++| .+..+|. .+..+++  |
T Consensus       114 L~~L~L~~N~i~~~~~~~~~~l~~L~~L~L~~N~l~~l~~~~~~~~~-~l~~L~~L~L~~N-~l~~l~~~~~~~l~~~~l  191 (361)
T 2xot_A          114 LEVLLLYNNHIVVVDRNAFEDMAQLQKLYLSQNQISRFPVELIKDGN-KLPKLMLLDLSSN-KLKKLPLTDLQKLPAWVK  191 (361)
T ss_dssp             CCEEECCSSCCCEECTTTTTTCTTCCEEECCSSCCCSCCGGGTC-----CTTCCEEECCSS-CCCCCCHHHHHHSCHHHH
T ss_pred             CCEEECCCCcccEECHHHhCCcccCCEEECCCCcCCeeCHHHhcCcc-cCCcCCEEECCCC-CCCccCHHHhhhccHhhc
Confidence            999999999999774  899999999999999999999887752111 6999999999996 5778884 5788887  4


Q ss_pred             ceeeccccc
Q 042541          678 EKLRITNCH  686 (695)
Q Consensus       678 ~~L~l~~~~  686 (695)
                      +.|+|++|+
T Consensus       192 ~~l~l~~N~  200 (361)
T 2xot_A          192 NGLYLHNNP  200 (361)
T ss_dssp             TTEECCSSC
T ss_pred             ceEEecCCC
Confidence            899999976

>3v47_A TOLL-like receptor 5B and variable lymphocyte REC chimeric protein; innate immunity, leucine-rich repeat, innate immune receptor system; HET: NAG; 2.47A {Danio rerio} PDB: 3v44_A*

Probab=99.19  E-value=5.7e-11  Score=129.06  Aligned_cols=137  Identities=19%  Similarity=0.260  Sum_probs=116.6

Q ss_pred             CCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--cccccccc
Q 042541          548 QGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNHL  625 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L  625 (695)
                      .+++|+.|.++.+......|..+..+++|++|++++|.+....   +..++.+++|++|+|++|.+..++  .++++++|
T Consensus       273 ~~~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~---~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~l~~L  349 (455)
T 3v47_A          273 EASGVKTCDLSKSKIFALLKSVFSHFTDLEQLTLAQNEINKID---DNAFWGLTHLLKLNLSQNFLGSIDSRMFENLDKL  349 (455)
T ss_dssp             TTSCCCEEECCSSCCCEECTTTTTTCTTCCEEECTTSCCCEEC---TTTTTTCTTCCEEECCSSCCCEECGGGGTTCTTC
T ss_pred             cccCceEEEecCccccccchhhcccCCCCCEEECCCCcccccC---hhHhcCcccCCEEECCCCccCCcChhHhcCcccC
Confidence            4578999999998888888889999999999999998774221   223788999999999999999764  88999999


Q ss_pred             cEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchh-hcCCCCCceeecccccCCCCCC
Q 042541          626 QKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDG-LCDIVSMEKLRITNCHRLSALP  692 (695)
Q Consensus       626 ~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~-i~~L~~L~~L~l~~~~~l~~lP  692 (695)
                      ++|+|++|.++.+++..+.    .+++|++|++++| .+..+|.. +..+++|+.|++++|+.....|
T Consensus       350 ~~L~Ls~N~l~~~~~~~~~----~l~~L~~L~L~~N-~l~~~~~~~~~~l~~L~~L~l~~N~l~~~~~  412 (455)
T 3v47_A          350 EVLDLSYNHIRALGDQSFL----GLPNLKELALDTN-QLKSVPDGIFDRLTSLQKIWLHTNPWDCSCP  412 (455)
T ss_dssp             CEEECCSSCCCEECTTTTT----TCTTCCEEECCSS-CCSCCCTTTTTTCTTCCEEECCSSCBCCCTT
T ss_pred             CEEECCCCcccccChhhcc----ccccccEEECCCC-ccccCCHhHhccCCcccEEEccCCCcccCCC
Confidence            9999999999999887766    8999999999996 56777765 6899999999999998666665

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens}

Probab=99.19  E-value=6.4e-11  Score=132.64  Aligned_cols=161  Identities=16%  Similarity=0.111  Sum_probs=108.0

Q ss_pred             CCccceEEeeecCCcccCCC-CCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCC
Q 042541          525 HPNNASLLSISTDETFSSNW-PDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKL  603 (695)
Q Consensus       525 ~~~~~r~l~~~~~~~~~~~~-~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L  603 (695)
                      .+..++++.+..+....... ....+++|++|.++.+......|..|.++++|++|++++|.+...   ....++.+++|
T Consensus        26 l~~~l~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~n~i~~i~~~~~~~l~~L~~L~L~~n~l~~~---~~~~~~~l~~L  102 (570)
T 2z63_A           26 LPFSTKNLDLSFNPLRHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQSL---ALGAFSGLSSL  102 (570)
T ss_dssp             SCSSCCEEECCSCCCCEECTTTTTTCSSCCEEECTTCCCCEECTTTTTTCTTCCEEECTTCCCCEE---CTTTTTTCTTC
T ss_pred             ccccccEEEccCCccCccChhHhhCCCCceEEECCCCcCCccCcccccCchhCCEEeCcCCcCCcc---CHhhhcCcccc
Confidence            34567777776654322211 223677888888877765555566788888888888888765321   11236778888


Q ss_pred             cEEEeccCCCCCcc--cccccccccEEeeccccCCccc-ccchhhhcccCCCccEEecccccccccCchhhcCCCCC---
Q 042541          604 KKIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVF-RNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSM---  677 (695)
Q Consensus       604 ~~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~-~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L---  677 (695)
                      ++|++++|.+..+|  .++++++|++|++++|.++.+. |..+.    .+++|++|++++|......|..++.+++|   
T Consensus       103 ~~L~L~~n~l~~l~~~~~~~l~~L~~L~L~~n~l~~~~lp~~~~----~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~~  178 (570)
T 2z63_A          103 QKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFS----NLTNLEHLDLSSNKIQSIYCTDLRVLHQMPLL  178 (570)
T ss_dssp             CEEECTTSCCCCSTTCSCTTCTTCCEEECCSSCCCCCCCCGGGG----GCTTCCEEECTTSCCCEECGGGGHHHHTCTTC
T ss_pred             ccccccccccccCCCccccccccccEEecCCCccceecChhhhc----ccCCCCEEeCcCCccceecHHHccchhccchh
Confidence            88888888888776  6778888888888888877632 33343    78888888888865433345567777777   


Q ss_pred             -ceeecccccCCCCCCC
Q 042541          678 -EKLRITNCHRLSALPE  693 (695)
Q Consensus       678 -~~L~l~~~~~l~~lP~  693 (695)
                       +.|++++|. +..+|+
T Consensus       179 ~~~L~l~~n~-l~~~~~  194 (570)
T 2z63_A          179 NLSLDLSLNP-MNFIQP  194 (570)
T ss_dssp             CCEEECTTCC-CCEECT
T ss_pred             hhhcccCCCC-ceecCH
Confidence             788888865 554443

>1xku_A Decorin; proteoglycan, leucine-rich repeat, structural protein; HET: NAG; 2.15A {Bos taurus} SCOP: c.10.2.7 PDB: 1xec_A* 1xcd_A*

Probab=99.18  E-value=1.6e-10  Score=119.74  Aligned_cols=151  Identities=13%  Similarity=0.188  Sum_probs=91.4

Q ss_pred             ccceEEeeecCCcccCCC-CCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcE
Q 042541          527 NNASLLSISTDETFSSNW-PDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKK  605 (695)
Q Consensus       527 ~~~r~l~~~~~~~~~~~~-~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~  605 (695)
                      ...+.+.+..+....... ....+++|+.|.++.+......|..+..+++|++|++++|.+.  .++.    .-.++|++
T Consensus        52 ~~l~~L~L~~n~i~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~--~l~~----~~~~~L~~  125 (330)
T 1xku_A           52 PDTALLDLQNNKITEIKDGDFKNLKNLHTLILINNKISKISPGAFAPLVKLERLYLSKNQLK--ELPE----KMPKTLQE  125 (330)
T ss_dssp             TTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSSCCS--BCCS----SCCTTCCE
T ss_pred             CCCeEEECCCCcCCEeChhhhccCCCCCEEECCCCcCCeeCHHHhcCCCCCCEEECCCCcCC--ccCh----hhcccccE
Confidence            455666665543322211 1225667777777666555555667777777777777776553  1111    11256777


Q ss_pred             EEeccCCCCCcc--cccccccccEEeeccccCCc--ccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceee
Q 042541          606 IRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQ--VFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLR  681 (695)
Q Consensus       606 L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~--~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~  681 (695)
                      |++++|.+..++  .++++++|++|++++|.+..  ..+..+.    .+++|++|++++| .+..+|..+.  ++|++|+
T Consensus       126 L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~~----~l~~L~~L~l~~n-~l~~l~~~~~--~~L~~L~  198 (330)
T 1xku_A          126 LRVHENEITKVRKSVFNGLNQMIVVELGTNPLKSSGIENGAFQ----GMKKLSYIRIADT-NITTIPQGLP--PSLTELH  198 (330)
T ss_dssp             EECCSSCCCBBCHHHHTTCTTCCEEECCSSCCCGGGBCTTGGG----GCTTCCEEECCSS-CCCSCCSSCC--TTCSEEE
T ss_pred             EECCCCcccccCHhHhcCCccccEEECCCCcCCccCcChhhcc----CCCCcCEEECCCC-ccccCCcccc--ccCCEEE
Confidence            777777777665  56777777777777776653  3344443    6777777777775 4566776543  6777777


Q ss_pred             cccccCCCCC
Q 042541          682 ITNCHRLSAL  691 (695)
Q Consensus       682 l~~~~~l~~l  691 (695)
                      +++|. +..+
T Consensus       199 l~~n~-l~~~  207 (330)
T 1xku_A          199 LDGNK-ITKV  207 (330)
T ss_dssp             CTTSC-CCEE
T ss_pred             CCCCc-CCcc
Confidence            77765 4433

>3j0a_A TOLL-like receptor 5; membrane protein, leucine-rich repeat, asymmetric homodimer, glycoprotein, immune system; HET: NAG FUC; 26.00A {Homo sapiens}

Probab=99.18  E-value=1.3e-10  Score=136.33  Aligned_cols=160  Identities=12%  Similarity=0.101  Sum_probs=107.3

Q ss_pred             CCccceEEeeecCCcccCCCC-CCCCCceEEEEEEccCccccC-ChhhcCCCCCcEEEEcccCCCCcccCcccccccCCC
Q 042541          525 HPNNASLLSISTDETFSSNWP-DMQGPEVKVVVLNIRTKKYVL-PDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSK  602 (695)
Q Consensus       525 ~~~~~r~l~~~~~~~~~~~~~-~~~~~~l~~L~l~~~~~~~~~-p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~  602 (695)
                      .+..+++|.+..+......+. ...+++|++|.++.+.....+ |..|.++++|++|+|++|.+...   .+..++++++
T Consensus        22 lp~~l~~LdLs~N~i~~i~~~~~~~l~~L~~LdLs~n~~~~~i~~~~f~~L~~L~~L~Ls~N~l~~~---~p~~~~~l~~   98 (844)
T 3j0a_A           22 VLNTTERLLLSFNYIRTVTASSFPFLEQLQLLELGSQYTPLTIDKEAFRNLPNLRILDLGSSKIYFL---HPDAFQGLFH   98 (844)
T ss_dssp             SCTTCCEEEEESCCCCEECSSSCSSCCSCSEEEECTTCCCCEECTTTTSSCTTCCEEECTTCCCCEE---CTTSSCSCSS
T ss_pred             CCCCcCEEECCCCcCCccChhHCcccccCeEEeCCCCCCccccCHHHhcCCCCCCEEECCCCcCccc---CHhHccCCcc
Confidence            456778888876654332222 236788888888887555555 66788888888888888766321   1233677888


Q ss_pred             CcEEEeccCCCCC-cc-c--ccccccccEEeeccccCCcccc-cchhhhcccCCCccEEecccccccccCchhhcCC--C
Q 042541          603 LKKIRLEHVSLPN-SL-A--TVRMNHLQKVSLVMCNVGQVFR-NSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDI--V  675 (695)
Q Consensus       603 L~~L~L~~~~l~~-lp-~--i~~l~~L~~L~l~~~~i~~~~~-~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L--~  675 (695)
                      |++|+|++|.+.. +| .  ++++++|++|+|++|.++.+++ ..+.    .+++|++|++++|......|..++.+  +
T Consensus        99 L~~L~Ls~n~l~~~~~~~~~~~~L~~L~~L~Ls~N~l~~~~~~~~~~----~L~~L~~L~Ls~N~i~~~~~~~l~~l~~~  174 (844)
T 3j0a_A           99 LFELRLYFCGLSDAVLKDGYFRNLKALTRLDLSKNQIRSLYLHPSFG----KLNSLKSIDFSSNQIFLVCEHELEPLQGK  174 (844)
T ss_dssp             CCCEECTTCCCSSCCSTTCCCSSCSSCCEEEEESCCCCCCCCCGGGG----TCSSCCEEEEESSCCCCCCSGGGHHHHHC
T ss_pred             cCEeeCcCCCCCcccccCccccccCCCCEEECCCCcccccccchhHh----hCCCCCEEECCCCcCCeeCHHHcccccCC
Confidence            8888888888773 45 3  7788888888888888777654 3444    78888888888765544555556555  5


Q ss_pred             CCceeecccccCCCCC
Q 042541          676 SMEKLRITNCHRLSAL  691 (695)
Q Consensus       676 ~L~~L~l~~~~~l~~l  691 (695)
                      +|+.|++++|+..+..
T Consensus       175 ~L~~L~L~~n~l~~~~  190 (844)
T 3j0a_A          175 TLSFFSLAANSLYSRV  190 (844)
T ss_dssp             SSCCCEECCSBSCCCC
T ss_pred             ccceEECCCCcccccc
Confidence            6666666665543333

>2ell_A Acidic leucine-rich nuclear phosphoprotein 32 FAM B; phapi2 protein, silver-stainable protein SSP29, acidic prote in leucines, structural genomics; NMR {Homo sapiens} PDB: 2rr6_A 2jqd_A

Probab=99.18  E-value=7.1e-11  Score=109.39  Aligned_cols=114  Identities=16%  Similarity=0.268  Sum_probs=95.8

Q ss_pred             CCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcccccccccccEEeeccccCCcccccchhhhcccCC
Q 042541          572 KMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFP  651 (695)
Q Consensus       572 ~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~  651 (695)
                      ..++|+.|++++|.+....++..  +..+++|++|++++|.++.++.++.+++|++|++++|.++..+|..+.    .++
T Consensus        22 ~~~~L~~L~l~~n~l~~~~i~~~--~~~l~~L~~L~l~~n~l~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~----~l~   95 (168)
T 2ell_A           22 TPAAVRELVLDNCKSNDGKIEGL--TAEFVNLEFLSLINVGLISVSNLPKLPKLKKLELSENRIFGGLDMLAE----KLP   95 (168)
T ss_dssp             CTTSCSEEECCSCBCBTTBCSSC--CGGGGGCCEEEEESSCCCCCSSCCCCSSCCEEEEESCCCCSCCCHHHH----HCT
T ss_pred             CcccCCEEECCCCCCChhhHHHH--HHhCCCCCEEeCcCCCCCChhhhccCCCCCEEECcCCcCchHHHHHHh----hCC
Confidence            45789999999998743344332  688999999999999998777788999999999999999987666664    699


Q ss_pred             CccEEecccccccccCc--hhhcCCCCCceeecccccCCCCCCC
Q 042541          652 NLLEMDIDYCNDLIELP--DGLCDIVSMEKLRITNCHRLSALPE  693 (695)
Q Consensus       652 ~L~~L~l~~c~~l~~lP--~~i~~L~~L~~L~l~~~~~l~~lP~  693 (695)
                      +|++|++++| .+..+|  ..++.+++|++|++++|+ +..+|.
T Consensus        96 ~L~~L~Ls~N-~l~~~~~~~~l~~l~~L~~L~l~~N~-l~~~~~  137 (168)
T 2ell_A           96 NLTHLNLSGN-KLKDISTLEPLKKLECLKSLDLFNCE-VTNLND  137 (168)
T ss_dssp             TCCEEECBSS-SCCSSGGGGGGSSCSCCCEEECCSSG-GGTSTT
T ss_pred             CCCEEeccCC-ccCcchhHHHHhcCCCCCEEEeeCCc-CcchHH
Confidence            9999999997 678877  689999999999999976 666664

>2z81_A CD282 antigen, TOLL-like receptor 2, variable lymphocyte recepto; TLR2, PAM3CSK4, lipopeptide, innate immunity, cytoplasmic VE glycoprotein; HET: NAG BMA MAN PCJ; 1.80A {Mus musculus} PDB: 2z82_A* 3a7c_A* 3a79_A* 3a7b_A* 2z7x_A*

Probab=99.18  E-value=4.9e-11  Score=132.95  Aligned_cols=153  Identities=14%  Similarity=0.107  Sum_probs=101.2

Q ss_pred             ccceEEeeecCCcccCCCC-CCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcE
Q 042541          527 NNASLLSISTDETFSSNWP-DMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKK  605 (695)
Q Consensus       527 ~~~r~l~~~~~~~~~~~~~-~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~  605 (695)
                      ...+++.+..+......+. ...+++|++|.++.+......|..|.++++|++|++++|.+...   ....++.+++|++
T Consensus        26 ~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~Ls~n~l~~~---~~~~~~~l~~L~~  102 (549)
T 2z81_A           26 AAMKSLDLSFNKITYIGHGDLRACANLQVLILKSSRINTIEGDAFYSLGSLEHLDLSDNHLSSL---SSSWFGPLSSLKY  102 (549)
T ss_dssp             TTCCEEECCSSCCCEECSSTTSSCTTCCEEECTTSCCCEECTTTTTTCTTCCEEECTTSCCCSC---CHHHHTTCTTCCE
T ss_pred             CCccEEECcCCccCccChhhhhcCCcccEEECCCCCcCccChhhccccccCCEEECCCCccCcc---CHHHhccCCCCcE
Confidence            4667777765543222221 23567777777777766666666777777777777777765321   1122667777777


Q ss_pred             EEeccCCCCC--cc-cccccccccEEeecccc-CCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceee
Q 042541          606 IRLEHVSLPN--SL-ATVRMNHLQKVSLVMCN-VGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLR  681 (695)
Q Consensus       606 L~L~~~~l~~--lp-~i~~l~~L~~L~l~~~~-i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~  681 (695)
                      |++++|.+..  .| .++++++|++|++++|. +..+++..+.    .+++|++|++++|......|..++++++|++|+
T Consensus       103 L~Ls~n~l~~~~~~~~~~~l~~L~~L~L~~n~~~~~~~~~~~~----~l~~L~~L~L~~n~l~~~~~~~l~~l~~L~~L~  178 (549)
T 2z81_A          103 LNLMGNPYQTLGVTSLFPNLTNLQTLRIGNVETFSEIRRIDFA----GLTSLNELEIKALSLRNYQSQSLKSIRDIHHLT  178 (549)
T ss_dssp             EECTTCCCSSSCSSCSCTTCTTCCEEEEEESSSCCEECTTTTT----TCCEEEEEEEEETTCCEECTTTTTTCSEEEEEE
T ss_pred             EECCCCcccccchhhhhhccCCccEEECCCCccccccCHhhhh----cccccCeeeccCCcccccChhhhhccccCceEe
Confidence            7777777763  45 67777777777777776 5566555554    677777777777665555777777777788887


Q ss_pred             ccccc
Q 042541          682 ITNCH  686 (695)
Q Consensus       682 l~~~~  686 (695)
                      +++|.
T Consensus       179 l~~n~  183 (549)
T 2z81_A          179 LHLSE  183 (549)
T ss_dssp             EECSB
T ss_pred             cccCc
Confidence            77754

>1xeu_A Internalin C; cellular invasion, leucine-rich repeat, cell invasion; 2.05A {Listeria monocytogenes}

Probab=99.17  E-value=1.1e-10  Score=116.79  Aligned_cols=147  Identities=14%  Similarity=0.147  Sum_probs=111.7

Q ss_pred             cceEEeeecCCcccCCCCCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEE
Q 042541          528 NASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIR  607 (695)
Q Consensus       528 ~~r~l~~~~~~~~~~~~~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~  607 (695)
                      ..+.+.+.+.... .......+++|+.|.++.+.... +|. +..+++|++|++++|.+..  ++.   +.. ++|++|+
T Consensus        42 ~L~~L~l~~n~i~-~l~~l~~l~~L~~L~L~~N~i~~-~~~-l~~l~~L~~L~L~~N~l~~--l~~---~~~-~~L~~L~  112 (263)
T 1xeu_A           42 GVQNFNGDNSNIQ-SLAGMQFFTNLKELHLSHNQISD-LSP-LKDLTKLEELSVNRNRLKN--LNG---IPS-ACLSRLF  112 (263)
T ss_dssp             TCSEEECTTSCCC-CCTTGGGCTTCCEEECCSSCCCC-CGG-GTTCSSCCEEECCSSCCSC--CTT---CCC-SSCCEEE
T ss_pred             cCcEEECcCCCcc-cchHHhhCCCCCEEECCCCccCC-Chh-hccCCCCCEEECCCCccCC--cCc---ccc-CcccEEE
Confidence            4556666544322 11222367899999998885544 344 8999999999999987742  222   333 8899999


Q ss_pred             eccCCCCCcccccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccccC
Q 042541          608 LEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHR  687 (695)
Q Consensus       608 L~~~~l~~lp~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~~  687 (695)
                      +++|.++.+|.++++++|++|++++|.++.++ .. .    .+++|++|++++| .+..+ ..+..+++|+.|++++|+ 
T Consensus       113 L~~N~l~~~~~l~~l~~L~~L~Ls~N~i~~~~-~l-~----~l~~L~~L~L~~N-~i~~~-~~l~~l~~L~~L~l~~N~-  183 (263)
T 1xeu_A          113 LDNNELRDTDSLIHLKNLEILSIRNNKLKSIV-ML-G----FLSKLEVLDLHGN-EITNT-GGLTRLKKVNWIDLTGQK-  183 (263)
T ss_dssp             CCSSCCSBSGGGTTCTTCCEEECTTSCCCBCG-GG-G----GCTTCCEEECTTS-CCCBC-TTSTTCCCCCEEEEEEEE-
T ss_pred             ccCCccCCChhhcCcccccEEECCCCcCCCCh-HH-c----cCCCCCEEECCCC-cCcch-HHhccCCCCCEEeCCCCc-
Confidence            99999998888889999999999999999875 33 3    8999999999996 46666 569999999999999976 


Q ss_pred             CCCCC
Q 042541          688 LSALP  692 (695)
Q Consensus       688 l~~lP  692 (695)
                      +...|
T Consensus       184 ~~~~~  188 (263)
T 1xeu_A          184 CVNEP  188 (263)
T ss_dssp             EECCC
T ss_pred             ccCCc
Confidence            54444

>4glp_A Monocyte differentiation antigen CD14; alpha beta BENT solenoid, LRR, lipopolysaccharide, serum, CD leucine-rich repeat, pattern recognition; 4.00A {Homo sapiens}

Probab=99.17  E-value=2.4e-11  Score=124.79  Aligned_cols=150  Identities=17%  Similarity=0.160  Sum_probs=92.2

Q ss_pred             CccceEEeeecCCcccCCCCC-CCCCceEEEEEEccCcccc--C--ChhhcCCCCCcEEEEcccCCCCcccCc-c-cccc
Q 042541          526 PNNASLLSISTDETFSSNWPD-MQGPEVKVVVLNIRTKKYV--L--PDFLQKMDELKVLIVTNYGFSPAELNN-F-RVLS  598 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~~~~~~-~~~~~l~~L~l~~~~~~~~--~--p~~~~~l~~Lr~L~l~~~~~~~~~~~~-~-~~l~  598 (695)
                      ....++|.+..+......+.. ..+++|+.|.++.|...+.  +  +..+..+++|++|++++|.+..  ++. . ..++
T Consensus       144 ~~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~~~~~l~~L~~L~Ls~N~l~~--l~~~~~~l~~  221 (310)
T 4glp_A          144 KPGLKVLSIAQAHSPAFSCEQVRAFPALTSLDLSDNPGLGERGLMAALCPHKFPAIQNLALRNTGMET--PTGVCAALAA  221 (310)
T ss_dssp             CSCCCEEEEECCSSCCCCTTSCCCCTTCCEEECCSCTTCHHHHHHTTSCTTSSCCCCSCBCCSSCCCC--HHHHHHHHHH
T ss_pred             ccCCCEEEeeCCCcchhhHHHhccCCCCCEEECCCCCCccchhhhHHHhhhcCCCCCEEECCCCCCCc--hHHHHHHHHh
Confidence            346667777655442222222 2567777777777754321  2  2234667777777777776531  111 0 1145


Q ss_pred             cCCCCcEEEeccCCCCCc-c-ccccc---ccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcC
Q 042541          599 ALSKLKKIRLEHVSLPNS-L-ATVRM---NHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCD  673 (695)
Q Consensus       599 ~l~~L~~L~L~~~~l~~l-p-~i~~l---~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~  673 (695)
                      .+++|++|+|++|.+..+ | .++.+   ++|++|+|++|.++.+|...       .++|++|++++| .+..+|. +..
T Consensus       222 ~l~~L~~L~Ls~N~l~~~~p~~~~~~~~~~~L~~L~Ls~N~l~~lp~~~-------~~~L~~L~Ls~N-~l~~~~~-~~~  292 (310)
T 4glp_A          222 AGVQPHSLDLSHNSLRATVNPSAPRCMWSSALNSLNLSFAGLEQVPKGL-------PAKLRVLDLSSN-RLNRAPQ-PDE  292 (310)
T ss_dssp             HTCCCSSEECTTSCCCCCCCSCCSSCCCCTTCCCEECCSSCCCSCCSCC-------CSCCSCEECCSC-CCCSCCC-TTS
T ss_pred             cCCCCCEEECCCCCCCccchhhHHhccCcCcCCEEECCCCCCCchhhhh-------cCCCCEEECCCC-cCCCCch-hhh
Confidence            667777888877777754 6 66655   57778888777777665433       257777777775 4566665 667


Q ss_pred             CCCCceeeccccc
Q 042541          674 IVSMEKLRITNCH  686 (695)
Q Consensus       674 L~~L~~L~l~~~~  686 (695)
                      +++|+.|++++|+
T Consensus       293 l~~L~~L~L~~N~  305 (310)
T 4glp_A          293 LPEVDNLTLDGNP  305 (310)
T ss_dssp             CCCCSCEECSSTT
T ss_pred             CCCccEEECcCCC
Confidence            7777788877765

>2ft3_A Biglycan; proteoglycan, dimer interface, structural protein, signaling; HET: NAG FLC; 3.40A {Bos taurus}

Probab=99.17  E-value=1.5e-10  Score=120.07  Aligned_cols=103  Identities=16%  Similarity=0.174  Sum_probs=47.3

Q ss_pred             CceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc-cccccccccEE
Q 042541          550 PEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL-ATVRMNHLQKV  628 (695)
Q Consensus       550 ~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp-~i~~l~~L~~L  628 (695)
                      ++++.|.++.+......|..+.++++|++|++++|.+...   .+..++.+++|++|++++|.+..+| .+.  ++|++|
T Consensus        54 ~~l~~L~l~~n~i~~~~~~~~~~l~~L~~L~L~~n~l~~~---~~~~~~~l~~L~~L~L~~n~l~~l~~~~~--~~L~~L  128 (332)
T 2ft3_A           54 PDTTLLDLQNNDISELRKDDFKGLQHLYALVLVNNKISKI---HEKAFSPLRKLQKLYISKNHLVEIPPNLP--SSLVEL  128 (332)
T ss_dssp             TTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSCCCEE---CGGGSTTCTTCCEEECCSSCCCSCCSSCC--TTCCEE
T ss_pred             CCCeEEECCCCcCCccCHhHhhCCCCCcEEECCCCccCcc---CHhHhhCcCCCCEEECCCCcCCccCcccc--ccCCEE
Confidence            3445555544443333334455555555555555443210   0112444555555555555555444 332  455555


Q ss_pred             eeccccCCcccccchhhhcccCCCccEEecccc
Q 042541          629 SLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYC  661 (695)
Q Consensus       629 ~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c  661 (695)
                      ++++|.++.+++..+.    .+++|++|++++|
T Consensus       129 ~l~~n~i~~~~~~~~~----~l~~L~~L~l~~n  157 (332)
T 2ft3_A          129 RIHDNRIRKVPKGVFS----GLRNMNCIEMGGN  157 (332)
T ss_dssp             ECCSSCCCCCCSGGGS----SCSSCCEEECCSC
T ss_pred             ECCCCccCccCHhHhC----CCccCCEEECCCC
Confidence            5555555544444333    4455555555543

>3t6q_A CD180 antigen; protein-protein complex, leucine rich repeat, MD-2 related L recognition, receptor, innate immunity, glycosylation, IMMU; HET: NAG BMA MAN; 1.90A {Mus musculus} PDB: 3b2d_A* 3rg1_A*

Probab=99.17  E-value=1e-10  Score=132.03  Aligned_cols=161  Identities=12%  Similarity=0.096  Sum_probs=126.3

Q ss_pred             CCccceEEeeecCCcccCCCC-CCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCC
Q 042541          525 HPNNASLLSISTDETFSSNWP-DMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKL  603 (695)
Q Consensus       525 ~~~~~r~l~~~~~~~~~~~~~-~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L  603 (695)
                      .+...+++.+.++......+. ...+++|++|.++.+......|..|.++++|++|++++|.+...   .+..++.+++|
T Consensus        31 l~~~l~~L~Ls~n~i~~~~~~~~~~l~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~Ls~n~l~~~---~~~~~~~l~~L  107 (606)
T 3t6q_A           31 LPNSTECLEFSFNVLPTIQNTTFSRLINLTFLDLTRCQIYWIHEDTFQSQHRLDTLVLTANPLIFM---AETALSGPKAL  107 (606)
T ss_dssp             SCTTCCEEECTTCCCSEECTTTSTTCTTCSEEECTTCCCCEECTTTTTTCTTCCEEECTTCCCSEE---CTTTTSSCTTC
T ss_pred             CCCcCcEEEccCCccCcCChhHhccCccceEEECCCCccceeChhhccCccccCeeeCCCCccccc---Chhhhcccccc
Confidence            445788898887654333222 23789999999999887777888999999999999999876421   12237899999


Q ss_pred             cEEEeccCCCCCc-c-cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCc--e
Q 042541          604 KKIRLEHVSLPNS-L-ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSME--K  679 (695)
Q Consensus       604 ~~L~L~~~~l~~l-p-~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~--~  679 (695)
                      ++|++++|.+..+ | .++++++|++|++++|.+..++...+.    .+++|++|++++|......|..++.+++|+  .
T Consensus       108 ~~L~L~~n~i~~l~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~----~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~l~  183 (606)
T 3t6q_A          108 KHLFFIQTGISSIDFIPLHNQKTLESLYLGSNHISSIKLPKGF----PTEKLKVLDFQNNAIHYLSKEDMSSLQQATNLS  183 (606)
T ss_dssp             CEEECTTSCCSCGGGSCCTTCTTCCEEECCSSCCCCCCCCTTC----CCTTCCEEECCSSCCCEECHHHHHTTTTCCSEE
T ss_pred             cEeeccccCcccCCcchhccCCcccEEECCCCcccccCccccc----CCcccCEEEcccCcccccChhhhhhhcccceeE
Confidence            9999999999987 4 899999999999999999986543333    799999999999754444467799999999  8


Q ss_pred             eecccccCCCCCCC
Q 042541          680 LRITNCHRLSALPE  693 (695)
Q Consensus       680 L~l~~~~~l~~lP~  693 (695)
                      |++++|. +..+|+
T Consensus       184 L~l~~n~-l~~~~~  196 (606)
T 3t6q_A          184 LNLNGND-IAGIEP  196 (606)
T ss_dssp             EECTTCC-CCEECT
T ss_pred             EecCCCc-cCccCh
Confidence            9999976 554443

>2z63_A TOLL-like receptor 4, variable lymphocyte recepto; TLR4, MD-2, LPS, immune system; HET: NAG FUL; 2.00A {Homo sapiens}

Probab=99.17  E-value=7.9e-11  Score=131.87  Aligned_cols=134  Identities=16%  Similarity=0.179  Sum_probs=96.3

Q ss_pred             CceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--cccccccccE
Q 042541          550 PEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNHLQK  627 (695)
Q Consensus       550 ~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L~~  627 (695)
                      ++++.|.++.+......+..|.++++|++|++++|.+..  + ....++.+++|++|+|++|.+..+|  .++++++|++
T Consensus        28 ~~l~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~n~i~~--i-~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~l~~L~~  104 (570)
T 2z63_A           28 FSTKNLDLSFNPLRHLGSYSFFSFPELQVLDLSRCEIQT--I-EDGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQK  104 (570)
T ss_dssp             SSCCEEECCSCCCCEECTTTTTTCSSCCEEECTTCCCCE--E-CTTTTTTCTTCCEEECTTCCCCEECTTTTTTCTTCCE
T ss_pred             ccccEEEccCCccCccChhHhhCCCCceEEECCCCcCCc--c-CcccccCchhCCEEeCcCCcCCccCHhhhcCcccccc
Confidence            467778887776655556677888888888888776532  1 1123677888888888888887665  7778888888


Q ss_pred             EeeccccCCcccccchhhhcccCCCccEEecccccccc-cCchhhcCCCCCceeecccccCCCCC
Q 042541          628 VSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLI-ELPDGLCDIVSMEKLRITNCHRLSAL  691 (695)
Q Consensus       628 L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~-~lP~~i~~L~~L~~L~l~~~~~l~~l  691 (695)
                      |++++|.++.+++..+.    .+++|++|++++|.... .+|..++++++|++|++++|. +..+
T Consensus       105 L~L~~n~l~~l~~~~~~----~l~~L~~L~L~~n~l~~~~lp~~~~~l~~L~~L~l~~n~-l~~~  164 (570)
T 2z63_A          105 LVAVETNLASLENFPIG----HLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNK-IQSI  164 (570)
T ss_dssp             EECTTSCCCCSTTCSCT----TCTTCCEEECCSSCCCCCCCCGGGGGCTTCCEEECTTSC-CCEE
T ss_pred             ccccccccccCCCcccc----ccccccEEecCCCccceecChhhhcccCCCCEEeCcCCc-ccee
Confidence            88888888877765444    78888888888764333 467888888888888888865 4444

>3t6q_A CD180 antigen; protein-protein complex, leucine rich repeat, MD-2 related L recognition, receptor, innate immunity, glycosylation, IMMU; HET: NAG BMA MAN; 1.90A {Mus musculus} PDB: 3b2d_A* 3rg1_A*

Probab=99.17  E-value=8.4e-11  Score=132.76  Aligned_cols=134  Identities=13%  Similarity=0.134  Sum_probs=81.1

Q ss_pred             CCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCc-c-cccccccc
Q 042541          548 QGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNS-L-ATVRMNHL  625 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~l-p-~i~~l~~L  625 (695)
                      .+++|+.|.++.+......|..+..+++|++|++++|.+....++....+..+++|++|++++|.+..+ | .++++++|
T Consensus       423 ~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L  502 (606)
T 3t6q_A          423 NLHLLKVLNLSHSLLDISSEQLFDGLPALQHLNLQGNHFPKGNIQKTNSLQTLGRLEILVLSFCDLSSIDQHAFTSLKMM  502 (606)
T ss_dssp             TCTTCCEEECTTCCCBTTCTTTTTTCTTCCEEECTTCBCGGGEECSSCGGGGCTTCCEEECTTSCCCEECTTTTTTCTTC
T ss_pred             CcccCCEEECCCCccCCcCHHHHhCCCCCCEEECCCCCCCccccccchhhccCCCccEEECCCCccCccChhhhccccCC
Confidence            455666666666655555555666666666666666655332222233456666667777766666644 3 66666677


Q ss_pred             cEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeeccccc
Q 042541          626 QKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCH  686 (695)
Q Consensus       626 ~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~  686 (695)
                      ++|+|++|.++..++..+.    .+++| .|++++|......|..++.+++|+.|++++|+
T Consensus       503 ~~L~Ls~N~l~~~~~~~l~----~l~~L-~L~L~~N~l~~~~~~~~~~l~~L~~L~l~~N~  558 (606)
T 3t6q_A          503 NHVDLSHNRLTSSSIEALS----HLKGI-YLNLASNHISIILPSLLPILSQQRTINLRQNP  558 (606)
T ss_dssp             CEEECCSSCCCGGGGGGGT----TCCSC-EEECCSSCCCCCCGGGHHHHHTSSEEECTTCC
T ss_pred             CEEECCCCccCcCChhHhC----ccccc-EEECcCCcccccCHhhcccCCCCCEEeCCCCC
Confidence            7777777766666655554    66666 66776654443344446666677777776665

>2je0_A Acidic leucine-rich nuclear phosphoprotein 32 FAM member A; nuclear protein; 2.40A {Homo sapiens} PDB: 2je1_A

Probab=99.17  E-value=4.9e-11  Score=108.06  Aligned_cols=114  Identities=18%  Similarity=0.300  Sum_probs=94.6

Q ss_pred             CCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcccccccccccEEeeccccCCcccccchhhhcccCC
Q 042541          572 KMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFP  651 (695)
Q Consensus       572 ~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~  651 (695)
                      ..++|+.|++++|.+....++.  .++.+++|++|++++|.++.++.++++++|++|++++|.++..+|..+.    .++
T Consensus        15 ~~~~l~~L~l~~n~l~~~~~~~--~~~~l~~L~~L~l~~n~l~~~~~~~~l~~L~~L~Ls~n~i~~~~~~~~~----~l~   88 (149)
T 2je0_A           15 TPSDVKELVLDNSRSNEGKLEG--LTDEFEELEFLSTINVGLTSIANLPKLNKLKKLELSDNRVSGGLEVLAE----KCP   88 (149)
T ss_dssp             CGGGCSEEECTTCBCBTTBCCS--CCTTCTTCCEEECTTSCCCCCTTCCCCTTCCEEECCSSCCCSCTHHHHH----HCT
T ss_pred             CCccCeEEEccCCcCChhHHHH--HHhhcCCCcEEECcCCCCCCchhhhcCCCCCEEECCCCcccchHHHHhh----hCC
Confidence            3478999999999874233333  3688999999999999998777788999999999999999986666654    699


Q ss_pred             CccEEecccccccccCc--hhhcCCCCCceeecccccCCCCCCC
Q 042541          652 NLLEMDIDYCNDLIELP--DGLCDIVSMEKLRITNCHRLSALPE  693 (695)
Q Consensus       652 ~L~~L~l~~c~~l~~lP--~~i~~L~~L~~L~l~~~~~l~~lP~  693 (695)
                      +|++|++++|. +..+|  ..++.+++|++|++++|+ +..+|.
T Consensus        89 ~L~~L~ls~N~-i~~~~~~~~~~~l~~L~~L~l~~N~-l~~~~~  130 (149)
T 2je0_A           89 NLTHLNLSGNK-IKDLSTIEPLKKLENLKSLDLFNCE-VTNLND  130 (149)
T ss_dssp             TCCEEECTTSC-CCSHHHHGGGGGCTTCCEEECTTCG-GGGSTT
T ss_pred             CCCEEECCCCc-CCChHHHHHHhhCCCCCEEeCcCCc-ccchHH
Confidence            99999999974 67765  789999999999999976 776664

>2wfh_A SLIT homolog 2 protein C-product; developmental protein, neurogenesis, splicing, glycoprotein, leucine-rich repeat, disulfide bond, differentiation; 1.80A {Homo sapiens}

Probab=99.16  E-value=1.8e-10  Score=109.20  Aligned_cols=111  Identities=18%  Similarity=0.235  Sum_probs=79.6

Q ss_pred             cCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--cccccccccEEeeccccCCcccccc
Q 042541          565 VLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFRNS  642 (695)
Q Consensus       565 ~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~  642 (695)
                      .+|..+  .++|++|++++|.+.  .++  ..+..+++|++|+|++|.++.++  .+.++++|++|+|++|.++.+++..
T Consensus        24 ~ip~~~--~~~l~~L~L~~n~i~--~ip--~~~~~l~~L~~L~Ls~N~i~~i~~~~f~~l~~L~~L~Ls~N~l~~i~~~~   97 (193)
T 2wfh_A           24 VLPKGI--PRDVTELYLDGNQFT--LVP--KELSNYKHLTLIDLSNNRISTLSNQSFSNMTQLLTLILSYNRLRCIPPRT   97 (193)
T ss_dssp             SCCSCC--CTTCCEEECCSSCCC--SCC--GGGGGCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCBCCTTT
T ss_pred             cCCCCC--CCCCCEEECCCCcCc--hhH--HHhhcccCCCEEECCCCcCCEeCHhHccCCCCCCEEECCCCccCEeCHHH
Confidence            445433  246788888877663  222  34677788888888888887666  6778888888888888888877766


Q ss_pred             hhhhcccCCCccEEecccccccccCchh-hcCCCCCceeeccccc
Q 042541          643 TFRISDAFPNLLEMDIDYCNDLIELPDG-LCDIVSMEKLRITNCH  686 (695)
Q Consensus       643 ~~~l~~~l~~L~~L~l~~c~~l~~lP~~-i~~L~~L~~L~l~~~~  686 (695)
                      +.    .+++|++|+|++| .+..+|.+ +..+++|++|++++|+
T Consensus        98 f~----~l~~L~~L~L~~N-~l~~~~~~~~~~l~~L~~L~L~~N~  137 (193)
T 2wfh_A           98 FD----GLKSLRLLSLHGN-DISVVPEGAFNDLSALSHLAIGANP  137 (193)
T ss_dssp             TT----TCTTCCEEECCSS-CCCBCCTTTTTTCTTCCEEECCSSC
T ss_pred             hC----CCCCCCEEECCCC-CCCeeChhhhhcCccccEEEeCCCC
Confidence            65    7788888888875 46667664 6778888888888765

>2z7x_B TOLL-like receptor 1, variable lymphocyte recepto; TLR2, TLR1, lipopeptide, innate immunity, glycoPro immune response, inflammatory response, leucine-rich repeat membrane, receptor; HET: NAG NDG MAN BMA PCJ; 2.10A {Homo sapiens}

Probab=99.16  E-value=1.3e-10  Score=128.64  Aligned_cols=136  Identities=10%  Similarity=0.184  Sum_probs=77.4

Q ss_pred             CCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCc-ccccccCCCCcEEEeccCCCCC-cc--cccccc
Q 042541          548 QGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNN-FRVLSALSKLKKIRLEHVSLPN-SL--ATVRMN  623 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~-~~~l~~l~~L~~L~L~~~~l~~-lp--~i~~l~  623 (695)
                      .+++|+.|.++.+......|..+..+++|++|++++|.+..  ++. +..++.+++|++|++++|.+.. +|  .+..++
T Consensus       322 ~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~N~l~~--l~~~~~~~~~l~~L~~L~Ls~N~l~~~l~~~~~~~l~  399 (520)
T 2z7x_B          322 KISPFLHLDFSNNLLTDTVFENCGHLTELETLILQMNQLKE--LSKIAEMTTQMKSLQQLDISQNSVSYDEKKGDCSWTK  399 (520)
T ss_dssp             SCCCCCEEECCSSCCCTTTTTTCCCCSSCCEEECCSSCCCB--HHHHHHHHTTCTTCCEEECCSSCCBCCGGGCSCCCCT
T ss_pred             hCCcccEEEeECCccChhhhhhhccCCCCCEEEccCCccCc--cccchHHHhhCCCCCEEECCCCcCCcccccchhccCc
Confidence            45666666666665555566666666666666666665531  111 1225566666666666666664 66  355666


Q ss_pred             cccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccccCCCCCCC
Q 042541          624 HLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPE  693 (695)
Q Consensus       624 ~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~~l~~lP~  693 (695)
                      +|++|++++|.+++..+..+      .++|++|++++| .+..+|.++..+++|++|++++|. +..+|.
T Consensus       400 ~L~~L~Ls~N~l~~~~~~~l------~~~L~~L~Ls~N-~l~~ip~~~~~l~~L~~L~L~~N~-l~~l~~  461 (520)
T 2z7x_B          400 SLLSLNMSSNILTDTIFRCL------PPRIKVLDLHSN-KIKSIPKQVVKLEALQELNVASNQ-LKSVPD  461 (520)
T ss_dssp             TCCEEECCSSCCCGGGGGSC------CTTCCEEECCSS-CCCCCCGGGGGCTTCCEEECCSSC-CCCCCT
T ss_pred             cCCEEECcCCCCCcchhhhh------cccCCEEECCCC-cccccchhhhcCCCCCEEECCCCc-CCccCH
Confidence            66666666666544332211      145666666654 344666665566666666666643 555554

>2z81_A CD282 antigen, TOLL-like receptor 2, variable lymphocyte recepto; TLR2, PAM3CSK4, lipopeptide, innate immunity, cytoplasmic VE glycoprotein; HET: NAG BMA MAN PCJ; 1.80A {Mus musculus} PDB: 2z82_A* 3a7c_A* 3a79_A* 3a7b_A* 2z7x_A*

Probab=99.16  E-value=5.2e-11  Score=132.72  Aligned_cols=154  Identities=10%  Similarity=0.103  Sum_probs=100.6

Q ss_pred             CccceEEeeecCCcccCCCC-CCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCc
Q 042541          526 PNNASLLSISTDETFSSNWP-DMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLK  604 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~~~~~-~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~  604 (695)
                      ....+++.+..+......+. ...+++|++|.++.+......|..++++++|++|++++|.+....  .++.++.+++|+
T Consensus        49 l~~L~~L~Ls~n~i~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~--~~~~~~~l~~L~  126 (549)
T 2z81_A           49 CANLQVLILKSSRINTIEGDAFYSLGSLEHLDLSDNHLSSLSSSWFGPLSSLKYLNLMGNPYQTLG--VTSLFPNLTNLQ  126 (549)
T ss_dssp             CTTCCEEECTTSCCCEECTTTTTTCTTCCEEECTTSCCCSCCHHHHTTCTTCCEEECTTCCCSSSC--SSCSCTTCTTCC
T ss_pred             CCcccEEECCCCCcCccChhhccccccCCEEECCCCccCccCHHHhccCCCCcEEECCCCcccccc--hhhhhhccCCcc
Confidence            34566776665543222211 235677777777777665555556777888888888777653211  122367777788


Q ss_pred             EEEeccCC-CCCcc--cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhh-cCCCCCcee
Q 042541          605 KIRLEHVS-LPNSL--ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGL-CDIVSMEKL  680 (695)
Q Consensus       605 ~L~L~~~~-l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i-~~L~~L~~L  680 (695)
                      +|++++|. +..+|  .++++++|++|++++|.++...|..+.    .+++|++|++++|. ...+|..+ +.+++|++|
T Consensus       127 ~L~L~~n~~~~~~~~~~~~~l~~L~~L~L~~n~l~~~~~~~l~----~l~~L~~L~l~~n~-~~~~~~~~~~~l~~L~~L  201 (549)
T 2z81_A          127 TLRIGNVETFSEIRRIDFAGLTSLNELEIKALSLRNYQSQSLK----SIRDIHHLTLHLSE-SAFLLEIFADILSSVRYL  201 (549)
T ss_dssp             EEEEEESSSCCEECTTTTTTCCEEEEEEEEETTCCEECTTTTT----TCSEEEEEEEECSB-STTHHHHHHHSTTTBSEE
T ss_pred             EEECCCCccccccCHhhhhcccccCeeeccCCcccccChhhhh----ccccCceEecccCc-ccccchhhHhhcccccEE
Confidence            88887776 55665  677777888888888877776665554    67778888877753 45566553 467788888


Q ss_pred             eccccc
Q 042541          681 RITNCH  686 (695)
Q Consensus       681 ~l~~~~  686 (695)
                      ++++|.
T Consensus       202 ~L~~n~  207 (549)
T 2z81_A          202 ELRDTN  207 (549)
T ss_dssp             EEESCB
T ss_pred             EccCCc
Confidence            887765

>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A*

Probab=99.15  E-value=1.3e-10  Score=133.14  Aligned_cols=160  Identities=17%  Similarity=0.227  Sum_probs=123.4

Q ss_pred             CCccceEEeeecCCcccCCCC-CCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCC
Q 042541          525 HPNNASLLSISTDETFSSNWP-DMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKL  603 (695)
Q Consensus       525 ~~~~~r~l~~~~~~~~~~~~~-~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L  603 (695)
                      .+..++++.+..+........ ...+++|++|.++.+......|..+.++++|++|++++|.+..  ++. ..++.+++|
T Consensus        23 ~~~~l~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~n~l~~--l~~-~~~~~l~~L   99 (680)
T 1ziw_A           23 LPTNITVLNLTHNQLRRLPAANFTRYSQLTSLDVGFNTISKLEPELCQKLPMLKVLNLQHNELSQ--LSD-KTFAFCTNL   99 (680)
T ss_dssp             SCTTCSEEECCSSCCCCCCGGGGGGGTTCSEEECCSSCCCCCCTTHHHHCTTCCEEECCSSCCCC--CCT-TTTTTCTTC
T ss_pred             cCCCCcEEECCCCCCCCcCHHHHhCCCcCcEEECCCCccCccCHHHHhcccCcCEEECCCCccCc--cCh-hhhccCCCC
Confidence            346788998877653322221 2367899999999887777778889999999999999887642  211 237889999


Q ss_pred             cEEEeccCCCCCcc--cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCch-hhc--CCCCCc
Q 042541          604 KKIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPD-GLC--DIVSME  678 (695)
Q Consensus       604 ~~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~-~i~--~L~~L~  678 (695)
                      ++|++++|.+..+|  .++++++|++|++++|.++..++..+.    .+++|++|++++|. +..+|. .++  .+++|+
T Consensus       100 ~~L~L~~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~~~~~~~----~l~~L~~L~L~~n~-l~~~~~~~~~~~~~~~L~  174 (680)
T 1ziw_A          100 TELHLMSNSIQKIKNNPFVKQKNLITLDLSHNGLSSTKLGTQV----QLENLQELLLSNNK-IQALKSEELDIFANSSLK  174 (680)
T ss_dssp             SEEECCSSCCCCCCSCTTTTCTTCCEEECCSSCCSCCCCCSSS----CCTTCCEEECCSSC-CCCBCHHHHGGGTTCEES
T ss_pred             CEEECCCCccCccChhHccccCCCCEEECCCCcccccCchhhc----ccccCCEEEccCCc-ccccCHHHhhcccccccc
Confidence            99999999998777  789999999999999999888887665    89999999999975 455554 343  568999


Q ss_pred             eeecccccCCCCCCC
Q 042541          679 KLRITNCHRLSALPE  693 (695)
Q Consensus       679 ~L~l~~~~~l~~lP~  693 (695)
                      +|++++|. +..+|+
T Consensus       175 ~L~L~~n~-l~~~~~  188 (680)
T 1ziw_A          175 KLELSSNQ-IKEFSP  188 (680)
T ss_dssp             EEECTTCC-CCCBCT
T ss_pred             EEECCCCc-ccccCh
Confidence            99999976 555543

>3j0a_A TOLL-like receptor 5; membrane protein, leucine-rich repeat, asymmetric homodimer, glycoprotein, immune system; HET: NAG FUC; 26.00A {Homo sapiens}

Probab=99.15  E-value=1.8e-10  Score=134.95  Aligned_cols=139  Identities=11%  Similarity=0.102  Sum_probs=112.0

Q ss_pred             CCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCc-c-cccccccc
Q 042541          548 QGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNS-L-ATVRMNHL  625 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~l-p-~i~~l~~L  625 (695)
                      .+++++.|.|+.+......|..|.++++|++|++++|... ..+ .+..+++|++|++|+|++|.+..+ | .++++++|
T Consensus        22 lp~~l~~LdLs~N~i~~i~~~~~~~l~~L~~LdLs~n~~~-~~i-~~~~f~~L~~L~~L~Ls~N~l~~~~p~~~~~l~~L   99 (844)
T 3j0a_A           22 VLNTTERLLLSFNYIRTVTASSFPFLEQLQLLELGSQYTP-LTI-DKEAFRNLPNLRILDLGSSKIYFLHPDAFQGLFHL   99 (844)
T ss_dssp             SCTTCCEEEEESCCCCEECSSSCSSCCSCSEEEECTTCCC-CEE-CTTTTSSCTTCCEEECTTCCCCEECTTSSCSCSSC
T ss_pred             CCCCcCEEECCCCcCCccChhHCcccccCeEEeCCCCCCc-ccc-CHHHhcCCCCCCEEECCCCcCcccCHhHccCCccc
Confidence            5678999999999887778889999999999999998552 122 123488999999999999999966 6 99999999


Q ss_pred             cEEeeccccCCccccc--chhhhcccCCCccEEecccccccccCc-hhhcCCCCCceeecccccCCCCCC
Q 042541          626 QKVSLVMCNVGQVFRN--STFRISDAFPNLLEMDIDYCNDLIELP-DGLCDIVSMEKLRITNCHRLSALP  692 (695)
Q Consensus       626 ~~L~l~~~~i~~~~~~--~~~~l~~~l~~L~~L~l~~c~~l~~lP-~~i~~L~~L~~L~l~~~~~l~~lP  692 (695)
                      ++|+|++|.+++..+.  .+.    .+++|++|++++|......| ..++++++|++|++++|..-+..|
T Consensus       100 ~~L~Ls~n~l~~~~~~~~~~~----~L~~L~~L~Ls~N~l~~~~~~~~~~~L~~L~~L~Ls~N~i~~~~~  165 (844)
T 3j0a_A          100 FELRLYFCGLSDAVLKDGYFR----NLKALTRLDLSKNQIRSLYLHPSFGKLNSLKSIDFSSNQIFLVCE  165 (844)
T ss_dssp             CCEECTTCCCSSCCSTTCCCS----SCSSCCEEEEESCCCCCCCCCGGGGTCSSCCEEEEESSCCCCCCS
T ss_pred             CEeeCcCCCCCcccccCcccc----ccCCCCEEECCCCcccccccchhHhhCCCCCEEECCCCcCCeeCH
Confidence            9999999999874332  244    89999999999976444333 579999999999999976433333

>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG; 2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A*

Probab=99.15  E-value=1.2e-10  Score=133.33  Aligned_cols=130  Identities=15%  Similarity=0.159  Sum_probs=77.9

Q ss_pred             CceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--cccccccccE
Q 042541          550 PEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNHLQK  627 (695)
Q Consensus       550 ~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L~~  627 (695)
                      ++++.|.++.+......+..|.++++|++|++++|.+...   .+..++.+++|++|+|++|.+..+|  .++++++|++
T Consensus        25 ~~l~~L~Ls~n~l~~~~~~~~~~l~~L~~L~Ls~n~l~~~---~~~~~~~l~~L~~L~L~~n~l~~l~~~~~~~l~~L~~  101 (680)
T 1ziw_A           25 TNITVLNLTHNQLRRLPAANFTRYSQLTSLDVGFNTISKL---EPELCQKLPMLKVLNLQHNELSQLSDKTFAFCTNLTE  101 (680)
T ss_dssp             TTCSEEECCSSCCCCCCGGGGGGGTTCSEEECCSSCCCCC---CTTHHHHCTTCCEEECCSSCCCCCCTTTTTTCTTCSE
T ss_pred             CCCcEEECCCCCCCCcCHHHHhCCCcCcEEECCCCccCcc---CHHHHhcccCcCEEECCCCccCccChhhhccCCCCCE
Confidence            4566666666554444444566666666666666554211   1122556666666666666666666  4666666666


Q ss_pred             EeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeeccccc
Q 042541          628 VSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCH  686 (695)
Q Consensus       628 L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~  686 (695)
                      |++++|.++.+++..+.    .+++|++|++++|......|..++++++|++|++++|.
T Consensus       102 L~L~~n~l~~~~~~~~~----~l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~n~  156 (680)
T 1ziw_A          102 LHLMSNSIQKIKNNPFV----KQKNLITLDLSHNGLSSTKLGTQVQLENLQELLLSNNK  156 (680)
T ss_dssp             EECCSSCCCCCCSCTTT----TCTTCCEEECCSSCCSCCCCCSSSCCTTCCEEECCSSC
T ss_pred             EECCCCccCccChhHcc----ccCCCCEEECCCCcccccCchhhcccccCCEEEccCCc
Confidence            66666666666655544    66666666666654444444556666666666666654

>4b8c_D Glucose-repressible alcohol dehydrogenase transcr effector; hydrolase-cell cycle complex; 3.41A {Saccharomyces cerevisiae S288C}

Probab=99.14  E-value=1.6e-11  Score=140.67  Aligned_cols=137  Identities=15%  Similarity=0.035  Sum_probs=105.9

Q ss_pred             CCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc-ccccccccc
Q 042541          548 QGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL-ATVRMNHLQ  626 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp-~i~~l~~L~  626 (695)
                      .+++|+.|.|+.+... .+|..+.++++|++|+|++|.+.  .++  +.++.|++|++|+|++|.++.+| .+++|++|+
T Consensus       222 ~l~~L~~L~Ls~n~l~-~l~~~~~~l~~L~~L~Ls~N~l~--~lp--~~~~~l~~L~~L~Ls~N~l~~lp~~~~~l~~L~  296 (727)
T 4b8c_D          222 DDQLWHALDLSNLQIF-NISANIFKYDFLTRLYLNGNSLT--ELP--AEIKNLSNLRVLDLSHNRLTSLPAELGSCFQLK  296 (727)
T ss_dssp             CCCCCCEEECTTSCCS-CCCGGGGGCCSCSCCBCTTSCCS--CCC--GGGGGGTTCCEEECTTSCCSSCCSSGGGGTTCS
T ss_pred             cCCCCcEEECCCCCCC-CCChhhcCCCCCCEEEeeCCcCc--ccC--hhhhCCCCCCEEeCcCCcCCccChhhcCCCCCC
Confidence            5678888888777654 77877778999999999998774  332  34889999999999999999999 999999999


Q ss_pred             EEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCC-CCceeecccccCCCCCCCC
Q 042541          627 KVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIV-SMEKLRITNCHRLSALPEG  694 (695)
Q Consensus       627 ~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~-~L~~L~l~~~~~l~~lP~~  694 (695)
                      +|+|++|.++.+|+.+.     .|++|++|+|++|...+.+|..++.+. .+..|+|++|...+.+|..
T Consensus       297 ~L~L~~N~l~~lp~~~~-----~l~~L~~L~L~~N~l~~~~p~~~~~~~~~~~~l~l~~N~l~~~~p~~  360 (727)
T 4b8c_D          297 YFYFFDNMVTTLPWEFG-----NLCNLQFLGVEGNPLEKQFLKILTEKSVTGLIFYLRDNRPEIPLPHE  360 (727)
T ss_dssp             EEECCSSCCCCCCSSTT-----SCTTCCCEECTTSCCCSHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
T ss_pred             EEECCCCCCCccChhhh-----cCCCccEEeCCCCccCCCChHHHhhcchhhhHHhhccCcccCcCccc
Confidence            99999999998877744     899999999999876666776665432 1223556665555555543

>3a79_B TLR6, VLRB.59, TOLL-like receptor 6, variable lymphocyte recepto; diacyl lipopeptide, innate immunity, Leu repeat, cell membrane, cytoplasmic vesicle; HET: PXS NAG BMA NDG; 2.90A {Mus musculus}

Probab=99.13  E-value=2.6e-10  Score=127.45  Aligned_cols=135  Identities=11%  Similarity=0.216  Sum_probs=74.4

Q ss_pred             CCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCc-ccccccCCCCcEEEeccCCCCC-cc--cccccc
Q 042541          548 QGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNN-FRVLSALSKLKKIRLEHVSLPN-SL--ATVRMN  623 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~-~~~l~~l~~L~~L~L~~~~l~~-lp--~i~~l~  623 (695)
                      .+++|+.|.++.+......|..+.++++|++|++++|.+..  ++. +..++.+++|++|++++|.+.. +|  .+..++
T Consensus       351 ~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~L~~N~l~~--~~~~~~~~~~l~~L~~L~l~~N~l~~~~~~~~~~~l~  428 (562)
T 3a79_B          351 SPSSFTFLNFTQNVFTDSVFQGCSTLKRLQTLILQRNGLKN--FFKVALMTKNMSSLETLDVSLNSLNSHAYDRTCAWAE  428 (562)
T ss_dssp             SCCCCCEEECCSSCCCTTTTTTCCSCSSCCEEECCSSCCCB--TTHHHHTTTTCTTCCEEECTTSCCBSCCSSCCCCCCT
T ss_pred             CCCCceEEECCCCccccchhhhhcccCCCCEEECCCCCcCC--cccchhhhcCCCCCCEEECCCCcCCCccChhhhcCcc
Confidence            45566666666665555556666666666666666655421  111 1124556666666666666654 55  355566


Q ss_pred             cccEEeeccccCCcccccchhhhcccC-CCccEEecccccccccCchhhcCCCCCceeecccccCCCCCCC
Q 042541          624 HLQKVSLVMCNVGQVFRNSTFRISDAF-PNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPE  693 (695)
Q Consensus       624 ~L~~L~l~~~~i~~~~~~~~~~l~~~l-~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~~l~~lP~  693 (695)
                      +|++|++++|.+++..+.       .+ ++|++|++++| .+..+|.++..+++|++|++++|. +..+|.
T Consensus       429 ~L~~L~l~~n~l~~~~~~-------~l~~~L~~L~L~~N-~l~~ip~~~~~l~~L~~L~L~~N~-l~~l~~  490 (562)
T 3a79_B          429 SILVLNLSSNMLTGSVFR-------CLPPKVKVLDLHNN-RIMSIPKDVTHLQALQELNVASNQ-LKSVPD  490 (562)
T ss_dssp             TCCEEECCSSCCCGGGGS-------SCCTTCSEEECCSS-CCCCCCTTTTSSCCCSEEECCSSC-CCCCCT
T ss_pred             cCCEEECCCCCCCcchhh-------hhcCcCCEEECCCC-cCcccChhhcCCCCCCEEECCCCC-CCCCCH
Confidence            666666666655432222       22 45666666654 445566555566666666666543 555554

>4fmz_A Internalin; leucine rich repeat, structural genomic center for structural genomics, JCSG, protein structure INI PSI-biology; HET: MSE; 1.91A {Listeria monocytogenes serotype 4B}

Probab=99.12  E-value=2.5e-10  Score=119.15  Aligned_cols=126  Identities=13%  Similarity=0.166  Sum_probs=84.0

Q ss_pred             CCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcccccccccccE
Q 042541          548 QGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSLATVRMNHLQK  627 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp~i~~l~~L~~  627 (695)
                      .+++|+.|.++.+.... +|. +..+++|++|++++|.+..     ++.+..+++|++|++++|.++.+|.+..+++|++
T Consensus       219 ~~~~L~~L~l~~n~l~~-~~~-~~~l~~L~~L~l~~n~l~~-----~~~~~~l~~L~~L~l~~n~l~~~~~~~~l~~L~~  291 (347)
T 4fmz_A          219 NMTRLNSLKIGNNKITD-LSP-LANLSQLTWLEIGTNQISD-----INAVKDLTKLKMLNVGSNQISDISVLNNLSQLNS  291 (347)
T ss_dssp             GCTTCCEEECCSSCCCC-CGG-GTTCTTCCEEECCSSCCCC-----CGGGTTCTTCCEEECCSSCCCCCGGGGGCTTCSE
T ss_pred             cCCcCCEEEccCCccCC-Ccc-hhcCCCCCEEECCCCccCC-----ChhHhcCCCcCEEEccCCccCCChhhcCCCCCCE
Confidence            55667777776664333 222 6677777777777765532     2336677777777777777776666667777777


Q ss_pred             EeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeeccccc
Q 042541          628 VSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCH  686 (695)
Q Consensus       628 L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~  686 (695)
                      |++++|.++..++..+.    .+++|++|++++|. +..+|. +..+++|+.|++++|+
T Consensus       292 L~L~~n~l~~~~~~~l~----~l~~L~~L~L~~n~-l~~~~~-~~~l~~L~~L~l~~N~  344 (347)
T 4fmz_A          292 LFLNNNQLGNEDMEVIG----GLTNLTTLFLSQNH-ITDIRP-LASLSKMDSADFANQV  344 (347)
T ss_dssp             EECCSSCCCGGGHHHHH----TCTTCSEEECCSSS-CCCCGG-GGGCTTCSEESSSCC-
T ss_pred             EECcCCcCCCcChhHhh----ccccCCEEEccCCc-cccccC-hhhhhccceeehhhhc
Confidence            77777777766665555    67777777777764 455554 7777777777777765

>4fmz_A Internalin; leucine rich repeat, structural genomic center for structural genomics, JCSG, protein structure INI PSI-biology; HET: MSE; 1.91A {Listeria monocytogenes serotype 4B}

Probab=99.11  E-value=2.4e-10  Score=119.29  Aligned_cols=151  Identities=12%  Similarity=0.129  Sum_probs=117.7

Q ss_pred             ccceEEeeecCCcccCCCCCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEE
Q 042541          527 NNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKI  606 (695)
Q Consensus       527 ~~~r~l~~~~~~~~~~~~~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L  606 (695)
                      ...+.+.+..+... .......+++|+.|.+..+......+  +..+++|++|++++|.+..     .+.+..+++|++|
T Consensus       177 ~~L~~L~l~~n~l~-~~~~~~~l~~L~~L~l~~n~l~~~~~--~~~~~~L~~L~l~~n~l~~-----~~~~~~l~~L~~L  248 (347)
T 4fmz_A          177 TDLYSLSLNYNQIE-DISPLASLTSLHYFTAYVNQITDITP--VANMTRLNSLKIGNNKITD-----LSPLANLSQLTWL  248 (347)
T ss_dssp             TTCSEEECTTSCCC-CCGGGGGCTTCCEEECCSSCCCCCGG--GGGCTTCCEEECCSSCCCC-----CGGGTTCTTCCEE
T ss_pred             CCCCEEEccCCccc-ccccccCCCccceeecccCCCCCCch--hhcCCcCCEEEccCCccCC-----CcchhcCCCCCEE
Confidence            45666766554322 11223467889999998875544333  7889999999999987642     2227899999999


Q ss_pred             EeccCCCCCcccccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeeccccc
Q 042541          607 RLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCH  686 (695)
Q Consensus       607 ~L~~~~l~~lp~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~  686 (695)
                      ++++|.++.++.+..+++|++|++++|.++.++ .. .    .+++|+.|++++|......|..++.+++|++|++++|+
T Consensus       249 ~l~~n~l~~~~~~~~l~~L~~L~l~~n~l~~~~-~~-~----~l~~L~~L~L~~n~l~~~~~~~l~~l~~L~~L~L~~n~  322 (347)
T 4fmz_A          249 EIGTNQISDINAVKDLTKLKMLNVGSNQISDIS-VL-N----NLSQLNSLFLNNNQLGNEDMEVIGGLTNLTTLFLSQNH  322 (347)
T ss_dssp             ECCSSCCCCCGGGTTCTTCCEEECCSSCCCCCG-GG-G----GCTTCSEEECCSSCCCGGGHHHHHTCTTCSEEECCSSS
T ss_pred             ECCCCccCCChhHhcCCCcCEEEccCCccCCCh-hh-c----CCCCCCEEECcCCcCCCcChhHhhccccCCEEEccCCc
Confidence            999999998888889999999999999998863 33 3    89999999999987666677889999999999999987


Q ss_pred             CCCCCC
Q 042541          687 RLSALP  692 (695)
Q Consensus       687 ~l~~lP  692 (695)
                       +..+|
T Consensus       323 -l~~~~  327 (347)
T 4fmz_A          323 -ITDIR  327 (347)
T ss_dssp             -CCCCG
T ss_pred             -ccccc
Confidence             55554

>2o6r_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 2.30A {Eptatretus burgeri}

Probab=99.10  E-value=4.1e-10  Score=105.19  Aligned_cols=106  Identities=17%  Similarity=0.227  Sum_probs=70.9

Q ss_pred             CCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--cccccccccEEeeccccCCcccccchhhhcccCC
Q 042541          574 DELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFP  651 (695)
Q Consensus       574 ~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~  651 (695)
                      ++|+.|++++|.+..  ++ ...++.+++|++|++++|.++.+|  .++.+++|++|++++|.++.+++..+.    .++
T Consensus        28 ~~l~~L~l~~n~l~~--~~-~~~~~~l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~N~l~~~~~~~~~----~l~  100 (177)
T 2o6r_A           28 SSATRLELESNKLQS--LP-HGVFDKLTQLTKLSLSQNQIQSLPDGVFDKLTKLTILYLHENKLQSLPNGVFD----KLT  100 (177)
T ss_dssp             TTCSEEECCSSCCCC--CC-TTTTTTCTTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTT----TCT
T ss_pred             CCCcEEEeCCCcccE--eC-HHHhcCcccccEEECCCCcceEeChhHccCCCccCEEECCCCCccccCHHHhh----CCc
Confidence            567777777766531  11 112566777777777777777666  456777777777777777777766554    677


Q ss_pred             CccEEecccccccccCchh-hcCCCCCceeecccccC
Q 042541          652 NLLEMDIDYCNDLIELPDG-LCDIVSMEKLRITNCHR  687 (695)
Q Consensus       652 ~L~~L~l~~c~~l~~lP~~-i~~L~~L~~L~l~~~~~  687 (695)
                      +|++|++++| .+..+|.. +..+++|++|++++|+.
T Consensus       101 ~L~~L~l~~N-~l~~~~~~~~~~l~~L~~L~l~~N~~  136 (177)
T 2o6r_A          101 QLKELALDTN-QLKSVPDGIFDRLTSLQKIWLHTNPW  136 (177)
T ss_dssp             TCCEEECCSS-CCSCCCTTTTTTCTTCCEEECCSSCB
T ss_pred             ccCEEECcCC-cceEeCHHHhcCCcccCEEEecCCCe
Confidence            7777777775 45666665 46677777777777663

>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=99.10  E-value=2.3e-10  Score=127.08  Aligned_cols=104  Identities=17%  Similarity=0.145  Sum_probs=52.0

Q ss_pred             CcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc-cccccccccEEeeccccCCcccccchhhhcccCCCcc
Q 042541          576 LKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL-ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLL  654 (695)
Q Consensus       576 Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp-~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~  654 (695)
                      |++|++++|.+..  +   +.++.+++|++|+|++|.++.+| .+++|++|++|+|++|.++++| .+.     .|++|+
T Consensus       443 L~~L~Ls~n~l~~--l---p~~~~l~~L~~L~Ls~N~l~~lp~~~~~l~~L~~L~Ls~N~l~~lp-~l~-----~l~~L~  511 (567)
T 1dce_A          443 VRVLHLAHKDLTV--L---CHLEQLLLVTHLDLSHNRLRALPPALAALRCLEVLQASDNALENVD-GVA-----NLPRLQ  511 (567)
T ss_dssp             CSEEECTTSCCSS--C---CCGGGGTTCCEEECCSSCCCCCCGGGGGCTTCCEEECCSSCCCCCG-GGT-----TCSSCC
T ss_pred             ceEEEecCCCCCC--C---cCccccccCcEeecCcccccccchhhhcCCCCCEEECCCCCCCCCc-ccC-----CCCCCc
Confidence            4555555544421  1   12455555555555555555555 5555555555555555555543 222     455555


Q ss_pred             EEecccccccccC--chhhcCCCCCceeecccccCCCCCC
Q 042541          655 EMDIDYCNDLIEL--PDGLCDIVSMEKLRITNCHRLSALP  692 (695)
Q Consensus       655 ~L~l~~c~~l~~l--P~~i~~L~~L~~L~l~~~~~l~~lP  692 (695)
                      +|+|++| .+..+  |..++.|++|+.|+|++|+ +..+|
T Consensus       512 ~L~Ls~N-~l~~~~~p~~l~~l~~L~~L~L~~N~-l~~~~  549 (567)
T 1dce_A          512 ELLLCNN-RLQQSAAIQPLVSCPRLVLLNLQGNS-LCQEE  549 (567)
T ss_dssp             EEECCSS-CCCSSSTTGGGGGCTTCCEEECTTSG-GGGSS
T ss_pred             EEECCCC-CCCCCCCcHHHhcCCCCCEEEecCCc-CCCCc
Confidence            5555553 23333  5555555555555555544 43333

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=99.08  E-value=4.3e-09  Score=108.63  Aligned_cols=170  Identities=17%  Similarity=0.152  Sum_probs=109.5

Q ss_pred             CCCCCCCcchHHHHHHHHHc-----CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHH
Q 042541          165 PVISPGLDVPLKELKMELFK-----DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKV  239 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~-----~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i  239 (695)
                      -+.++|++..++.+..++..     .....|.|+|++|+|||++|+.+++  ...    ...++++.+......++    
T Consensus        11 ~~~~ig~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~i~~--~~~----~~~~~~~~~~~~~~~~l----   80 (324)
T 1hqc_A           11 LDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAH--ELG----VNLRVTSGPAIEKPGDL----   80 (324)
T ss_dssp             TTTCCSCHHHHHHHHHHHHHHHHHCSCCCCCEEECCTTCCCHHHHHHHHH--HHT----CCEEEECTTTCCSHHHH----
T ss_pred             HHHhhCHHHHHHHHHHHHHHHHccCCCCCcEEEECCCCCCHHHHHHHHHH--HhC----CCEEEEeccccCChHHH----
Confidence            45689999999998887762     3346789999999999999999987  332    22445554433222221    


Q ss_pred             HHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChHH----HhhhccC------------------CCCC
Q 042541          240 LHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSESL----LQKLGFQ------------------LPDY  297 (695)
Q Consensus       240 ~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~~----~~~l~~~------------------~~gs  297 (695)
                                           ...+..-..+..+|++||+.......    +..+...                  .++.
T Consensus        81 ---------------------~~~l~~~~~~~~~l~lDEi~~l~~~~~~~L~~~l~~~~~~~v~~~~~~~~~~~~~~~~~  139 (324)
T 1hqc_A           81 ---------------------AAILANSLEEGDILFIDEIHRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRF  139 (324)
T ss_dssp             ---------------------HHHHTTTCCTTCEEEETTTTSCCHHHHHHHHHHHHHSEEEECCSSSSSCCCEEEECCCC
T ss_pred             ---------------------HHHHHHhccCCCEEEEECCcccccchHHHHHHHHHhhhhHHhccccccccccccCCCCE
Confidence                                 12221101356789999998776432    1111111                  1245


Q ss_pred             EEEEEcCCCC-------CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHHHhh
Q 042541          298 KILVTSRSEF-------PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGGSL  368 (695)
Q Consensus       298 ~iivTtR~~~-------~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~~~L  368 (695)
                      .+|.||....       ...+..+.+.+++.++..+++...+.....   .-..+....|++.++|.|..+..+...+
T Consensus       140 ~~i~~t~~~~~~~~~l~~R~~~~i~l~~~~~~e~~~~l~~~~~~~~~---~~~~~~~~~l~~~~~G~~r~l~~~l~~~  214 (324)
T 1hqc_A          140 TLIGATTRPGLITAPLLSRFGIVEHLEYYTPEELAQGVMRDARLLGV---RITEEAALEIGRRSRGTMRVAKRLFRRV  214 (324)
T ss_dssp             EEEEEESCCSSCSCSTTTTCSCEEECCCCCHHHHHHHHHHHHHTTTC---CCCHHHHHHHHHHSCSCHHHHHHHHHHH
T ss_pred             EEEEeCCCcccCCHHHHhcccEEEecCCCCHHHHHHHHHHHHHhcCC---CCCHHHHHHHHHHccCCHHHHHHHHHHH
Confidence            6776666441       122347899999999999999887654322   1236778999999999998887665543

>3o53_A Protein LRIM1, AGAP006348-PA; leucine-rich repeat, protein binding; HET: NAG; 2.00A {Anopheles gambiae}

Probab=99.08  E-value=4.9e-11  Score=122.92  Aligned_cols=154  Identities=13%  Similarity=0.003  Sum_probs=122.0

Q ss_pred             CccceEEeeecCCcccCCC-CCCCCCceEEEEEEccCccccCChhh-cCCCCCcEEEEcccCCCCcccCcccccccCCCC
Q 042541          526 PNNASLLSISTDETFSSNW-PDMQGPEVKVVVLNIRTKKYVLPDFL-QKMDELKVLIVTNYGFSPAELNNFRVLSALSKL  603 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~~~~-~~~~~~~l~~L~l~~~~~~~~~p~~~-~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L  603 (695)
                      ....+.+.+..+....... ....+++|+.|.++.+......|..+ ..+++|++|++++|.+..     .+....+++|
T Consensus       119 ~~~L~~L~l~~N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~~~l~~L~~L~L~~N~l~~-----~~~~~~l~~L  193 (317)
T 3o53_A          119 GQGKKNIYLANNKITMLRDLDEGCRSRVQYLDLKLNEIDTVNFAELAASSDTLEHLNLQYNFIYD-----VKGQVVFAKL  193 (317)
T ss_dssp             CSSCEEEECCSSCCCSGGGBCTGGGSSEEEEECTTSCCCEEEGGGGGGGTTTCCEEECTTSCCCE-----EECCCCCTTC
T ss_pred             cCCCCEEECCCCCCCCccchhhhccCCCCEEECCCCCCCcccHHHHhhccCcCCEEECCCCcCcc-----cccccccccC
Confidence            3457788877654322211 12357899999999987766666655 578999999999987742     2334568999


Q ss_pred             cEEEeccCCCCCcc-cccccccccEEeeccccCCcccccchhhhcccCCCccEEeccccccc-ccCchhhcCCCCCceee
Q 042541          604 KKIRLEHVSLPNSL-ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDL-IELPDGLCDIVSMEKLR  681 (695)
Q Consensus       604 ~~L~L~~~~l~~lp-~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l-~~lP~~i~~L~~L~~L~  681 (695)
                      ++|+|++|.++.+| .+..+++|++|++++|.++.+|+...     .+++|+.|++++|... ..+|..++.+++|+.|+
T Consensus       194 ~~L~Ls~N~l~~l~~~~~~l~~L~~L~L~~N~l~~l~~~~~-----~l~~L~~L~l~~N~~~~~~~~~~~~~~~~L~~l~  268 (317)
T 3o53_A          194 KTLDLSSNKLAFMGPEFQSAAGVTWISLRNNKLVLIEKALR-----FSQNLEHFDLRGNGFHCGTLRDFFSKNQRVQTVA  268 (317)
T ss_dssp             CEEECCSSCCCEECGGGGGGTTCSEEECTTSCCCEECTTCC-----CCTTCCEEECTTCCCBHHHHHHHHHTCHHHHHHH
T ss_pred             CEEECCCCcCCcchhhhcccCcccEEECcCCcccchhhHhh-----cCCCCCEEEccCCCccCcCHHHHHhccccceEEE
Confidence            99999999999999 99999999999999999998877654     8999999999998655 57888899999999999


Q ss_pred             cccccCCC
Q 042541          682 ITNCHRLS  689 (695)
Q Consensus       682 l~~~~~l~  689 (695)
                      +++|+.+.
T Consensus       269 l~~~~~l~  276 (317)
T 3o53_A          269 KQTVKKLT  276 (317)
T ss_dssp             HHHHHHHH
T ss_pred             CCCchhcc
Confidence            99665444

>2z7x_B TOLL-like receptor 1, variable lymphocyte recepto; TLR2, TLR1, lipopeptide, innate immunity, glycoPro immune response, inflammatory response, leucine-rich repeat membrane, receptor; HET: NAG NDG MAN BMA PCJ; 2.10A {Homo sapiens}

Probab=99.07  E-value=6.1e-10  Score=123.14  Aligned_cols=153  Identities=14%  Similarity=0.168  Sum_probs=121.5

Q ss_pred             CccceEEeeecCCcccCCCCC-CCCCceEEEEEEccCccc--cCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCC
Q 042541          526 PNNASLLSISTDETFSSNWPD-MQGPEVKVVVLNIRTKKY--VLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSK  602 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~~~~~~-~~~~~l~~L~l~~~~~~~--~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~  602 (695)
                      ....+++.+.++......+.. ..+++|+.|.++.+....  .+|..+..+++|++|++++|.+... ++. ..+..+++
T Consensus       323 l~~L~~L~Ls~n~l~~~~~~~~~~l~~L~~L~L~~N~l~~l~~~~~~~~~l~~L~~L~Ls~N~l~~~-l~~-~~~~~l~~  400 (520)
T 2z7x_B          323 ISPFLHLDFSNNLLTDTVFENCGHLTELETLILQMNQLKELSKIAEMTTQMKSLQQLDISQNSVSYD-EKK-GDCSWTKS  400 (520)
T ss_dssp             CCCCCEEECCSSCCCTTTTTTCCCCSSCCEEECCSSCCCBHHHHHHHHTTCTTCCEEECCSSCCBCC-GGG-CSCCCCTT
T ss_pred             CCcccEEEeECCccChhhhhhhccCCCCCEEEccCCccCccccchHHHhhCCCCCEEECCCCcCCcc-ccc-chhccCcc
Confidence            456778888766543322222 378999999999986654  6778899999999999999877421 211 13678899


Q ss_pred             CcEEEeccCCCC-Ccc-cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchh-hcCCCCCce
Q 042541          603 LKKIRLEHVSLP-NSL-ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDG-LCDIVSMEK  679 (695)
Q Consensus       603 L~~L~L~~~~l~-~lp-~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~-i~~L~~L~~  679 (695)
                      |++|++++|.++ .+| .+.  ++|++|++++|.++.+|+..+     .+++|++|++++| .+..+|.. +..+++|+.
T Consensus       401 L~~L~Ls~N~l~~~~~~~l~--~~L~~L~Ls~N~l~~ip~~~~-----~l~~L~~L~L~~N-~l~~l~~~~~~~l~~L~~  472 (520)
T 2z7x_B          401 LLSLNMSSNILTDTIFRCLP--PRIKVLDLHSNKIKSIPKQVV-----KLEALQELNVASN-QLKSVPDGIFDRLTSLQK  472 (520)
T ss_dssp             CCEEECCSSCCCGGGGGSCC--TTCCEEECCSSCCCCCCGGGG-----GCTTCCEEECCSS-CCCCCCTTTTTTCTTCCE
T ss_pred             CCEEECcCCCCCcchhhhhc--ccCCEEECCCCcccccchhhh-----cCCCCCEEECCCC-cCCccCHHHhccCCcccE
Confidence            999999999997 566 543  799999999999998888776     8999999999997 57799987 899999999


Q ss_pred             eecccccCC
Q 042541          680 LRITNCHRL  688 (695)
Q Consensus       680 L~l~~~~~l  688 (695)
                      |++++|+..
T Consensus       473 L~l~~N~~~  481 (520)
T 2z7x_B          473 IWLHTNPWD  481 (520)
T ss_dssp             EECCSSCBC
T ss_pred             EECcCCCCc
Confidence            999998743

>1xeu_A Internalin C; cellular invasion, leucine-rich repeat, cell invasion; 2.05A {Listeria monocytogenes}

Probab=99.06  E-value=5.2e-10  Score=111.75  Aligned_cols=127  Identities=18%  Similarity=0.119  Sum_probs=103.6

Q ss_pred             CCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcccccccccccE
Q 042541          548 QGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSLATVRMNHLQK  627 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp~i~~l~~L~~  627 (695)
                      .+++|+.|.++.+.. ..+| .+..+++|++|++++|.+..  +   +.++.+++|++|++++|.++.+|.+.. .+|++
T Consensus        39 ~l~~L~~L~l~~n~i-~~l~-~l~~l~~L~~L~L~~N~i~~--~---~~l~~l~~L~~L~L~~N~l~~l~~~~~-~~L~~  110 (263)
T 1xeu_A           39 ELSGVQNFNGDNSNI-QSLA-GMQFFTNLKELHLSHNQISD--L---SPLKDLTKLEELSVNRNRLKNLNGIPS-ACLSR  110 (263)
T ss_dssp             HHTTCSEEECTTSCC-CCCT-TGGGCTTCCEEECCSSCCCC--C---GGGTTCSSCCEEECCSSCCSCCTTCCC-SSCCE
T ss_pred             hcCcCcEEECcCCCc-ccch-HHhhCCCCCEEECCCCccCC--C---hhhccCCCCCEEECCCCccCCcCcccc-CcccE
Confidence            467889999987743 3455 68899999999999987742  2   227899999999999999999883333 99999


Q ss_pred             EeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccccCCCCC
Q 042541          628 VSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSAL  691 (695)
Q Consensus       628 L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~~l~~l  691 (695)
                      |++++|.++.++ ...     .+++|+.|++++| .+..+| .++.+++|++|++++|. +..+
T Consensus       111 L~L~~N~l~~~~-~l~-----~l~~L~~L~Ls~N-~i~~~~-~l~~l~~L~~L~L~~N~-i~~~  165 (263)
T 1xeu_A          111 LFLDNNELRDTD-SLI-----HLKNLEILSIRNN-KLKSIV-MLGFLSKLEVLDLHGNE-ITNT  165 (263)
T ss_dssp             EECCSSCCSBSG-GGT-----TCTTCCEEECTTS-CCCBCG-GGGGCTTCCEEECTTSC-CCBC
T ss_pred             EEccCCccCCCh-hhc-----CcccccEEECCCC-cCCCCh-HHccCCCCCEEECCCCc-Ccch
Confidence            999999999864 333     8999999999996 577887 69999999999999976 5544

>4g8a_A TOLL-like receptor 4; leucine rich repeat MD-2 related lipid recognition, receptor immunity, lipid binding, glycosylation, immune system; HET: NAG LP4 LP5 DAO MYR KDO; 2.40A {Homo sapiens} PDB: 3fxi_A*

Probab=99.06  E-value=2.6e-10  Score=129.29  Aligned_cols=133  Identities=14%  Similarity=0.140  Sum_probs=103.7

Q ss_pred             CCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--cccccccc
Q 042541          548 QGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNHL  625 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L  625 (695)
                      .+++++.+.++.+......|..+..++.|++|++++|.......+  ..+..+++|++|+|++|.++.++  .++++++|
T Consensus       443 ~l~~l~~l~ls~n~l~~~~~~~~~~~~~L~~L~Ls~N~~~~~~~~--~~~~~l~~L~~L~Ls~N~L~~l~~~~f~~l~~L  520 (635)
T 4g8a_A          443 SLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLP--DIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSL  520 (635)
T ss_dssp             TCTTCCEEECTTSCCEECCTTTTTTCTTCCEEECTTCEEGGGEEC--SCCTTCTTCCEEECTTSCCCEECTTTTTTCTTC
T ss_pred             cccccccccccccccccccccccccchhhhhhhhhhcccccccCc--hhhhhccccCEEECCCCccCCcChHHHcCCCCC
Confidence            456667777766666666677778888888888887754221111  23778899999999999999765  88899999


Q ss_pred             cEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCC-CCCceeeccccc
Q 042541          626 QKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDI-VSMEKLRITNCH  686 (695)
Q Consensus       626 ~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L-~~L~~L~l~~~~  686 (695)
                      ++|+|++|+++.+++..+.    .+++|++|+|++|......|..+..+ ++|++|+|++|+
T Consensus       521 ~~L~Ls~N~l~~l~~~~~~----~l~~L~~L~Ls~N~l~~~~~~~l~~l~~~L~~L~L~~Np  578 (635)
T 4g8a_A          521 QVLNMSHNNFFSLDTFPYK----CLNSLQVLDYSLNHIMTSKKQELQHFPSSLAFLNLTQND  578 (635)
T ss_dssp             CEEECTTSCCCBCCCGGGT----TCTTCCEEECTTSCCCBCCSSCTTCCCTTCCEEECTTCC
T ss_pred             CEEECCCCcCCCCChhHHh----CCCCCCEEECCCCcCCCCCHHHHHhhhCcCCEEEeeCCC
Confidence            9999999999999888776    89999999999976555556678887 689999999876

>3a79_B TLR6, VLRB.59, TOLL-like receptor 6, variable lymphocyte recepto; diacyl lipopeptide, innate immunity, Leu repeat, cell membrane, cytoplasmic vesicle; HET: PXS NAG BMA NDG; 2.90A {Mus musculus}

Probab=99.05  E-value=6.2e-10  Score=124.32  Aligned_cols=153  Identities=14%  Similarity=0.186  Sum_probs=120.7

Q ss_pred             CccceEEeeecCCcccCCCCC-CCCCceEEEEEEccCccc--cCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCC
Q 042541          526 PNNASLLSISTDETFSSNWPD-MQGPEVKVVVLNIRTKKY--VLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSK  602 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~~~~~~-~~~~~l~~L~l~~~~~~~--~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~  602 (695)
                      ....+++.+..+......+.. ..+++|+.|.++.+....  .+|..+.++++|++|++++|.+... ++. ..+..+++
T Consensus       352 l~~L~~L~l~~n~l~~~~~~~~~~l~~L~~L~L~~N~l~~~~~~~~~~~~l~~L~~L~l~~N~l~~~-~~~-~~~~~l~~  429 (562)
T 3a79_B          352 PSSFTFLNFTQNVFTDSVFQGCSTLKRLQTLILQRNGLKNFFKVALMTKNMSSLETLDVSLNSLNSH-AYD-RTCAWAES  429 (562)
T ss_dssp             CCCCCEEECCSSCCCTTTTTTCCSCSSCCEEECCSSCCCBTTHHHHTTTTCTTCCEEECTTSCCBSC-CSS-CCCCCCTT
T ss_pred             CCCceEEECCCCccccchhhhhcccCCCCEEECCCCCcCCcccchhhhcCCCCCCEEECCCCcCCCc-cCh-hhhcCccc
Confidence            456778887766543322222 368999999999885544  4567789999999999999877421 211 13678899


Q ss_pred             CcEEEeccCCCC-Ccc-cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchh-hcCCCCCce
Q 042541          603 LKKIRLEHVSLP-NSL-ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDG-LCDIVSMEK  679 (695)
Q Consensus       603 L~~L~L~~~~l~-~lp-~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~-i~~L~~L~~  679 (695)
                      |++|++++|.++ .+| .+.  ++|++|+|++|.++.+|+..+     .+++|++|++++| .+..+|.. +..+++|+.
T Consensus       430 L~~L~l~~n~l~~~~~~~l~--~~L~~L~L~~N~l~~ip~~~~-----~l~~L~~L~L~~N-~l~~l~~~~~~~l~~L~~  501 (562)
T 3a79_B          430 ILVLNLSSNMLTGSVFRCLP--PKVKVLDLHNNRIMSIPKDVT-----HLQALQELNVASN-QLKSVPDGVFDRLTSLQY  501 (562)
T ss_dssp             CCEEECCSSCCCGGGGSSCC--TTCSEEECCSSCCCCCCTTTT-----SSCCCSEEECCSS-CCCCCCTTSTTTCTTCCC
T ss_pred             CCEEECCCCCCCcchhhhhc--CcCCEEECCCCcCcccChhhc-----CCCCCCEEECCCC-CCCCCCHHHHhcCCCCCE
Confidence            999999999997 555 443  799999999999999888877     8999999999996 57799998 999999999


Q ss_pred             eecccccCC
Q 042541          680 LRITNCHRL  688 (695)
Q Consensus       680 L~l~~~~~l  688 (695)
                      |++++|+..
T Consensus       502 L~l~~N~~~  510 (562)
T 3a79_B          502 IWLHDNPWD  510 (562)
T ss_dssp             EECCSCCBC
T ss_pred             EEecCCCcC
Confidence            999998744

>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=99.04  E-value=4.2e-10  Score=124.88  Aligned_cols=120  Identities=18%  Similarity=0.170  Sum_probs=94.9

Q ss_pred             eEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcccccccccccEEeec
Q 042541          552 VKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSLATVRMNHLQKVSLV  631 (695)
Q Consensus       552 l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp~i~~l~~L~~L~l~  631 (695)
                      |+.|.++.|... .+|. ++.+++|++|+|++|.+.  .++  +.++.|++|++|+|++|.++.+|.+++|++|++|+|+
T Consensus       443 L~~L~Ls~n~l~-~lp~-~~~l~~L~~L~Ls~N~l~--~lp--~~~~~l~~L~~L~Ls~N~l~~lp~l~~l~~L~~L~Ls  516 (567)
T 1dce_A          443 VRVLHLAHKDLT-VLCH-LEQLLLVTHLDLSHNRLR--ALP--PALAALRCLEVLQASDNALENVDGVANLPRLQELLLC  516 (567)
T ss_dssp             CSEEECTTSCCS-SCCC-GGGGTTCCEEECCSSCCC--CCC--GGGGGCTTCCEEECCSSCCCCCGGGTTCSSCCEEECC
T ss_pred             ceEEEecCCCCC-CCcC-ccccccCcEeecCccccc--ccc--hhhhcCCCCCEEECCCCCCCCCcccCCCCCCcEEECC
Confidence            455666555433 3676 889999999999998874  333  3588999999999999999998888899999999999


Q ss_pred             cccCCccc-ccchhhhcccCCCccEEecccccccccCchhh----cCCCCCceeec
Q 042541          632 MCNVGQVF-RNSTFRISDAFPNLLEMDIDYCNDLIELPDGL----CDIVSMEKLRI  682 (695)
Q Consensus       632 ~~~i~~~~-~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i----~~L~~L~~L~l  682 (695)
                      +|.++.++ |..+.    .|++|++|+|++| .+..+|+.+    ..+++|+.|++
T Consensus       517 ~N~l~~~~~p~~l~----~l~~L~~L~L~~N-~l~~~~~~~~~l~~~lp~L~~L~l  567 (567)
T 1dce_A          517 NNRLQQSAAIQPLV----SCPRLVLLNLQGN-SLCQEEGIQERLAEMLPSVSSILT  567 (567)
T ss_dssp             SSCCCSSSTTGGGG----GCTTCCEEECTTS-GGGGSSSCTTHHHHHCTTCSEEEC
T ss_pred             CCCCCCCCCcHHHh----cCCCCCEEEecCC-cCCCCccHHHHHHHHCcccCccCC
Confidence            99999985 55554    8999999999996 466666543    34889999875

>2r9u_A Variable lymphocyte receptor; adaptive immunity, VLR, leucine-rich repeat, LRR, system; 2.10A {Petromyzon marinus}

Probab=99.03  E-value=6.6e-10  Score=103.35  Aligned_cols=81  Identities=12%  Similarity=0.198  Sum_probs=39.7

Q ss_pred             CCCcEEEeccCCCCCcc--cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchh-hcCCCCC
Q 042541          601 SKLKKIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDG-LCDIVSM  677 (695)
Q Consensus       601 ~~L~~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~-i~~L~~L  677 (695)
                      .+|++|+|++|.+..++  .++++++|++|+|++|.++.+|+..+.    .+++|++|+|++| .+..+|.+ ++.+++|
T Consensus        33 ~~L~~L~Ls~N~l~~~~~~~~~~l~~L~~L~Ls~N~l~~i~~~~~~----~l~~L~~L~L~~N-~l~~l~~~~~~~l~~L  107 (174)
T 2r9u_A           33 TDKQRLWLNNNQITKLEPGVFDHLVNLQQLYFNSNKLTAIPTGVFD----KLTQLTQLDLNDN-HLKSIPRGAFDNLKSL  107 (174)
T ss_dssp             TTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTTTT----TCTTCCEEECCSS-CCCCCCTTTTTTCTTC
T ss_pred             CCCcEEEeCCCCccccCHHHhcCCcCCCEEECCCCCCCccChhHhC----CcchhhEEECCCC-ccceeCHHHhccccCC
Confidence            34555555555555442  444555555555555555555444433    4555555555543 34444443 4455555


Q ss_pred             ceeeccccc
Q 042541          678 EKLRITNCH  686 (695)
Q Consensus       678 ~~L~l~~~~  686 (695)
                      ++|+|++|+
T Consensus       108 ~~L~L~~N~  116 (174)
T 2r9u_A          108 THIYLYNNP  116 (174)
T ss_dssp             SEEECCSSC
T ss_pred             CEEEeCCCC
Confidence            555555543

>3bz5_A Internalin-J, INLJ; leucine rich repeat (LRR), cysteine ladder, asparagine ladder, virulence factor, solenoid, cell WALL; 2.70A {Listeria monocytogenes}

Probab=99.03  E-value=1.2e-09  Score=118.32  Aligned_cols=79  Identities=13%  Similarity=0.180  Sum_probs=37.2

Q ss_pred             cccCCCCcEEEeccCCCCCcccccccccccEEeecccc-CCcccccchhhhcccCCCccEEecccccccccCchhhcCCC
Q 042541          597 LSALSKLKKIRLEHVSLPNSLATVRMNHLQKVSLVMCN-VGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIV  675 (695)
Q Consensus       597 l~~l~~L~~L~L~~~~l~~lp~i~~l~~L~~L~l~~~~-i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~  675 (695)
                      ++.+++|++|++++|.++.+| ++++++|++|++++|. +..+  ...     .+++|+.|++++| .+..+|  ++.++
T Consensus       123 ~~~l~~L~~L~l~~N~l~~l~-l~~l~~L~~L~l~~n~~~~~~--~~~-----~l~~L~~L~ls~n-~l~~l~--l~~l~  191 (457)
T 3bz5_A          123 VSQNPLLTYLNCARNTLTEID-VSHNTQLTELDCHLNKKITKL--DVT-----PQTQLTTLDCSFN-KITELD--VSQNK  191 (457)
T ss_dssp             CTTCTTCCEEECTTSCCSCCC-CTTCTTCCEEECTTCSCCCCC--CCT-----TCTTCCEEECCSS-CCCCCC--CTTCT
T ss_pred             CCCCCcCCEEECCCCccceec-cccCCcCCEEECCCCCccccc--ccc-----cCCcCCEEECCCC-ccceec--cccCC
Confidence            344444444444444444443 3344444444444442 2222  111     4555555555554 344454  55555


Q ss_pred             CCceeeccccc
Q 042541          676 SMEKLRITNCH  686 (695)
Q Consensus       676 ~L~~L~l~~~~  686 (695)
                      +|+.|++++|.
T Consensus       192 ~L~~L~l~~N~  202 (457)
T 3bz5_A          192 LLNRLNCDTNN  202 (457)
T ss_dssp             TCCEEECCSSC
T ss_pred             CCCEEECcCCc
Confidence            66666665543

>3bz5_A Internalin-J, INLJ; leucine rich repeat (LRR), cysteine ladder, asparagine ladder, virulence factor, solenoid, cell WALL; 2.70A {Listeria monocytogenes}

Probab=99.03  E-value=7.8e-10  Score=119.80  Aligned_cols=129  Identities=13%  Similarity=0.110  Sum_probs=82.0

Q ss_pred             CCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcccccccccccE
Q 042541          548 QGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSLATVRMNHLQK  627 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp~i~~l~~L~~  627 (695)
                      .+++|+.|.++.+.... +|  +..+++|+.|++++|.+...      .++.+++|++|++++|.++.+| ++.+++|++
T Consensus       168 ~l~~L~~L~ls~n~l~~-l~--l~~l~~L~~L~l~~N~l~~~------~l~~l~~L~~L~Ls~N~l~~ip-~~~l~~L~~  237 (457)
T 3bz5_A          168 PQTQLTTLDCSFNKITE-LD--VSQNKLLNRLNCDTNNITKL------DLNQNIQLTFLDCSSNKLTEID-VTPLTQLTY  237 (457)
T ss_dssp             TCTTCCEEECCSSCCCC-CC--CTTCTTCCEEECCSSCCSCC------CCTTCTTCSEEECCSSCCSCCC-CTTCTTCSE
T ss_pred             cCCcCCEEECCCCccce-ec--cccCCCCCEEECcCCcCCee------ccccCCCCCEEECcCCcccccC-ccccCCCCE
Confidence            45666666666654333 33  56667777777776655321      1667788888888888888777 667788888


Q ss_pred             EeeccccCCcccccchhhhcccCC-------CccEEecccccccccCchhhcCCCCCceeecccccCCCCCC
Q 042541          628 VSLVMCNVGQVFRNSTFRISDAFP-------NLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALP  692 (695)
Q Consensus       628 L~l~~~~i~~~~~~~~~~l~~~l~-------~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~~l~~lP  692 (695)
                      |++++|.+++.|+..+.    .|.       +|+.|++++|..++.+|  ++.+++|+.|++++|..++.+|
T Consensus       238 L~l~~N~l~~~~~~~l~----~L~~L~l~~n~L~~L~l~~n~~~~~~~--~~~l~~L~~L~Ls~n~~l~~l~  303 (457)
T 3bz5_A          238 FDCSVNPLTELDVSTLS----KLTTLHCIQTDLLEIDLTHNTQLIYFQ--AEGCRKIKELDVTHNTQLYLLD  303 (457)
T ss_dssp             EECCSSCCSCCCCTTCT----TCCEEECTTCCCSCCCCTTCTTCCEEE--CTTCTTCCCCCCTTCTTCCEEE
T ss_pred             EEeeCCcCCCcCHHHCC----CCCEEeccCCCCCEEECCCCccCCccc--ccccccCCEEECCCCcccceec
Confidence            88888888777654332    232       44555555555555555  3456666666666666555554

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=99.01  E-value=2.2e-09  Score=110.79  Aligned_cols=178  Identities=13%  Similarity=0.143  Sum_probs=113.8

Q ss_pred             CCCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhcccccc-ccCCCcEEEEEeCCCCCHHHHHHHHHHhc
Q 042541          165 PVISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQ-GKFKDDIFYVTVSKNPNVKAIVQKVLHHK  243 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~-~~f~~~~~wv~~~~~~~~~~~~~~i~~~l  243 (695)
                      -..++|++..++.+..++..+..+.+.|+|++|+||||+|+.+++.  +. ..+...+++++.+.......+ ++++..+
T Consensus        20 ~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~l~~~--l~~~~~~~~~~~~~~~~~~~~~~i-~~~~~~~   96 (323)
T 1sxj_B           20 LSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHE--LLGRSYADGVLELNASDDRGIDVV-RNQIKHF   96 (323)
T ss_dssp             GGGCCSCTHHHHHHHHHHHSCCCCCEEEECSTTSSHHHHHHHHHHH--HHGGGHHHHEEEECTTSCCSHHHH-HTHHHHH
T ss_pred             HHHHHCCHHHHHHHHHHHHcCCCCeEEEECcCCCCHHHHHHHHHHH--hcCCcccCCEEEecCccccChHHH-HHHHHHH
Confidence            3568999999999999998776555999999999999999999873  31 122222444444433232221 1122111


Q ss_pred             CCCCCCCCChHHHHHHHHHHHHhc-CCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCC------CCCC
Q 042541          244 GYPVPEFQTDEAAINDLERFFKQM-RIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFP------QFGS  312 (695)
Q Consensus       244 ~~~~~~~~~~~~~~~~l~~~~~~l-~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~------~~~~  312 (695)
                      ...                 ...+ .+++.++|+||++.....    ++..+....+++.+|+||.....      ....
T Consensus        97 ~~~-----------------~~~~~~~~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~~~~~~l~~~l~sr~~  159 (323)
T 1sxj_B           97 AQK-----------------KLHLPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCA  159 (323)
T ss_dssp             HHB-----------------CCCCCTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSE
T ss_pred             Hhc-----------------cccCCCCCceEEEEECcccCCHHHHHHHHHHHhccCCCceEEEEeCChhhchhHHHhhce
Confidence            100                 0011 356899999999876543    23333334456788888865421      1223


Q ss_pred             eEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhH-HHHHH
Q 042541          313 VHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLA-LKVVG  365 (695)
Q Consensus       313 ~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLa-i~~~~  365 (695)
                      .+.+.+++.++..+++...+.....   .-.++.+..|++.|+|.|.. +..+.
T Consensus       160 ~i~~~~~~~~~~~~~l~~~~~~~~~---~~~~~~~~~l~~~~~G~~r~a~~~l~  210 (323)
T 1sxj_B          160 ILRYSKLSDEDVLKRLLQIIKLEDV---KYTNDGLEAIIFTAEGDMRQAINNLQ  210 (323)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHHHTC---CBCHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             EEeecCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHcCCCHHHHHHHHH
Confidence            8999999999999999887643221   12356788999999999954 44443

>1ds9_A Outer arm dynein; leucine-rich repeat, beta-BETA-alpha cylinder, flagella, contractIle protein; NMR {Chlamydomonas reinhardtii} SCOP: c.10.3.1 PDB: 1m9l_A

Probab=99.01  E-value=1.4e-11  Score=117.67  Aligned_cols=109  Identities=12%  Similarity=0.165  Sum_probs=54.6

Q ss_pred             CChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc-cccccccccEEeeccccCCcccccchh
Q 042541          566 LPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL-ATVRMNHLQKVSLVMCNVGQVFRNSTF  644 (695)
Q Consensus       566 ~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp-~i~~l~~L~~L~l~~~~i~~~~~~~~~  644 (695)
                      +|..+..+++|++|++++|.+..  ++   .+..+++|++|++++|.+..+| .++.+++|++|++++|.++.+| .. .
T Consensus        40 l~~~~~~l~~L~~L~ls~n~l~~--l~---~~~~l~~L~~L~l~~n~l~~l~~~~~~~~~L~~L~L~~N~l~~l~-~~-~  112 (198)
T 1ds9_A           40 MDATLSTLKACKHLALSTNNIEK--IS---SLSGMENLRILSLGRNLIKKIENLDAVADTLEELWISYNQIASLS-GI-E  112 (198)
T ss_dssp             CHHHHHHTTTCSEEECSEEEESC--CC---CHHHHTTCCEEEEEEEEECSCSSHHHHHHHCSEEEEEEEECCCHH-HH-H
T ss_pred             hhHHHhcCCCCCEEECCCCCCcc--cc---ccccCCCCCEEECCCCCcccccchhhcCCcCCEEECcCCcCCcCC-cc-c
Confidence            33355555555555555554421  11   3455555555555555555555 4445555555555555555533 22 1


Q ss_pred             hhcccCCCccEEecccccccccCch--hhcCCCCCceeeccccc
Q 042541          645 RISDAFPNLLEMDIDYCNDLIELPD--GLCDIVSMEKLRITNCH  686 (695)
Q Consensus       645 ~l~~~l~~L~~L~l~~c~~l~~lP~--~i~~L~~L~~L~l~~~~  686 (695)
                          .+++|++|++++| .+..+|.  .+..+++|++|++++|+
T Consensus       113 ----~l~~L~~L~l~~N-~i~~~~~~~~l~~l~~L~~L~l~~N~  151 (198)
T 1ds9_A          113 ----KLVNLRVLYMSNN-KITNWGEIDKLAALDKLEDLLLAGNP  151 (198)
T ss_dssp             ----HHHHSSEEEESEE-ECCCHHHHHHHTTTTTCSEEEECSCH
T ss_pred             ----cCCCCCEEECCCC-cCCchhHHHHHhcCCCCCEEEecCCc
Confidence                4555555555553 2344432  45555555555555544

>2ast_B S-phase kinase-associated protein 2; SCF-substrate complex, LRR, cell cycle, protein turnover COM ligase-ligase inhibitor complex; HET: TPO; 2.30A {Homo sapiens} SCOP: a.158.1.1 c.10.1.3 PDB: 2ass_B 1fqv_A* 1fs2_A

Probab=99.01  E-value=5.8e-11  Score=123.42  Aligned_cols=155  Identities=17%  Similarity=0.204  Sum_probs=114.8

Q ss_pred             CccceEEeeecCCcccC-CC-CCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEccc-CCCCcccCcccccccCCC
Q 042541          526 PNNASLLSISTDETFSS-NW-PDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNY-GFSPAELNNFRVLSALSK  602 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~~-~~-~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~-~~~~~~~~~~~~l~~l~~  602 (695)
                      ....+++.+.+...... .+ ....+++|+.|.++.+......|..+..+++|++|++++| .+....++  ..+..+++
T Consensus        92 ~~~L~~L~L~~~~l~~~~~~~~~~~~~~L~~L~L~~~~l~~~~~~~l~~~~~L~~L~L~~~~~l~~~~l~--~~~~~~~~  169 (336)
T 2ast_B           92 PFRVQHMDLSNSVIEVSTLHGILSQCSKLQNLSLEGLRLSDPIVNTLAKNSNLVRLNLSGCSGFSEFALQ--TLLSSCSR  169 (336)
T ss_dssp             CBCCCEEECTTCEECHHHHHHHHTTBCCCSEEECTTCBCCHHHHHHHTTCTTCSEEECTTCBSCCHHHHH--HHHHHCTT
T ss_pred             CCCCCEEEccCCCcCHHHHHHHHhhCCCCCEEeCcCcccCHHHHHHHhcCCCCCEEECCCCCCCCHHHHH--HHHhcCCC
Confidence            35677787766542111 11 1136789999999888766677788889999999999988 44322222  22678999


Q ss_pred             CcEEEeccC-CCCC--cc-cccccc-cccEEeecccc--CC-cccccchhhhcccCCCccEEeccccccc-ccCchhhcC
Q 042541          603 LKKIRLEHV-SLPN--SL-ATVRMN-HLQKVSLVMCN--VG-QVFRNSTFRISDAFPNLLEMDIDYCNDL-IELPDGLCD  673 (695)
Q Consensus       603 L~~L~L~~~-~l~~--lp-~i~~l~-~L~~L~l~~~~--i~-~~~~~~~~~l~~~l~~L~~L~l~~c~~l-~~lP~~i~~  673 (695)
                      |++|++++| .++.  +| .++.++ +|++|++++|.  ++ ...+..+.    .+++|+.|++++|..+ ...|..+++
T Consensus       170 L~~L~l~~~~~l~~~~~~~~~~~l~~~L~~L~l~~~~~~~~~~~l~~~~~----~~~~L~~L~l~~~~~l~~~~~~~l~~  245 (336)
T 2ast_B          170 LDELNLSWCFDFTEKHVQVAVAHVSETITQLNLSGYRKNLQKSDLSTLVR----RCPNLVHLDLSDSVMLKNDCFQEFFQ  245 (336)
T ss_dssp             CCEEECCCCTTCCHHHHHHHHHHSCTTCCEEECCSCGGGSCHHHHHHHHH----HCTTCSEEECTTCTTCCGGGGGGGGG
T ss_pred             CCEEcCCCCCCcChHHHHHHHHhcccCCCEEEeCCCcccCCHHHHHHHHh----hCCCCCEEeCCCCCcCCHHHHHHHhC
Confidence            999999999 8883  67 788999 99999999994  43 22233333    7999999999998744 466778999


Q ss_pred             CCCCceeeccccc
Q 042541          674 IVSMEKLRITNCH  686 (695)
Q Consensus       674 L~~L~~L~l~~~~  686 (695)
                      +++|++|++++|.
T Consensus       246 l~~L~~L~l~~~~  258 (336)
T 2ast_B          246 LNYLQHLSLSRCY  258 (336)
T ss_dssp             CTTCCEEECTTCT
T ss_pred             CCCCCEeeCCCCC
Confidence            9999999999986

>1o6v_A Internalin A; bacterial infection, extracellular recognition, cell WALL attached, leucine rich repeat; 1.5A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 1o6s_A* 1o6t_A 2omz_A 2omy_A 2omw_A 2omv_A 2omt_A 2omx_A 2omu_A

Probab=99.01  E-value=1.6e-09  Score=118.00  Aligned_cols=150  Identities=13%  Similarity=0.157  Sum_probs=101.8

Q ss_pred             ccceEEeeecCCcccCCCCCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEE
Q 042541          527 NNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKI  606 (695)
Q Consensus       527 ~~~r~l~~~~~~~~~~~~~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L  606 (695)
                      ...+++.+..+.... ......+++|+.|.++.+..... |. +..+++|+.|++++|.+..     .+.++.+++|++|
T Consensus       243 ~~L~~L~l~~n~l~~-~~~~~~l~~L~~L~l~~n~l~~~-~~-~~~l~~L~~L~L~~n~l~~-----~~~~~~l~~L~~L  314 (466)
T 1o6v_A          243 TNLTDLDLANNQISN-LAPLSGLTKLTELKLGANQISNI-SP-LAGLTALTNLELNENQLED-----ISPISNLKNLTYL  314 (466)
T ss_dssp             TTCSEEECCSSCCCC-CGGGTTCTTCSEEECCSSCCCCC-GG-GTTCTTCSEEECCSSCCSC-----CGGGGGCTTCSEE
T ss_pred             CCCCEEECCCCcccc-chhhhcCCCCCEEECCCCccCcc-cc-ccCCCccCeEEcCCCcccC-----chhhcCCCCCCEE
Confidence            345566655443211 11233567788888877654433 32 6778888888888776532     2226778888888


Q ss_pred             EeccCCCCCcccccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeeccccc
Q 042541          607 RLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCH  686 (695)
Q Consensus       607 ~L~~~~l~~lp~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~  686 (695)
                      ++++|.+..++.++.+++|++|++++|.++..+ ...     .+++|+.|++++|.. ..++. +..+++|+.|++++|.
T Consensus       315 ~L~~n~l~~~~~~~~l~~L~~L~l~~n~l~~~~-~l~-----~l~~L~~L~l~~n~l-~~~~~-~~~l~~L~~L~l~~n~  386 (466)
T 1o6v_A          315 TLYFNNISDISPVSSLTKLQRLFFYNNKVSDVS-SLA-----NLTNINWLSAGHNQI-SDLTP-LANLTRITQLGLNDQA  386 (466)
T ss_dssp             ECCSSCCSCCGGGGGCTTCCEEECCSSCCCCCG-GGT-----TCTTCCEEECCSSCC-CBCGG-GTTCTTCCEEECCCEE
T ss_pred             ECcCCcCCCchhhccCccCCEeECCCCccCCch-hhc-----cCCCCCEEeCCCCcc-Cccch-hhcCCCCCEEeccCCc
Confidence            888888876665678888888888888887763 332     788899999988754 44444 8888999999998876


Q ss_pred             CCCCCCC
Q 042541          687 RLSALPE  693 (695)
Q Consensus       687 ~l~~lP~  693 (695)
                       +..+|.
T Consensus       387 -~~~~p~  392 (466)
T 1o6v_A          387 -WTNAPV  392 (466)
T ss_dssp             -EECCCB
T ss_pred             -ccCCch
Confidence             444443

>2wfh_A SLIT homolog 2 protein C-product; developmental protein, neurogenesis, splicing, glycoprotein, leucine-rich repeat, disulfide bond, differentiation; 1.80A {Homo sapiens}

Probab=99.00  E-value=1.7e-09  Score=102.43  Aligned_cols=106  Identities=19%  Similarity=0.275  Sum_probs=88.1

Q ss_pred             cEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc-cccccccccEEeeccccCCcccccchhhhcccCCCccE
Q 042541          577 KVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL-ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLE  655 (695)
Q Consensus       577 r~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp-~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~  655 (695)
                      ++++++++++.  .++.    +-..+|++|+|++|.++.+| .+.++++|++|+|++|.++.+++..+.    .+++|++
T Consensus        13 ~~l~~~~~~l~--~ip~----~~~~~l~~L~L~~n~i~~ip~~~~~l~~L~~L~Ls~N~i~~i~~~~f~----~l~~L~~   82 (193)
T 2wfh_A           13 TVVRCSNKGLK--VLPK----GIPRDVTELYLDGNQFTLVPKELSNYKHLTLIDLSNNRISTLSNQSFS----NMTQLLT   82 (193)
T ss_dssp             TEEECTTSCCS--SCCS----CCCTTCCEEECCSSCCCSCCGGGGGCTTCCEEECCSSCCCCCCTTTTT----TCTTCCE
T ss_pred             CEEEcCCCCCC--cCCC----CCCCCCCEEECCCCcCchhHHHhhcccCCCEEECCCCcCCEeCHhHcc----CCCCCCE
Confidence            57888877653  2221    12357999999999999999 999999999999999999999988776    8999999


Q ss_pred             EecccccccccCch-hhcCCCCCceeecccccCCCCCCCC
Q 042541          656 MDIDYCNDLIELPD-GLCDIVSMEKLRITNCHRLSALPEG  694 (695)
Q Consensus       656 L~l~~c~~l~~lP~-~i~~L~~L~~L~l~~~~~l~~lP~~  694 (695)
                      |+|++|. +..+|. .|+.+++|++|+|++|. +..+|.+
T Consensus        83 L~Ls~N~-l~~i~~~~f~~l~~L~~L~L~~N~-l~~~~~~  120 (193)
T 2wfh_A           83 LILSYNR-LRCIPPRTFDGLKSLRLLSLHGND-ISVVPEG  120 (193)
T ss_dssp             EECCSSC-CCBCCTTTTTTCTTCCEEECCSSC-CCBCCTT
T ss_pred             EECCCCc-cCEeCHHHhCCCCCCCEEECCCCC-CCeeChh
Confidence            9999965 666664 69999999999999965 8888864

>2ast_B S-phase kinase-associated protein 2; SCF-substrate complex, LRR, cell cycle, protein turnover COM ligase-ligase inhibitor complex; HET: TPO; 2.30A {Homo sapiens} SCOP: a.158.1.1 c.10.1.3 PDB: 2ass_B 1fqv_A* 1fs2_A

Probab=98.99  E-value=1.4e-10  Score=120.46  Aligned_cols=152  Identities=14%  Similarity=0.170  Sum_probs=111.9

Q ss_pred             CccceEEeeecCCcccCCCC-CCCCCceEEEEEEcc-Cccc-cCChhhcCCCCCcEEEEccc-CCCCcccCcccccccCC
Q 042541          526 PNNASLLSISTDETFSSNWP-DMQGPEVKVVVLNIR-TKKY-VLPDFLQKMDELKVLIVTNY-GFSPAELNNFRVLSALS  601 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~~~~~-~~~~~~l~~L~l~~~-~~~~-~~p~~~~~l~~Lr~L~l~~~-~~~~~~~~~~~~l~~l~  601 (695)
                      ....++|.+.+.......+. -..+++|+.|.++.+ .... .+|..+.++++|++|++++| .+....++  ..+..++
T Consensus       117 ~~~L~~L~L~~~~l~~~~~~~l~~~~~L~~L~L~~~~~l~~~~l~~~~~~~~~L~~L~l~~~~~l~~~~~~--~~~~~l~  194 (336)
T 2ast_B          117 CSKLQNLSLEGLRLSDPIVNTLAKNSNLVRLNLSGCSGFSEFALQTLLSSCSRLDELNLSWCFDFTEKHVQ--VAVAHVS  194 (336)
T ss_dssp             BCCCSEEECTTCBCCHHHHHHHTTCTTCSEEECTTCBSCCHHHHHHHHHHCTTCCEEECCCCTTCCHHHHH--HHHHHSC
T ss_pred             CCCCCEEeCcCcccCHHHHHHHhcCCCCCEEECCCCCCCCHHHHHHHHhcCCCCCEEcCCCCCCcChHHHH--HHHHhcc
Confidence            45778888876542211111 125899999999988 3443 46777889999999999998 66432222  2377899


Q ss_pred             -CCcEEEeccC--CCC--Ccc-cccccccccEEeecccc-CCcccccchhhhcccCCCccEEecccccccccCch---hh
Q 042541          602 -KLKKIRLEHV--SLP--NSL-ATVRMNHLQKVSLVMCN-VGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPD---GL  671 (695)
Q Consensus       602 -~L~~L~L~~~--~l~--~lp-~i~~l~~L~~L~l~~~~-i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~---~i  671 (695)
                       +|++|++++|  .++  .+| .++++++|++|++++|. ++...+..+.    .+++|++|++++|..+  .|.   .+
T Consensus       195 ~~L~~L~l~~~~~~~~~~~l~~~~~~~~~L~~L~l~~~~~l~~~~~~~l~----~l~~L~~L~l~~~~~~--~~~~~~~l  268 (336)
T 2ast_B          195 ETITQLNLSGYRKNLQKSDLSTLVRRCPNLVHLDLSDSVMLKNDCFQEFF----QLNYLQHLSLSRCYDI--IPETLLEL  268 (336)
T ss_dssp             TTCCEEECCSCGGGSCHHHHHHHHHHCTTCSEEECTTCTTCCGGGGGGGG----GCTTCCEEECTTCTTC--CGGGGGGG
T ss_pred             cCCCEEEeCCCcccCCHHHHHHHHhhCCCCCEEeCCCCCcCCHHHHHHHh----CCCCCCEeeCCCCCCC--CHHHHHHH
Confidence             9999999999  454  677 88899999999999998 6544333344    8999999999998632  333   58


Q ss_pred             cCCCCCceeecccc
Q 042541          672 CDIVSMEKLRITNC  685 (695)
Q Consensus       672 ~~L~~L~~L~l~~~  685 (695)
                      +++++|+.|++++|
T Consensus       269 ~~~~~L~~L~l~~~  282 (336)
T 2ast_B          269 GEIPTLKTLQVFGI  282 (336)
T ss_dssp             GGCTTCCEEECTTS
T ss_pred             hcCCCCCEEeccCc
Confidence            88999999999998

>3g39_A Variable lymphocyte receptor VLRB.2D; antibody, X-RAY, crystallography, immune system; 1.55A {Petromyzon marinus} PDB: 3g3a_A 3g3b_A 3twi_D

Probab=98.99  E-value=1.4e-09  Score=100.84  Aligned_cols=81  Identities=12%  Similarity=0.172  Sum_probs=43.7

Q ss_pred             CCCcEEEeccCCCCCcc--cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchh-hcCCCCC
Q 042541          601 SKLKKIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDG-LCDIVSM  677 (695)
Q Consensus       601 ~~L~~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~-i~~L~~L  677 (695)
                      .+|++|+|++|.++.++  .++++++|++|+|++|.++.+++..+.    .+++|++|+|++| .+..+|.. +.++++|
T Consensus        30 ~~l~~L~L~~N~i~~~~~~~~~~l~~L~~L~Ls~N~l~~l~~~~f~----~l~~L~~L~L~~N-~l~~~~~~~~~~l~~L  104 (170)
T 3g39_A           30 TTTQVLYLYDNQITKLEPGVFDRLTQLTRLDLDNNQLTVLPAGVFD----KLTQLTQLSLNDN-QLKSIPRGAFDNLKSL  104 (170)
T ss_dssp             TTCSEEECCSSCCCCCCTTTTTTCTTCSEEECCSSCCCCCCTTTTT----TCTTCCEEECCSS-CCCCCCTTTTTTCTTC
T ss_pred             CCCcEEEcCCCcCCccChhhhcCcccCCEEECCCCCcCccChhhcc----CCCCCCEEECCCC-ccCEeCHHHhcCCCCC
Confidence            44555555555555443  455555555555555555555555443    5555555555553 34444443 5555555


Q ss_pred             ceeeccccc
Q 042541          678 EKLRITNCH  686 (695)
Q Consensus       678 ~~L~l~~~~  686 (695)
                      ++|+|++|+
T Consensus       105 ~~L~L~~N~  113 (170)
T 3g39_A          105 THIWLLNNP  113 (170)
T ss_dssp             CEEECCSSC
T ss_pred             CEEEeCCCC
Confidence            555555544

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A}

Probab=98.96  E-value=2.2e-09  Score=118.55  Aligned_cols=149  Identities=9%  Similarity=0.060  Sum_probs=98.9

Q ss_pred             CccceEEeeecCCcccCCCCCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcE
Q 042541          526 PNNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKK  605 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~~~~~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~  605 (695)
                      ....++|.+.++.... .+.  -..+|+.|.++.|.... +|.   .+++|++|++++|.+..  ++.     .+++|++
T Consensus        99 l~~L~~L~Ls~N~l~~-ip~--l~~~L~~L~Ls~N~l~~-lp~---~l~~L~~L~Ls~N~l~~--lp~-----~l~~L~~  164 (571)
T 3cvr_A           99 PASLEYLDACDNRLST-LPE--LPASLKHLDVDNNQLTM-LPE---LPALLEYINADNNQLTM--LPE-----LPTSLEV  164 (571)
T ss_dssp             CTTCCEEECCSSCCSC-CCC--CCTTCCEEECCSSCCSC-CCC---CCTTCCEEECCSSCCSC--CCC-----CCTTCCE
T ss_pred             cCCCCEEEccCCCCCC-cch--hhcCCCEEECCCCcCCC-CCC---cCccccEEeCCCCccCc--CCC-----cCCCcCE
Confidence            3456666665543222 111  12267777777765444 555   56778888888776632  221     4678889


Q ss_pred             EEeccCCCCCcccccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccc
Q 042541          606 IRLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNC  685 (695)
Q Consensus       606 L~L~~~~l~~lp~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~  685 (695)
                      |+|++|.++.+|.++  ++|++|+|++|.|+.+|+ +...+....+.|+.|+|++| .+..+|.+++++++|+.|+|++|
T Consensus       165 L~Ls~N~L~~lp~l~--~~L~~L~Ls~N~L~~lp~-~~~~L~~~~~~L~~L~Ls~N-~l~~lp~~l~~l~~L~~L~L~~N  240 (571)
T 3cvr_A          165 LSVRNNQLTFLPELP--ESLEALDVSTNLLESLPA-VPVRNHHSEETEIFFRCREN-RITHIPENILSLDPTCTIILEDN  240 (571)
T ss_dssp             EECCSSCCSCCCCCC--TTCCEEECCSSCCSSCCC-CC--------CCEEEECCSS-CCCCCCGGGGGSCTTEEEECCSS
T ss_pred             EECCCCCCCCcchhh--CCCCEEECcCCCCCchhh-HHHhhhcccccceEEecCCC-cceecCHHHhcCCCCCEEEeeCC
Confidence            999998888888533  789999999999887776 33111111233399999986 67889999999999999999998


Q ss_pred             cCCCCCC
Q 042541          686 HRLSALP  692 (695)
Q Consensus       686 ~~l~~lP  692 (695)
                      +..+.+|
T Consensus       241 ~l~~~~p  247 (571)
T 3cvr_A          241 PLSSRIR  247 (571)
T ss_dssp             SCCHHHH
T ss_pred             cCCCcCH
Confidence            7555444

>4ay9_X Follicle-stimulating hormone receptor; hormone-receptor complex, leucine-rich repeats, LRR, GPCR; HET: TYS NAG; 2.50A {Homo sapiens} PDB: 1xwd_C*

Probab=98.96  E-value=5.1e-09  Score=109.31  Aligned_cols=126  Identities=16%  Similarity=0.226  Sum_probs=63.3

Q ss_pred             cCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEecc-CCCCCcc--cccccc-cccEEeeccccC
Q 042541          560 RTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEH-VSLPNSL--ATVRMN-HLQKVSLVMCNV  635 (695)
Q Consensus       560 ~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~-~~l~~lp--~i~~l~-~L~~L~l~~~~i  635 (695)
                      +......|..|..+++|++|++++|.+...  +.. .+....++..|++.+ +.+..+|  .+..+. .|++|+|++|.+
T Consensus        90 N~l~~l~~~~f~~l~~L~~L~l~~n~l~~~--~~~-~~~~~~~l~~l~l~~~~~i~~l~~~~f~~~~~~l~~L~L~~N~i  166 (350)
T 4ay9_X           90 NNLLYINPEAFQNLPNLQYLLISNTGIKHL--PDV-HKIHSLQKVLLDIQDNINIHTIERNSFVGLSFESVILWLNKNGI  166 (350)
T ss_dssp             TTCCEECTTSBCCCTTCCEEEEEEECCSSC--CCC-TTCCBSSCEEEEEESCTTCCEECTTSSTTSBSSCEEEECCSSCC
T ss_pred             CcccccCchhhhhccccccccccccccccC--Cch-hhcccchhhhhhhccccccccccccchhhcchhhhhhccccccc
Confidence            333333455666777777777777654311  110 011222333444432 2333333  233332 355566666666


Q ss_pred             CcccccchhhhcccCCCccEEecccccccccCchh-hcCCCCCceeecccccCCCCCCCC
Q 042541          636 GQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDG-LCDIVSMEKLRITNCHRLSALPEG  694 (695)
Q Consensus       636 ~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~-i~~L~~L~~L~l~~~~~l~~lP~~  694 (695)
                      +.+++..+     ..++|+.|++.+|+.++.+|.. |..+++|+.|++++|. +..+|.+
T Consensus       167 ~~i~~~~f-----~~~~L~~l~l~~~n~l~~i~~~~f~~l~~L~~LdLs~N~-l~~lp~~  220 (350)
T 4ay9_X          167 QEIHNSAF-----NGTQLDELNLSDNNNLEELPNDVFHGASGPVILDISRTR-IHSLPSY  220 (350)
T ss_dssp             CEECTTSS-----TTEEEEEEECTTCTTCCCCCTTTTTTEECCSEEECTTSC-CCCCCSS
T ss_pred             cCCChhhc-----cccchhHHhhccCCcccCCCHHHhccCcccchhhcCCCC-cCccChh
Confidence            65555555     4555666666655566666643 4566666666666643 5555543

>2o6r_A Variable lymphocyte receptor B; leucine-rich repeat protein, LRR, immune system; 2.30A {Eptatretus burgeri}

Probab=98.96  E-value=4e-09  Score=98.39  Aligned_cols=113  Identities=14%  Similarity=0.103  Sum_probs=92.5

Q ss_pred             CCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--ccccccccc
Q 042541          549 GPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNHLQ  626 (695)
Q Consensus       549 ~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L~  626 (695)
                      .++++.|.++.+......+..+..+++|++|++++|.+..  ++ ...++.+++|++|++++|.++.+|  .++++++|+
T Consensus        27 ~~~l~~L~l~~n~l~~~~~~~~~~l~~L~~L~l~~n~l~~--~~-~~~~~~l~~L~~L~l~~N~l~~~~~~~~~~l~~L~  103 (177)
T 2o6r_A           27 PSSATRLELESNKLQSLPHGVFDKLTQLTKLSLSQNQIQS--LP-DGVFDKLTKLTILYLHENKLQSLPNGVFDKLTQLK  103 (177)
T ss_dssp             CTTCSEEECCSSCCCCCCTTTTTTCTTCSEEECCSSCCCC--CC-TTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCC
T ss_pred             CCCCcEEEeCCCcccEeCHHHhcCcccccEEECCCCcceE--eC-hhHccCCCccCEEECCCCCccccCHHHhhCCcccC
Confidence            4688999998887665555678999999999999987742  11 122678999999999999999888  578999999


Q ss_pred             EEeeccccCCcccccchhhhcccCCCccEEecccccccccCc
Q 042541          627 KVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELP  668 (695)
Q Consensus       627 ~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP  668 (695)
                      +|++++|.++.+|+..+.    .+++|++|++++|......|
T Consensus       104 ~L~l~~N~l~~~~~~~~~----~l~~L~~L~l~~N~~~~~~~  141 (177)
T 2o6r_A          104 ELALDTNQLKSVPDGIFD----RLTSLQKIWLHTNPWDCSCP  141 (177)
T ss_dssp             EEECCSSCCSCCCTTTTT----TCTTCCEEECCSSCBCCCHH
T ss_pred             EEECcCCcceEeCHHHhc----CCcccCEEEecCCCeeccCc
Confidence            999999999999988765    79999999999976544433

>3cvr_A Invasion plasmid antigen; leucine rich repeat and alpha fold, ligase; 2.80A {Shigella flexneri 2A}

Probab=98.95  E-value=1.7e-09  Score=119.55  Aligned_cols=139  Identities=18%  Similarity=0.126  Sum_probs=101.1

Q ss_pred             ccceEEeeecCCcccCCCCCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEE
Q 042541          527 NNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKI  606 (695)
Q Consensus       527 ~~~r~l~~~~~~~~~~~~~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L  606 (695)
                      ...+.|.+.++... ..+  ..+++|+.|.++.|.... +|. +.+  +|++|++++|.+..  ++.     .+++|++|
T Consensus        80 ~~L~~L~Ls~N~l~-~ip--~~l~~L~~L~Ls~N~l~~-ip~-l~~--~L~~L~Ls~N~l~~--lp~-----~l~~L~~L  145 (571)
T 3cvr_A           80 PQITVLEITQNALI-SLP--ELPASLEYLDACDNRLST-LPE-LPA--SLKHLDVDNNQLTM--LPE-----LPALLEYI  145 (571)
T ss_dssp             TTCSEEECCSSCCS-CCC--CCCTTCCEEECCSSCCSC-CCC-CCT--TCCEEECCSSCCSC--CCC-----CCTTCCEE
T ss_pred             CCCCEEECcCCCCc-ccc--cccCCCCEEEccCCCCCC-cch-hhc--CCCEEECCCCcCCC--CCC-----cCccccEE
Confidence            45777777665433 222  356888999888886554 666 554  89999999887642  222     57889999


Q ss_pred             EeccCCCCCcccccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCC-------ce
Q 042541          607 RLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSM-------EK  679 (695)
Q Consensus       607 ~L~~~~l~~lp~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L-------~~  679 (695)
                      +|++|.++.+|.  .+++|++|+|++|.++.+|+  +     . ++|+.|+|++| .+..+|. +..  +|       +.
T Consensus       146 ~Ls~N~l~~lp~--~l~~L~~L~Ls~N~L~~lp~--l-----~-~~L~~L~Ls~N-~L~~lp~-~~~--~L~~~~~~L~~  211 (571)
T 3cvr_A          146 NADNNQLTMLPE--LPTSLEVLSVRNNQLTFLPE--L-----P-ESLEALDVSTN-LLESLPA-VPV--RNHHSEETEIF  211 (571)
T ss_dssp             ECCSSCCSCCCC--CCTTCCEEECCSSCCSCCCC--C-----C-TTCCEEECCSS-CCSSCCC-CC----------CCEE
T ss_pred             eCCCCccCcCCC--cCCCcCEEECCCCCCCCcch--h-----h-CCCCEEECcCC-CCCchhh-HHH--hhhcccccceE
Confidence            999999888884  56789999999998888666  4     4 78999999986 5778887 655  77       99


Q ss_pred             eecccccCCCCCCCC
Q 042541          680 LRITNCHRLSALPEG  694 (695)
Q Consensus       680 L~l~~~~~l~~lP~~  694 (695)
                      |+|++|. +..+|.+
T Consensus       212 L~Ls~N~-l~~lp~~  225 (571)
T 3cvr_A          212 FRCRENR-ITHIPEN  225 (571)
T ss_dssp             EECCSSC-CCCCCGG
T ss_pred             EecCCCc-ceecCHH
Confidence            9998865 7788864

>1jl5_A Outer protein YOPM; leucine-rich repeat, molecular pathogenesis, effector protein, virulence factor, toxin; 2.10A {Yersinia pestis} SCOP: c.10.2.6 PDB: 1g9u_A

Probab=98.92  E-value=7.9e-09  Score=111.75  Aligned_cols=143  Identities=17%  Similarity=0.120  Sum_probs=79.4

Q ss_pred             ccceEEeeecCCcccCCCCCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEE
Q 042541          527 NNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKI  606 (695)
Q Consensus       527 ~~~r~l~~~~~~~~~~~~~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L  606 (695)
                      ...+++.+..+.... ..  ...++|+.|.++.+.... +| .++++++|++|++++|.+..  ++.     ...+|++|
T Consensus       111 ~~L~~L~l~~n~l~~-l~--~~~~~L~~L~L~~n~l~~-lp-~~~~l~~L~~L~l~~N~l~~--lp~-----~~~~L~~L  178 (454)
T 1jl5_A          111 QSLKSLLVDNNNLKA-LS--DLPPLLEYLGVSNNQLEK-LP-ELQNSSFLKIIDVDNNSLKK--LPD-----LPPSLEFI  178 (454)
T ss_dssp             TTCCEEECCSSCCSC-CC--SCCTTCCEEECCSSCCSS-CC-CCTTCTTCCEEECCSSCCSC--CCC-----CCTTCCEE
T ss_pred             CCCcEEECCCCccCc-cc--CCCCCCCEEECcCCCCCC-Cc-ccCCCCCCCEEECCCCcCcc--cCC-----CcccccEE
Confidence            455666665443211 10  112577777777765543 66 47778888888888776532  211     12356666


Q ss_pred             EeccCCCCCcccccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeeccccc
Q 042541          607 RLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCH  686 (695)
Q Consensus       607 ~L~~~~l~~lp~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~  686 (695)
                      ++++|.+..+|.++++++|++|++++|.++++|.        ..++|++|++++| .+..+|. ++.+++|++|++++|.
T Consensus       179 ~L~~n~l~~l~~~~~l~~L~~L~l~~N~l~~l~~--------~~~~L~~L~l~~n-~l~~lp~-~~~l~~L~~L~l~~N~  248 (454)
T 1jl5_A          179 AAGNNQLEELPELQNLPFLTAIYADNNSLKKLPD--------LPLSLESIVAGNN-ILEELPE-LQNLPFLTTIYADNNL  248 (454)
T ss_dssp             ECCSSCCSSCCCCTTCTTCCEEECCSSCCSSCCC--------CCTTCCEEECCSS-CCSSCCC-CTTCTTCCEEECCSSC
T ss_pred             ECcCCcCCcCccccCCCCCCEEECCCCcCCcCCC--------CcCcccEEECcCC-cCCcccc-cCCCCCCCEEECCCCc
Confidence            6666666665555666666666666666655432        2235555555554 3345553 5555555555555543


Q ss_pred             CCCCCC
Q 042541          687 RLSALP  692 (695)
Q Consensus       687 ~l~~lP  692 (695)
                       +..+|
T Consensus       249 -l~~l~  253 (454)
T 1jl5_A          249 -LKTLP  253 (454)
T ss_dssp             -CSSCC
T ss_pred             -CCccc
Confidence             44444

>1ds9_A Outer arm dynein; leucine-rich repeat, beta-BETA-alpha cylinder, flagella, contractIle protein; NMR {Chlamydomonas reinhardtii} SCOP: c.10.3.1 PDB: 1m9l_A

Probab=98.91  E-value=7.2e-11  Score=112.63  Aligned_cols=124  Identities=10%  Similarity=0.123  Sum_probs=100.5

Q ss_pred             CCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcccccccccccE
Q 042541          548 QGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSLATVRMNHLQK  627 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp~i~~l~~L~~  627 (695)
                      .+++|+.|.++.+.... +| .+..+++|++|++++|.+.  .++.  .+..+++|++|++++|.+..+|.++.+++|++
T Consensus        46 ~l~~L~~L~ls~n~l~~-l~-~~~~l~~L~~L~l~~n~l~--~l~~--~~~~~~~L~~L~L~~N~l~~l~~~~~l~~L~~  119 (198)
T 1ds9_A           46 TLKACKHLALSTNNIEK-IS-SLSGMENLRILSLGRNLIK--KIEN--LDAVADTLEELWISYNQIASLSGIEKLVNLRV  119 (198)
T ss_dssp             HTTTCSEEECSEEEESC-CC-CHHHHTTCCEEEEEEEEEC--SCSS--HHHHHHHCSEEEEEEEECCCHHHHHHHHHSSE
T ss_pred             cCCCCCEEECCCCCCcc-cc-ccccCCCCCEEECCCCCcc--cccc--hhhcCCcCCEEECcCCcCCcCCccccCCCCCE
Confidence            56789999998875444 67 8899999999999998774  3332  35677899999999999999888889999999


Q ss_pred             EeeccccCCcccc-cchhhhcccCCCccEEecccccccccCchh----------hcCCCCCceee
Q 042541          628 VSLVMCNVGQVFR-NSTFRISDAFPNLLEMDIDYCNDLIELPDG----------LCDIVSMEKLR  681 (695)
Q Consensus       628 L~l~~~~i~~~~~-~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~----------i~~L~~L~~L~  681 (695)
                      |++++|.++.+++ ..+.    .+++|++|++++|......|..          +..+++|+.|+
T Consensus       120 L~l~~N~i~~~~~~~~l~----~l~~L~~L~l~~N~l~~~~~~~~~~~~~~~~~~~~l~~L~~Ld  180 (198)
T 1ds9_A          120 LYMSNNKITNWGEIDKLA----ALDKLEDLLLAGNPLYNDYKENNATSEYRIEVVKRLPNLKKLD  180 (198)
T ss_dssp             EEESEEECCCHHHHHHHT----TTTTCSEEEECSCHHHHHHHTTTTHHHHHHHHHHHCSSCSEEC
T ss_pred             EECCCCcCCchhHHHHHh----cCCCCCEEEecCCccccccccccchHHHHHHHHHhCCCcEEEC
Confidence            9999999998765 3333    8999999999998654444432          88999999998

>1o6v_A Internalin A; bacterial infection, extracellular recognition, cell WALL attached, leucine rich repeat; 1.5A {Listeria monocytogenes} SCOP: b.1.18.15 c.10.2.1 PDB: 1o6s_A* 1o6t_A 2omz_A 2omy_A 2omw_A 2omv_A 2omt_A 2omx_A 2omu_A

Probab=98.90  E-value=5.4e-09  Score=113.79  Aligned_cols=146  Identities=14%  Similarity=0.145  Sum_probs=109.9

Q ss_pred             ccceEEeeecCCcccCCCCCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEE
Q 042541          527 NNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKI  606 (695)
Q Consensus       527 ~~~r~l~~~~~~~~~~~~~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L  606 (695)
                      ...+.+.+..+.... ......+++|+.|.++.+......|  +..+++|+.|++++|.+..     .+.+..+++|++|
T Consensus       221 ~~L~~L~l~~n~l~~-~~~l~~l~~L~~L~l~~n~l~~~~~--~~~l~~L~~L~l~~n~l~~-----~~~~~~l~~L~~L  292 (466)
T 1o6v_A          221 TNLDELSLNGNQLKD-IGTLASLTNLTDLDLANNQISNLAP--LSGLTKLTELKLGANQISN-----ISPLAGLTALTNL  292 (466)
T ss_dssp             TTCCEEECCSSCCCC-CGGGGGCTTCSEEECCSSCCCCCGG--GTTCTTCSEEECCSSCCCC-----CGGGTTCTTCSEE
T ss_pred             CCCCEEECCCCCccc-chhhhcCCCCCEEECCCCccccchh--hhcCCCCCEEECCCCccCc-----cccccCCCccCeE
Confidence            456666665543211 1122357888888888775544333  7888899999998886642     1227788999999


Q ss_pred             EeccCCCCCcccccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeeccccc
Q 042541          607 RLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCH  686 (695)
Q Consensus       607 ~L~~~~l~~lp~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~  686 (695)
                      ++++|.+..++.++.+++|++|++++|.+++.++ . .    .+++|+.|++++| .+..+| .+.++++|+.|++++|.
T Consensus       293 ~L~~n~l~~~~~~~~l~~L~~L~L~~n~l~~~~~-~-~----~l~~L~~L~l~~n-~l~~~~-~l~~l~~L~~L~l~~n~  364 (466)
T 1o6v_A          293 ELNENQLEDISPISNLKNLTYLTLYFNNISDISP-V-S----SLTKLQRLFFYNN-KVSDVS-SLANLTNINWLSAGHNQ  364 (466)
T ss_dssp             ECCSSCCSCCGGGGGCTTCSEEECCSSCCSCCGG-G-G----GCTTCCEEECCSS-CCCCCG-GGTTCTTCCEEECCSSC
T ss_pred             EcCCCcccCchhhcCCCCCCEEECcCCcCCCchh-h-c----cCccCCEeECCCC-ccCCch-hhccCCCCCEEeCCCCc
Confidence            9999999887777889999999999999988776 3 3    7999999999997 566665 69999999999999987


Q ss_pred             CC
Q 042541          687 RL  688 (695)
Q Consensus       687 ~l  688 (695)
                      ..
T Consensus       365 l~  366 (466)
T 1o6v_A          365 IS  366 (466)
T ss_dssp             CC
T ss_pred             cC
Confidence            43

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=98.90  E-value=5.6e-09  Score=107.85  Aligned_cols=176  Identities=14%  Similarity=0.173  Sum_probs=112.7

Q ss_pred             CCCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccc-cCCCcEEEEEeCCCCCHHHHHHHHHHhc
Q 042541          165 PVISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQG-KFKDDIFYVTVSKNPNVKAIVQKVLHHK  243 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~-~f~~~~~wv~~~~~~~~~~~~~~i~~~l  243 (695)
                      -..++|++..++.+..++..+..+.+.|+|++|+||||+|+.+++.  +.. .+...++.++.+....... ..      
T Consensus        24 ~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~la~~l~~~--l~~~~~~~~~~~~~~~~~~~~~~-~~------   94 (327)
T 1iqp_A           24 LDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARE--LFGENWRHNFLELNASDERGINV-IR------   94 (327)
T ss_dssp             TTTCCSCHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHHHHHHHH--HHGGGHHHHEEEEETTCHHHHHT-TH------
T ss_pred             HHHhhCCHHHHHHHHHHHHcCCCCeEEEECcCCCCHHHHHHHHHHH--hcCCcccCceEEeeccccCchHH-HH------
Confidence            3458999999999999998776666999999999999999999873  211 1111133343332111100 00      


Q ss_pred             CCCCCCCCChHHHHHHHHHHHHh--c-CCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCCC------C
Q 042541          244 GYPVPEFQTDEAAINDLERFFKQ--M-RIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFPQ------F  310 (695)
Q Consensus       244 ~~~~~~~~~~~~~~~~l~~~~~~--l-~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~~------~  310 (695)
                                    ..+......  + .+++.++|+||++.....    ++..+.....++++|+||......      .
T Consensus        95 --------------~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~l~sr  160 (327)
T 1iqp_A           95 --------------EKVKEFARTKPIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSR  160 (327)
T ss_dssp             --------------HHHHHHHHSCCGGGCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHT
T ss_pred             --------------HHHHHHHhhCCcCCCCCeEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCCccccCHHHHhh
Confidence                          111111111  1 267889999999876543    333333344578888888664211      1


Q ss_pred             CCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHHH
Q 042541          311 GSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGG  366 (695)
Q Consensus       311 ~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~~  366 (695)
                      ...+.+.+++.++...++...+.....   .-..+....|++.++|.|..+..+..
T Consensus       161 ~~~~~~~~l~~~~~~~~l~~~~~~~~~---~~~~~~~~~l~~~~~g~~r~~~~~l~  213 (327)
T 1iqp_A          161 CAIFRFRPLRDEDIAKRLRYIAENEGL---ELTEEGLQAILYIAEGDMRRAINILQ  213 (327)
T ss_dssp             EEEEECCCCCHHHHHHHHHHHHHTTTC---EECHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             CcEEEecCCCHHHHHHHHHHHHHhcCC---CCCHHHHHHHHHHCCCCHHHHHHHHH
Confidence            227899999999999999887643322   12356788999999999986654433

>1w8a_A SLIT protein; signaling protein, secreted protein, AXON guidance, leucine-rich repeat glycoprotein, EGF-like domain, signal protein; 2.8A {Drosophila melanogaster} SCOP: c.10.2.7

Probab=98.89  E-value=5.1e-09  Score=99.10  Aligned_cols=103  Identities=15%  Similarity=0.180  Sum_probs=83.3

Q ss_pred             cEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc-c--ccccccccEEeeccccCCcccccchhhhcccCCCc
Q 042541          577 KVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL-A--TVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNL  653 (695)
Q Consensus       577 r~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp-~--i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L  653 (695)
                      ++++++++++.  .++.  .+  ..+|++|++++|.+..+| .  ++++++|++|+|++|.++.++|..+.    .+++|
T Consensus        11 ~~l~~s~~~l~--~ip~--~~--~~~l~~L~l~~n~i~~~~~~~~~~~l~~L~~L~Ls~N~l~~~~~~~~~----~l~~L   80 (192)
T 1w8a_A           11 TTVDCTGRGLK--EIPR--DI--PLHTTELLLNDNELGRISSDGLFGRLPHLVKLELKRNQLTGIEPNAFE----GASHI   80 (192)
T ss_dssp             TEEECTTSCCS--SCCS--CC--CTTCSEEECCSCCCCSBCCSCSGGGCTTCCEEECCSSCCCCBCTTTTT----TCTTC
T ss_pred             CEEEcCCCCcC--cCcc--CC--CCCCCEEECCCCcCCccCCccccccCCCCCEEECCCCCCCCcCHhHcC----CcccC
Confidence            78888887662  2221  12  238999999999999887 4  89999999999999999999887776    89999


Q ss_pred             cEEecccccccccCc-hhhcCCCCCceeecccccCCCCC
Q 042541          654 LEMDIDYCNDLIELP-DGLCDIVSMEKLRITNCHRLSAL  691 (695)
Q Consensus       654 ~~L~l~~c~~l~~lP-~~i~~L~~L~~L~l~~~~~l~~l  691 (695)
                      ++|+|++|. +..+| ..++.+++|++|+|++|. +..+
T Consensus        81 ~~L~Ls~N~-l~~~~~~~~~~l~~L~~L~L~~N~-l~~~  117 (192)
T 1w8a_A           81 QELQLGENK-IKEISNKMFLGLHQLKTLNLYDNQ-ISCV  117 (192)
T ss_dssp             CEEECCSCC-CCEECSSSSTTCTTCCEEECCSSC-CCEE
T ss_pred             CEEECCCCc-CCccCHHHhcCCCCCCEEECCCCc-CCee
Confidence            999999975 55555 458999999999999977 5444

>3g06_A SSPH2 (leucine-rich repeat protein); E3 ubiquitin ligase, leucine rich repeat domain, type three effector, salmonella virulence factor; 1.90A {Salmonella typhimurium}

Probab=98.87  E-value=6e-09  Score=116.53  Aligned_cols=78  Identities=17%  Similarity=0.155  Sum_probs=56.8

Q ss_pred             CCCcEEEeccCCCCCcccccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCcee
Q 042541          601 SKLKKIRLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKL  680 (695)
Q Consensus       601 ~~L~~L~L~~~~l~~lp~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L  680 (695)
                      ++|++|++++|.++.+|  ..+++|++|+|++|.++.+|+        .+++|+.|+|++| .+..+|.+++++++|+.|
T Consensus       221 ~~L~~L~Ls~N~L~~lp--~~l~~L~~L~Ls~N~L~~lp~--------~~~~L~~L~Ls~N-~L~~lp~~l~~l~~L~~L  289 (622)
T 3g06_A          221 SGLKELIVSGNRLTSLP--VLPSELKELMVSGNRLTSLPM--------LPSGLLSLSVYRN-QLTRLPESLIHLSSETTV  289 (622)
T ss_dssp             TTCCEEECCSSCCSCCC--CCCTTCCEEECCSSCCSCCCC--------CCTTCCEEECCSS-CCCSCCGGGGGSCTTCEE
T ss_pred             CCCCEEEccCCccCcCC--CCCCcCcEEECCCCCCCcCCc--------ccccCcEEeCCCC-CCCcCCHHHhhccccCEE
Confidence            45666666666666665  334667777777776666554        4678899999986 567899999999999999


Q ss_pred             ecccccCCC
Q 042541          681 RITNCHRLS  689 (695)
Q Consensus       681 ~l~~~~~l~  689 (695)
                      +|++|+..+
T Consensus       290 ~L~~N~l~~  298 (622)
T 3g06_A          290 NLEGNPLSE  298 (622)
T ss_dssp             ECCSCCCCH
T ss_pred             EecCCCCCC
Confidence            999987443

>3g06_A SSPH2 (leucine-rich repeat protein); E3 ubiquitin ligase, leucine rich repeat domain, type three effector, salmonella virulence factor; 1.90A {Salmonella typhimurium}

Probab=98.86  E-value=2.5e-08  Score=111.51  Aligned_cols=39  Identities=26%  Similarity=0.260  Sum_probs=19.5

Q ss_pred             CCCccEEecccccccccCchhhcCCCCCceeecccccCCCCCCC
Q 042541          650 FPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPE  693 (695)
Q Consensus       650 l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~~l~~lP~  693 (695)
                      +++|+.|++++| .+..+|.   .+++|+.|+|++|. +..+|.
T Consensus       240 l~~L~~L~Ls~N-~L~~lp~---~~~~L~~L~Ls~N~-L~~lp~  278 (622)
T 3g06_A          240 PSELKELMVSGN-RLTSLPM---LPSGLLSLSVYRNQ-LTRLPE  278 (622)
T ss_dssp             CTTCCEEECCSS-CCSCCCC---CCTTCCEEECCSSC-CCSCCG
T ss_pred             CCcCcEEECCCC-CCCcCCc---ccccCcEEeCCCCC-CCcCCH
Confidence            444555555543 3444544   34555555665543 445554

>4ay9_X Follicle-stimulating hormone receptor; hormone-receptor complex, leucine-rich repeats, LRR, GPCR; HET: TYS NAG; 2.50A {Homo sapiens} PDB: 1xwd_C*

Probab=98.84  E-value=9.7e-09  Score=107.20  Aligned_cols=161  Identities=12%  Similarity=0.130  Sum_probs=102.2

Q ss_pred             CccceEEeeecCCcccCCCC-CCCCCceEEEEEEccCccccCCh-hhcCCCCCcEE-EEcccCCCCcccCcccccccCCC
Q 042541          526 PNNASLLSISTDETFSSNWP-DMQGPEVKVVVLNIRTKKYVLPD-FLQKMDELKVL-IVTNYGFSPAELNNFRVLSALSK  602 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~~~~~-~~~~~~l~~L~l~~~~~~~~~p~-~~~~l~~Lr~L-~l~~~~~~~~~~~~~~~l~~l~~  602 (695)
                      +..++.|.+..+........ ...+++|+.|.|+.|.....+|. .|.++++|..+ .+.+|.+..  + ....+..+++
T Consensus        29 ~~~l~~L~Ls~N~i~~i~~~~f~~l~~L~~L~Ls~N~i~~~i~~~~f~~L~~l~~~l~~~~N~l~~--l-~~~~f~~l~~  105 (350)
T 4ay9_X           29 PRNAIELRFVLTKLRVIQKGAFSGFGDLEKIEISQNDVLEVIEADVFSNLPKLHEIRIEKANNLLY--I-NPEAFQNLPN  105 (350)
T ss_dssp             CTTCSEEEEESCCCSEECTTSSTTCTTCCEEEEECCTTCCEECTTSBCSCTTCCEEEEEEETTCCE--E-CTTSBCCCTT
T ss_pred             CCCCCEEEccCCcCCCcCHHHHcCCCCCCEEECcCCCCCCccChhHhhcchhhhhhhcccCCcccc--c-Cchhhhhccc
Confidence            34566666665543221111 13566777777777655444443 56666666543 333443321  1 1122566777


Q ss_pred             CcEEEeccCCCCCcc--cccccccccEEeeccc-cCCcccccchhhhcccC-CCccEEecccccccccCchhhcCCCCCc
Q 042541          603 LKKIRLEHVSLPNSL--ATVRMNHLQKVSLVMC-NVGQVFRNSTFRISDAF-PNLLEMDIDYCNDLIELPDGLCDIVSME  678 (695)
Q Consensus       603 L~~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~-~i~~~~~~~~~~l~~~l-~~L~~L~l~~c~~l~~lP~~i~~L~~L~  678 (695)
                      |++|++++|.+..+|  .+....++.+|++.++ .+..+++..+.    .+ ..|++|++++| .+..+|.++....+|+
T Consensus       106 L~~L~l~~n~l~~~~~~~~~~~~~l~~l~l~~~~~i~~l~~~~f~----~~~~~l~~L~L~~N-~i~~i~~~~f~~~~L~  180 (350)
T 4ay9_X          106 LQYLLISNTGIKHLPDVHKIHSLQKVLLDIQDNINIHTIERNSFV----GLSFESVILWLNKN-GIQEIHNSAFNGTQLD  180 (350)
T ss_dssp             CCEEEEEEECCSSCCCCTTCCBSSCEEEEEESCTTCCEECTTSST----TSBSSCEEEECCSS-CCCEECTTSSTTEEEE
T ss_pred             cccccccccccccCCchhhcccchhhhhhhccccccccccccchh----hcchhhhhhccccc-cccCCChhhccccchh
Confidence            777777777777666  4455566777777654 56666665543    44 46888999985 6788998888888999


Q ss_pred             eeecccccCCCCCCCC
Q 042541          679 KLRITNCHRLSALPEG  694 (695)
Q Consensus       679 ~L~l~~~~~l~~lP~~  694 (695)
                      .|++.+|+.++.+|.+
T Consensus       181 ~l~l~~~n~l~~i~~~  196 (350)
T 4ay9_X          181 ELNLSDNNNLEELPND  196 (350)
T ss_dssp             EEECTTCTTCCCCCTT
T ss_pred             HHhhccCCcccCCCHH
Confidence            9999988889999875

>2ca6_A RAN GTPase-activating protein 1; GAP, GTPase activation, hemihedral twinning, leucine-rich repeat protein, LRR, merohedral twinning; 2.2A {Schizosaccharomyces pombe} SCOP: c.10.1.2 PDB: 1k5g_C* 1k5d_C 1yrg_A

Probab=98.80  E-value=1e-09  Score=116.40  Aligned_cols=136  Identities=13%  Similarity=0.120  Sum_probs=103.4

Q ss_pred             CceEEEEEEccCcc-ccCC---hhhcCCCCCcEEEEcccCCCCcccC-ccc-ccccCCCCcEEEeccCCC-----CCcc-
Q 042541          550 PEVKVVVLNIRTKK-YVLP---DFLQKMDELKVLIVTNYGFSPAELN-NFR-VLSALSKLKKIRLEHVSL-----PNSL-  617 (695)
Q Consensus       550 ~~l~~L~l~~~~~~-~~~p---~~~~~l~~Lr~L~l~~~~~~~~~~~-~~~-~l~~l~~L~~L~L~~~~l-----~~lp-  617 (695)
                      ++|+.|.++.|... ..+|   ..+..+++|++|++++|.+....+. ..+ .+..+++|++|+|++|.+     ..+| 
T Consensus       159 ~~L~~L~L~~n~l~~~~~~~l~~~l~~~~~L~~L~L~~n~l~~~g~~~l~~~~l~~~~~L~~L~Ls~n~l~~~g~~~l~~  238 (386)
T 2ca6_A          159 PPLRSIICGRNRLENGSMKEWAKTFQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQDNTFTHLGSSALAI  238 (386)
T ss_dssp             CCCCEEECCSSCCTGGGHHHHHHHHHHCTTCCEEECCSSCCCHHHHHHHHHTTGGGCTTCCEEECCSSCCHHHHHHHHHH
T ss_pred             CCCcEEECCCCCCCcHHHHHHHHHHHhCCCcCEEECcCCCCCHhHHHHHHHHHhhcCCCccEEECcCCCCCcHHHHHHHH
Confidence            78888988888554 3444   5677899999999999877432211 112 478899999999999999     5678 


Q ss_pred             cccccccccEEeeccccCCccc----ccchhhhcccCCCccEEecccccccc----cCchhh-cCCCCCceeecccccC
Q 042541          618 ATVRMNHLQKVSLVMCNVGQVF----RNSTFRISDAFPNLLEMDIDYCNDLI----ELPDGL-CDIVSMEKLRITNCHR  687 (695)
Q Consensus       618 ~i~~l~~L~~L~l~~~~i~~~~----~~~~~~l~~~l~~L~~L~l~~c~~l~----~lP~~i-~~L~~L~~L~l~~~~~  687 (695)
                      .+..+++|++|+|++|.++...    +..+. . ..+++|++|+|++|....    .+|..+ .++++|++|++++|+.
T Consensus       239 ~l~~~~~L~~L~L~~n~i~~~~~~~l~~~l~-~-~~~~~L~~L~L~~n~i~~~g~~~l~~~l~~~l~~L~~L~l~~N~l  315 (386)
T 2ca6_A          239 ALKSWPNLRELGLNDCLLSARGAAAVVDAFS-K-LENIGLQTLRLQYNEIELDAVRTLKTVIDEKMPDLLFLELNGNRF  315 (386)
T ss_dssp             HGGGCTTCCEEECTTCCCCHHHHHHHHHHHH-T-CSSCCCCEEECCSSCCBHHHHHHHHHHHHHHCTTCCEEECTTSBS
T ss_pred             HHccCCCcCEEECCCCCCchhhHHHHHHHHh-h-ccCCCeEEEECcCCcCCHHHHHHHHHHHHhcCCCceEEEccCCcC
Confidence            8899999999999999987641    22210 0 038999999999975433    399888 7799999999999873

>1jl5_A Outer protein YOPM; leucine-rich repeat, molecular pathogenesis, effector protein, virulence factor, toxin; 2.10A {Yersinia pestis} SCOP: c.10.2.6 PDB: 1g9u_A

Probab=98.80  E-value=1.9e-08  Score=108.83  Aligned_cols=142  Identities=24%  Similarity=0.197  Sum_probs=104.6

Q ss_pred             CccceEEeeecCCcccCCCCCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcE
Q 042541          526 PNNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKK  605 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~~~~~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~  605 (695)
                      +...+++.+..+.... .+  ..+++|+.|.++.+.... +|..   .++|++|++++|.+..  ++   .++.+++|++
T Consensus        90 ~~~L~~L~l~~n~l~~-lp--~~~~~L~~L~l~~n~l~~-l~~~---~~~L~~L~L~~n~l~~--lp---~~~~l~~L~~  157 (454)
T 1jl5_A           90 PPHLESLVASCNSLTE-LP--ELPQSLKSLLVDNNNLKA-LSDL---PPLLEYLGVSNNQLEK--LP---ELQNSSFLKI  157 (454)
T ss_dssp             CTTCSEEECCSSCCSS-CC--CCCTTCCEEECCSSCCSC-CCSC---CTTCCEEECCSSCCSS--CC---CCTTCTTCCE
T ss_pred             cCCCCEEEccCCcCCc-cc--cccCCCcEEECCCCccCc-ccCC---CCCCCEEECcCCCCCC--Cc---ccCCCCCCCE
Confidence            4567888876654322 11  134789999988774432 3321   2689999999987642  33   4889999999


Q ss_pred             EEeccCCCCCcc-cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeeccc
Q 042541          606 IRLEHVSLPNSL-ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITN  684 (695)
Q Consensus       606 L~L~~~~l~~lp-~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~  684 (695)
                      |++++|.++.+| .+   .+|++|++++|.++.+| ...     .+++|++|++++| .+..+|...   ++|++|++++
T Consensus       158 L~l~~N~l~~lp~~~---~~L~~L~L~~n~l~~l~-~~~-----~l~~L~~L~l~~N-~l~~l~~~~---~~L~~L~l~~  224 (454)
T 1jl5_A          158 IDVDNNSLKKLPDLP---PSLEFIAAGNNQLEELP-ELQ-----NLPFLTAIYADNN-SLKKLPDLP---LSLESIVAGN  224 (454)
T ss_dssp             EECCSSCCSCCCCCC---TTCCEEECCSSCCSSCC-CCT-----TCTTCCEEECCSS-CCSSCCCCC---TTCCEEECCS
T ss_pred             EECCCCcCcccCCCc---ccccEEECcCCcCCcCc-ccc-----CCCCCCEEECCCC-cCCcCCCCc---CcccEEECcC
Confidence            999999999888 43   48999999999998865 443     8999999999997 466677643   5899999999


Q ss_pred             ccCCCCCCC
Q 042541          685 CHRLSALPE  693 (695)
Q Consensus       685 ~~~l~~lP~  693 (695)
                      |. +..+|.
T Consensus       225 n~-l~~lp~  232 (454)
T 1jl5_A          225 NI-LEELPE  232 (454)
T ss_dssp             SC-CSSCCC
T ss_pred             Cc-CCcccc
Confidence            75 778874

>2ca6_A RAN GTPase-activating protein 1; GAP, GTPase activation, hemihedral twinning, leucine-rich repeat protein, LRR, merohedral twinning; 2.2A {Schizosaccharomyces pombe} SCOP: c.10.1.2 PDB: 1k5g_C* 1k5d_C 1yrg_A

Probab=98.79  E-value=1.2e-09  Score=115.93  Aligned_cols=156  Identities=12%  Similarity=0.150  Sum_probs=95.9

Q ss_pred             CccceEEeeecCCcccCC----C-CCCCCCceEEEEEEccCccc----cCChhhcCC---------CCCcEEEEcccCCC
Q 042541          526 PNNASLLSISTDETFSSN----W-PDMQGPEVKVVVLNIRTKKY----VLPDFLQKM---------DELKVLIVTNYGFS  587 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~~~----~-~~~~~~~l~~L~l~~~~~~~----~~p~~~~~l---------~~Lr~L~l~~~~~~  587 (695)
                      ....++|.+..+......    + .-..+++|+.|.|+.|....    .++..+..+         ++|++|++++|.+.
T Consensus        93 ~~~L~~L~Ls~n~l~~~~~~~l~~~l~~~~~L~~L~L~~n~l~~~~~~~l~~~l~~l~~~~~~~~~~~L~~L~L~~n~l~  172 (386)
T 2ca6_A           93 CPKLHTVRLSDNAFGPTAQEPLIDFLSKHTPLEHLYLHNNGLGPQAGAKIARALQELAVNKKAKNAPPLRSIICGRNRLE  172 (386)
T ss_dssp             CTTCCEEECCSCCCCTTTHHHHHHHHHHCTTCCEEECCSSCCHHHHHHHHHHHHHHHHHHHHHHTCCCCCEEECCSSCCT
T ss_pred             CCcccEEECCCCcCCHHHHHHHHHHHHhCCCCCEEECcCCCCCHHHHHHHHHHHHHHhhhhhcccCCCCcEEECCCCCCC
Confidence            345667766554332110    0 00246777777777765432    233334444         77888888777664


Q ss_pred             CcccCcc-cccccCCCCcEEEeccCCCC------Ccc-cccccccccEEeeccccCC-----cccccchhhhcccCCCcc
Q 042541          588 PAELNNF-RVLSALSKLKKIRLEHVSLP------NSL-ATVRMNHLQKVSLVMCNVG-----QVFRNSTFRISDAFPNLL  654 (695)
Q Consensus       588 ~~~~~~~-~~l~~l~~L~~L~L~~~~l~------~lp-~i~~l~~L~~L~l~~~~i~-----~~~~~~~~~l~~~l~~L~  654 (695)
                      ...++.+ ..+..+++|++|++++|.+.      -+| .+.++++|++|+|++|.++     .++. .+.    .+++|+
T Consensus       173 ~~~~~~l~~~l~~~~~L~~L~L~~n~l~~~g~~~l~~~~l~~~~~L~~L~Ls~n~l~~~g~~~l~~-~l~----~~~~L~  247 (386)
T 2ca6_A          173 NGSMKEWAKTFQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQDNTFTHLGSSALAI-ALK----SWPNLR  247 (386)
T ss_dssp             GGGHHHHHHHHHHCTTCCEEECCSSCCCHHHHHHHHHTTGGGCTTCCEEECCSSCCHHHHHHHHHH-HGG----GCTTCC
T ss_pred             cHHHHHHHHHHHhCCCcCEEECcCCCCCHhHHHHHHHHHhhcCCCccEEECcCCCCCcHHHHHHHH-HHc----cCCCcC
Confidence            3333221 23567778888888888877      345 6777888888888888774     2333 222    678888


Q ss_pred             EEeccccccccc----Cchhh--cCCCCCceeeccccc
Q 042541          655 EMDIDYCNDLIE----LPDGL--CDIVSMEKLRITNCH  686 (695)
Q Consensus       655 ~L~l~~c~~l~~----lP~~i--~~L~~L~~L~l~~~~  686 (695)
                      +|+|++|.....    +|..+  +++++|++|+|++|.
T Consensus       248 ~L~L~~n~i~~~~~~~l~~~l~~~~~~~L~~L~L~~n~  285 (386)
T 2ca6_A          248 ELGLNDCLLSARGAAAVVDAFSKLENIGLQTLRLQYNE  285 (386)
T ss_dssp             EEECTTCCCCHHHHHHHHHHHHTCSSCCCCEEECCSSC
T ss_pred             EEECCCCCCchhhHHHHHHHHhhccCCCeEEEECcCCc
Confidence            888888753322    46666  448888888888876

>2r9u_A Variable lymphocyte receptor; adaptive immunity, VLR, leucine-rich repeat, LRR, system; 2.10A {Petromyzon marinus}

Probab=98.78  E-value=2e-08  Score=93.27  Aligned_cols=96  Identities=13%  Similarity=0.075  Sum_probs=70.3

Q ss_pred             ccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--cccccccccEEeeccccCCccccc
Q 042541          564 YVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFRN  641 (695)
Q Consensus       564 ~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~  641 (695)
                      ..+|..+.  ++|++|+|++|.+....   ...++.+++|++|+|++|.++.+|  .++++++|++|+|++|.++.+++.
T Consensus        25 ~~iP~~~~--~~L~~L~Ls~N~l~~~~---~~~~~~l~~L~~L~Ls~N~l~~i~~~~~~~l~~L~~L~L~~N~l~~l~~~   99 (174)
T 2r9u_A           25 ASVPAGIP--TDKQRLWLNNNQITKLE---PGVFDHLVNLQQLYFNSNKLTAIPTGVFDKLTQLTQLDLNDNHLKSIPRG   99 (174)
T ss_dssp             SSCCSCCC--TTCSEEECCSSCCCCCC---TTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTT
T ss_pred             CccCCCcC--CCCcEEEeCCCCccccC---HHHhcCCcCCCEEECCCCCCCccChhHhCCcchhhEEECCCCccceeCHH
Confidence            45665543  77888888888764211   123678888888888888888888  457888888888888888888887


Q ss_pred             chhhhcccCCCccEEecccccccccCch
Q 042541          642 STFRISDAFPNLLEMDIDYCNDLIELPD  669 (695)
Q Consensus       642 ~~~~l~~~l~~L~~L~l~~c~~l~~lP~  669 (695)
                      .+.    .+++|++|+|++|. +...|.
T Consensus       100 ~~~----~l~~L~~L~L~~N~-~~c~~~  122 (174)
T 2r9u_A          100 AFD----NLKSLTHIYLYNNP-WDCECR  122 (174)
T ss_dssp             TTT----TCTTCSEEECCSSC-BCTTBG
T ss_pred             Hhc----cccCCCEEEeCCCC-cccccc
Confidence            665    78888888888853 444444

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=98.76  E-value=4.7e-08  Score=98.83  Aligned_cols=165  Identities=7%  Similarity=0.070  Sum_probs=105.7

Q ss_pred             CCCCCcchHHHHHHHHH----cCCceEEEEEcCCCCcHHHHHHHHhccccccc---cC-CCcEEEEEeCCCCCHHHHHHH
Q 042541          167 ISPGLDVPLKELKMELF----KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQG---KF-KDDIFYVTVSKNPNVKAIVQK  238 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~----~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~---~f-~~~~~wv~~~~~~~~~~~~~~  238 (695)
                      .+.||++|.++|...|.    .+..+.+.|+|++|+|||++++.+++......   .. ...++++++....+...++..
T Consensus        21 ~L~~Re~E~~~i~~~L~~~i~~~~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~~~~t~~~~~~~  100 (318)
T 3te6_A           21 LLKSQVEDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELAGMDALYEK  100 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTCCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETTCCC--HHHHHH
T ss_pred             ccCCHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEeccccCCHHHHHHH
Confidence            47899999999988776    45678899999999999999999998422111   11 122557777788888999999


Q ss_pred             HHHhcCCCCCCCCChHHHHHHHHHHHHhc---CCCcEEEEEeCCCCCC-hHHH-hhhcc-CCCCC--EEEEEcCC-CCC-
Q 042541          239 VLHHKGYPVPEFQTDEAAINDLERFFKQM---RIEAILLVLDDVWPGS-ESLL-QKLGF-QLPDY--KILVTSRS-EFP-  308 (695)
Q Consensus       239 i~~~l~~~~~~~~~~~~~~~~l~~~~~~l---~~~~~LlVlDdv~~~~-~~~~-~~l~~-~~~gs--~iivTtR~-~~~-  308 (695)
                      |.+++.+......   .....+..++..+   .+++++++||+++... +..+ .-+.+ ...++  .||.++.. ... 
T Consensus       101 I~~~L~g~~~~~~---~~~~~L~~~f~~~~~~~~~~~ii~lDE~d~l~~q~~L~~l~~~~~~~~s~~~vI~i~n~~d~~~  177 (318)
T 3te6_A          101 IWFAISKENLCGD---ISLEALNFYITNVPKAKKRKTLILIQNPENLLSEKILQYFEKWISSKNSKLSIICVGGHNVTIR  177 (318)
T ss_dssp             HHHHHSCCC--CC---CCHHHHHHHHHHSCGGGSCEEEEEEECCSSSCCTHHHHHHHHHHHCSSCCEEEEEECCSSCCCH
T ss_pred             HHHHhcCCCCCch---HHHHHHHHHHHHhhhccCCceEEEEecHHHhhcchHHHHHHhcccccCCcEEEEEEecCcccch
Confidence            9999865422111   1234455556443   5678999999987653 2222 22221 12333  33333433 211 


Q ss_pred             ---------CCC-CeEecCCCChHHHHHHHHHhccC
Q 042541          309 ---------QFG-SVHYLKPLTYEAARTLFLHSANL  334 (695)
Q Consensus       309 ---------~~~-~~~~l~~L~~~ea~~Lf~~~~~~  334 (695)
                               ..+ ..+.+.+++.+|-.+++.+++..
T Consensus       178 ~~L~~~v~SR~~~~~i~F~pYt~~el~~Il~~Rl~~  213 (318)
T 3te6_A          178 EQINIMPSLKAHFTEIKLNKVDKNELQQMIITRLKS  213 (318)
T ss_dssp             HHHHTCHHHHTTEEEEECCCCCHHHHHHHHHHHHHH
T ss_pred             hhcchhhhccCCceEEEeCCCCHHHHHHHHHHHHHh
Confidence                     122 36899999999999999887643

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=98.75  E-value=1.3e-07  Score=99.41  Aligned_cols=185  Identities=17%  Similarity=0.108  Sum_probs=108.6

Q ss_pred             CCCCCCcchHHHHHHHHHcCC-ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcC
Q 042541          166 VISPGLDVPLKELKMELFKDG-RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKG  244 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~~-~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~  244 (695)
                      ..++|++..++.+...+..+. ...+.|+|++|+||||+|+.+++.......+.    ...+....    ....+.....
T Consensus        16 ~~~vg~~~~~~~L~~~l~~~~~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~----~~~~~~~~----~~~~~~~~~~   87 (373)
T 1jr3_A           16 ADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGIT----ATPCGVCD----NCREIEQGRF   87 (373)
T ss_dssp             TTSCSCHHHHHHHHHHHHHTCCCSEEEEESCTTSSHHHHHHHHHHHHSCTTCSC----SSCCSSSH----HHHHHHTSCC
T ss_pred             hhccCcHHHHHHHHHHHHhCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCC----CCCCcccH----HHHHHhccCC
Confidence            458999999999999988654 46789999999999999999987321111100    00000000    0011110000


Q ss_pred             C-----CCCCCCChHHHHHHHHHHHHh-----cCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCC--
Q 042541          245 Y-----PVPEFQTDEAAINDLERFFKQ-----MRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFP--  308 (695)
Q Consensus       245 ~-----~~~~~~~~~~~~~~l~~~~~~-----l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~--  308 (695)
                      .     ........    +.+..+++.     ..+++.++|+||++.....    ++..+.....+..+|++|.....  
T Consensus        88 ~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~Ll~~le~~~~~~~~Il~~~~~~~l~  163 (373)
T 1jr3_A           88 VDLIEIDAASRTKV----EDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLP  163 (373)
T ss_dssp             SSCEEEETTCSCCS----SCHHHHHHHTTSCCSSSSSEEEEEECGGGSCHHHHHHHHHHHHSCCSSEEEEEEESCGGGSC
T ss_pred             CceEEecccccCCH----HHHHHHHHHHhhccccCCeEEEEEECcchhcHHHHHHHHHHHhcCCCceEEEEEeCChHhCc
Confidence            0     00000000    112222222     2466789999999776543    33334334446677777764421  


Q ss_pred             ----CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHH
Q 042541          309 ----QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVG  365 (695)
Q Consensus       309 ----~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~  365 (695)
                          .....+.+.+++.++..+++...+.....   .-..+.+..|++.++|.|..+..+.
T Consensus       164 ~~l~sr~~~i~~~~l~~~~~~~~l~~~~~~~~~---~~~~~a~~~l~~~~~G~~r~~~~~l  221 (373)
T 1jr3_A          164 VTILSRCLQFHLKALDVEQIRHQLEHILNEEHI---AHEPRALQLLARAAEGSLRDALSLT  221 (373)
T ss_dssp             HHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTC---CBCHHHHHHHHHHSSSCHHHHHHHH
T ss_pred             HHHHhheeEeeCCCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHCCCCHHHHHHHH
Confidence                12247899999999999999876533221   1235678889999999998776654

>3g39_A Variable lymphocyte receptor VLRB.2D; antibody, X-RAY, crystallography, immune system; 1.55A {Petromyzon marinus} PDB: 3g3a_A 3g3b_A 3twi_D

Probab=98.73  E-value=2.5e-08  Score=92.26  Aligned_cols=89  Identities=16%  Similarity=0.155  Sum_probs=64.9

Q ss_pred             cCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--cccccccccEEeeccccCCcccccc
Q 042541          565 VLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFRNS  642 (695)
Q Consensus       565 ~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~  642 (695)
                      .+|..+  .++|++|+|++|.+....   ...+..+++|++|+|++|.++.+|  .++++++|++|+|++|.++.+++..
T Consensus        23 ~ip~~~--~~~l~~L~L~~N~i~~~~---~~~~~~l~~L~~L~Ls~N~l~~l~~~~f~~l~~L~~L~L~~N~l~~~~~~~   97 (170)
T 3g39_A           23 SVPTGI--PTTTQVLYLYDNQITKLE---PGVFDRLTQLTRLDLDNNQLTVLPAGVFDKLTQLTQLSLNDNQLKSIPRGA   97 (170)
T ss_dssp             SCCSCC--CTTCSEEECCSSCCCCCC---TTTTTTCTTCSEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCCCCTTT
T ss_pred             ccCccC--CCCCcEEEcCCCcCCccC---hhhhcCcccCCEEECCCCCcCccChhhccCCCCCCEEECCCCccCEeCHHH
Confidence            455544  367888888887664211   123677888888888888888777  4578888888888888888888776


Q ss_pred             hhhhcccCCCccEEeccccc
Q 042541          643 TFRISDAFPNLLEMDIDYCN  662 (695)
Q Consensus       643 ~~~l~~~l~~L~~L~l~~c~  662 (695)
                      +.    .+++|++|+|++|.
T Consensus        98 ~~----~l~~L~~L~L~~N~  113 (170)
T 3g39_A           98 FD----NLKSLTHIWLLNNP  113 (170)
T ss_dssp             TT----TCTTCCEEECCSSC
T ss_pred             hc----CCCCCCEEEeCCCC
Confidence            65    78888888888754

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=98.70  E-value=4.5e-08  Score=100.61  Aligned_cols=174  Identities=14%  Similarity=0.164  Sum_probs=110.1

Q ss_pred             CCCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccc-cccCCCcEEEEEeCCCCCHHHHHHHHHHhc
Q 042541          165 PVISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQV-QGKFKDDIFYVTVSKNPNVKAIVQKVLHHK  243 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~-~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l  243 (695)
                      -..++|++..++.+..++..+..+.+.|+|++|+|||++|+.+++.  + ...+...++.++.+......          
T Consensus        16 ~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~l~~~--l~~~~~~~~~~~~~~~~~~~~~----------   83 (319)
T 2chq_A           16 LDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARD--LFGENWRDNFIEMNASDERGID----------   83 (319)
T ss_dssp             GGGSCSCHHHHHHHHTTTTTTCCCCEEEESSSSSSHHHHHHHHHHH--HHTTCHHHHCEEEETTSTTCTT----------
T ss_pred             HHHHhCCHHHHHHHHHHHhCCCCCeEEEECcCCcCHHHHHHHHHHH--hcCCcccCCeEEEeCccccChH----------
Confidence            3458999999999988887666555999999999999999999873  2 11122113344444321110          


Q ss_pred             CCCCCCCCChHHHHHHHHHHHHh--c-CCCcEEEEEeCCCCCChHHHhh----hccCCCCCEEEEEcCCCCC------CC
Q 042541          244 GYPVPEFQTDEAAINDLERFFKQ--M-RIEAILLVLDDVWPGSESLLQK----LGFQLPDYKILVTSRSEFP------QF  310 (695)
Q Consensus       244 ~~~~~~~~~~~~~~~~l~~~~~~--l-~~~~~LlVlDdv~~~~~~~~~~----l~~~~~gs~iivTtR~~~~------~~  310 (695)
                              ....   .+......  + .+++.++|+||++.........    +....+++.+|+||.....      ..
T Consensus        84 --------~~~~---~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~~l~~~l~sr  152 (319)
T 2chq_A           84 --------VVRH---KIKEFARTAPIGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVSRIIEPIQSR  152 (319)
T ss_dssp             --------TSSH---HHHHHHHSCCSSSCCCEEEEEETGGGSCHHHHHTTGGGTSSSSSSEEEEEEESCGGGSCHHHHTT
T ss_pred             --------HHHH---HHHHHHhcCCCCCCCceEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCChhhcchHHHhh
Confidence                    0001   11111111  1 2668999999997765432222    2223346778877765421      12


Q ss_pred             CCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHH
Q 042541          311 GSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVV  364 (695)
Q Consensus       311 ~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~  364 (695)
                      ...+.+.+++.++..+++...+.....   .-..+....|++.++|.+..+...
T Consensus       153 ~~~i~~~~~~~~~~~~~l~~~~~~~~~---~i~~~~l~~l~~~~~G~~r~~~~~  203 (319)
T 2chq_A          153 CAVFRFKPVPKEAMKKRLLEICEKEGV---KITEDGLEALIYISGGDFRKAINA  203 (319)
T ss_dssp             CEEEECCCCCHHHHHHHHHHHHHTTCC---CBCHHHHHHHHHTTTTCHHHHHHH
T ss_pred             CeEEEecCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHcCCCHHHHHHH
Confidence            238999999999999999887653322   123667889999999999865544

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.64  E-value=3.7e-07  Score=95.16  Aligned_cols=188  Identities=14%  Similarity=0.068  Sum_probs=113.5

Q ss_pred             CCCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcC
Q 042541          165 PVISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKG  244 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~  244 (695)
                      -..++|++..++.+..++..+..+.+.|+|++|+||||+|+.+++.......+...+..++.+.......+. +.+..+.
T Consensus        36 ~~~i~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~  114 (353)
T 1sxj_D           36 LDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVR-EKVKNFA  114 (353)
T ss_dssp             TTTCCSCCTTHHHHHHHTTCTTCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHHT-THHHHHH
T ss_pred             HHHhhCCHHHHHHHHHHHhcCCCCEEEEECCCCCCHHHHHHHHHHHhCCCcccccceEEEccccccchHHHH-HHHHHHh
Confidence            356899999999999998876545589999999999999999987321111233334455555433333222 1111110


Q ss_pred             -CCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCCCC------CCe
Q 042541          245 -YPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFPQF------GSV  313 (695)
Q Consensus       245 -~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~~~------~~~  313 (695)
                       .........  .     . ...-.++.-++++|++......    ++..+.......++|++|.......      ...
T Consensus       115 ~~~~~~~~~~--~-----~-~~~~~~~~~vliiDE~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~l~sR~~~  186 (353)
T 1sxj_D          115 RLTVSKPSKH--D-----L-ENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSK  186 (353)
T ss_dssp             HSCCCCCCTT--H-----H-HHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHHSEE
T ss_pred             hhcccccchh--h-----c-ccCCCCCceEEEEECCCccCHHHHHHHHHHHHhcCCCceEEEEeCchhhCcchhhccCce
Confidence             000000000  0     0 0111245679999998766532    3333433445677777775442111      127


Q ss_pred             EecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHH
Q 042541          314 HYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVV  364 (695)
Q Consensus       314 ~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~  364 (695)
                      +.+.+++.++....+...+.....   .-.++....|++.++|.|..+..+
T Consensus       187 i~~~~~~~~~~~~~l~~~~~~~~~---~i~~~~l~~l~~~~~G~~r~~~~~  234 (353)
T 1sxj_D          187 FRFKALDASNAIDRLRFISEQENV---KCDDGVLERILDISAGDLRRGITL  234 (353)
T ss_dssp             EECCCCCHHHHHHHHHHHHHTTTC---CCCHHHHHHHHHHTSSCHHHHHHH
T ss_pred             EEeCCCCHHHHHHHHHHHHHHhCC---CCCHHHHHHHHHHcCCCHHHHHHH
Confidence            889999999999999887643222   123678899999999999865544

>2ifg_A High affinity nerve growth factor receptor; TRK, TRKA, receptor-ligand complex transferase; HET: NAG NDG MAN BMA; 3.40A {Homo sapiens} SCOP: b.1.1.4 b.1.1.4 c.10.2.7

Probab=98.63  E-value=5.1e-08  Score=101.53  Aligned_cols=92  Identities=17%  Similarity=0.184  Sum_probs=70.3

Q ss_pred             ccccCChhhcCCCCCcEEEEcc-cCCCCcccCcccccccCCCCcEEEeccCCCCCcc--cccccccccEEeeccccCCcc
Q 042541          562 KKYVLPDFLQKMDELKVLIVTN-YGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQV  638 (695)
Q Consensus       562 ~~~~~p~~~~~l~~Lr~L~l~~-~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~  638 (695)
                      ....+|. +..+.+|+.|+|++ |.+..  ++ ...++.|++|++|+|++|.+..+|  .+++|++|++|+|++|.++.+
T Consensus        20 ~l~~ip~-l~~~~~L~~L~l~~~n~l~~--~~-~~~~~~l~~L~~L~l~~N~l~~~~~~~~~~l~~L~~L~l~~N~l~~~   95 (347)
T 2ifg_A           20 ALDSLHH-LPGAENLTELYIENQQHLQH--LE-LRDLRGLGELRNLTIVKSGLRFVAPDAFHFTPRLSRLNLSFNALESL   95 (347)
T ss_dssp             CCTTTTT-SCSCSCCSEEECCSCSSCCE--EC-GGGSCSCCCCSEEECCSSCCCEECTTGGGSCSCCCEEECCSSCCSCC
T ss_pred             CCCccCC-CCCCCCeeEEEccCCCCCCC--cC-hhHhccccCCCEEECCCCccceeCHHHhcCCcCCCEEeCCCCcccee
Confidence            4456788 88888899999985 66531  11 123778888999999999888766  778899999999999988888


Q ss_pred             cccchhhhcccCCCccEEeccccc
Q 042541          639 FRNSTFRISDAFPNLLEMDIDYCN  662 (695)
Q Consensus       639 ~~~~~~~l~~~l~~L~~L~l~~c~  662 (695)
                      |+..+.    .++ |+.|+|.+|.
T Consensus        96 ~~~~~~----~~~-L~~l~l~~N~  114 (347)
T 2ifg_A           96 SWKTVQ----GLS-LQELVLSGNP  114 (347)
T ss_dssp             CSTTTC----SCC-CCEEECCSSC
T ss_pred             CHHHcc----cCC-ceEEEeeCCC
Confidence            887774    344 8889888754

>3goz_A Leucine-rich repeat-containing protein; LEGL7, NESG, LGR148, structural genomics, PSI-2, protein structure initiative; 2.10A {Legionella pneumophila subsp}

Probab=98.59  E-value=2.5e-08  Score=104.61  Aligned_cols=164  Identities=15%  Similarity=0.167  Sum_probs=105.8

Q ss_pred             CCccceEEeeecCCcccCCC----CC-CCCC-ceEEEEEEccCccccCChhhcCC-----CCCcEEEEcccCCCCcccCc
Q 042541          525 HPNNASLLSISTDETFSSNW----PD-MQGP-EVKVVVLNIRTKKYVLPDFLQKM-----DELKVLIVTNYGFSPAELNN  593 (695)
Q Consensus       525 ~~~~~r~l~~~~~~~~~~~~----~~-~~~~-~l~~L~l~~~~~~~~~p~~~~~l-----~~Lr~L~l~~~~~~~~~~~~  593 (695)
                      .+...++|.+..+.......    .. ..++ +|+.|.++.|......+..+..+     ++|++|++++|.+.......
T Consensus        20 ~~~~L~~L~Ls~n~l~~~~~~~l~~~l~~~~~~L~~L~Ls~N~l~~~~~~~l~~~l~~~~~~L~~L~Ls~n~l~~~~~~~   99 (362)
T 3goz_A           20 IPHGVTSLDLSLNNLYSISTVELIQAFANTPASVTSLNLSGNSLGFKNSDELVQILAAIPANVTSLNLSGNFLSYKSSDE   99 (362)
T ss_dssp             SCTTCCEEECTTSCGGGSCHHHHHHHHHTCCTTCCEEECCSSCGGGSCHHHHHHHHHTSCTTCCEEECCSSCGGGSCHHH
T ss_pred             CCCCceEEEccCCCCChHHHHHHHHHHHhCCCceeEEECcCCCCCHHHHHHHHHHHhccCCCccEEECcCCcCChHHHHH
Confidence            34558888887665332221    11 1466 89999998886666555555554     89999999998764322111


Q ss_pred             c-cccccC-CCCcEEEeccCCCCCcc--cccc-----cccccEEeeccccCCcccccchh-hhcccCC-CccEEeccccc
Q 042541          594 F-RVLSAL-SKLKKIRLEHVSLPNSL--ATVR-----MNHLQKVSLVMCNVGQVFRNSTF-RISDAFP-NLLEMDIDYCN  662 (695)
Q Consensus       594 ~-~~l~~l-~~L~~L~L~~~~l~~lp--~i~~-----l~~L~~L~l~~~~i~~~~~~~~~-~l~~~l~-~L~~L~l~~c~  662 (695)
                      + ..+..+ ++|++|+|++|.++..+  .++.     .++|++|+|++|.++......+. .+. .++ +|++|+|++|.
T Consensus       100 l~~~l~~~~~~L~~L~Ls~N~l~~~~~~~l~~~l~~~~~~L~~L~Ls~N~l~~~~~~~l~~~l~-~~~~~L~~L~Ls~n~  178 (362)
T 3goz_A          100 LVKTLAAIPFTITVLDLGWNDFSSKSSSEFKQAFSNLPASITSLNLRGNDLGIKSSDELIQILA-AIPANVNSLNLRGNN  178 (362)
T ss_dssp             HHHHHHTSCTTCCEEECCSSCGGGSCHHHHHHHHTTSCTTCCEEECTTSCGGGSCHHHHHHHHH-TSCTTCCEEECTTSC
T ss_pred             HHHHHHhCCCCccEEECcCCcCCcHHHHHHHHHHHhCCCceeEEEccCCcCCHHHHHHHHHHHh-cCCccccEeeecCCC
Confidence            1 113444 78999999999988555  4333     25899999999988753322211 111 444 89999999975


Q ss_pred             ccccCch----hhcCC-CCCceeecccccCCCC
Q 042541          663 DLIELPD----GLCDI-VSMEKLRITNCHRLSA  690 (695)
Q Consensus       663 ~l~~lP~----~i~~L-~~L~~L~l~~~~~l~~  690 (695)
                      .-...|.    .+..+ ++|++|+|++|. ++.
T Consensus       179 l~~~~~~~l~~~l~~~~~~L~~L~Ls~N~-i~~  210 (362)
T 3goz_A          179 LASKNCAELAKFLASIPASVTSLDLSANL-LGL  210 (362)
T ss_dssp             GGGSCHHHHHHHHHTSCTTCCEEECTTSC-GGG
T ss_pred             CchhhHHHHHHHHHhCCCCCCEEECCCCC-CCh
Confidence            4334443    34455 599999999976 554

>3goz_A Leucine-rich repeat-containing protein; LEGL7, NESG, LGR148, structural genomics, PSI-2, protein structure initiative; 2.10A {Legionella pneumophila subsp}

Probab=98.58  E-value=2.1e-08  Score=105.24  Aligned_cols=163  Identities=15%  Similarity=0.122  Sum_probs=112.8

Q ss_pred             cceEEeeecCCcccCCCCCC-C-----CCceEEEEEEccCccccCCh----hhcCC-CCCcEEEEcccCCCCcccCcc-c
Q 042541          528 NASLLSISTDETFSSNWPDM-Q-----GPEVKVVVLNIRTKKYVLPD----FLQKM-DELKVLIVTNYGFSPAELNNF-R  595 (695)
Q Consensus       528 ~~r~l~~~~~~~~~~~~~~~-~-----~~~l~~L~l~~~~~~~~~p~----~~~~l-~~Lr~L~l~~~~~~~~~~~~~-~  595 (695)
                      ..++|.+..+......+..+ .     +++|+.|.++.+......+.    .+..+ ++|++|++++|.+.......+ .
T Consensus        52 ~L~~L~Ls~N~l~~~~~~~l~~~l~~~~~~L~~L~Ls~n~l~~~~~~~l~~~l~~~~~~L~~L~Ls~N~l~~~~~~~l~~  131 (362)
T 3goz_A           52 SVTSLNLSGNSLGFKNSDELVQILAAIPANVTSLNLSGNFLSYKSSDELVKTLAAIPFTITVLDLGWNDFSSKSSSEFKQ  131 (362)
T ss_dssp             TCCEEECCSSCGGGSCHHHHHHHHHTSCTTCCEEECCSSCGGGSCHHHHHHHHHTSCTTCCEEECCSSCGGGSCHHHHHH
T ss_pred             ceeEEECcCCCCCHHHHHHHHHHHhccCCCccEEECcCCcCChHHHHHHHHHHHhCCCCccEEECcCCcCCcHHHHHHHH
Confidence            78888887765433222111 1     38999999999876555554    34555 899999999998743322111 1


Q ss_pred             cccc-CCCCcEEEeccCCCC-----Ccc-cccccc-cccEEeeccccCCcccccchhhhcccC-CCccEEeccccccccc
Q 042541          596 VLSA-LSKLKKIRLEHVSLP-----NSL-ATVRMN-HLQKVSLVMCNVGQVFRNSTFRISDAF-PNLLEMDIDYCNDLIE  666 (695)
Q Consensus       596 ~l~~-l~~L~~L~L~~~~l~-----~lp-~i~~l~-~L~~L~l~~~~i~~~~~~~~~~l~~~l-~~L~~L~l~~c~~l~~  666 (695)
                      .+.. ..+|++|+|++|.+.     .++ .+..++ +|++|+|++|.++...+..+...-..+ ++|++|+|++|. +..
T Consensus       132 ~l~~~~~~L~~L~Ls~N~l~~~~~~~l~~~l~~~~~~L~~L~Ls~n~l~~~~~~~l~~~l~~~~~~L~~L~Ls~N~-i~~  210 (362)
T 3goz_A          132 AFSNLPASITSLNLRGNDLGIKSSDELIQILAAIPANVNSLNLRGNNLASKNCAELAKFLASIPASVTSLDLSANL-LGL  210 (362)
T ss_dssp             HHTTSCTTCCEEECTTSCGGGSCHHHHHHHHHTSCTTCCEEECTTSCGGGSCHHHHHHHHHTSCTTCCEEECTTSC-GGG
T ss_pred             HHHhCCCceeEEEccCCcCCHHHHHHHHHHHhcCCccccEeeecCCCCchhhHHHHHHHHHhCCCCCCEEECCCCC-CCh
Confidence            1334 368999999999987     444 556666 999999999999876654333111145 599999999975 565


Q ss_pred             -----CchhhcCC-CCCceeecccccCCCCCC
Q 042541          667 -----LPDGLCDI-VSMEKLRITNCHRLSALP  692 (695)
Q Consensus       667 -----lP~~i~~L-~~L~~L~l~~~~~l~~lP  692 (695)
                           +|..+..+ ++|++|+|++|. ++..+
T Consensus       211 ~~~~~l~~~l~~~~~~L~~L~Ls~N~-l~~~~  241 (362)
T 3goz_A          211 KSYAELAYIFSSIPNHVVSLNLCLNC-LHGPS  241 (362)
T ss_dssp             SCHHHHHHHHHHSCTTCCEEECCSSC-CCCCC
T ss_pred             hHHHHHHHHHhcCCCCceEEECcCCC-CCcHH
Confidence                 77778775 599999999976 65543

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=98.53  E-value=1.5e-06  Score=89.92  Aligned_cols=166  Identities=17%  Similarity=0.177  Sum_probs=105.0

Q ss_pred             CCCCCCCcchHHHHHHHHHc-----CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHH
Q 042541          165 PVISPGLDVPLKELKMELFK-----DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKV  239 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~-----~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i  239 (695)
                      -+.++|++..++++..++..     .....|.|+|++|+|||++|+.+++  .....    .+.++.+.....       
T Consensus        28 ~~~iiG~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~ia~--~~~~~----~~~~~~~~~~~~-------   94 (338)
T 3pfi_A           28 FDGYIGQESIKKNLNVFIAAAKKRNECLDHILFSGPAGLGKTTLANIISY--EMSAN----IKTTAAPMIEKS-------   94 (338)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHHTTSCCCCEEEECSTTSSHHHHHHHHHH--HTTCC----EEEEEGGGCCSH-------
T ss_pred             HHHhCChHHHHHHHHHHHHHHHhcCCCCCeEEEECcCCCCHHHHHHHHHH--HhCCC----eEEecchhccch-------
Confidence            45689999999999888872     3356789999999999999999987  33222    334444322111       


Q ss_pred             HHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhccC------------------CCCC
Q 042541          240 LHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGFQ------------------LPDY  297 (695)
Q Consensus       240 ~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~------------------~~gs  297 (695)
                                        ..+...+.. ..+..+|+||++......    ++..+...                  .++.
T Consensus        95 ------------------~~~~~~~~~-~~~~~vl~lDEi~~l~~~~~~~Ll~~l~~~~~~~~~~~~~~~~~~~~~~~~~  155 (338)
T 3pfi_A           95 ------------------GDLAAILTN-LSEGDILFIDEIHRLSPAIEEVLYPAMEDYRLDIIIGSGPAAQTIKIDLPKF  155 (338)
T ss_dssp             ------------------HHHHHHHHT-CCTTCEEEEETGGGCCHHHHHHHHHHHHTSCC---------CCCCCCCCCCC
T ss_pred             ------------------hHHHHHHHh-ccCCCEEEEechhhcCHHHHHHHHHHHHhccchhhcccCccccceecCCCCe
Confidence                              112222222 245678999999776543    22222111                  1124


Q ss_pred             EEEEEcCCCC-------CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHH
Q 042541          298 KILVTSRSEF-------PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVG  365 (695)
Q Consensus       298 ~iivTtR~~~-------~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~  365 (695)
                      .+|.||....       ...+..+.+.+++.++...++...+.....   .-..+....|++.+.|.|-.+..+.
T Consensus       156 ~~i~atn~~~~l~~~L~~R~~~~i~l~~~~~~e~~~il~~~~~~~~~---~~~~~~~~~l~~~~~G~~r~l~~~l  227 (338)
T 3pfi_A          156 TLIGATTRAGMLSNPLRDRFGMQFRLEFYKDSELALILQKAALKLNK---TCEEKAALEIAKRSRSTPRIALRLL  227 (338)
T ss_dssp             EEEEEESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHTTC---EECHHHHHHHHHTTTTCHHHHHHHH
T ss_pred             EEEEeCCCccccCHHHHhhcCEEeeCCCcCHHHHHHHHHHHHHhcCC---CCCHHHHHHHHHHHCcCHHHHHHHH
Confidence            5666555431       123358999999999999999877643221   1236778889999999996655443

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.52  E-value=4.9e-07  Score=99.14  Aligned_cols=184  Identities=13%  Similarity=0.120  Sum_probs=107.4

Q ss_pred             CCCCCCCcchHHHHHHHHHc-----------------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeC
Q 042541          165 PVISPGLDVPLKELKMELFK-----------------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVS  227 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~-----------------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~  227 (695)
                      -..++|++..++++..++..                 +..+.+.|+|++|+||||+|+.+++.  .    ...++.++.+
T Consensus        38 ~~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~--l----~~~~i~in~s  111 (516)
T 1sxj_A           38 LQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQE--L----GYDILEQNAS  111 (516)
T ss_dssp             GGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHH--T----TCEEEEECTT
T ss_pred             HHHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHH--c----CCCEEEEeCC
Confidence            35689999999999999874                 13478999999999999999999873  3    2335566666


Q ss_pred             CCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCh------HHHhhhccCCCCCEEEE
Q 042541          228 KNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSE------SLLQKLGFQLPDYKILV  301 (695)
Q Consensus       228 ~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~------~~~~~l~~~~~gs~iiv  301 (695)
                      .......+ ...+........- ..   ....... .....+++.+|++|+++....      ..+..+... .+..||+
T Consensus       112 ~~~~~~~~-~~~i~~~~~~~~~-~~---~~~~~~~-~~~~~~~~~vliIDEid~l~~~~~~~l~~L~~~l~~-~~~~iIl  184 (516)
T 1sxj_A          112 DVRSKTLL-NAGVKNALDNMSV-VG---YFKHNEE-AQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCRK-TSTPLIL  184 (516)
T ss_dssp             SCCCHHHH-HHTGGGGTTBCCS-TT---TTTC-----CCSSTTSEEEEECSGGGCCTTSTTHHHHHHHHHHH-CSSCEEE
T ss_pred             CcchHHHH-HHHHHHHhccccH-HH---HHhhhhh-hhhccCCCeEEEEECCCccchhhHHHHHHHHHHHHh-cCCCEEE
Confidence            55554322 2222222111000 00   0000000 001246789999999965432      112222211 2344555


Q ss_pred             EcCCCC-C------CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCch-hHHHHH
Q 042541          302 TSRSEF-P------QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCP-LALKVV  364 (695)
Q Consensus       302 TtR~~~-~------~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~P-Lai~~~  364 (695)
                      ++.... .      .....+.+++++.++..+.+...+......   -.++....|++.++|.+ .++..+
T Consensus       185 i~~~~~~~~l~~l~~r~~~i~f~~~~~~~~~~~L~~i~~~~~~~---i~~~~l~~la~~s~GdiR~~i~~L  252 (516)
T 1sxj_A          185 ICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFK---LDPNVIDRLIQTTRGDIRQVINLL  252 (516)
T ss_dssp             EESCTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHHHTCC---CCTTHHHHHHHHTTTCHHHHHHHH
T ss_pred             EEcCCCCccchhhHhceEEEEeCCCCHHHHHHHHHHHHHHcCCC---CCHHHHHHHHHHcCCcHHHHHHHH
Confidence            544331 1      122378999999999999988766433221   12456888999999954 445544

>1z7x_W Ribonuclease inhibitor; leucine-rich repeat, enzyme- inhibitor complex, structural genomics, protein structure initiative, PSI, CESG; HET: CIT; 1.95A {Homo sapiens} SCOP: c.10.1.1 PDB: 2q4g_W* 2bex_A 1a4y_A 2bnh_A 1dfj_I

Probab=98.51  E-value=1.9e-08  Score=109.22  Aligned_cols=35  Identities=23%  Similarity=0.285  Sum_probs=16.2

Q ss_pred             CCcEEEeccCCCC-----Ccc-cccccccccEEeeccccCC
Q 042541          602 KLKKIRLEHVSLP-----NSL-ATVRMNHLQKVSLVMCNVG  636 (695)
Q Consensus       602 ~L~~L~L~~~~l~-----~lp-~i~~l~~L~~L~l~~~~i~  636 (695)
                      +|++|+|++|.++     .+| .+.++++|++|++++|.++
T Consensus        86 ~L~~L~L~~n~i~~~~~~~l~~~l~~~~~L~~L~Ls~n~i~  126 (461)
T 1z7x_W           86 KIQKLSLQNCCLTGAGCGVLSSTLRTLPTLQELHLSDNLLG  126 (461)
T ss_dssp             CCCEEECTTSCCBGGGHHHHHHHTTSCTTCCEEECCSSBCH
T ss_pred             ceeEEEccCCCCCHHHHHHHHHHHccCCceeEEECCCCcCc
Confidence            3445555554444     223 4444445555555544443

>2ifg_A High affinity nerve growth factor receptor; TRK, TRKA, receptor-ligand complex transferase; HET: NAG NDG MAN BMA; 3.40A {Homo sapiens} SCOP: b.1.1.4 b.1.1.4 c.10.2.7

Probab=98.49  E-value=2.1e-07  Score=96.90  Aligned_cols=85  Identities=15%  Similarity=0.138  Sum_probs=39.7

Q ss_pred             CCceEEEEEEc-cCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc-ccccccccc
Q 042541          549 GPEVKVVVLNI-RTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL-ATVRMNHLQ  626 (695)
Q Consensus       549 ~~~l~~L~l~~-~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp-~i~~l~~L~  626 (695)
                      +++|+.|.|+. |......|..|.++++|+.|+|++|.+...   ....++.|++|++|+|++|.+..+| .+.....|+
T Consensus        30 ~~~L~~L~l~~~n~l~~~~~~~~~~l~~L~~L~l~~N~l~~~---~~~~~~~l~~L~~L~l~~N~l~~~~~~~~~~~~L~  106 (347)
T 2ifg_A           30 AENLTELYIENQQHLQHLELRDLRGLGELRNLTIVKSGLRFV---APDAFHFTPRLSRLNLSFNALESLSWKTVQGLSLQ  106 (347)
T ss_dssp             CSCCSEEECCSCSSCCEECGGGSCSCCCCSEEECCSSCCCEE---CTTGGGSCSCCCEEECCSSCCSCCCSTTTCSCCCC
T ss_pred             CCCeeEEEccCCCCCCCcChhHhccccCCCEEECCCCcccee---CHHHhcCCcCCCEEeCCCCccceeCHHHcccCCce
Confidence            34455555553 333333334455555555555555544211   0112445555555555555555555 222222255


Q ss_pred             EEeeccccCC
Q 042541          627 KVSLVMCNVG  636 (695)
Q Consensus       627 ~L~l~~~~i~  636 (695)
                      +|+|.+|.+.
T Consensus       107 ~l~l~~N~~~  116 (347)
T 2ifg_A          107 ELVLSGNPLH  116 (347)
T ss_dssp             EEECCSSCCC
T ss_pred             EEEeeCCCcc
Confidence            5555555544

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=98.48  E-value=3.2e-07  Score=89.91  Aligned_cols=166  Identities=16%  Similarity=0.141  Sum_probs=100.9

Q ss_pred             CCCCCCc---chHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHh
Q 042541          166 VISPGLD---VPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHH  242 (695)
Q Consensus       166 ~~~vGr~---~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~  242 (695)
                      +.|+|.+   ..++.+..++..+..+.+.|+|++|+||||||+.+++  ....... .+.|++++.....          
T Consensus        28 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~ll~G~~G~GKT~la~~l~~--~~~~~~~-~~~~~~~~~~~~~----------   94 (242)
T 3bos_A           28 TSYYPAAGNDELIGALKSAASGDGVQAIYLWGPVKSGRTHLIHAACA--RANELER-RSFYIPLGIHASI----------   94 (242)
T ss_dssp             TTSCC--CCHHHHHHHHHHHHTCSCSEEEEECSTTSSHHHHHHHHHH--HHHHTTC-CEEEEEGGGGGGS----------
T ss_pred             hhccCCCCCHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHH--HHHHcCC-eEEEEEHHHHHHH----------
Confidence            4567633   4455665655555678899999999999999999987  3332222 2668877542110          


Q ss_pred             cCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH------HHhhhccC-CCCC-EEEEEcCCCCC---CC-
Q 042541          243 KGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES------LLQKLGFQ-LPDY-KILVTSRSEFP---QF-  310 (695)
Q Consensus       243 l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~------~~~~l~~~-~~gs-~iivTtR~~~~---~~-  310 (695)
                      +                 .+.++.+ .++.+||+||++.....      +...+... ..+. ++|+||+....   .. 
T Consensus        95 ~-----------------~~~~~~~-~~~~vliiDe~~~~~~~~~~~~~l~~~l~~~~~~~~~~ii~~~~~~~~~~~~~~  156 (242)
T 3bos_A           95 S-----------------TALLEGL-EQFDLICIDDVDAVAGHPLWEEAIFDLYNRVAEQKRGSLIVSASASPMEAGFVL  156 (242)
T ss_dssp             C-----------------GGGGTTG-GGSSEEEEETGGGGTTCHHHHHHHHHHHHHHHHHCSCEEEEEESSCTTTTTCCC
T ss_pred             H-----------------HHHHHhc-cCCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCCeEEEEcCCCHHHHHHhh
Confidence            0                 0001111 34679999998654321      12211111 1232 58888775432   11 


Q ss_pred             ---------CCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHH
Q 042541          311 ---------GSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVG  365 (695)
Q Consensus       311 ---------~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~  365 (695)
                               +..+.+++++.++..+++...+.....   .-..+....|++.++|.+..+..+.
T Consensus       157 ~~l~~r~~~~~~i~l~~~~~~~~~~~l~~~~~~~~~---~~~~~~~~~l~~~~~g~~r~l~~~l  217 (242)
T 3bos_A          157 PDLVSRMHWGLTYQLQPMMDDEKLAALQRRAAMRGL---QLPEDVGRFLLNRMARDLRTLFDVL  217 (242)
T ss_dssp             HHHHHHHHHSEEEECCCCCGGGHHHHHHHHHHHTTC---CCCHHHHHHHHHHTTTCHHHHHHHH
T ss_pred             hhhhhHhhcCceEEeCCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHccCCHHHHHHHH
Confidence                     147899999999999999887643221   1236778899999999887665543

>1z7x_W Ribonuclease inhibitor; leucine-rich repeat, enzyme- inhibitor complex, structural genomics, protein structure initiative, PSI, CESG; HET: CIT; 1.95A {Homo sapiens} SCOP: c.10.1.1 PDB: 2q4g_W* 2bex_A 1a4y_A 2bnh_A 1dfj_I

Probab=98.45  E-value=2.7e-08  Score=108.05  Aligned_cols=135  Identities=19%  Similarity=0.226  Sum_probs=75.5

Q ss_pred             CCCceEEEEEEccCcccc----C-ChhhcCCCCCcEEEEcccCCCCcccCc-ccccccCCCCcEEEeccCCCCCcc--cc
Q 042541          548 QGPEVKVVVLNIRTKKYV----L-PDFLQKMDELKVLIVTNYGFSPAELNN-FRVLSALSKLKKIRLEHVSLPNSL--AT  619 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~----~-p~~~~~l~~Lr~L~l~~~~~~~~~~~~-~~~l~~l~~L~~L~L~~~~l~~lp--~i  619 (695)
                      .+++|+.|.++.+.....    + +..+..+++|++|++++|.+....... ...+..+++|++|++++|.+...+  .+
T Consensus       225 ~~~~L~~L~Ls~n~l~~~~~~~l~~~~~~~~~~L~~L~L~~n~l~~~~~~~l~~~l~~~~~L~~L~Ls~n~i~~~~~~~l  304 (461)
T 1z7x_W          225 SKASLRELALGSNKLGDVGMAELCPGLLHPSSRLRTLWIWECGITAKGCGDLCRVLRAKESLKELSLAGNELGDEGARLL  304 (461)
T ss_dssp             HCTTCCEEECCSSBCHHHHHHHHHHHHTSTTCCCCEEECTTSCCCHHHHHHHHHHHHHCTTCCEEECTTCCCHHHHHHHH
T ss_pred             hCCCccEEeccCCcCChHHHHHHHHHHhcCCCCceEEECcCCCCCHHHHHHHHHHHhhCCCcceEECCCCCCchHHHHHH
Confidence            356777777766633221    1 122335677777777776553222111 122555777777777777765222  22


Q ss_pred             cc-----cccccEEeeccccCCccc----ccchhhhcccCCCccEEecccccccccCchhhcC-----CCCCceeecccc
Q 042541          620 VR-----MNHLQKVSLVMCNVGQVF----RNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCD-----IVSMEKLRITNC  685 (695)
Q Consensus       620 ~~-----l~~L~~L~l~~~~i~~~~----~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~-----L~~L~~L~l~~~  685 (695)
                      ..     .++|++|++++|.++...    +..+.    .+++|++|++++|..-..-+..+..     .++|++|++++|
T Consensus       305 ~~~l~~~~~~L~~L~L~~n~l~~~~~~~l~~~l~----~~~~L~~L~Ls~n~i~~~~~~~l~~~l~~~~~~L~~L~L~~n  380 (461)
T 1z7x_W          305 CETLLEPGCQLESLWVKSCSFTAACCSHFSSVLA----QNRFLLELQISNNRLEDAGVRELCQGLGQPGSVLRVLWLADC  380 (461)
T ss_dssp             HHHHTSTTCCCCEEECTTSCCBGGGHHHHHHHHH----HCSSCCEEECCSSBCHHHHHHHHHHHHTSTTCCCCEEECTTS
T ss_pred             HHHhccCCccceeeEcCCCCCchHHHHHHHHHHh----hCCCccEEEccCCccccccHHHHHHHHcCCCCceEEEECCCC
Confidence            22     257777777777766532    11122    5678888888876422222333332     668888888887


Q ss_pred             c
Q 042541          686 H  686 (695)
Q Consensus       686 ~  686 (695)
                      .
T Consensus       381 ~  381 (461)
T 1z7x_W          381 D  381 (461)
T ss_dssp             C
T ss_pred             C
Confidence            5

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.41  E-value=1.2e-06  Score=91.48  Aligned_cols=187  Identities=12%  Similarity=0.041  Sum_probs=105.3

Q ss_pred             CCCCCCCcchHHHHHHHH-HcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCc-----------------------
Q 042541          165 PVISPGLDVPLKELKMEL-FKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDD-----------------------  220 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L-~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~-----------------------  220 (695)
                      -+.++|.+..++.+..++ ..+..+.+.|+|+.|+||||+|+.++..  +...-...                       
T Consensus        13 ~~~~vg~~~~~~~l~~~~~~~~~~~~~ll~Gp~G~GKTtl~~~la~~--l~~~~~g~i~~~~~~~~~~~~~~~~~~~~~~   90 (354)
T 1sxj_E           13 LNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLES--IFGPGVYRLKIDVRQFVTASNRKLELNVVSS   90 (354)
T ss_dssp             GGGCCSCHHHHHHHHTTTTCTTCCCCEEEECSTTSSHHHHHHTHHHH--HSCTTCCC------------------CCEEC
T ss_pred             HHHhcCCHHHHHHHHHHHhhCCCCCeEEEECCCCCCHHHHHHHHHHH--HcCCCCCeEEecceeecccccccceeeeecc
Confidence            356799999999998888 5554444999999999999999988762  11110000                       


Q ss_pred             --EEEEEeCCCC-CHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhccC
Q 042541          221 --IFYVTVSKNP-NVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGFQ  293 (695)
Q Consensus       221 --~~wv~~~~~~-~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~  293 (695)
                        .+.+..+... ......++++..+....+-    ....     .+..+.+++-++|+|++...+..    ++..+...
T Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~----~~~~-----~ls~l~~~~~vlilDE~~~L~~~~~~~L~~~le~~  161 (354)
T 1sxj_E           91 PYHLEITPSDMGNNDRIVIQELLKEVAQMEQV----DFQD-----SKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKY  161 (354)
T ss_dssp             SSEEEECCC----CCHHHHHHHHHHHTTTTC---------------------CCEEEEEECTTSSCHHHHHHHHHHHHHS
T ss_pred             cceEEecHhhcCCcchHHHHHHHHHHHHhccc----cccc-----cccccCCCCeEEEEeCccccCHHHHHHHHHHHHhh
Confidence              1111111100 0000122222222110000    0000     00001346779999999876543    33444434


Q ss_pred             CCCCEEEEEcCCCCC------CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCc-hHHHHHHHHhcCCchhHHHHHH
Q 042541          294 LPDYKILVTSRSEFP------QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPD-ENIVSKILRACKGCPLALKVVG  365 (695)
Q Consensus       294 ~~gs~iivTtR~~~~------~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~-~~~~~~I~~~c~G~PLai~~~~  365 (695)
                      .+++.+|++|.....      .-...+++.+++.++..+.+...+......   -. ++.+..|++.++|.+..+..+.
T Consensus       162 ~~~~~~Il~t~~~~~l~~~l~sR~~~~~~~~~~~~~~~~~l~~~~~~~~~~---~~~~~~l~~i~~~~~G~~r~a~~~l  237 (354)
T 1sxj_E          162 SKNIRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERIQ---LETKDILKRIAQASNGNLRVSLLML  237 (354)
T ss_dssp             TTTEEEEEEESCSCSSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCE---ECCSHHHHHHHHHHTTCHHHHHHHH
T ss_pred             cCCCEEEEEeCCHHHHHHHHHhhceEEecCCcCHHHHHHHHHHHHHHcCCC---CCcHHHHHHHHHHcCCCHHHHHHHH
Confidence            456788887766422      112378999999999999998776432211   12 4678899999999987655443

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=98.40  E-value=8.1e-07  Score=83.45  Aligned_cols=45  Identities=22%  Similarity=0.227  Sum_probs=40.2

Q ss_pred             CCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhcc
Q 042541          166 VISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      +.++||+++++++.+.+.....+.+.|+|++|+|||+||+.+++.
T Consensus        22 ~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l~~~~~~~   66 (195)
T 1jbk_A           22 DPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQR   66 (195)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             cccccchHHHHHHHHHHhcCCCCceEEECCCCCCHHHHHHHHHHH
Confidence            457999999999999998766778899999999999999999873

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=98.40  E-value=6.3e-06  Score=82.34  Aligned_cols=185  Identities=14%  Similarity=0.100  Sum_probs=101.7

Q ss_pred             CCCCCCcchHHHHHHH-------HH---cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHH
Q 042541          166 VISPGLDVPLKELKME-------LF---KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAI  235 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~-------L~---~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~  235 (695)
                      ..++|....++++...       +.   ....+.+.|+|++|+|||+||+.+++.  ..    ...+.++.+..      
T Consensus        33 ~~~i~~~~~~~~i~~~~~~l~~~l~~~~~~~~~~vLl~G~~GtGKT~la~~ia~~--~~----~~~~~i~~~~~------  100 (272)
T 1d2n_A           33 NGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEE--SN----FPFIKICSPDK------  100 (272)
T ss_dssp             TCCCCCSHHHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHHH--HT----CSEEEEECGGG------
T ss_pred             cCCCCccHHHHHHHHHHHHHHHHHhccCCCCCeEEEEECCCCCcHHHHHHHHHHH--hC----CCEEEEeCHHH------
Confidence            3578988887777663       32   334578999999999999999999873  21    21334443321      


Q ss_pred             HHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCC----------ChHHHhhh---ccCC--CC--C
Q 042541          236 VQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPG----------SESLLQKL---GFQL--PD--Y  297 (695)
Q Consensus       236 ~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~----------~~~~~~~l---~~~~--~g--s  297 (695)
                             +.+     .........+...+ .....+..+|+|||++..          ...++..+   ....  ++  .
T Consensus       101 -------~~g-----~~~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~l~~L~~~~~~~~~~~~~~  168 (272)
T 1d2n_A          101 -------MIG-----FSETAKCQAMKKIFDDAYKSQLSCVVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKL  168 (272)
T ss_dssp             -------CTT-----CCHHHHHHHHHHHHHHHHTSSEEEEEECCHHHHTTCBTTTTBCCHHHHHHHHHHTTCCCSTTCEE
T ss_pred             -------hcC-----CchHHHHHHHHHHHHHHHhcCCcEEEEEChhhhhccCCCChhHHHHHHHHHHHHhcCccCCCCCE
Confidence                   110     01222223444455 333467899999997542          22222222   2211  23  3


Q ss_pred             EEEEEcCCC--------CCCCCCeEecCCCCh-HHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCC------chhHHH
Q 042541          298 KILVTSRSE--------FPQFGSVHYLKPLTY-EAARTLFLHSANLQDGNSYIPDENIVSKILRACKG------CPLALK  362 (695)
Q Consensus       298 ~iivTtR~~--------~~~~~~~~~l~~L~~-~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G------~PLai~  362 (695)
                      .||.||...        .......+.+++++. ++-..++.+..        .-..+....|++.+.|      ++-++.
T Consensus       169 ~ii~ttn~~~~l~~~~l~~rf~~~i~~p~l~~r~~i~~i~~~~~--------~~~~~~~~~l~~~~~g~~~~g~ir~l~~  240 (272)
T 1d2n_A          169 LIIGTTSRKDVLQEMEMLNAFSTTIHVPNIATGEQLLEALELLG--------NFKDKERTTIAQQVKGKKVWIGIKKLLM  240 (272)
T ss_dssp             EEEEEESCHHHHHHTTCTTTSSEEEECCCEEEHHHHHHHHHHHT--------CSCHHHHHHHHHHHTTSEEEECHHHHHH
T ss_pred             EEEEecCChhhcchhhhhcccceEEcCCCccHHHHHHHHHHhcC--------CCCHHHHHHHHHHhcCCCccccHHHHHH
Confidence            455566654        112234788999988 66666665431        1135668889998888      344444


Q ss_pred             HHHHhhCCCCHHHHHHHHHH
Q 042541          363 VVGGSLCGKHEVFWQRMVKE  382 (695)
Q Consensus       363 ~~~~~L~~~~~~~w~~~l~~  382 (695)
                      .+-......+...+...++.
T Consensus       241 ~l~~a~~~~~~~~~~~~~~~  260 (272)
T 1d2n_A          241 LIEMSLQMDPEYRVRKFLAL  260 (272)
T ss_dssp             HHHHHTTSCGGGHHHHHHHH
T ss_pred             HHHHHhhhchHHHHHHHHHH
Confidence            44333332333444444443

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=98.37  E-value=3.9e-06  Score=86.30  Aligned_cols=167  Identities=16%  Similarity=0.111  Sum_probs=101.6

Q ss_pred             CCCCCCCcchHHHHHHHHHcCC-ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhc
Q 042541          165 PVISPGLDVPLKELKMELFKDG-RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHK  243 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~-~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l  243 (695)
                      -+.++|.+..++.+..++..+. ..++.+.|++|+|||++|+.+++  ..    ...++.++.+.. .... ++..+.  
T Consensus        25 ~~~ivg~~~~~~~l~~~l~~~~~~~~~L~~G~~G~GKT~la~~la~--~l----~~~~~~i~~~~~-~~~~-i~~~~~--   94 (324)
T 3u61_B           25 IDECILPAFDKETFKSITSKGKIPHIILHSPSPGTGKTTVAKALCH--DV----NADMMFVNGSDC-KIDF-VRGPLT--   94 (324)
T ss_dssp             TTTSCCCHHHHHHHHHHHHTTCCCSEEEECSSTTSSHHHHHHHHHH--HT----TEEEEEEETTTC-CHHH-HHTHHH--
T ss_pred             HHHHhCcHHHHHHHHHHHHcCCCCeEEEeeCcCCCCHHHHHHHHHH--Hh----CCCEEEEccccc-CHHH-HHHHHH--
Confidence            3568999999999999998655 46778888899999999999987  33    222455654432 1221 111111  


Q ss_pred             CCCCCCCCChHHHHHHHHHHHHh--cCCCcEEEEEeCCCCCC-hH----HHhhhccCCCCCEEEEEcCCCCCCC------
Q 042541          244 GYPVPEFQTDEAAINDLERFFKQ--MRIEAILLVLDDVWPGS-ES----LLQKLGFQLPDYKILVTSRSEFPQF------  310 (695)
Q Consensus       244 ~~~~~~~~~~~~~~~~l~~~~~~--l~~~~~LlVlDdv~~~~-~~----~~~~l~~~~~gs~iivTtR~~~~~~------  310 (695)
                                        .....  ..+++.++++||++... ..    ++..+.....++.+|+||.......      
T Consensus        95 ------------------~~~~~~~~~~~~~vliiDEi~~l~~~~~~~~L~~~le~~~~~~~iI~~~n~~~~l~~~l~sR  156 (324)
T 3u61_B           95 ------------------NFASAASFDGRQKVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANNIDGIIKPLQSR  156 (324)
T ss_dssp             ------------------HHHHBCCCSSCEEEEEEESCCCGGGHHHHHHHHHHHHHHGGGCEEEEEESSGGGSCTTHHHH
T ss_pred             ------------------HHHhhcccCCCCeEEEEECCcccCcHHHHHHHHHHHHhCCCCcEEEEEeCCccccCHHHHhh
Confidence                              11111  13478899999998765 33    2222222234678888887653211      


Q ss_pred             CCeEecCCCChHHHHHH-------HHHhccCCCCCCCCCch-HHHHHHHHhcCCchhHHH
Q 042541          311 GSVHYLKPLTYEAARTL-------FLHSANLQDGNSYIPDE-NIVSKILRACKGCPLALK  362 (695)
Q Consensus       311 ~~~~~l~~L~~~ea~~L-------f~~~~~~~~~~~~~~~~-~~~~~I~~~c~G~PLai~  362 (695)
                      ...+.+++++.++-.++       +...+.....  . -.. +....|++.++|.+..+.
T Consensus       157 ~~~i~~~~~~~~e~~~il~~~~~~l~~~~~~~~~--~-~~~~~~~~~l~~~~~gd~R~a~  213 (324)
T 3u61_B          157 CRVITFGQPTDEDKIEMMKQMIRRLTEICKHEGI--A-IADMKVVAALVKKNFPDFRKTI  213 (324)
T ss_dssp             SEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHTC--C-BSCHHHHHHHHHHTCSCTTHHH
T ss_pred             CcEEEeCCCCHHHHHHHHHHHHHHHHHHHHHcCC--C-CCcHHHHHHHHHhCCCCHHHHH
Confidence            12789999998874333       2222221111  1 123 778889999998876443

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=98.36  E-value=7.1e-06  Score=82.55  Aligned_cols=171  Identities=14%  Similarity=0.140  Sum_probs=100.8

Q ss_pred             CCCCCCCcchHHHHHHHHHc-------------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCC
Q 042541          165 PVISPGLDVPLKELKMELFK-------------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPN  231 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~-------------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~  231 (695)
                      -+.++|.+..+++|.+.+..             ...+-+.|+|++|+|||+||+.+++.  .    ....+.++.+... 
T Consensus        16 ~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~--~----~~~~~~v~~~~~~-   88 (285)
T 3h4m_A           16 YEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATE--T----NATFIRVVGSELV-   88 (285)
T ss_dssp             GGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHH--T----TCEEEEEEGGGGC-
T ss_pred             HHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHH--h----CCCEEEEehHHHH-
Confidence            35689999999999887752             34567999999999999999999873  2    2223344432211 


Q ss_pred             HHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCC-----------ChH-------HHhhhc-
Q 042541          232 VKAIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPG-----------SES-------LLQKLG-  291 (695)
Q Consensus       232 ~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~-----------~~~-------~~~~l~-  291 (695)
                                   ..     ........+...+ .....++.+|+|||++..           ...       ++..+. 
T Consensus        89 -------------~~-----~~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~l~~ll~~~~~  150 (285)
T 3h4m_A           89 -------------KK-----FIGEGASLVKDIFKLAKEKAPSIIFIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEMDG  150 (285)
T ss_dssp             -------------CC-----STTHHHHHHHHHHHHHHHTCSEEEEEETTHHHHBCCSSSCCGGGGHHHHHHHHHHHHHHT
T ss_pred             -------------Hh-----ccchHHHHHHHHHHHHHHcCCeEEEEECHHHhcccCccccCCccHHHHHHHHHHHHHhhC
Confidence                         00     0111122233333 222456789999998542           111       112221 


Q ss_pred             -cCCCCCEEEEEcCCCC-------C--CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCC-chhH
Q 042541          292 -FQLPDYKILVTSRSEF-------P--QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKG-CPLA  360 (695)
Q Consensus       292 -~~~~gs~iivTtR~~~-------~--~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G-~PLa  360 (695)
                       ....+..||.||....       .  .....+.+++.+.++..+++...+......    .......|++.+.| .|-.
T Consensus       151 ~~~~~~~~vI~ttn~~~~l~~~l~~~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~----~~~~~~~l~~~~~g~~~~~  226 (285)
T 3h4m_A          151 FDARGDVKIIGATNRPDILDPAILRPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLA----EDVNLEEIAKMTEGCVGAE  226 (285)
T ss_dssp             TCSSSSEEEEEECSCGGGBCHHHHSTTSEEEEEECCCCCHHHHHHHHHHHHTTSCBC----TTCCHHHHHHHCTTCCHHH
T ss_pred             CCCCCCEEEEEeCCCchhcCHHHcCCCcCCeEEEECCCCHHHHHHHHHHHHhcCCCC----CcCCHHHHHHHcCCCCHHH
Confidence             1223556777776541       1  222378999999999999998876543221    11225677788877 4544


Q ss_pred             HHHH
Q 042541          361 LKVV  364 (695)
Q Consensus       361 i~~~  364 (695)
                      |..+
T Consensus       227 i~~l  230 (285)
T 3h4m_A          227 LKAI  230 (285)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            4443

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=98.31  E-value=1.3e-05  Score=85.64  Aligned_cols=170  Identities=16%  Similarity=0.156  Sum_probs=102.9

Q ss_pred             CCCCCCCcchH---HHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCC-CCHHHHHHHHH
Q 042541          165 PVISPGLDVPL---KELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKN-PNVKAIVQKVL  240 (695)
Q Consensus       165 ~~~~vGr~~~~---~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~-~~~~~~~~~i~  240 (695)
                      -+.+||.+..+   ..+...+..+....+.|+|++|+||||||+.+++  .....      ++.++.. ....++ +.++
T Consensus        25 l~~ivGq~~~~~~~~~L~~~i~~~~~~~vLL~GppGtGKTtlAr~ia~--~~~~~------f~~l~a~~~~~~~i-r~~~   95 (447)
T 3pvs_A           25 LAQYIGQQHLLAAGKPLPRAIEAGHLHSMILWGPPGTGKTTLAEVIAR--YANAD------VERISAVTSGVKEI-REAI   95 (447)
T ss_dssp             TTTCCSCHHHHSTTSHHHHHHHHTCCCEEEEECSTTSSHHHHHHHHHH--HTTCE------EEEEETTTCCHHHH-HHHH
T ss_pred             HHHhCCcHHHHhchHHHHHHHHcCCCcEEEEECCCCCcHHHHHHHHHH--HhCCC------eEEEEeccCCHHHH-HHHH
Confidence            35679998887   7788888877778899999999999999999987  33222      3333321 122211 1111


Q ss_pred             HhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEE-EcCCCCCC------
Q 042541          241 HHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILV-TSRSEFPQ------  309 (695)
Q Consensus       241 ~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iiv-TtR~~~~~------  309 (695)
                      ..                 ...  ....+++.+|++|+++.....    ++..+..  ....+|. ||.+....      
T Consensus        96 ~~-----------------a~~--~~~~~~~~iLfIDEI~~l~~~~q~~LL~~le~--~~v~lI~att~n~~~~l~~aL~  154 (447)
T 3pvs_A           96 ER-----------------ARQ--NRNAGRRTILFVDEVHRFNKSQQDAFLPHIED--GTITFIGATTENPSFELNSALL  154 (447)
T ss_dssp             HH-----------------HHH--HHHTTCCEEEEEETTTCC------CCHHHHHT--TSCEEEEEESSCGGGSSCHHHH
T ss_pred             HH-----------------HHH--hhhcCCCcEEEEeChhhhCHHHHHHHHHHHhc--CceEEEecCCCCcccccCHHHh
Confidence            11                 111  111467899999999766432    2222222  2234444 44443211      


Q ss_pred             -CCCeEecCCCChHHHHHHHHHhccCCCCC---C-CCCchHHHHHHHHhcCCchhHHHHH
Q 042541          310 -FGSVHYLKPLTYEAARTLFLHSANLQDGN---S-YIPDENIVSKILRACKGCPLALKVV  364 (695)
Q Consensus       310 -~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~---~-~~~~~~~~~~I~~~c~G~PLai~~~  364 (695)
                       -...+.+.+++.++...++.+.+......   . ..-..+....|++.++|.+..+..+
T Consensus       155 sR~~v~~l~~l~~edi~~il~~~l~~~~~~~~~~~~~i~~~al~~L~~~~~Gd~R~lln~  214 (447)
T 3pvs_A          155 SRARVYLLKSLSTEDIEQVLTQAMEDKTRGYGGQDIVLPDETRRAIAELVNGDARRALNT  214 (447)
T ss_dssp             TTEEEEECCCCCHHHHHHHHHHHHHCTTTSSTTSSEECCHHHHHHHHHHHCSCHHHHHHH
T ss_pred             CceeEEeeCCcCHHHHHHHHHHHHHHHhhhhccccCcCCHHHHHHHHHHCCCCHHHHHHH
Confidence             11278899999999999998876542111   1 1123677889999999988755544

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=98.29  E-value=4.4e-06  Score=89.39  Aligned_cols=175  Identities=18%  Similarity=0.194  Sum_probs=104.3

Q ss_pred             CCC-CCcch--HHHHHHHHHcCC-ceEEEEEcCCCCcHHHHHHHHhccccccccC-CCcEEEEEeCCCCCHHHHHHHHHH
Q 042541          167 ISP-GLDVP--LKELKMELFKDG-RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKF-KDDIFYVTVSKNPNVKAIVQKVLH  241 (695)
Q Consensus       167 ~~v-Gr~~~--~~~l~~~L~~~~-~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f-~~~~~wv~~~~~~~~~~~~~~i~~  241 (695)
                      .|| |....  ...+......++ ...+.|+|++|+||||||+.+++  .....+ ...+++++...      +...+..
T Consensus       106 ~fv~g~~n~~a~~~~~~~a~~~~~~~~lll~Gp~G~GKTtLa~aia~--~l~~~~~~~~v~~v~~~~------~~~~~~~  177 (440)
T 2z4s_A          106 NFVVGPGNSFAYHAALEVAKHPGRYNPLFIYGGVGLGKTHLLQSIGN--YVVQNEPDLRVMYITSEK------FLNDLVD  177 (440)
T ss_dssp             GCCCCTTTHHHHHHHHHHHHSTTSSCCEEEECSSSSSHHHHHHHHHH--HHHHHCCSSCEEEEEHHH------HHHHHHH
T ss_pred             hcCCCCchHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHH--HHHHhCCCCeEEEeeHHH------HHHHHHH
Confidence            344 75543  333334443433 57899999999999999999998  444433 33355665443      3444444


Q ss_pred             hcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCh--H----HHhhhcc-CCCCCEEEEEcCCCCC------
Q 042541          242 HKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSE--S----LLQKLGF-QLPDYKILVTSRSEFP------  308 (695)
Q Consensus       242 ~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~--~----~~~~l~~-~~~gs~iivTtR~~~~------  308 (695)
                      .+...     .       ...+...++.+..+|++||++....  .    ++..+.. ...|..||+||.....      
T Consensus       178 ~~~~~-----~-------~~~~~~~~~~~~~vL~IDEi~~l~~~~~~q~~l~~~l~~l~~~~~~iIitt~~~~~~l~~l~  245 (440)
T 2z4s_A          178 SMKEG-----K-------LNEFREKYRKKVDILLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQ  245 (440)
T ss_dssp             HHHTT-----C-------HHHHHHHHTTTCSEEEEECGGGGSSCHHHHHHHHHHHHHHHTTTCEEEEEESSCGGGCSSCC
T ss_pred             HHHcc-----c-------HHHHHHHhcCCCCEEEEeCcccccCChHHHHHHHHHHHHHHHCCCeEEEEECCCHHHHHHHH
Confidence            43221     0       1112233333678999999965431  1    2222221 2357789998886421      


Q ss_pred             -------CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHH
Q 042541          309 -------QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVV  364 (695)
Q Consensus       309 -------~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~  364 (695)
                             ..+..+.+++++.++-.+++.+.+......   -..+....|++.++|.+..+.-+
T Consensus       246 ~~L~sR~~~g~~i~l~~p~~e~r~~iL~~~~~~~~~~---i~~e~l~~la~~~~gn~R~l~~~  305 (440)
T 2z4s_A          246 DRLVSRFQMGLVAKLEPPDEETRKSIARKMLEIEHGE---LPEEVLNFVAENVDDNLRRLRGA  305 (440)
T ss_dssp             HHHHHHHHSSBCCBCCCCCHHHHHHHHHHHHHHHTCC---CCTTHHHHHHHHCCSCHHHHHHH
T ss_pred             HHHHhhccCCeEEEeCCCCHHHHHHHHHHHHHHcCCC---CCHHHHHHHHHhcCCCHHHHHHH
Confidence                   113468899999999999998876432211   12456788999999988655433

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=98.28  E-value=1.4e-05  Score=82.41  Aligned_cols=162  Identities=17%  Similarity=0.172  Sum_probs=100.1

Q ss_pred             cchHHHHHHHHHcCC-ceEEEEEcCCCCcHHHHHHHHhccccccccC---------------------CCcEEEEEeC--
Q 042541          172 DVPLKELKMELFKDG-RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKF---------------------KDDIFYVTVS--  227 (695)
Q Consensus       172 ~~~~~~l~~~L~~~~-~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f---------------------~~~~~wv~~~--  227 (695)
                      ++..+.+...+..+. ...+.++|+.|+|||++|+.+++.  +....                     .. +.++...  
T Consensus         8 ~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a~~la~~--l~~~~~~~~~~c~~c~~c~~~~~~~~~d-~~~~~~~~~   84 (334)
T 1a5t_A            8 RPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRY--LLCQQPQGHKSCGHCRGCQLMQAGTHPD-YYTLAPEKG   84 (334)
T ss_dssp             HHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHHH--HTCSSCBTTBCCSCSHHHHHHHHTCCTT-EEEECCCTT
T ss_pred             HHHHHHHHHHHHcCCcceeEEEECCCCchHHHHHHHHHHH--HhCCCCCCCCCCCCCHHHHHHhcCCCCC-EEEEecccc
Confidence            445667777777655 457999999999999999998763  21111                     11 2333221  


Q ss_pred             -CCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEE
Q 042541          228 -KNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVT  302 (695)
Q Consensus       228 -~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivT  302 (695)
                       ....+.. .+++.+.+...                   ...+++-++|+|+++.....    ++..+....+++.+|++
T Consensus        85 ~~~~~i~~-ir~l~~~~~~~-------------------~~~~~~kvviIdead~l~~~a~naLLk~lEep~~~~~~Il~  144 (334)
T 1a5t_A           85 KNTLGVDA-VREVTEKLNEH-------------------ARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLA  144 (334)
T ss_dssp             CSSBCHHH-HHHHHHHTTSC-------------------CTTSSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEE
T ss_pred             CCCCCHHH-HHHHHHHHhhc-------------------cccCCcEEEEECchhhcCHHHHHHHHHHhcCCCCCeEEEEE
Confidence             1111111 11222222111                   01366889999999876533    44555555556777777


Q ss_pred             cCCCCC------CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHH
Q 042541          303 SRSEFP------QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVV  364 (695)
Q Consensus       303 tR~~~~------~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~  364 (695)
                      |.....      .-...+.+.+++.++..+.+....        .-..+.+..+++.++|.|..+..+
T Consensus       145 t~~~~~l~~ti~SRc~~~~~~~~~~~~~~~~L~~~~--------~~~~~~~~~l~~~s~G~~r~a~~~  204 (334)
T 1a5t_A          145 TREPERLLATLRSRCRLHYLAPPPEQYAVTWLSREV--------TMSQDALLAALRLSAGSPGAALAL  204 (334)
T ss_dssp             ESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHC--------CCCHHHHHHHHHHTTTCHHHHHHT
T ss_pred             eCChHhCcHHHhhcceeeeCCCCCHHHHHHHHHHhc--------CCCHHHHHHHHHHcCCCHHHHHHH
Confidence            765421      122378999999999999998775        113566788999999999765443

>2p1m_B Transport inhibitor response 1 protein; F-BOX, leucine rich repeat, signaling protein; HET: IHP; 1.80A {Arabidopsis thaliana} PDB: 2p1n_B* 2p1o_B* 2p1p_B* 2p1q_B* 3c6n_B* 3c6o_B* 3c6p_B*

Probab=98.26  E-value=1.8e-07  Score=104.98  Aligned_cols=134  Identities=16%  Similarity=0.175  Sum_probs=68.9

Q ss_pred             CCceEEEEEEccCccccCChhhc-CCCCCcEEEEcccC-CCCcccCcccccccCCCCcEEEeccCCCCC-----cc-ccc
Q 042541          549 GPEVKVVVLNIRTKKYVLPDFLQ-KMDELKVLIVTNYG-FSPAELNNFRVLSALSKLKKIRLEHVSLPN-----SL-ATV  620 (695)
Q Consensus       549 ~~~l~~L~l~~~~~~~~~p~~~~-~l~~Lr~L~l~~~~-~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~-----lp-~i~  620 (695)
                      +++|+.|.++.+......+..+. .+++|++|++.+|. +....+..  ...++++|++|+|++|.++.     ++ ...
T Consensus       104 ~~~L~~L~L~~~~~~~~~~~~l~~~~~~L~~L~L~~~~~~~~~~l~~--~~~~~~~L~~L~L~~~~i~~~~~~~l~~~~~  181 (594)
T 2p1m_B          104 YTWLEEIRLKRMVVTDDCLELIAKSFKNFKVLVLSSCEGFSTDGLAA--IAATCRNLKELDLRESDVDDVSGHWLSHFPD  181 (594)
T ss_dssp             CTTCCEEEEESCBCCHHHHHHHHHHCTTCCEEEEESCEEEEHHHHHH--HHHHCTTCCEEECTTCEEECCCGGGGGGSCT
T ss_pred             CCCCCeEEeeCcEEcHHHHHHHHHhCCCCcEEeCCCcCCCCHHHHHH--HHHhCCCCCEEeCcCCccCCcchHHHHHHhh
Confidence            45666666666544333333333 46667777766652 21111111  13356667777776665432     22 223


Q ss_pred             ccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccc
Q 042541          621 RMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNC  685 (695)
Q Consensus       621 ~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~  685 (695)
                      .+++|++|++++|. ..+....+..+...+++|++|++++|..+..+|..+.++++|++|++.+|
T Consensus       182 ~~~~L~~L~l~~~~-~~~~~~~l~~l~~~~~~L~~L~L~~~~~~~~l~~~~~~~~~L~~L~l~~~  245 (594)
T 2p1m_B          182 TYTSLVSLNISCLA-SEVSFSALERLVTRCPNLKSLKLNRAVPLEKLATLLQRAPQLEELGTGGY  245 (594)
T ss_dssp             TCCCCCEEECTTCC-SCCCHHHHHHHHHHCTTCCEEECCTTSCHHHHHHHHHHCTTCSEEECSBC
T ss_pred             cCCcCcEEEecccC-CcCCHHHHHHHHHhCCCCcEEecCCCCcHHHHHHHHhcCCcceEcccccc
Confidence            45566777776665 22222222111114566777777666555556666666666666665443

>3un9_A NLR family member X1; leucine rich repeat (LRR), antiviral signaling, MAVS, TRAF6, UQCRC2, immune system; 2.65A {Homo sapiens}

Probab=98.23  E-value=1.1e-07  Score=99.65  Aligned_cols=136  Identities=15%  Similarity=0.130  Sum_probs=75.9

Q ss_pred             CceEEEEEEccCccccC-ChhhcCCCCCcEEEEcccCCCCcccCccc-cc-ccCCCCcEEEeccCCCCC-----cc-ccc
Q 042541          550 PEVKVVVLNIRTKKYVL-PDFLQKMDELKVLIVTNYGFSPAELNNFR-VL-SALSKLKKIRLEHVSLPN-----SL-ATV  620 (695)
Q Consensus       550 ~~l~~L~l~~~~~~~~~-p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~-~l-~~l~~L~~L~L~~~~l~~-----lp-~i~  620 (695)
                      ++|+.|.|+.|.....- ......+++|+.|+|++|.+.......+. .+ ...++|+.|+|++|.++.     ++ .+.
T Consensus       101 ~~L~~L~Ls~n~l~~~~~~~l~~~L~~L~~L~Ls~n~l~~~~~~~L~~~L~~~~~~L~~L~Ls~n~l~~~~~~~l~~~L~  180 (372)
T 3un9_A          101 HALDEVNLASCQLDPAGLRTLLPVFLRARKLGLQLNSLGPEACKDLRDLLLHDQCQITTLRLSNNPLTAAGVAVLMEGLA  180 (372)
T ss_dssp             SCEEEEECTTCCCCHHHHHHTHHHHHTEEEEECCSSCCCHHHHHHHHHHHHSTTCCCCEEECCSSCCHHHHHHHHHHHHH
T ss_pred             CCceEEEecCCCCCHHHHHHHHHHHHhccHhhcCCCCCCHHHHHHHHHHHHhcCCccceeeCCCCCCChHHHHHHHHHHh
Confidence            45666666666432211 11223345677788877766432221111 11 235667888888877753     33 445


Q ss_pred             ccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccc-----cCchhhcCCCCCceeeccccc
Q 042541          621 RMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLI-----ELPDGLCDIVSMEKLRITNCH  686 (695)
Q Consensus       621 ~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~-----~lP~~i~~L~~L~~L~l~~~~  686 (695)
                      .+++|++|+|++|.++......+...-...++|++|+|++|. +.     .++..+...++|++|+|++|.
T Consensus       181 ~~~~L~~L~Ls~N~l~~~g~~~L~~~L~~~~~L~~L~Ls~N~-i~~~g~~~l~~~L~~~~~L~~L~Ls~N~  250 (372)
T 3un9_A          181 GNTSVTHLSLLHTGLGDEGLELLAAQLDRNRQLQELNVAYNG-AGDTAALALARAAREHPSLELLHLYFNE  250 (372)
T ss_dssp             TCSSCCEEECTTSSCHHHHHHHHHHHGGGCSCCCEEECCSSC-CCHHHHHHHHHHHHHCSSCCEEECTTSS
T ss_pred             cCCCcCEEeCCCCCCCcHHHHHHHHHHhcCCCcCeEECCCCC-CCHHHHHHHHHHHHhCCCCCEEeccCCC
Confidence            677788888888776542211110000156678888887764 33     244555666778888887765

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=98.21  E-value=5.7e-05  Score=74.74  Aligned_cols=172  Identities=11%  Similarity=0.093  Sum_probs=97.9

Q ss_pred             CCCCCCcchHHHHHHHHH---c---------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHH
Q 042541          166 VISPGLDVPLKELKMELF---K---------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVK  233 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~---~---------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~  233 (695)
                      +.++|.+..++.+.+++.   .         ...+-|.|+|++|+|||++|+.+++  ...    ...+.++.+...+  
T Consensus         6 ~~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~vll~G~~GtGKT~la~~la~--~~~----~~~~~~~~~~~~~--   77 (262)
T 2qz4_A            6 KDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVAT--EAQ----VPFLAMAGAEFVE--   77 (262)
T ss_dssp             TSSCSCHHHHHHHHHHHHHHHCCC------CCCCCEEEEESCTTSSHHHHHHHHHH--HHT----CCEEEEETTTTSS--
T ss_pred             HHhCCHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEECCCCCCHHHHHHHHHH--HhC----CCEEEechHHHHh--
Confidence            457999988877766543   1         2245688999999999999999987  332    2244555544211  


Q ss_pred             HHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCC---------------hH----HHhhhccC
Q 042541          234 AIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGS---------------ES----LLQKLGFQ  293 (695)
Q Consensus       234 ~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~---------------~~----~~~~l~~~  293 (695)
                              ..         .......+..++ ......+.+|++||++...               ..    ++..+...
T Consensus        78 --------~~---------~~~~~~~~~~~~~~a~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~  140 (262)
T 2qz4_A           78 --------VI---------GGLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGFSNTEEEQTLNQLLVEMDGM  140 (262)
T ss_dssp             --------SS---------TTHHHHHHHHHHHHHHHTCSEEEEEECC-------------------CHHHHHHHHHHHTC
T ss_pred             --------hc---------cChhHHHHHHHHHHHHhcCCeEEEEeCcchhhccccccccCccchhHHHHHHHHHHHhhCc
Confidence                    00         011122333444 2223567999999997541               01    22222211


Q ss_pred             --CCCCEEEEEcCCCC------C---CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchh-HH
Q 042541          294 --LPDYKILVTSRSEF------P---QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPL-AL  361 (695)
Q Consensus       294 --~~gs~iivTtR~~~------~---~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PL-ai  361 (695)
                        ..+..||.||....      .   .....+.++..+.++-.+++...+.....  ..........+++.+.|.+- .|
T Consensus       141 ~~~~~~~vi~~tn~~~~ld~~l~~~~R~~~~i~i~~p~~~~r~~il~~~~~~~~~--~~~~~~~~~~l~~~~~g~~~~~l  218 (262)
T 2qz4_A          141 GTTDHVIVLASTNRADILDGALMRPGRLDRHVFIDLPTLQERREIFEQHLKSLKL--TQSSTFYSQRLAELTPGFSGADI  218 (262)
T ss_dssp             CTTCCEEEEEEESCGGGGGSGGGSTTSCCEEEECCSCCHHHHHHHHHHHHHHTTC--CBTHHHHHHHHHHTCTTCCHHHH
T ss_pred             CCCCCEEEEecCCChhhcCHHHhcCCcCCeEEEeCCcCHHHHHHHHHHHHHhCCC--CcchhhHHHHHHHHCCCCCHHHH
Confidence              22445666665431      1   23347889999999999999876643222  11112235788888888754 44


Q ss_pred             HHH
Q 042541          362 KVV  364 (695)
Q Consensus       362 ~~~  364 (695)
                      ..+
T Consensus       219 ~~l  221 (262)
T 2qz4_A          219 ANI  221 (262)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            443

>3sb4_A Hypothetical leucine rich repeat protein; LRR, right-handed beta-alpha superhelix, leucine-rich repeat structural genomics; HET: MSE PG4; 1.99A {Bacteroides thetaiotaomicron}

Probab=98.20  E-value=2.7e-06  Score=87.66  Aligned_cols=87  Identities=8%  Similarity=0.102  Sum_probs=75.4

Q ss_pred             CCCCcEEEeccCCCCCcc--cccccccccEEeeccccCCcccccchhhhcccCCCcc-EEecccccccccCc-hhhcCCC
Q 042541          600 LSKLKKIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLL-EMDIDYCNDLIELP-DGLCDIV  675 (695)
Q Consensus       600 l~~L~~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~-~L~l~~c~~l~~lP-~~i~~L~  675 (695)
                      +++|+.|+|.+|+++.+|  .+.++.+|+.|+|..| ++.+++..|.    .+++|+ .+++.+  .+..++ ..|.+++
T Consensus       225 ~~~L~~l~L~~n~i~~I~~~aF~~~~~L~~l~l~~n-i~~I~~~aF~----~~~~L~~~l~l~~--~l~~I~~~aF~~c~  297 (329)
T 3sb4_A          225 MPNLVSLDISKTNATTIPDFTFAQKKYLLKIKLPHN-LKTIGQRVFS----NCGRLAGTLELPA--SVTAIEFGAFMGCD  297 (329)
T ss_dssp             CTTCCEEECTTBCCCEECTTTTTTCTTCCEEECCTT-CCEECTTTTT----TCTTCCEEEEECT--TCCEECTTTTTTCT
T ss_pred             cCCCeEEECCCCCcceecHhhhhCCCCCCEEECCcc-cceehHHHhh----CChhccEEEEEcc--cceEEchhhhhCCc
Confidence            789999999999999999  8999999999999998 8888888887    899999 999987  577776 4589999


Q ss_pred             CCceeecccccCCCCCCCC
Q 042541          676 SMEKLRITNCHRLSALPEG  694 (695)
Q Consensus       676 ~L~~L~l~~~~~l~~lP~~  694 (695)
                      +|+.|++++++ +..+|.+
T Consensus       298 ~L~~l~l~~n~-i~~I~~~  315 (329)
T 3sb4_A          298 NLRYVLATGDK-ITTLGDE  315 (329)
T ss_dssp             TEEEEEECSSC-CCEECTT
T ss_pred             cCCEEEeCCCc-cCccchh
Confidence            99999998754 7777653

>3ogk_B Coronatine-insensitive protein 1; leucine rich repeat, ubiquitin ligase, SCF, protein binding; HET: OGK; 2.80A {Arabidopsis thaliana} PDB: 3ogl_B* 3ogm_B*

Probab=98.19  E-value=1.3e-06  Score=97.80  Aligned_cols=131  Identities=13%  Similarity=0.012  Sum_probs=67.7

Q ss_pred             CCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc-ccccccccc
Q 042541          548 QGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL-ATVRMNHLQ  626 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp-~i~~l~~L~  626 (695)
                      .+++|+.|.+..+... .+|..+..+++|+.|++..+.........+..+..+++|+.|++.++....+| .+..+++|+
T Consensus       218 ~~~~L~~L~L~~~~~~-~l~~~~~~~~~L~~L~l~~~~~~~~~~~~~~~l~~~~~L~~L~l~~~~~~~l~~~~~~~~~L~  296 (592)
T 3ogk_B          218 NCRSLVSVKVGDFEIL-ELVGFFKAAANLEEFCGGSLNEDIGMPEKYMNLVFPRKLCRLGLSYMGPNEMPILFPFAAQIR  296 (592)
T ss_dssp             HCTTCCEEECSSCBGG-GGHHHHHHCTTCCEEEECBCCCCTTCTTSSSCCCCCTTCCEEEETTCCTTTGGGGGGGGGGCC
T ss_pred             hCCCCcEEeccCccHH-HHHHHHhhhhHHHhhcccccccccchHHHHHHhhccccccccCccccchhHHHHHHhhcCCCc
Confidence            4567777777665332 25566667777777777643221111112223555666666666665555666 666677777


Q ss_pred             EEeeccccCCcccc-cchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecc
Q 042541          627 KVSLVMCNVGQVFR-NSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRIT  683 (695)
Q Consensus       627 ~L~l~~~~i~~~~~-~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~  683 (695)
                      +|+|++|.++.... ....    .+++|++|++++|..-..++.-+..+++|++|+++
T Consensus       297 ~L~Ls~~~l~~~~~~~~~~----~~~~L~~L~L~~~~~~~~l~~~~~~~~~L~~L~L~  350 (592)
T 3ogk_B          297 KLDLLYALLETEDHCTLIQ----KCPNLEVLETRNVIGDRGLEVLAQYCKQLKRLRIE  350 (592)
T ss_dssp             EEEETTCCCCHHHHHHHHT----TCTTCCEEEEEGGGHHHHHHHHHHHCTTCCEEEEE
T ss_pred             EEecCCCcCCHHHHHHHHH----hCcCCCEEeccCccCHHHHHHHHHhCCCCCEEEee
Confidence            77777766432211 1111    45555555555332222233333444555555555

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=98.18  E-value=5.4e-05  Score=79.18  Aligned_cols=193  Identities=7%  Similarity=-0.027  Sum_probs=103.6

Q ss_pred             CCCCCCCcchHHHH---HHHHHcCC--ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCC----CCCHHHH
Q 042541          165 PVISPGLDVPLKEL---KMELFKDG--RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSK----NPNVKAI  235 (695)
Q Consensus       165 ~~~~vGr~~~~~~l---~~~L~~~~--~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~----~~~~~~~  235 (695)
                      -+.+||++..++.+   ...+..+.  .+.+.|+|++|+|||++|+.+++  ......+  .+.+....    .....+.
T Consensus        43 ~~~ivG~~~~~~~l~~l~~~~~~~~~~~~~vLl~GppGtGKT~la~~la~--~l~~~~~--~~~~~~~~~~~~~~~~~~~  118 (368)
T 3uk6_A           43 SQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQ--ALGPDTP--FTAIAGSEIFSLEMSKTEA  118 (368)
T ss_dssp             ETTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEEESTTSSHHHHHHHHHH--HHCSSCC--EEEEEGGGGSCSSSCHHHH
T ss_pred             hhhccChHHHHHHHHHHHHHHHcCCCCCCEEEEECCCCCCHHHHHHHHHH--HhcccCC--cccccchhhhhcccchhHH
Confidence            34689999887764   44444443  35899999999999999999998  3332222  22333222    2334444


Q ss_pred             HHHHHHhcCC-C--------------------C-------CC--CCChHHHHHHHHHHHHh--cCCC----cEEEEEeCC
Q 042541          236 VQKVLHHKGY-P--------------------V-------PE--FQTDEAAINDLERFFKQ--MRIE----AILLVLDDV  279 (695)
Q Consensus       236 ~~~i~~~l~~-~--------------------~-------~~--~~~~~~~~~~l~~~~~~--l~~~----~~LlVlDdv  279 (695)
                      +.+.+..... .                    .       ..  ..........+......  ..++    +.+|++|++
T Consensus       119 ~~~~~~~~~~~~~~~~~~~~~~~~~ld~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~g~~~~~~~vl~IDEi  198 (368)
T 3uk6_A          119 LTQAFRRSIGVRIKAGAVHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVAEWREEGKAEIIPGVLFIDEV  198 (368)
T ss_dssp             HHHHHHHSBEECC------CEEHHHHHHHTC----CCSCC-------CHHHHHHHHHHHHHHHHHTC---CBCEEEEESG
T ss_pred             HHHHHHHHHHHHhhhhccccccHhhhhhhhcccccchhhccCcccccHHHHHHHHHHHHHHhhhhccccccCceEEEhhc
Confidence            4444333110 0                    0       00  00011222222222211  1233    469999999


Q ss_pred             CCCChHHHhhh---ccCCCCCEEEEEcCCC-----------CCCC-------CCeEecCCCChHHHHHHHHHhccCCCCC
Q 042541          280 WPGSESLLQKL---GFQLPDYKILVTSRSE-----------FPQF-------GSVHYLKPLTYEAARTLFLHSANLQDGN  338 (695)
Q Consensus       280 ~~~~~~~~~~l---~~~~~gs~iivTtR~~-----------~~~~-------~~~~~l~~L~~~ea~~Lf~~~~~~~~~~  338 (695)
                      ..........+   ....+...++++|...           ....       ...+.+++++.++..+++...+..... 
T Consensus       199 ~~l~~~~~~~L~~~le~~~~~~~ii~t~~~~~~i~~t~~~~~~~l~~~l~sR~~~i~~~~~~~~e~~~il~~~~~~~~~-  277 (368)
T 3uk6_A          199 HMLDIESFSFLNRALESDMAPVLIMATNRGITRIRGTSYQSPHGIPIDLLDRLLIVSTTPYSEKDTKQILRIRCEEEDV-  277 (368)
T ss_dssp             GGSBHHHHHHHHHHTTCTTCCEEEEEESCSEEECBTSSCEEETTCCHHHHTTEEEEEECCCCHHHHHHHHHHHHHHTTC-
T ss_pred             cccChHHHHHHHHHhhCcCCCeeeeecccceeeeeccCCCCcccCCHHHHhhccEEEecCCCHHHHHHHHHHHHHHcCC-
Confidence            87654422222   2222223344444311           0000       115789999999999999977653222 


Q ss_pred             CCCCchHHHHHHHHhcC-CchhHHHHH
Q 042541          339 SYIPDENIVSKILRACK-GCPLALKVV  364 (695)
Q Consensus       339 ~~~~~~~~~~~I~~~c~-G~PLai~~~  364 (695)
                        .-..+....|++.+. |.|..+..+
T Consensus       278 --~~~~~~l~~l~~~~~~G~~r~~~~l  302 (368)
T 3uk6_A          278 --EMSEDAYTVLTRIGLETSLRYAIQL  302 (368)
T ss_dssp             --CBCHHHHHHHHHHHHHSCHHHHHHH
T ss_pred             --CCCHHHHHHHHHHhcCCCHHHHHHH
Confidence              123677888999997 777655544

>2p1m_B Transport inhibitor response 1 protein; F-BOX, leucine rich repeat, signaling protein; HET: IHP; 1.80A {Arabidopsis thaliana} PDB: 2p1n_B* 2p1o_B* 2p1p_B* 2p1q_B* 3c6n_B* 3c6o_B* 3c6p_B*

Probab=98.17  E-value=3.7e-07  Score=102.47  Aligned_cols=116  Identities=12%  Similarity=0.199  Sum_probs=84.0

Q ss_pred             hcCCCCCcEEEEcccCCCCcccCcccccc-cCCCCcEEEeccC-CCCC--cc-cccccccccEEeeccccCCcccccchh
Q 042541          570 LQKMDELKVLIVTNYGFSPAELNNFRVLS-ALSKLKKIRLEHV-SLPN--SL-ATVRMNHLQKVSLVMCNVGQVFRNSTF  644 (695)
Q Consensus       570 ~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~-~l~~L~~L~L~~~-~l~~--lp-~i~~l~~L~~L~l~~~~i~~~~~~~~~  644 (695)
                      ...+++|+.|++++|.+....+   ..+. .+++|++|+|.+| .+..  ++ .+.++++|++|+|++|.++...+..+.
T Consensus       101 ~~~~~~L~~L~L~~~~~~~~~~---~~l~~~~~~L~~L~L~~~~~~~~~~l~~~~~~~~~L~~L~L~~~~i~~~~~~~l~  177 (594)
T 2p1m_B          101 SSSYTWLEEIRLKRMVVTDDCL---ELIAKSFKNFKVLVLSSCEGFSTDGLAAIAATCRNLKELDLRESDVDDVSGHWLS  177 (594)
T ss_dssp             HHHCTTCCEEEEESCBCCHHHH---HHHHHHCTTCCEEEEESCEEEEHHHHHHHHHHCTTCCEEECTTCEEECCCGGGGG
T ss_pred             HHhCCCCCeEEeeCcEEcHHHH---HHHHHhCCCCcEEeCCCcCCCCHHHHHHHHHhCCCCCEEeCcCCccCCcchHHHH
Confidence            4578899999999987643222   2243 6899999999998 5553  56 556899999999999987765544444


Q ss_pred             hhcccCCCccEEeccccc-cc--ccCchhhcCCCCCceeecccccCC
Q 042541          645 RISDAFPNLLEMDIDYCN-DL--IELPDGLCDIVSMEKLRITNCHRL  688 (695)
Q Consensus       645 ~l~~~l~~L~~L~l~~c~-~l--~~lP~~i~~L~~L~~L~l~~~~~l  688 (695)
                      .++..+++|+.|++++|. .+  ..++.-+.++++|++|++++|..+
T Consensus       178 ~~~~~~~~L~~L~l~~~~~~~~~~~l~~l~~~~~~L~~L~L~~~~~~  224 (594)
T 2p1m_B          178 HFPDTYTSLVSLNISCLASEVSFSALERLVTRCPNLKSLKLNRAVPL  224 (594)
T ss_dssp             GSCTTCCCCCEEECTTCCSCCCHHHHHHHHHHCTTCCEEECCTTSCH
T ss_pred             HHhhcCCcCcEEEecccCCcCCHHHHHHHHHhCCCCcEEecCCCCcH
Confidence            444478899999999985 11  112222456799999999998443

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=98.16  E-value=1.4e-05  Score=82.75  Aligned_cols=171  Identities=12%  Similarity=0.136  Sum_probs=103.3

Q ss_pred             CCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhcccccc-ccCCCcEEEEEeCCCCCHHHHHHHHHHhcC
Q 042541          166 VISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQ-GKFKDDIFYVTVSKNPNVKAIVQKVLHHKG  244 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~-~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~  244 (695)
                      ..++|.+..++.|...+..++.+.+.++|+.|+||||+|+.+++.  +. ..+...+.-++.+.......+. ++     
T Consensus        25 ~~~~g~~~~~~~L~~~i~~g~~~~~ll~Gp~G~GKTtla~~la~~--l~~~~~~~~~~~~~~~~~~~~~~ir-~~-----   96 (340)
T 1sxj_C           25 DEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALARE--IYGKNYSNMVLELNASDDRGIDVVR-NQ-----   96 (340)
T ss_dssp             GGCCSCHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHHHHHHH--HHTTSHHHHEEEECTTSCCSHHHHH-TH-----
T ss_pred             HHhcCcHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHH--HcCCCccceEEEEcCcccccHHHHH-HH-----
Confidence            456898888888888888776555899999999999999999873  21 1111112233333222221111 11     


Q ss_pred             CCCCCCCChHHHHHHHHHHHHh---cCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCC------CCC
Q 042541          245 YPVPEFQTDEAAINDLERFFKQ---MRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFP------QFG  311 (695)
Q Consensus       245 ~~~~~~~~~~~~~~~l~~~~~~---l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~------~~~  311 (695)
                                     +....+.   ..+..-++|+|+++.....    ++..+......+.+|++|.....      .-.
T Consensus        97 ---------------i~~~~~~~~~~~~~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~n~~~~i~~~i~sR~  161 (340)
T 1sxj_C           97 ---------------IKDFASTRQIFSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQC  161 (340)
T ss_dssp             ---------------HHHHHHBCCSSSCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTS
T ss_pred             ---------------HHHHHhhcccCCCCceEEEEeCCCCCCHHHHHHHHHHHhcCCCCeEEEEEecCccccchhHHhhc
Confidence                           1111111   1245789999998765432    33333333456677777654321      112


Q ss_pred             CeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHH
Q 042541          312 SVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALK  362 (695)
Q Consensus       312 ~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~  362 (695)
                      ..+.+.+++.++..+.+...+.....   .-..+..+.|++.++|.+.-+.
T Consensus       162 ~~~~~~~l~~~~~~~~l~~~~~~~~~---~i~~~~~~~i~~~s~G~~r~~~  209 (340)
T 1sxj_C          162 TRFRFQPLPQEAIERRIANVLVHEKL---KLSPNAEKALIELSNGDMRRVL  209 (340)
T ss_dssp             EEEECCCCCHHHHHHHHHHHHHTTTC---CBCHHHHHHHHHHHTTCHHHHH
T ss_pred             eeEeccCCCHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHcCCCHHHHH
Confidence            36889999999998888876632221   1135678889999999887443

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens}

Probab=98.15  E-value=3.1e-05  Score=80.53  Aligned_cols=173  Identities=10%  Similarity=0.094  Sum_probs=102.8

Q ss_pred             CCCCCCcchHHHHHHHHHc------------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHH
Q 042541          166 VISPGLDVPLKELKMELFK------------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVK  233 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~------------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~  233 (695)
                      +.++|.+..++.|.+.+..            ...+.|.|+|++|+|||+||+.+++.  .    ....+.++.+.-..  
T Consensus        84 ~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~--~----~~~~~~i~~~~l~~--  155 (357)
T 3d8b_A           84 EDIAGVEFAKATIKEIVVWPMLRPDIFTGLRGPPKGILLFGPPGTGKTLIGKCIASQ--S----GATFFSISASSLTS--  155 (357)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGSCCSEEEEESSTTSSHHHHHHHHHHH--T----TCEEEEEEGGGGCC--
T ss_pred             HHhCChHHHHHHHHHHHHHHhhChHhHhhccCCCceEEEECCCCCCHHHHHHHHHHH--c----CCeEEEEehHHhhc--
Confidence            4579999999999887641            23578999999999999999999873  2    22244555543211  


Q ss_pred             HHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCC---------------hHHHhhhccC----
Q 042541          234 AIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGS---------------ESLLQKLGFQ----  293 (695)
Q Consensus       234 ~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~---------------~~~~~~l~~~----  293 (695)
                                  .     ........+..++ .....++.+|+||+++...               ..++..+...    
T Consensus       156 ------------~-----~~g~~~~~~~~~~~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~  218 (357)
T 3d8b_A          156 ------------K-----WVGEGEKMVRALFAVARCQQPAVIFIDEIDSLLSQRGDGEHESSRRIKTEFLVQLDGATTSS  218 (357)
T ss_dssp             ------------S-----STTHHHHHHHHHHHHHHHTCSEEEEEETHHHHTBC------CHHHHHHHHHHHHHHC----C
T ss_pred             ------------c-----ccchHHHHHHHHHHHHHhcCCeEEEEeCchhhhccCCCCcchHHHHHHHHHHHHHhcccccC
Confidence                        0     0011122233333 2223567899999984220               0122222211    


Q ss_pred             CCCCEEEEEcCCCC-------CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCC-chhHHHHHH
Q 042541          294 LPDYKILVTSRSEF-------PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKG-CPLALKVVG  365 (695)
Q Consensus       294 ~~gs~iivTtR~~~-------~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G-~PLai~~~~  365 (695)
                      ..+..||.||....       ......+.+...+.++..+++...+.....   .-..+....|++.+.| .+-.|..+.
T Consensus       219 ~~~v~vI~atn~~~~l~~~l~~Rf~~~i~i~~p~~~~r~~il~~~~~~~~~---~l~~~~l~~la~~t~G~s~~dl~~l~  295 (357)
T 3d8b_A          219 EDRILVVGATNRPQEIDEAARRRLVKRLYIPLPEASARKQIVINLMSKEQC---CLSEEEIEQIVQQSDAFSGADMTQLC  295 (357)
T ss_dssp             CCCEEEEEEESCGGGBCHHHHTTCCEEEECCCCCHHHHHHHHHHHHHTSCB---CCCHHHHHHHHHHTTTCCHHHHHHHH
T ss_pred             CCCEEEEEecCChhhCCHHHHhhCceEEEeCCcCHHHHHHHHHHHHhhcCC---CccHHHHHHHHHHcCCCCHHHHHHHH
Confidence            12345555664431       123347788899999999988876643221   1135678889999998 455666654


Q ss_pred             H
Q 042541          366 G  366 (695)
Q Consensus       366 ~  366 (695)
                      .
T Consensus       296 ~  296 (357)
T 3d8b_A          296 R  296 (357)
T ss_dssp             H
T ss_pred             H
Confidence            4

>3ogk_B Coronatine-insensitive protein 1; leucine rich repeat, ubiquitin ligase, SCF, protein binding; HET: OGK; 2.80A {Arabidopsis thaliana} PDB: 3ogl_B* 3ogm_B*

Probab=98.14  E-value=8.1e-07  Score=99.60  Aligned_cols=83  Identities=11%  Similarity=0.109  Sum_probs=37.2

Q ss_pred             CCceEEEEEEccCcccc----CChhhcCCCCCcEEEEcccCCCCcccCcc-cccccCCCCcEEEeccCCCCCcc-ccccc
Q 042541          549 GPEVKVVVLNIRTKKYV----LPDFLQKMDELKVLIVTNYGFSPAELNNF-RVLSALSKLKKIRLEHVSLPNSL-ATVRM  622 (695)
Q Consensus       549 ~~~l~~L~l~~~~~~~~----~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~-~~l~~l~~L~~L~L~~~~l~~lp-~i~~l  622 (695)
                      +++|+.|.++.+.....    ++..+..+++|++|++++|.+.......+ ..+..+++|+.|++++|.+..+| .++++
T Consensus       163 ~~~L~~L~L~~~~~~~~~~~~l~~~~~~~~~L~~L~L~~n~~~~~~~~~l~~~~~~~~~L~~L~L~~~~~~~l~~~~~~~  242 (592)
T 3ogk_B          163 CRKIKTLLMEESSFSEKDGKWLHELAQHNTSLEVLNFYMTEFAKISPKDLETIARNCRSLVSVKVGDFEILELVGFFKAA  242 (592)
T ss_dssp             CTTCSEEECTTCEEECCCSHHHHHHHHHCCCCCEEECTTCCCSSCCHHHHHHHHHHCTTCCEEECSSCBGGGGHHHHHHC
T ss_pred             CCCCCEEECccccccCcchhHHHHHHhcCCCccEEEeeccCCCccCHHHHHHHHhhCCCCcEEeccCccHHHHHHHHhhh
Confidence            45555555554422111    23334445555555555544421000011 11334555555555555555555 55555


Q ss_pred             ccccEEeec
Q 042541          623 NHLQKVSLV  631 (695)
Q Consensus       623 ~~L~~L~l~  631 (695)
                      ++|++|+++
T Consensus       243 ~~L~~L~l~  251 (592)
T 3ogk_B          243 ANLEEFCGG  251 (592)
T ss_dssp             TTCCEEEEC
T ss_pred             hHHHhhccc
Confidence            555555554

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=98.14  E-value=4.7e-05  Score=77.81  Aligned_cols=174  Identities=14%  Similarity=0.164  Sum_probs=100.8

Q ss_pred             CCCCCCcchHHHHHHHHHc------------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHH
Q 042541          166 VISPGLDVPLKELKMELFK------------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVK  233 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~------------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~  233 (695)
                      +.++|.+..++.|.+.+..            ...+-|.|+|++|+|||+||+.+++.  ..   ....+.++.+.-.+  
T Consensus        12 ~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~--~~---~~~~~~i~~~~l~~--   84 (322)
T 1xwi_A           12 SDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATE--AN---NSTFFSISSSDLVS--   84 (322)
T ss_dssp             GGSCSCHHHHHHHHHHHHHHHHCGGGSCTTCCCCSEEEEESSSSSCHHHHHHHHHHH--TT---SCEEEEEECCSSCC--
T ss_pred             HHhcCHHHHHHHHHHHHHHHHhCHHHHhCCCCCCceEEEECCCCccHHHHHHHHHHH--cC---CCcEEEEEhHHHHh--
Confidence            4578999988888877641            12467999999999999999999973  21   11133444432210  


Q ss_pred             HHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCC--------h---H----HHhhhcc---CC
Q 042541          234 AIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGS--------E---S----LLQKLGF---QL  294 (695)
Q Consensus       234 ~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~--------~---~----~~~~l~~---~~  294 (695)
                                  ...  ...+.   .+..++ .....++.+|++|+++...        .   .    ++..+..   ..
T Consensus        85 ------------~~~--g~~~~---~~~~lf~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~ld~~~~~~  147 (322)
T 1xwi_A           85 ------------KWL--GESEK---LVKNLFQLARENKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDN  147 (322)
T ss_dssp             ------------SSC--CSCHH---HHHHHHHHHHHTSSEEEEEETTTGGGCCSSSCCTTHHHHHHHHHHHHHHCSSSCC
T ss_pred             ------------hhh--hHHHH---HHHHHHHHHHhcCCcEEEeecHHHhccccccccchHHHHHHHHHHHHHhcccccC
Confidence                        000  01122   223333 2223678999999996431        0   1    1222221   12


Q ss_pred             CCCEEEEEcCCCC-------CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCc-hhHHHHHHH
Q 042541          295 PDYKILVTSRSEF-------PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGC-PLALKVVGG  366 (695)
Q Consensus       295 ~gs~iivTtR~~~-------~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~-PLai~~~~~  366 (695)
                      .+..||.||....       ......+.++..+.++-.+++.........   .........|++.+.|. +-.|..+..
T Consensus       148 ~~v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~---~l~~~~l~~la~~t~G~sgadl~~l~~  224 (322)
T 1xwi_A          148 DGILVLGATNIPWVLDSAIRRRFEKRIYIPLPEPHARAAMFKLHLGTTQN---SLTEADFRELGRKTDGYSGADISIIVR  224 (322)
T ss_dssp             TTEEEEEEESCTTTSCHHHHHTCCEEEECCCCCHHHHHHHHHHHHTTCCB---CCCHHHHHHHHHTCTTCCHHHHHHHHH
T ss_pred             CCEEEEEecCCcccCCHHHHhhcCeEEEeCCcCHHHHHHHHHHHHhcCCC---CCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            3445555664431       123347788888999999999887643221   11355678899999887 444555443

>3un9_A NLR family member X1; leucine rich repeat (LRR), antiviral signaling, MAVS, TRAF6, UQCRC2, immune system; 2.65A {Homo sapiens}

Probab=98.13  E-value=1.9e-07  Score=97.94  Aligned_cols=136  Identities=13%  Similarity=0.070  Sum_probs=90.3

Q ss_pred             CceEEEEEEccCcccc----CChhhc-CCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--cc---
Q 042541          550 PEVKVVVLNIRTKKYV----LPDFLQ-KMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--AT---  619 (695)
Q Consensus       550 ~~l~~L~l~~~~~~~~----~p~~~~-~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i---  619 (695)
                      ++++.|.++.+.....    +...+. ..++|+.|+|++|.+....+..+  ...+.+|++|+|++|.++...  .+   
T Consensus        72 ~~L~~L~Ls~n~l~~~~~~~l~~~L~~~~~~L~~L~Ls~n~l~~~~~~~l--~~~L~~L~~L~Ls~n~l~~~~~~~L~~~  149 (372)
T 3un9_A           72 SSLRQLNLAGVRMTPVKCTVVAAVLGSGRHALDEVNLASCQLDPAGLRTL--LPVFLRARKLGLQLNSLGPEACKDLRDL  149 (372)
T ss_dssp             TTCCEEECTTSCCCHHHHHHHHHHHSSCSSCEEEEECTTCCCCHHHHHHT--HHHHHTEEEEECCSSCCCHHHHHHHHHH
T ss_pred             hhCCEEEecCCCCCHHHHHHHHHHHhhCCCCceEEEecCCCCCHHHHHHH--HHHHHhccHhhcCCCCCCHHHHHHHHHH
Confidence            3455666655543322    223333 23799999999998754332222  345678999999999997433  33   


Q ss_pred             --cccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccc-----cCchhhcCCCCCceeecccccCCC
Q 042541          620 --VRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLI-----ELPDGLCDIVSMEKLRITNCHRLS  689 (695)
Q Consensus       620 --~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~-----~lP~~i~~L~~L~~L~l~~~~~l~  689 (695)
                        ...++|++|+|++|.++......+...-..+++|++|+|++|. ++     .++..+...++|++|+|++|. ++
T Consensus       150 L~~~~~~L~~L~Ls~n~l~~~~~~~l~~~L~~~~~L~~L~Ls~N~-l~~~g~~~L~~~L~~~~~L~~L~Ls~N~-i~  224 (372)
T 3un9_A          150 LLHDQCQITTLRLSNNPLTAAGVAVLMEGLAGNTSVTHLSLLHTG-LGDEGLELLAAQLDRNRQLQELNVAYNG-AG  224 (372)
T ss_dssp             HHSTTCCCCEEECCSSCCHHHHHHHHHHHHHTCSSCCEEECTTSS-CHHHHHHHHHHHGGGCSCCCEEECCSSC-CC
T ss_pred             HHhcCCccceeeCCCCCCChHHHHHHHHHHhcCCCcCEEeCCCCC-CCcHHHHHHHHHHhcCCCcCeEECCCCC-CC
Confidence              2457899999999988653221111000168899999999975 44     346678888999999999986 44

>2ra8_A Uncharacterized protein Q64V53_bacfr; WGR domain, LRR domain, leucine rich repeats, BFR43, structural genomics, PSI-2; 1.95A {Bacteroides fragilis}

Probab=98.12  E-value=1.3e-06  Score=90.70  Aligned_cols=133  Identities=17%  Similarity=0.158  Sum_probs=65.7

Q ss_pred             CCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccC--C------CCCcc--
Q 042541          548 QGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHV--S------LPNSL--  617 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~--~------l~~lp--  617 (695)
                      .+|+|+.|.+.++.. ..+|. +. +++|+.|++..+++....+..+. ...+++|++|+|+.+  .      +..+.  
T Consensus       170 ~~P~L~~L~L~g~~~-l~l~~-~~-~~~L~~L~L~~~~l~~~~l~~l~-~~~lp~L~~L~L~~~~~~~~~~~~~~~l~~~  245 (362)
T 2ra8_A          170 AMPLLNNLKIKGTNN-LSIGK-KP-RPNLKSLEIISGGLPDSVVEDIL-GSDLPNLEKLVLYVGVEDYGFDGDMNVFRPL  245 (362)
T ss_dssp             TCTTCCEEEEECCBT-CBCCS-CB-CTTCSEEEEECSBCCHHHHHHHH-HSBCTTCCEEEEECBCGGGTCCSCGGGTGGG
T ss_pred             cCCCCcEEEEeCCCC-ceecc-cc-CCCCcEEEEecCCCChHHHHHHH-HccCCCCcEEEEeccccccccchhHHHHHHH
Confidence            346666666665521 12333 22 66677777766554221111110 125667777766421  1      11111  


Q ss_pred             -cccccccccEEeeccccCCcccccchhhhcccCCCccEEeccccccccc-----CchhhcCCCCCceeeccccc
Q 042541          618 -ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIE-----LPDGLCDIVSMEKLRITNCH  686 (695)
Q Consensus       618 -~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~-----lP~~i~~L~~L~~L~l~~~~  686 (695)
                       ..+.+++|++|+|++|.+...........| .+++|++|+|++|. ++.     ++.++.++++|+.|+|++|.
T Consensus       246 l~~~~~p~Lr~L~L~~~~i~~~~~~~la~a~-~~~~L~~LdLs~n~-L~d~G~~~L~~~L~~l~~L~~L~L~~n~  318 (362)
T 2ra8_A          246 FSKDRFPNLKWLGIVDAEEQNVVVEMFLESD-ILPQLETMDISAGV-LTDEGARLLLDHVDKIKHLKFINMKYNY  318 (362)
T ss_dssp             SCTTTCTTCCEEEEESCTTHHHHHHHHHHCS-SGGGCSEEECCSSC-CBHHHHHHHHTTHHHHTTCSEEECCSBB
T ss_pred             HhcCCCCCcCEEeCCCCCCchHHHHHHHhCc-cCCCCCEEECCCCC-CChHHHHHHHhhcccCCcceEEECCCCc
Confidence             112466777777777665532111111112 46677777776643 332     44555666777777777654

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C

Probab=98.10  E-value=1.7e-05  Score=81.32  Aligned_cols=173  Identities=16%  Similarity=0.181  Sum_probs=102.3

Q ss_pred             CCCCCCcchHHHHHHHHH------------cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHH
Q 042541          166 VISPGLDVPLKELKMELF------------KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVK  233 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~------------~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~  233 (695)
                      +.++|.+..++.|.+.+.            ....+-|.|+|++|+|||+||+.+++  ...    ...+.++.+.     
T Consensus        18 ~di~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~--~~~----~~~~~v~~~~-----   86 (322)
T 3eie_A           18 EDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVAT--EAN----STFFSVSSSD-----   86 (322)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCGGGCCTTCCCCCEEEEECSSSSCHHHHHHHHHH--HHT----CEEEEEEHHH-----
T ss_pred             HHhcChHHHHHHHHHHHHHHHhCHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHH--HHC----CCEEEEchHH-----
Confidence            457999999999988773            11246799999999999999999987  332    2233443321     


Q ss_pred             HHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCC---------------hHHHhhhc---cCC
Q 042541          234 AIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGS---------------ESLLQKLG---FQL  294 (695)
Q Consensus       234 ~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~---------------~~~~~~l~---~~~  294 (695)
                       +    ....         .......+..++ .....++.+|+||+++...               ..++..+.   ...
T Consensus        87 -l----~~~~---------~g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~  152 (322)
T 3eie_A           87 -L----VSKW---------MGESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGNDS  152 (322)
T ss_dssp             -H----HTTT---------GGGHHHHHHHHHHHHHHTSSEEEEEECGGGGSCC------CCTHHHHHHHHHHHGGGGTSC
T ss_pred             -H----hhcc---------cchHHHHHHHHHHHHHhcCCeEEEechhhhhhccCCCCcchHHHHHHHHHHHHhccccccC
Confidence             1    1110         011122233333 2224567899999986431               11222222   223


Q ss_pred             CCCEEEEEcCCCCC-------CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCc-hhHHHHHHH
Q 042541          295 PDYKILVTSRSEFP-------QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGC-PLALKVVGG  366 (695)
Q Consensus       295 ~gs~iivTtR~~~~-------~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~-PLai~~~~~  366 (695)
                      .+..||.||.....       .....+.++..+.++-.+++...+.....   .........|++.+.|. +-.|..+..
T Consensus       153 ~~v~vi~atn~~~~ld~al~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~---~~~~~~l~~la~~t~g~sg~di~~l~~  229 (322)
T 3eie_A          153 QGVLVLGATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMFEINVGDTPC---VLTKEDYRTLGAMTEGYSGSDIAVVVK  229 (322)
T ss_dssp             CCEEEEEEESCGGGSCHHHHHHCCEEEECCCCCHHHHHHHHHHHHTTCCC---CCCHHHHHHHHHTTTTCCHHHHHHHHH
T ss_pred             CceEEEEecCChhhCCHHHHcccCeEEEeCCCCHHHHHHHHHHHhccCCC---CCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            34556656654311       23347788889999999999987754322   11355678899999884 545554443

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=98.10  E-value=1e-05  Score=75.34  Aligned_cols=44  Identities=20%  Similarity=0.209  Sum_probs=39.7

Q ss_pred             CCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          166 VISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..++||+.+++.+.+.+.....+.+.|+|++|+|||+||+.+++
T Consensus        22 ~~~~g~~~~~~~l~~~l~~~~~~~vll~G~~G~GKT~la~~~~~   65 (187)
T 2p65_A           22 DPVIGRDTEIRRAIQILSRRTKNNPILLGDPGVGKTAIVEGLAI   65 (187)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSSSCEEEEESCGGGCHHHHHHHHHH
T ss_pred             chhhcchHHHHHHHHHHhCCCCCceEEECCCCCCHHHHHHHHHH
Confidence            45799999999999999876677889999999999999999987

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus}

Probab=98.07  E-value=3.4e-05  Score=78.15  Aligned_cols=166  Identities=13%  Similarity=0.152  Sum_probs=95.4

Q ss_pred             CCCCCCcchHHHHHHHHHc-------------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCH
Q 042541          166 VISPGLDVPLKELKMELFK-------------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNV  232 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~-------------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~  232 (695)
                      +.++|.+..+++|.+.+..             ...+.|.|+|++|+|||+||+.+++  ...    ...+.++      .
T Consensus        15 ~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~--~~~----~~~i~v~------~   82 (301)
T 3cf0_A           15 EDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIAN--ECQ----ANFISIK------G   82 (301)
T ss_dssp             GGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHH--HTT----CEEEEEC------H
T ss_pred             HHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHH--HhC----CCEEEEE------h
Confidence            4579999988888877652             3356799999999999999999997  332    2222332      2


Q ss_pred             HHHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCC------------------hHHHhhhccC
Q 042541          233 KAIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGS------------------ESLLQKLGFQ  293 (695)
Q Consensus       233 ~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~------------------~~~~~~l~~~  293 (695)
                      .++.....   +..      .    ..+..++ ......+.++++|+++...                  ..++..+...
T Consensus        83 ~~l~~~~~---g~~------~----~~~~~~f~~a~~~~p~il~iDEid~l~~~~~~~~~~~~~~~~~~~~~lL~~l~~~  149 (301)
T 3cf0_A           83 PELLTMWF---GES------E----ANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGM  149 (301)
T ss_dssp             HHHHHHHH---TTC------T----THHHHHHHHHHHTCSEEEEECSTTHHHHHHTTTTCCSSCSCCHHHHHHHHHHHSS
T ss_pred             HHHHhhhc---Cch------H----HHHHHHHHHHHhcCCeEEEEEChHHHhhccCCCcCCcchHHHHHHHHHHHHhhcc
Confidence            23333221   211      0    1123333 2223568999999986311                  1123333211


Q ss_pred             --CCCCEEEEEcCCCC------C---CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhH
Q 042541          294 --LPDYKILVTSRSEF------P---QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLA  360 (695)
Q Consensus       294 --~~gs~iivTtR~~~------~---~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLa  360 (695)
                        ..+..||.||....      .   .....+.++..+.++-.+++.............    ....+++.+.|.|-+
T Consensus       150 ~~~~~v~vi~atn~~~~ld~al~r~gRf~~~i~i~~p~~~~r~~il~~~l~~~~~~~~~----~~~~la~~~~g~sg~  223 (301)
T 3cf0_A          150 STKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDV----DLEFLAKMTNGFSGA  223 (301)
T ss_dssp             CTTSSEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCSSC----CHHHHHHTCSSCCHH
T ss_pred             cCCCCEEEEEecCCccccChHHhcCCccceEEecCCcCHHHHHHHHHHHHccCCCCccc----hHHHHHHHcCCCCHH
Confidence              22456666665441      1   223378899999999889888766433211111    134566677776643

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=98.05  E-value=4e-05  Score=78.58  Aligned_cols=165  Identities=17%  Similarity=0.124  Sum_probs=94.5

Q ss_pred             CCCcc--hHHHHHHHHHcC--CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcC
Q 042541          169 PGLDV--PLKELKMELFKD--GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKG  244 (695)
Q Consensus       169 vGr~~--~~~~l~~~L~~~--~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~  244 (695)
                      +|...  ....+...+..+  ....+.|+|++|+||||||+.+++.  .... ...+++++..      ++...+...+.
T Consensus        15 ~g~~~~~a~~~~~~~~~~~~~~~~~lll~G~~GtGKT~la~~i~~~--~~~~-~~~~~~i~~~------~~~~~~~~~~~   85 (324)
T 1l8q_A           15 VGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNE--AKKR-GYRVIYSSAD------DFAQAMVEHLK   85 (324)
T ss_dssp             CCTTTHHHHHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHH--HHHT-TCCEEEEEHH------HHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHhCcCCCCCeEEEECCCCCcHHHHHHHHHHH--HHHC-CCEEEEEEHH------HHHHHHHHHHH
Confidence            36443  234444544443  2467899999999999999999883  3222 2235566543      23333333321


Q ss_pred             CCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCCh--H----HHhhhcc-CCCCCEEEEEcCCCCC---C-----
Q 042541          245 YPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSE--S----LLQKLGF-QLPDYKILVTSRSEFP---Q-----  309 (695)
Q Consensus       245 ~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~--~----~~~~l~~-~~~gs~iivTtR~~~~---~-----  309 (695)
                      ..     .    ...+   ...+ .+..+|++||+.....  +    +...+.. ...|..||+||.....   .     
T Consensus        86 ~~-----~----~~~~---~~~~-~~~~vL~iDEi~~l~~~~~~~~~l~~~l~~~~~~~~~iii~~~~~~~~l~~l~~~L  152 (324)
T 1l8q_A           86 KG-----T----INEF---RNMY-KSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRL  152 (324)
T ss_dssp             HT-----C----HHHH---HHHH-HTCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHH
T ss_pred             cC-----c----HHHH---HHHh-cCCCEEEEcCcccccCChHHHHHHHHHHHHHHHCCCeEEEEecCChHHHHHhhhHh
Confidence            10     0    1111   1112 2367999999865431  1    2222211 1246678888865421   1     


Q ss_pred             -----CCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhH
Q 042541          310 -----FGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLA  360 (695)
Q Consensus       310 -----~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLa  360 (695)
                           .+..+.+++ +.++..+++...+.....   .-.++....|++.+ |..-.
T Consensus       153 ~sR~~~~~~i~l~~-~~~e~~~il~~~~~~~~~---~l~~~~l~~l~~~~-g~~r~  203 (324)
T 1l8q_A          153 VSRFEGGILVEIEL-DNKTRFKIIKEKLKEFNL---ELRKEVIDYLLENT-KNVRE  203 (324)
T ss_dssp             HHHHHTSEEEECCC-CHHHHHHHHHHHHHHTTC---CCCHHHHHHHHHHC-SSHHH
T ss_pred             hhcccCceEEEeCC-CHHHHHHHHHHHHHhcCC---CCCHHHHHHHHHhC-CCHHH
Confidence                 123688999 999999999887643222   12366788889988 77653

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*

Probab=98.03  E-value=2.8e-05  Score=80.75  Aligned_cols=172  Identities=16%  Similarity=0.181  Sum_probs=99.3

Q ss_pred             CCCCCCcchHHHHHHHHHc------------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHH
Q 042541          166 VISPGLDVPLKELKMELFK------------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVK  233 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~------------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~  233 (695)
                      +.++|.+..++.|.+.+..            ...+-|.|+|++|+|||+||+.+++.  ..    ...+.++.+      
T Consensus        51 ~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~--~~----~~~~~v~~~------  118 (355)
T 2qp9_X           51 EDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATE--AN----STFFSVSSS------  118 (355)
T ss_dssp             GGSCCGGGHHHHHHHHTHHHHHCGGGGCSSCCCCCCEEEECSTTSCHHHHHHHHHHH--HT----CEEEEEEHH------
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhCHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHH--hC----CCEEEeeHH------
Confidence            4579999999999887631            11345889999999999999999983  32    223344332      


Q ss_pred             HHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCCh---------------HHHhhhc---cCC
Q 042541          234 AIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGSE---------------SLLQKLG---FQL  294 (695)
Q Consensus       234 ~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~~---------------~~~~~l~---~~~  294 (695)
                      ++    .....+      ...   ..+..++ .....++.+|+||+++....               .++..+.   ...
T Consensus       119 ~l----~~~~~g------~~~---~~~~~~f~~a~~~~~~vl~iDEid~l~~~r~~~~~~~~~~~~~~ll~~l~~~~~~~  185 (355)
T 2qp9_X          119 DL----VSKWMG------ESE---KLVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGNDS  185 (355)
T ss_dssp             HH----HSCC---------CH---HHHHHHHHHHHHTSSEEEEEECGGGGTC------CTHHHHHHHHHHHHHHHCC---
T ss_pred             HH----hhhhcc------hHH---HHHHHHHHHHHHcCCeEEEEechHhhcccCCCCcchHHHHHHHHHHHHhhcccccC
Confidence            11    111100      111   2223333 22235789999999864321               1222221   112


Q ss_pred             CCCEEEEEcCCCC-------CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCc-hhHHHHHH
Q 042541          295 PDYKILVTSRSEF-------PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGC-PLALKVVG  365 (695)
Q Consensus       295 ~gs~iivTtR~~~-------~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~-PLai~~~~  365 (695)
                      .+..||.||....       ......+.++..+.++-.+++...+.....   .........|++.+.|. +-.|..+.
T Consensus       186 ~~v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~---~~~~~~l~~la~~t~G~sg~dl~~l~  261 (355)
T 2qp9_X          186 QGVLVLGATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMFEINVGDTPS---VLTKEDYRTLGAMTEGYSGSDIAVVV  261 (355)
T ss_dssp             CCEEEEEEESCGGGSCHHHHHTCCEEEECCCCCHHHHHHHHHHHHTTSCB---CCCHHHHHHHHHHTTTCCHHHHHHHH
T ss_pred             CCeEEEeecCCcccCCHHHHcccCEEEEeCCcCHHHHHHHHHHHHhhCCC---CCCHHHHHHHHHHcCCCCHHHHHHHH
Confidence            3445555665431       123347788999999999999887643321   11245678899999884 54455443

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.02  E-value=0.00013  Score=75.60  Aligned_cols=164  Identities=16%  Similarity=0.186  Sum_probs=97.5

Q ss_pred             CCCCCCcchHHHHHHHHH----c---------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCH
Q 042541          166 VISPGLDVPLKELKMELF----K---------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNV  232 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~----~---------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~  232 (695)
                      +.+.|.++.+++|.+.+.    .         ..++=|.++|++|+|||.||+++++  .....    .+.++.+.-.+ 
T Consensus       148 ~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTllAkAiA~--e~~~~----f~~v~~s~l~s-  220 (405)
T 4b4t_J          148 DMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAH--HTDCK----FIRVSGAELVQ-  220 (405)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHHHHHH--HHTCE----EEEEEGGGGSC-
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHHHHHH--hhCCC----ceEEEhHHhhc-
Confidence            456889988888877654    1         1256789999999999999999998  33222    34554443211 


Q ss_pred             HHHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCCh-----------H-------HHhhhcc-
Q 042541          233 KAIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGSE-----------S-------LLQKLGF-  292 (695)
Q Consensus       233 ~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~~-----------~-------~~~~l~~-  292 (695)
                                   .     -..+....++.++ ..-...+++|++|+++....           .       ++..+.. 
T Consensus       221 -------------k-----~vGese~~vr~lF~~Ar~~aP~IIFiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~  282 (405)
T 4b4t_J          221 -------------K-----YIGEGSRMVRELFVMAREHAPSIIFMDEIDSIGSTRVEGSGGGDSEVQRTMLELLNQLDGF  282 (405)
T ss_dssp             -------------S-----STTHHHHHHHHHHHHHHHTCSEEEEEESSSCCTTSCSCSSSGGGGHHHHHHHHHHHHHHTT
T ss_pred             -------------c-----ccchHHHHHHHHHHHHHHhCCceEeeecchhhccCCCCCCCCCcHHHHHHHHHHHHhhhcc
Confidence                         0     1122234445555 33346789999999864320           0       2222221 


Q ss_pred             -CCCCCEEEEEcCCCC---------CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCch
Q 042541          293 -QLPDYKILVTSRSEF---------PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCP  358 (695)
Q Consensus       293 -~~~gs~iivTtR~~~---------~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~P  358 (695)
                       ...+..||.||....         ......+.++.-+.++-.++|+.+..........    -...|++.+.|+-
T Consensus       283 ~~~~~V~vIaATNrpd~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~l~~dv----dl~~lA~~t~G~S  354 (405)
T 4b4t_J          283 ETSKNIKIIMATNRLDILDPALLRPGRIDRKIEFPPPSVAARAEILRIHSRKMNLTRGI----NLRKVAEKMNGCS  354 (405)
T ss_dssp             TCCCCEEEEEEESCSSSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSBCCSSC----CHHHHHHHCCSCC
T ss_pred             CCCCCeEEEeccCChhhCCHhHcCCCcCceEEEcCCcCHHHHHHHHHHHhcCCCCCccC----CHHHHHHHCCCCC
Confidence             122345555665441         1344588899889999899998766433221111    1567888888753

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=98.02  E-value=1.9e-05  Score=70.50  Aligned_cols=109  Identities=13%  Similarity=0.071  Sum_probs=66.0

Q ss_pred             CCCCCcchHHHHHHHHH--cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcC
Q 042541          167 ISPGLDVPLKELKMELF--KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKG  244 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~--~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~  244 (695)
                      .++|++..++++.+.+.  .....-|.|+|.+|+|||++|+.+++.. .+...+  .+ ++++...+.            
T Consensus         2 ~iiG~s~~~~~~~~~~~~~a~~~~~vll~G~~GtGKt~lA~~i~~~~-~~~~~~--~v-~~~~~~~~~------------   65 (145)
T 3n70_A            2 ELIGRSEWINQYRRRLQQLSETDIAVWLYGAPGTGRMTGARYLHQFG-RNAQGE--FV-YRELTPDNA------------   65 (145)
T ss_dssp             --CCSSHHHHHHHHHHHHHTTCCSCEEEESSTTSSHHHHHHHHHHSS-TTTTSC--CE-EEECCTTTS------------
T ss_pred             CceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCCHHHHHHHHHHhC-CccCCC--EE-EECCCCCcc------------
Confidence            47999999999998876  2334557899999999999999998731 111222  33 666543221            


Q ss_pred             CCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCC
Q 042541          245 YPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSE  306 (695)
Q Consensus       245 ~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~  306 (695)
                            ..       ....++..  +...|++|+++.....    ++..+.......++|+||...
T Consensus        66 ------~~-------~~~~~~~a--~~g~l~ldei~~l~~~~q~~Ll~~l~~~~~~~~~I~~t~~~  116 (145)
T 3n70_A           66 ------PQ-------LNDFIALA--QGGTLVLSHPEHLTREQQYHLVQLQSQEHRPFRLIGIGDTS  116 (145)
T ss_dssp             ------SC-------HHHHHHHH--TTSCEEEECGGGSCHHHHHHHHHHHHSSSCSSCEEEEESSC
T ss_pred             ------hh-------hhcHHHHc--CCcEEEEcChHHCCHHHHHHHHHHHhhcCCCEEEEEECCcC
Confidence                  00       11112111  2357899999877643    333343334457888888643

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=98.01  E-value=6.6e-05  Score=79.08  Aligned_cols=174  Identities=14%  Similarity=0.156  Sum_probs=100.3

Q ss_pred             CCCCCCCcchHHHHHHHHH------------cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCH
Q 042541          165 PVISPGLDVPLKELKMELF------------KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNV  232 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~------------~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~  232 (695)
                      -+.++|.+..++.|.+++.            ....+-|.|+|++|+|||+||+.+++.  .    ...++.++.+.-...
T Consensus       114 ~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vLL~GppGtGKT~la~aia~~--~----~~~~~~v~~~~l~~~  187 (389)
T 3vfd_A          114 FDDIAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAE--S----NATFFNISAASLTSK  187 (389)
T ss_dssp             GGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGCCCSEEEEESSTTSCHHHHHHHHHHH--T----TCEEEEECSCCC---
T ss_pred             hHHhCCHHHHHHHHHHHHHHhccCHHHhcccCCCCceEEEECCCCCCHHHHHHHHHHh--h----cCcEEEeeHHHhhcc
Confidence            3568999999999988773            122468999999999999999999873  2    222344444332210


Q ss_pred             HHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHH-hcCCCcEEEEEeCCCCCC-----------hH----HHhhhc---cC
Q 042541          233 KAIVQKVLHHKGYPVPEFQTDEAAINDLERFFK-QMRIEAILLVLDDVWPGS-----------ES----LLQKLG---FQ  293 (695)
Q Consensus       233 ~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~-~l~~~~~LlVlDdv~~~~-----------~~----~~~~l~---~~  293 (695)
                        .       .+       ...   ..+..++. .....+.+|+||+++...           ..    ++..+.   ..
T Consensus       188 --~-------~g-------~~~---~~~~~~~~~a~~~~~~il~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~  248 (389)
T 3vfd_A          188 --Y-------VG-------EGE---KLVRALFAVARELQPSIIFIDQVDSLLCERREGEHDASRRLKTEFLIEFDGVQSA  248 (389)
T ss_dssp             --------------------CH---HHHHHHHHHHHHSSSEEEEEETGGGGC--------CTHHHHHHHHHHHHHHHC--
T ss_pred             --c-------cc-------hHH---HHHHHHHHHHHhcCCeEEEEECchhhcccCCCccchHHHHHHHHHHHHhhccccc
Confidence              0       00       011   12223331 113456899999995431           11    111111   11


Q ss_pred             -CCCCEEEEEcCCCC-------CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchh-HHHHH
Q 042541          294 -LPDYKILVTSRSEF-------PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPL-ALKVV  364 (695)
Q Consensus       294 -~~gs~iivTtR~~~-------~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PL-ai~~~  364 (695)
                       ..+..||.||....       ......+.+...+.++..+++...+.....   .-..+....|++.+.|..- +|..+
T Consensus       249 ~~~~v~vI~atn~~~~l~~~l~~R~~~~i~i~~p~~~~r~~il~~~~~~~~~---~l~~~~~~~la~~~~g~~~~~l~~L  325 (389)
T 3vfd_A          249 GDDRVLVMGATNRPQELDEAVLRRFIKRVYVSLPNEETRLLLLKNLLCKQGS---PLTQKELAQLARMTDGYSGSDLTAL  325 (389)
T ss_dssp             ---CEEEEEEESCGGGCCHHHHTTCCEEEECCCCCHHHHHHHHHHHHTTSCC---CSCHHHHHHHHHHTTTCCHHHHHHH
T ss_pred             CCCCEEEEEecCCchhcCHHHHcCcceEEEcCCcCHHHHHHHHHHHHHhcCC---CCCHHHHHHHHHHcCCCCHHHHHHH
Confidence             12344555665431       123346889999999999999877644322   1235677889999988644 55555


Q ss_pred             HH
Q 042541          365 GG  366 (695)
Q Consensus       365 ~~  366 (695)
                      ..
T Consensus       326 ~~  327 (389)
T 3vfd_A          326 AK  327 (389)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=98.01  E-value=0.00013  Score=73.79  Aligned_cols=172  Identities=13%  Similarity=0.169  Sum_probs=99.2

Q ss_pred             CCCCCCcchHHHHHHHHHc------------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHH
Q 042541          166 VISPGLDVPLKELKMELFK------------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVK  233 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~------------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~  233 (695)
                      +.++|.+..++.+.+.+..            ...+.+.|+|++|+||||+|+.+++.  .    ....+.++.+....  
T Consensus        21 ~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la~~la~~--~----~~~~~~i~~~~l~~--   92 (297)
T 3b9p_A           21 TDIAGQDVAKQALQEMVILPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLARAVATE--C----SATFLNISAASLTS--   92 (297)
T ss_dssp             GGSCCCHHHHHHHHHHTHHHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHHHHHHHH--T----TCEEEEEESTTTSS--
T ss_pred             HHhCChHHHHHHHHHHHHhhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHHHHHHHH--h----CCCeEEeeHHHHhh--
Confidence            4679999999998887642            23568899999999999999999873  2    22233444433211  


Q ss_pred             HHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCC-----------hH----HHhhhcc---CC
Q 042541          234 AIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGS-----------ES----LLQKLGF---QL  294 (695)
Q Consensus       234 ~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~-----------~~----~~~~l~~---~~  294 (695)
                                  ...  .....   .+...+ .....++.+|++|++....           ..    ++..+..   ..
T Consensus        93 ------------~~~--~~~~~---~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~  155 (297)
T 3b9p_A           93 ------------KYV--GDGEK---LVRALFAVARHMQPSIIFIDEVDSLLSERSSSEHEASRRLKTEFLVEFDGLPGNP  155 (297)
T ss_dssp             ------------SSC--SCHHH---HHHHHHHHHHHTCSEEEEEETGGGTSBCC-----CCSHHHHHHHHHHHHHCC---
T ss_pred             ------------ccc--chHHH---HHHHHHHHHHHcCCcEEEeccHHHhccccccCcchHHHHHHHHHHHHHhcccccC
Confidence                        000  01111   222222 2223567899999985431           11    1221111   11


Q ss_pred             --CCCEEEEEcCCCC-------CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchh-HHHHH
Q 042541          295 --PDYKILVTSRSEF-------PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPL-ALKVV  364 (695)
Q Consensus       295 --~gs~iivTtR~~~-------~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PL-ai~~~  364 (695)
                        .+..||.||....       ......+.++..+.++...++...+.....   .-..+....|++.+.|.+- ++..+
T Consensus       156 ~~~~v~vi~~tn~~~~l~~~l~~R~~~~i~~~~p~~~~r~~il~~~~~~~~~---~~~~~~~~~la~~~~g~~~~~l~~l  232 (297)
T 3b9p_A          156 DGDRIVVLAATNRPQELDEAALRRFTKRVYVSLPDEQTRELLLNRLLQKQGS---PLDTEALRRLAKITDGYSGSDLTAL  232 (297)
T ss_dssp             ---CEEEEEEESCGGGBCHHHHHHCCEEEECCCCCHHHHHHHHHHHHGGGSC---CSCHHHHHHHHHHTTTCCHHHHHHH
T ss_pred             CCCcEEEEeecCChhhCCHHHHhhCCeEEEeCCcCHHHHHHHHHHHHHhcCC---CCCHHHHHHHHHHcCCCCHHHHHHH
Confidence              2345555665431       122346778888888888888776543221   1135567889999999875 55444


Q ss_pred             H
Q 042541          365 G  365 (695)
Q Consensus       365 ~  365 (695)
                      .
T Consensus       233 ~  233 (297)
T 3b9p_A          233 A  233 (297)
T ss_dssp             H
T ss_pred             H
Confidence            3

>3e4g_A ATP synthase subunit S, mitochondrial; leucine-rich repeat, CF0, hydrogen ION transport, inner membrane, ION transport, membrane, mitochondrion; 0.96A {Bos taurus} PDB: 3e3z_A 3dze_A 3e2j_A

Probab=97.98  E-value=3.7e-06  Score=76.81  Aligned_cols=86  Identities=14%  Similarity=0.227  Sum_probs=58.5

Q ss_pred             CCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCC-CCCcc--ccccc----ccccEEeecccc-CCcccccchhh
Q 042541          574 DELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVS-LPNSL--ATVRM----NHLQKVSLVMCN-VGQVFRNSTFR  645 (695)
Q Consensus       574 ~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~-l~~lp--~i~~l----~~L~~L~l~~~~-i~~~~~~~~~~  645 (695)
                      .+|+.||+++|.+....+.   .+..+++|+.|+|++|. ++.-.  .+..+    ++|++|+|++|. |+..-   ...
T Consensus        61 ~~L~~LDLs~~~Itd~GL~---~L~~~~~L~~L~L~~C~~ItD~gL~~L~~~~~~~~~L~~L~Ls~C~~ITD~G---l~~  134 (176)
T 3e4g_A           61 YKIQAIDATDSCIMSIGFD---HMEGLQYVEKIRLCKCHYIEDGCLERLSQLENLQKSMLEMEIISCGNVTDKG---IIA  134 (176)
T ss_dssp             CCEEEEEEESCCCCGGGGG---GGTTCSCCCEEEEESCTTCCHHHHHHHHTCHHHHHHCCEEEEESCTTCCHHH---HHH
T ss_pred             ceEeEEeCcCCCccHHHHH---HhcCCCCCCEEEeCCCCccCHHHHHHHHhcccccCCCCEEEcCCCCcCCHHH---HHH
Confidence            4699999999876554443   36788889999998885 66332  45554    368888888884 65421   112


Q ss_pred             hcccCCCccEEeccccccccc
Q 042541          646 ISDAFPNLLEMDIDYCNDLIE  666 (695)
Q Consensus       646 l~~~l~~L~~L~l~~c~~l~~  666 (695)
                      +. .+++|+.|++++|..++.
T Consensus       135 L~-~~~~L~~L~L~~c~~Itd  154 (176)
T 3e4g_A          135 LH-HFRNLKYLFLSDLPGVKE  154 (176)
T ss_dssp             GG-GCTTCCEEEEESCTTCCC
T ss_pred             Hh-cCCCCCEEECCCCCCCCc
Confidence            22 678888888888876654

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A

Probab=97.94  E-value=0.00022  Score=76.31  Aligned_cols=173  Identities=14%  Similarity=0.193  Sum_probs=98.4

Q ss_pred             CCCCCCcchHHHHHHHHH------------cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHH
Q 042541          166 VISPGLDVPLKELKMELF------------KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVK  233 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~------------~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~  233 (695)
                      +.++|.+..++.|.+.+.            ....+-|.|+|++|+|||+||+.+++.  ..   ..  -++.++...   
T Consensus       134 ~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~lA~aia~~--~~---~~--~~~~v~~~~---  203 (444)
T 2zan_A          134 SDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATE--AN---NS--TFFSISSSD---  203 (444)
T ss_dssp             GGSCSCHHHHHHHHHHHTHHHHCTTTTSGGGCCCSEEEEECSTTSSHHHHHHHHHHH--CC---SS--EEEEECCC----
T ss_pred             HHhcCHHHHHHHHHHHHHHHhhCHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHH--cC---CC--CEEEEeHHH---
Confidence            467999999998888763            123467999999999999999999973  21   11  233443321   


Q ss_pred             HHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCC-----------hHHHhhhcc-------CC
Q 042541          234 AIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGS-----------ESLLQKLGF-------QL  294 (695)
Q Consensus       234 ~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~-----------~~~~~~l~~-------~~  294 (695)
                       +....   .+...    .      .+..++ .....++.+|+||+++...           ......+..       ..
T Consensus       204 -l~~~~---~g~~~----~------~~~~~f~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~  269 (444)
T 2zan_A          204 -LVSKW---LGESE----K------LVKNLFQLARENKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDN  269 (444)
T ss_dssp             ------------CC----C------THHHHHHHHHHSCSEEEEESCTTTTCCCSSCCCCGGGHHHHHHHHTTTTCSSCCC
T ss_pred             -HHhhh---cchHH----H------HHHHHHHHHHHcCCeEEEEechHhhccCCCCccccHHHHHHHHHHHHHhCcccCC
Confidence             11111   11110    0      112222 1113568899999997541           112222221       12


Q ss_pred             CCCEEEEEcCCCC-------CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCc-hhHHHHHH
Q 042541          295 PDYKILVTSRSEF-------PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGC-PLALKVVG  365 (695)
Q Consensus       295 ~gs~iivTtR~~~-------~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~-PLai~~~~  365 (695)
                      .+..||.||....       ......+.++..+.++-..+|...+......   ........|++.+.|. +-.|..+.
T Consensus       270 ~~v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~~---l~~~~l~~la~~t~G~sgadl~~l~  345 (444)
T 2zan_A          270 DGILVLGATNIPWVLDSAIRRRFEKRIYIPLPEAHARAAMFRLHLGSTQNS---LTEADFQELGRKTDGYSGADISIIV  345 (444)
T ss_dssp             SSCEEEEEESCGGGSCHHHHTTCCEEEECCCCCHHHHHHHHHHHHTTSCEE---CCHHHHHHHHHHTTTCCHHHHHHHH
T ss_pred             CCEEEEecCCCccccCHHHHhhcceEEEeCCcCHHHHHHHHHHHHhcCCCC---CCHHHHHHHHHHcCCCCHHHHHHHH
Confidence            3456666665431       2333477888888888888888776432211   1245678889999884 44454443

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.93  E-value=0.00032  Score=73.87  Aligned_cols=164  Identities=14%  Similarity=0.141  Sum_probs=96.3

Q ss_pred             CCCCCCcchHHHHHHHHH----c---------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCH
Q 042541          166 VISPGLDVPLKELKMELF----K---------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNV  232 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~----~---------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~  232 (695)
                      +.+.|.++.+++|.+.+.    .         ..++=|.++|++|+|||.||+++++.  ..    ...+.++.+.-.+ 
T Consensus       181 ~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTllAkAiA~e--~~----~~~~~v~~s~l~s-  253 (437)
T 4b4t_L          181 DGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAAT--IG----ANFIFSPASGIVD-  253 (437)
T ss_dssp             GGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHH--HT----CEEEEEEGGGTCC-
T ss_pred             hHhCChHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHHHHHHHHH--hC----CCEEEEehhhhcc-
Confidence            456788888888877664    1         22577999999999999999999983  32    2244555443211 


Q ss_pred             HHHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCC-----------h-------HHHhhhcc-
Q 042541          233 KAIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGS-----------E-------SLLQKLGF-  292 (695)
Q Consensus       233 ~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~-----------~-------~~~~~l~~-  292 (695)
                                   .     ...+....++.++ ..-...+++|++|+++...           .       .++..+.. 
T Consensus       254 -------------k-----~~Gese~~ir~~F~~A~~~~P~IifiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~  315 (437)
T 4b4t_L          254 -------------K-----YIGESARIIREMFAYAKEHEPCIIFMDEVDAIGGRRFSEGTSADREIQRTLMELLTQMDGF  315 (437)
T ss_dssp             -------------S-----SSSHHHHHHHHHHHHHHHSCSEEEEEECCCSSSCCCSSSCCSSTTHHHHHHHHHHHHHHSS
T ss_pred             -------------c-----cchHHHHHHHHHHHHHHhcCCceeeeecccccccccccCCCCcchHHHHHHHHHHHHhhcc
Confidence                         0     1112223344444 3334678999999986421           0       02222221 


Q ss_pred             -CCCCCEEEEEcCCCC------CCCC---CeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCch
Q 042541          293 -QLPDYKILVTSRSEF------PQFG---SVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCP  358 (695)
Q Consensus       293 -~~~gs~iivTtR~~~------~~~~---~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~P  358 (695)
                       ...+..||.||....      ...|   ..+.++.-+.++-.++|+.+..........    ....|++.+.|+-
T Consensus       316 ~~~~~vivI~ATNrp~~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~d~----dl~~lA~~t~G~s  387 (437)
T 4b4t_L          316 DNLGQTKIIMATNRPDTLDPALLRPGRLDRKVEIPLPNEAGRLEIFKIHTAKVKKTGEF----DFEAAVKMSDGFN  387 (437)
T ss_dssp             SCTTSSEEEEEESSTTSSCTTTTSTTSEEEEECCCCCCHHHHHHHHHHHHHTSCBCSCC----CHHHHHHTCCSCC
T ss_pred             cCCCCeEEEEecCCchhhCHHHhCCCccceeeecCCcCHHHHHHHHHHHhcCCCCCccc----CHHHHHHhCCCCC
Confidence             223456777776541      1223   267788888888888887765433221111    1567788888753

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=97.93  E-value=3.1e-05  Score=83.51  Aligned_cols=140  Identities=11%  Similarity=0.097  Sum_probs=79.3

Q ss_pred             CCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccC------CCcEEEEEeCCCCCHHHHHHHH
Q 042541          166 VISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKF------KDDIFYVTVSKNPNVKAIVQKV  239 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f------~~~~~wv~~~~~~~~~~~~~~i  239 (695)
                      +.+|||+.+++++...|......-+.|+|++|+|||++|+.+++  .+...+      ...++.++++.           
T Consensus       180 d~iiGr~~~i~~l~~~l~r~~~~~~LL~G~pG~GKT~la~~la~--~l~~~~~p~~l~~~~~~~l~~~~-----------  246 (468)
T 3pxg_A          180 DPVIGRSKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQ--QIINNEVPEILRDKRVMTLDMGT-----------  246 (468)
T ss_dssp             CCCCCCHHHHHHHHHHHHCSSSCEEEEESCTTTTTHHHHHHHHH--HHHSSCSCTTTSSCCEECC---------------
T ss_pred             CCccCcHHHHHHHHHHHhccCCCCeEEECCCCCCHHHHHHHHHH--HHHhCCCChhhcCCeEEEeeCCc-----------
Confidence            45899999999999999866566778999999999999999987  332211      22233333330           


Q ss_pred             HHhcCCCCCCCCChHHHHHHHHHHHHh-cCCCcEEEEEeCCCCCChHHHhhhccCC-C-CCEEEEEcCCCC-----CCCC
Q 042541          240 LHHKGYPVPEFQTDEAAINDLERFFKQ-MRIEAILLVLDDVWPGSESLLQKLGFQL-P-DYKILVTSRSEF-----PQFG  311 (695)
Q Consensus       240 ~~~l~~~~~~~~~~~~~~~~l~~~~~~-l~~~~~LlVlDdv~~~~~~~~~~l~~~~-~-gs~iivTtR~~~-----~~~~  311 (695)
                        ...+.         ....+..++.. -..++.+|++|.  ..  .....+.... . ..++|.+|....     ....
T Consensus       247 --~~~g~---------~e~~~~~~~~~~~~~~~~iLfiD~--~~--~a~~~L~~~L~~g~v~vI~at~~~e~~~~~~~~~  311 (468)
T 3pxg_A          247 --KYRGE---------FEDRLKKVMDEIRQAGNIILFIDA--AI--DASNILKPSLARGELQCIGATTLDEYRKYIEKDA  311 (468)
T ss_dssp             -----------------CTTHHHHHHHHHTCCCCEEEECC------------CCCTTSSSCEEEEECCTTTTHHHHTTCS
T ss_pred             --cccch---------HHHHHHHHHHHHHhcCCeEEEEeC--ch--hHHHHHHHhhcCCCEEEEecCCHHHHHHHhhcCH
Confidence              00000         00122333321 135678999991  11  1112222211 2 356666554432     1111


Q ss_pred             ------CeEecCCCChHHHHHHHHHhcc
Q 042541          312 ------SVHYLKPLTYEAARTLFLHSAN  333 (695)
Q Consensus       312 ------~~~~l~~L~~~ea~~Lf~~~~~  333 (695)
                            ..+.+++.+.++..+++...+.
T Consensus       312 al~~Rf~~i~v~~p~~e~~~~iL~~~~~  339 (468)
T 3pxg_A          312 ALERRFQPIQVDQPSVDESIQILQGLRD  339 (468)
T ss_dssp             HHHHSEEEEECCCCCHHHHHHHHHHTTT
T ss_pred             HHHHhCccceeCCCCHHHHHHHHHHHHH
Confidence                  1688999999999999987653

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=97.92  E-value=4e-05  Score=77.98  Aligned_cols=146  Identities=14%  Similarity=0.107  Sum_probs=85.0

Q ss_pred             CCCCCcchHHHHHHHHH---------------cCCceEEEEEcCCCCcHHHHHHHHhccccccccC-CCcEEEEEeCCCC
Q 042541          167 ISPGLDVPLKELKMELF---------------KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKF-KDDIFYVTVSKNP  230 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~---------------~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f-~~~~~wv~~~~~~  230 (695)
                      .++|.+..++.|.+.+.               ......+.|+|++|+|||++|+.+++........ ...++.++.+.  
T Consensus        32 ~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~~~~vll~G~~GtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~--  109 (309)
T 3syl_A           32 ELIGLKPVKDRIRETAALLLVERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGLLHRLGYVRKGHLVSVTRDD--  109 (309)
T ss_dssp             HSSSCHHHHHHHHHHHHHHHHHHHHHHHTCCSSCCCCEEEEEECTTSSHHHHHHHHHHHHHHTTSSSSCCEEEECGGG--
T ss_pred             HccChHHHHHHHHHHHHHHHhHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHhcCCcCCCcEEEEcHHH--
Confidence            46999998888877654               2234579999999999999999887732111111 11133333221  


Q ss_pred             CHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCC---------ChH----HHhhhccCCCCC
Q 042541          231 NVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPG---------SES----LLQKLGFQLPDY  297 (695)
Q Consensus       231 ~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~---------~~~----~~~~l~~~~~gs  297 (695)
                                  +......  ..   ...+...++..  +..+|++|+++..         ...    ++..+.....+.
T Consensus       110 ------------l~~~~~g--~~---~~~~~~~~~~~--~~~vl~iDEid~l~~~~~~~~~~~~~~~~Ll~~l~~~~~~~  170 (309)
T 3syl_A          110 ------------LVGQYIG--HT---APKTKEVLKRA--MGGVLFIDEAYYLYRPDNERDYGQEAIEILLQVMENNRDDL  170 (309)
T ss_dssp             ------------TCCSSTT--CH---HHHHHHHHHHH--TTSEEEEETGGGSCCCC---CCTHHHHHHHHHHHHHCTTTC
T ss_pred             ------------hhhhccc--cc---HHHHHHHHHhc--CCCEEEEEChhhhccCCCcccccHHHHHHHHHHHhcCCCCE
Confidence                        1110000  11   12233444222  3469999999743         322    333344444567


Q ss_pred             EEEEEcCCCC--------C----CCCCeEecCCCChHHHHHHHHHhcc
Q 042541          298 KILVTSRSEF--------P----QFGSVHYLKPLTYEAARTLFLHSAN  333 (695)
Q Consensus       298 ~iivTtR~~~--------~----~~~~~~~l~~L~~~ea~~Lf~~~~~  333 (695)
                      .+|+||....        .    .....+.+++++.++-.+++...+.
T Consensus       171 ~~i~~~~~~~~~~~~~~~~~l~~R~~~~i~~~~~~~~~~~~il~~~l~  218 (309)
T 3syl_A          171 VVILAGYADRMENFFQSNPGFRSRIAHHIEFPDYSDEELFEIAGHMLD  218 (309)
T ss_dssp             EEEEEECHHHHHHHHHHSTTHHHHEEEEEEECCCCHHHHHHHHHHHHH
T ss_pred             EEEEeCChHHHHHHHhhCHHHHHhCCeEEEcCCcCHHHHHHHHHHHHH
Confidence            8888775320        1    1224789999999999999987664

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=97.90  E-value=4e-05  Score=71.15  Aligned_cols=112  Identities=15%  Similarity=0.166  Sum_probs=60.3

Q ss_pred             hHHHHHHHHHc---CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCC
Q 042541          174 PLKELKMELFK---DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEF  250 (695)
Q Consensus       174 ~~~~l~~~L~~---~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~  250 (695)
                      .++.+.+++.+   .....+.|+|++|+|||||++.+++.......+.  +++++      ..++...+.........  
T Consensus        22 ~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~~g~~--~~~~~------~~~~~~~~~~~~~~~~~--   91 (180)
T 3ec2_A           22 ALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLAVATLKAIYEKKGIR--GYFFD------TKDLIFRLKHLMDEGKD--   91 (180)
T ss_dssp             HHHHHHHHHHSCCGGGCCEEEECCSSSSSHHHHHHHHHHHHHHHSCCC--CCEEE------HHHHHHHHHHHHHHTCC--
T ss_pred             HHHHHHHHHHhccccCCCEEEEECCCCCCHHHHHHHHHHHHHHHcCCe--EEEEE------HHHHHHHHHHHhcCchH--
Confidence            34444444432   2357899999999999999999988322122222  33544      34444444443321110  


Q ss_pred             CChHHHHHHHHHHHHhcCCCcEEEEEeCCCC--CChHHHhh----hcc-CCCCCEEEEEcCCC
Q 042541          251 QTDEAAINDLERFFKQMRIEAILLVLDDVWP--GSESLLQK----LGF-QLPDYKILVTSRSE  306 (695)
Q Consensus       251 ~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~--~~~~~~~~----l~~-~~~gs~iivTtR~~  306 (695)
                         ...       ++.+ .+.-+|||||++.  .+.+....    +.. ...|..+|+||...
T Consensus        92 ---~~~-------~~~~-~~~~llilDE~~~~~~~~~~~~~l~~ll~~~~~~~~~ii~tsn~~  143 (180)
T 3ec2_A           92 ---TKF-------LKTV-LNSPVLVLDDLGSERLSDWQRELISYIITYRYNNLKSTIITTNYS  143 (180)
T ss_dssp             ---SHH-------HHHH-HTCSEEEEETCSSSCCCHHHHHHHHHHHHHHHHTTCEEEEECCCC
T ss_pred             ---HHH-------HHHh-cCCCEEEEeCCCCCcCCHHHHHHHHHHHHHHHHcCCCEEEEcCCC
Confidence               011       1111 2456899999973  33332111    111 12578899988744

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.85  E-value=0.00032  Score=73.67  Aligned_cols=163  Identities=14%  Similarity=0.118  Sum_probs=96.0

Q ss_pred             CCCCCCcchHHHHHHHHH----c---------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCH
Q 042541          166 VISPGLDVPLKELKMELF----K---------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNV  232 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~----~---------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~  232 (695)
                      +.+.|.++.+++|.+.+.    .         ..++-|.++|++|+|||.||+++++  .....    .+.++.+.-.+ 
T Consensus       209 ~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlLAkAiA~--e~~~~----fi~vs~s~L~s-  281 (467)
T 4b4t_H          209 SDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVAN--RTDAT----FIRVIGSELVQ-  281 (467)
T ss_dssp             SSCTTCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHHHHHHH--HHTCE----EEEEEGGGGCC-
T ss_pred             HHhccHHHHHHHHHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHHHHHHh--ccCCC----eEEEEhHHhhc-
Confidence            357888888888877543    1         2367799999999999999999998  33222    34454443110 


Q ss_pred             HHHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCCh-----------H-------HHhhhccC
Q 042541          233 KAIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGSE-----------S-------LLQKLGFQ  293 (695)
Q Consensus       233 ~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~~-----------~-------~~~~l~~~  293 (695)
                                   .     -..+....++.++ ..-...+++|++|+++....           .       ++..+...
T Consensus       282 -------------k-----~vGesek~ir~lF~~Ar~~aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~  343 (467)
T 4b4t_H          282 -------------K-----YVGEGARMVRELFEMARTKKACIIFFDEIDAVGGARFDDGAGGDNEVQRTMLELITQLDGF  343 (467)
T ss_dssp             -------------C-----SSSHHHHHHHHHHHHHHHTCSEEEEEECCTTTSBCCSSSSCGGGGHHHHHHHHHHHHHHSS
T ss_pred             -------------c-----cCCHHHHHHHHHHHHHHhcCCceEeecccccccccccCcCCCccHHHHHHHHHHHHHhhcc
Confidence                         0     1112223344444 33346789999999864320           0       22222222


Q ss_pred             C--CCCEEEEEcCCCC---------CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCc
Q 042541          294 L--PDYKILVTSRSEF---------PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGC  357 (695)
Q Consensus       294 ~--~gs~iivTtR~~~---------~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~  357 (695)
                      .  .+..||.||....         ......+.++.-+.++-.++|+.+..........    ....|++.|.|.
T Consensus       344 ~~~~~ViVIaATNrpd~LDpALlRpGRFD~~I~i~lPd~~~R~~Ilk~~l~~~~l~~dv----dl~~LA~~T~Gf  414 (467)
T 4b4t_H          344 DPRGNIKVMFATNRPNTLDPALLRPGRIDRKVEFSLPDLEGRANIFRIHSKSMSVERGI----RWELISRLCPNS  414 (467)
T ss_dssp             CCTTTEEEEEECSCTTSBCHHHHSTTTCCEEECCCCCCHHHHHHHHHHHHTTSCBCSSC----CHHHHHHHCCSC
T ss_pred             CCCCcEEEEeCCCCcccCChhhhccccccEEEEeCCcCHHHHHHHHHHHhcCCCCCCCC----CHHHHHHHCCCC
Confidence            2  2334555665441         1334478888888888889998766433221111    146788888875

>3e4g_A ATP synthase subunit S, mitochondrial; leucine-rich repeat, CF0, hydrogen ION transport, inner membrane, ION transport, membrane, mitochondrion; 0.96A {Bos taurus} PDB: 3e3z_A 3dze_A 3e2j_A

Probab=97.82  E-value=1.5e-05  Score=72.73  Aligned_cols=80  Identities=10%  Similarity=0.099  Sum_probs=38.0

Q ss_pred             ceEEEEEEccCccccCChhhcCCCCCcEEEEcccC-CCCcccCcccccccC----CCCcEEEeccCC-CCCcc--ccccc
Q 042541          551 EVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYG-FSPAELNNFRVLSAL----SKLKKIRLEHVS-LPNSL--ATVRM  622 (695)
Q Consensus       551 ~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~-~~~~~~~~~~~l~~l----~~L~~L~L~~~~-l~~lp--~i~~l  622 (695)
                      +|+.|+++.+.....--..+.++++|+.|+|++|. +....+..   ++.+    ++|++|+|++|. ++.-.  .+.++
T Consensus        62 ~L~~LDLs~~~Itd~GL~~L~~~~~L~~L~L~~C~~ItD~gL~~---L~~~~~~~~~L~~L~Ls~C~~ITD~Gl~~L~~~  138 (176)
T 3e4g_A           62 KIQAIDATDSCIMSIGFDHMEGLQYVEKIRLCKCHYIEDGCLER---LSQLENLQKSMLEMEIISCGNVTDKGIIALHHF  138 (176)
T ss_dssp             CEEEEEEESCCCCGGGGGGGTTCSCCCEEEEESCTTCCHHHHHH---HHTCHHHHHHCCEEEEESCTTCCHHHHHHGGGC
T ss_pred             eEeEEeCcCCCccHHHHHHhcCCCCCCEEEeCCCCccCHHHHHH---HHhcccccCCCCEEEcCCCCcCCHHHHHHHhcC
Confidence            45666665553222212234556666666666553 22222211   2222    246666666653 55322  44455


Q ss_pred             ccccEEeeccc
Q 042541          623 NHLQKVSLVMC  633 (695)
Q Consensus       623 ~~L~~L~l~~~  633 (695)
                      ++|++|+|++|
T Consensus       139 ~~L~~L~L~~c  149 (176)
T 3e4g_A          139 RNLKYLFLSDL  149 (176)
T ss_dssp             TTCCEEEEESC
T ss_pred             CCCCEEECCCC
Confidence            66666666666

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=97.81  E-value=0.00016  Score=73.00  Aligned_cols=141  Identities=14%  Similarity=0.063  Sum_probs=89.6

Q ss_pred             CCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhcccc-ccccCCCcEEEEEeCC-CCCHHHHHHHHHHhcCCCC
Q 042541          170 GLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQ-VQGKFKDDIFYVTVSK-NPNVKAIVQKVLHHKGYPV  247 (695)
Q Consensus       170 Gr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~-~~~~f~~~~~wv~~~~-~~~~~~~~~~i~~~l~~~~  247 (695)
                      |-++.++.+...+..+..+...++|+.|+||||+|+.+.+... ....... +.+++.++ ...+..+ +++++.+....
T Consensus         1 g~~~~~~~L~~~i~~~~~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d-~~~l~~~~~~~~id~i-r~li~~~~~~p   78 (305)
T 2gno_A            1 GAKDQLETLKRIIEKSEGISILINGEDLSYPREVSLELPEYVEKFPPKASD-VLEIDPEGENIGIDDI-RTIKDFLNYSP   78 (305)
T ss_dssp             ---CHHHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTT-EEEECCSSSCBCHHHH-HHHHHHHTSCC
T ss_pred             ChHHHHHHHHHHHHCCCCcEEEEECCCCCCHHHHHHHHHHhCchhhccCCC-EEEEcCCcCCCCHHHH-HHHHHHHhhcc
Confidence            4456677888888866678999999999999999999986311 1112233 45655443 2333332 33444332211


Q ss_pred             CCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCC-----CCCCCeEecCC
Q 042541          248 PEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEF-----PQFGSVHYLKP  318 (695)
Q Consensus       248 ~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~-----~~~~~~~~l~~  318 (695)
                                         ..+++-++|+|+++.....    ++..+....+.+.+|++|.+..     .... .+++++
T Consensus        79 -------------------~~~~~kvviIdead~lt~~a~naLLk~LEep~~~t~fIl~t~~~~kl~~tI~SR-~~~f~~  138 (305)
T 2gno_A           79 -------------------ELYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLLPTIKSR-VFRVVV  138 (305)
T ss_dssp             -------------------SSSSSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCGGGSCHHHHTT-SEEEEC
T ss_pred             -------------------ccCCceEEEeccHHHhCHHHHHHHHHHHhCCCCCeEEEEEECChHhChHHHHce-eEeCCC
Confidence                               1356789999999776533    4455555556778887765441     1112 899999


Q ss_pred             CChHHHHHHHHHhc
Q 042541          319 LTYEAARTLFLHSA  332 (695)
Q Consensus       319 L~~~ea~~Lf~~~~  332 (695)
                      +++++..+.+.+.+
T Consensus       139 l~~~~i~~~L~~~~  152 (305)
T 2gno_A          139 NVPKEFRDLVKEKI  152 (305)
T ss_dssp             CCCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHh
Confidence            99999999998775

>1io0_A Tropomodulin; LRR protein, right-handed super-helix, protein binding; 1.45A {Gallus gallus} SCOP: c.10.1.1

Probab=97.81  E-value=6.9e-06  Score=76.78  Aligned_cols=119  Identities=13%  Similarity=0.064  Sum_probs=78.0

Q ss_pred             CChhhcCCCCCcEEEEccc-CCCCcccCcc-cccccCCCCcEEEeccCCCCC-----cc-cccccccccEEeeccccCCc
Q 042541          566 LPDFLQKMDELKVLIVTNY-GFSPAELNNF-RVLSALSKLKKIRLEHVSLPN-----SL-ATVRMNHLQKVSLVMCNVGQ  637 (695)
Q Consensus       566 ~p~~~~~l~~Lr~L~l~~~-~~~~~~~~~~-~~l~~l~~L~~L~L~~~~l~~-----lp-~i~~l~~L~~L~l~~~~i~~  637 (695)
                      +...+...+.|+.|+|++| .+.......+ ..+...++|++|+|++|.+..     +. .+...++|++|+|++|.|..
T Consensus        28 l~~~l~~~~~L~~L~L~~n~~i~~~g~~~l~~~L~~~~~L~~L~Ls~n~i~~~g~~~l~~~L~~n~~L~~L~L~~N~i~~  107 (185)
T 1io0_A           28 LKRIQNNDPDLEEVNLNNIMNIPVPTLKACAEALKTNTYVKKFSIVGTRSNDPVAFALAEMLKVNNTLKSLNVESNFISG  107 (185)
T ss_dssp             HHHHHTTCTTCCEEECTTCTTCCHHHHHHHHHHHTTCCSCCEEECTTSCCCHHHHHHHHHHHHHCSSCCEEECCSSCCCH
T ss_pred             HHHHHhcCCCCCEEEecCCCCCCHHHHHHHHHHHHhCCCcCEEECcCCCCChHHHHHHHHHHHhCCCcCEEECcCCcCCH
Confidence            3445677888999999887 6643332222 235566788999999988863     33 45566789999999998775


Q ss_pred             ccccch-hhhcccCCCccEEec--cccccccc-----CchhhcCCCCCceeeccccc
Q 042541          638 VFRNST-FRISDAFPNLLEMDI--DYCNDLIE-----LPDGLCDIVSMEKLRITNCH  686 (695)
Q Consensus       638 ~~~~~~-~~l~~~l~~L~~L~l--~~c~~l~~-----lP~~i~~L~~L~~L~l~~~~  686 (695)
                      .--..+ ..+. ..++|++|+|  ++| .++.     +...+...++|++|+|++|.
T Consensus       108 ~g~~~l~~~L~-~n~~L~~L~L~~~~N-~i~~~g~~~l~~~L~~n~~L~~L~L~~n~  162 (185)
T 1io0_A          108 SGILALVEALQ-SNTSLIELRIDNQSQ-PLGNNVEMEIANMLEKNTTLLKFGYHFTQ  162 (185)
T ss_dssp             HHHHHHHHGGG-GCSSCCEEECCCCSS-CCCHHHHHHHHHHHHHCSSCCEEECCCSS
T ss_pred             HHHHHHHHHHH-hCCCceEEEecCCCC-CCCHHHHHHHHHHHHhCCCcCEEeccCCC
Confidence            211111 1111 5678999999  554 3443     44556677899999998875

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=97.80  E-value=9.8e-05  Score=86.00  Aligned_cols=171  Identities=12%  Similarity=0.127  Sum_probs=91.4

Q ss_pred             CCCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccc-----cC-CCcEEEEEeCCCCCHHHHHHH
Q 042541          165 PVISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQG-----KF-KDDIFYVTVSKNPNVKAIVQK  238 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~-----~f-~~~~~wv~~~~~~~~~~~~~~  238 (695)
                      -+.+|||+.+++++++.|......-+.|+|++|+|||++|+.+++.  +..     .. ...+++++++.-..       
T Consensus       169 ld~viGr~~~i~~l~~~l~~~~~~~vlL~G~pG~GKT~la~~la~~--l~~~~~p~~l~~~~~~~l~~~~l~~-------  239 (854)
T 1qvr_A          169 LDPVIGRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQR--IVKGDVPEGLKGKRIVSLQMGSLLA-------  239 (854)
T ss_dssp             SCCCCSCHHHHHHHHHHHHCSSCCCCEEEECTTSCHHHHHHHHHHH--HHHTCSCTTSTTCEEEEECC------------
T ss_pred             CcccCCcHHHHHHHHHHHhcCCCCceEEEcCCCCCHHHHHHHHHHH--HhcCCCchhhcCCeEEEeehHHhhc-------
Confidence            3457999999999999998766667889999999999999999873  311     11 23344554432110       


Q ss_pred             HHHhcCCCCCCCCChHHHHHHHHHHHHhc--CCCcEEEEEeCCCCCC--------hH---HHhhhccCCCCCEEEEEcC-
Q 042541          239 VLHHKGYPVPEFQTDEAAINDLERFFKQM--RIEAILLVLDDVWPGS--------ES---LLQKLGFQLPDYKILVTSR-  304 (695)
Q Consensus       239 i~~~l~~~~~~~~~~~~~~~~l~~~~~~l--~~~~~LlVlDdv~~~~--------~~---~~~~l~~~~~gs~iivTtR-  304 (695)
                           +..     ...+....+..++..+  .+++.+|++|++....        ..   .+..+... .+..+|.+|. 
T Consensus       240 -----g~~-----~~g~~~~~l~~~~~~~~~~~~~~iL~IDEi~~l~~~~~~~g~~~~~~~L~~~l~~-~~i~~I~at~~  308 (854)
T 1qvr_A          240 -----GAK-----YRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKAEGAVDAGNMLKPALAR-GELRLIGATTL  308 (854)
T ss_dssp             ----------------CHHHHHHHHHHHHHTTCSSEEEEECCC-------------------HHHHHT-TCCCEEEEECH
T ss_pred             -----cCc-----cchHHHHHHHHHHHHHHhcCCCeEEEEecHHHHhccCCccchHHHHHHHHHHHhC-CCeEEEEecCc
Confidence                 000     0011223344444333  2468999999996543        11   12222211 2344555443 


Q ss_pred             CC------CCC---CCCeEecCCCChHHHHHHHHHhccCCCCC-CCCCchHHHHHHHHhcC
Q 042541          305 SE------FPQ---FGSVHYLKPLTYEAARTLFLHSANLQDGN-SYIPDENIVSKILRACK  355 (695)
Q Consensus       305 ~~------~~~---~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~-~~~~~~~~~~~I~~~c~  355 (695)
                      ..      ...   --..+.+++++.++..+++.......... ...-..+....+++.+.
T Consensus       309 ~~~~~~~~d~aL~rRf~~i~l~~p~~~e~~~iL~~~~~~~~~~~~~~i~~~al~~~~~ls~  369 (854)
T 1qvr_A          309 DEYREIEKDPALERRFQPVYVDEPTVEETISILRGLKEKYEVHHGVRISDSAIIAAATLSH  369 (854)
T ss_dssp             HHHHHHTTCTTTCSCCCCEEECCCCHHHHHHHHHHHHHHHHHHTTCEECHHHHHHHHHHHH
T ss_pred             hHHhhhccCHHHHhCCceEEeCCCCHHHHHHHHHhhhhhhhhhcCCCCCHHHHHHHHHHHh
Confidence            21      111   11258899999999999987543211000 00112455666666663

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=97.78  E-value=5.6e-05  Score=71.57  Aligned_cols=117  Identities=14%  Similarity=0.139  Sum_probs=62.6

Q ss_pred             CCCCCcc----hHHHHHHHHHcCC----ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHH
Q 042541          167 ISPGLDV----PLKELKMELFKDG----RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQK  238 (695)
Q Consensus       167 ~~vGr~~----~~~~l~~~L~~~~----~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~  238 (695)
                      .|++.+.    .++.+..++....    .+.+.|+|++|+|||+||+.+++  ........ ++|++++      ++...
T Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~G~~GtGKT~la~~i~~--~~~~~~~~-~~~~~~~------~~~~~   96 (202)
T 2w58_A           26 DVDLNDDGRIKAIRFAERFVAEYEPGKKMKGLYLHGSFGVGKTYLLAAIAN--ELAKRNVS-SLIVYVP------ELFRE   96 (202)
T ss_dssp             SSCCSSHHHHHHHHHHHHHHHHCCSSCCCCEEEEECSTTSSHHHHHHHHHH--HHHTTTCC-EEEEEHH------HHHHH
T ss_pred             hccCCChhHHHHHHHHHHHHHHhhhccCCCeEEEECCCCCCHHHHHHHHHH--HHHHcCCe-EEEEEhH------HHHHH
Confidence            4565443    3444555555331    27899999999999999999998  33333223 6677654      44455


Q ss_pred             HHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCC--hH----HHhhhc-cC-CCCCEEEEEcCC
Q 042541          239 VLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGS--ES----LLQKLG-FQ-LPDYKILVTSRS  305 (695)
Q Consensus       239 i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~--~~----~~~~l~-~~-~~gs~iivTtR~  305 (695)
                      +.......     ......    ..+   .. .-+|||||++...  .+    ++..+. .. ..+..+|+||..
T Consensus        97 ~~~~~~~~-----~~~~~~----~~~---~~-~~~lilDei~~~~~~~~~~~~ll~~~l~~~~~~~~~~i~tsn~  158 (202)
T 2w58_A           97 LKHSLQDQ-----TMNEKL----DYI---KK-VPVLMLDDLGAEAMSSWVRDDVFGPILQYRMFENLPTFFTSNF  158 (202)
T ss_dssp             HHHC---C-----CCHHHH----HHH---HH-SSEEEEEEECCC---CCGGGTTHHHHHHHHHHTTCCEEEEESS
T ss_pred             HHHHhccc-----hHHHHH----HHh---cC-CCEEEEcCCCCCcCCHHHHHHHHHHHHHHHHhCCCCEEEEcCC
Confidence            54433211     111111    112   11 2399999995532  11    222111 11 245678888873

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.74  E-value=0.00059  Score=70.95  Aligned_cols=163  Identities=12%  Similarity=0.101  Sum_probs=93.1

Q ss_pred             CCCCCCcchHHHHHHHHH----c---------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCH
Q 042541          166 VISPGLDVPLKELKMELF----K---------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNV  232 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~----~---------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~  232 (695)
                      +.+.|.++.+++|.+.+.    .         ..++=|.++|++|+|||.||+++++.  ....    .+.++.++-.  
T Consensus       182 ~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~e--~~~~----fi~v~~s~l~--  253 (437)
T 4b4t_I          182 SDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQ--TSAT----FLRIVGSELI--  253 (437)
T ss_dssp             GGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHHHHH--HTCE----EEEEESGGGC--
T ss_pred             eecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHHHHH--hCCC----EEEEEHHHhh--
Confidence            456788988888877654    1         22577999999999999999999983  3222    3344433211  


Q ss_pred             HHHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCC------------h--H----HHhhhcc-
Q 042541          233 KAIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGS------------E--S----LLQKLGF-  292 (695)
Q Consensus       233 ~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~------------~--~----~~~~l~~-  292 (695)
                                  ..     ...+....++.++ ..-...+++|++|+++...            .  .    ++..+.. 
T Consensus       254 ------------sk-----~vGesek~ir~lF~~Ar~~aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~LL~~lDg~  316 (437)
T 4b4t_I          254 ------------QK-----YLGDGPRLCRQIFKVAGENAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGF  316 (437)
T ss_dssp             ------------CS-----SSSHHHHHHHHHHHHHHHTCSEEEEEEEESSSSCCCSCSSCSSCCHHHHHHHHHHHHHHHC
T ss_pred             ------------hc-----cCchHHHHHHHHHHHHHhcCCcEEEEehhhhhcccCCCCCCCccHHHHHHHHHHHHHhhCc
Confidence                        00     1112223344444 2224678999999985321            0  0    2222221 


Q ss_pred             -CCCCCEEEEEcCCCC------CCCCC---eEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCc
Q 042541          293 -QLPDYKILVTSRSEF------PQFGS---VHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGC  357 (695)
Q Consensus       293 -~~~gs~iivTtR~~~------~~~~~---~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~  357 (695)
                       ...+..||.||-...      ...|.   .+.++.-+.++-.++|..+..........    ....|++.+.|+
T Consensus       317 ~~~~~ViVIaATNrpd~LDpALlRpGRfD~~I~v~lPd~~~R~~Il~~~l~~~~l~~dv----dl~~LA~~T~Gf  387 (437)
T 4b4t_I          317 DDRGDVKVIMATNKIETLDPALIRPGRIDRKILFENPDLSTKKKILGIHTSKMNLSEDV----NLETLVTTKDDL  387 (437)
T ss_dssp             CCSSSEEEEEEESCSTTCCTTSSCTTTEEEEECCCCCCHHHHHHHHHHHHTTSCBCSCC----CHHHHHHHCCSC
T ss_pred             CCCCCEEEEEeCCChhhcCHHHhcCCceeEEEEcCCcCHHHHHHHHHHHhcCCCCCCcC----CHHHHHHhCCCC
Confidence             122345555665441      12233   57788888888888888766432221111    156777888775

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*

Probab=97.73  E-value=0.00016  Score=73.34  Aligned_cols=57  Identities=23%  Similarity=0.263  Sum_probs=42.3

Q ss_pred             CCCCCCcchHHHHHHHHHc--------------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCC
Q 042541          166 VISPGLDVPLKELKMELFK--------------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSK  228 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~--------------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~  228 (695)
                      ..++|.+..++.+...+..              ....-+.|+|++|+|||++|+.+++.  .    ....+.++.+.
T Consensus        15 ~~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~--l----~~~~~~i~~~~   85 (310)
T 1ofh_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKL--A----NAPFIKVEATK   85 (310)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHH--H----TCCEEEEEGGG
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhhhhcccccccCCCceEEEECCCCCCHHHHHHHHHHH--h----CCCEEEEcchh
Confidence            3579999999999877753              23466889999999999999999873  3    22245666554

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.73  E-value=0.00032  Score=73.74  Aligned_cols=163  Identities=13%  Similarity=0.098  Sum_probs=93.3

Q ss_pred             CCCCCCcchHHHHHHHHH----c---------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCH
Q 042541          166 VISPGLDVPLKELKMELF----K---------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNV  232 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~----~---------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~  232 (695)
                      +.+.|.++.+++|.+.+.    .         ..++-|.++|++|+|||.||+++++  ....    ..+.++.+.-.  
T Consensus       181 ~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAiA~--e~~~----~f~~v~~s~l~--  252 (434)
T 4b4t_M          181 SDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAA--QTNA----TFLKLAAPQLV--  252 (434)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHH--HHTC----EEEEEEGGGGC--
T ss_pred             HhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHHHH--HhCC----CEEEEehhhhh--
Confidence            467889988888877643    1         2257799999999999999999998  3322    23455544311  


Q ss_pred             HHHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCC-------C----hH-------HHhhhccC
Q 042541          233 KAIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPG-------S----ES-------LLQKLGFQ  293 (695)
Q Consensus       233 ~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~-------~----~~-------~~~~l~~~  293 (695)
                                  ..     ...+....++.++ ..-...+++|++|+++..       .    ..       ++..+...
T Consensus       253 ------------~~-----~vGese~~ir~lF~~A~~~aP~IifiDEiDal~~~R~~~~~~~~~~~~~~~~~lL~~ldg~  315 (434)
T 4b4t_M          253 ------------QM-----YIGEGAKLVRDAFALAKEKAPTIIFIDELDAIGTKRFDSEKSGDREVQRTMLELLNQLDGF  315 (434)
T ss_dssp             ------------SS-----CSSHHHHHHHHHHHHHHHHCSEEEEEECTHHHHCCCSSGGGGTTHHHHHHHHHHHHHHTTS
T ss_pred             ------------hc-----ccchHHHHHHHHHHHHHhcCCeEEeecchhhhhhccCCCCCCCchHHHHHHHHHHHHhhcc
Confidence                        00     1111223344444 222456899999998421       0    00       22222221


Q ss_pred             --CCCCEEEEEcCCCC------CCCCC---eEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCc
Q 042541          294 --LPDYKILVTSRSEF------PQFGS---VHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGC  357 (695)
Q Consensus       294 --~~gs~iivTtR~~~------~~~~~---~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~  357 (695)
                        ..+..||.||....      ...|.   .+.++.-+.++-.++|+.+..........    -...|++.+.|+
T Consensus       316 ~~~~~ViVIaaTNrp~~LD~AllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~dv----dl~~lA~~t~G~  386 (434)
T 4b4t_M          316 SSDDRVKVLAATNRVDVLDPALLRSGRLDRKIEFPLPSEDSRAQILQIHSRKMTTDDDI----NWQELARSTDEF  386 (434)
T ss_dssp             CSSCSSEEEEECSSCCCCCTTTCSTTSEEEEEECCCCCHHHHHHHHHHHHHHSCBCSCC----CHHHHHHHCSSC
T ss_pred             CCCCCEEEEEeCCCchhcCHhHhcCCceeEEEEeCCcCHHHHHHHHHHHhcCCCCCCcC----CHHHHHHhCCCC
Confidence              22345665776542      12233   67888888888888887655332211111    146678888775

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=97.69  E-value=7.4e-05  Score=66.39  Aligned_cols=43  Identities=14%  Similarity=0.155  Sum_probs=33.5

Q ss_pred             CCCCCcchHHHHHHHHH--cCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          167 ISPGLDVPLKELKMELF--KDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~--~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .++|++..++++.+.+.  .....-|.|+|.+|+|||++|+.+++
T Consensus         5 ~~iG~s~~~~~l~~~~~~~~~~~~~vll~G~~GtGKt~lA~~i~~   49 (143)
T 3co5_A            5 DKLGNSAAIQEMNREVEAAAKRTSPVFLTGEAGSPFETVARYFHK   49 (143)
T ss_dssp             ---CCCHHHHHHHHHHHHHHTCSSCEEEEEETTCCHHHHHGGGCC
T ss_pred             CceeCCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHH
Confidence            46999999999888876  23334578999999999999999987

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.68  E-value=0.00051  Score=72.17  Aligned_cols=163  Identities=17%  Similarity=0.150  Sum_probs=90.1

Q ss_pred             CCCCCCcchHHHHHHHHH----c---------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCH
Q 042541          166 VISPGLDVPLKELKMELF----K---------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNV  232 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~----~---------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~  232 (695)
                      +.+.|.++.+++|.+.+.    .         ..++=|.++|++|+|||+||+++++.  ..    ...+.++.++-.+ 
T Consensus       172 ~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~lakAiA~~--~~----~~~~~v~~~~l~~-  244 (428)
T 4b4t_K          172 ADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANS--TK----AAFIRVNGSEFVH-  244 (428)
T ss_dssp             GGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHHHHHHHH--HT----CEEEEEEGGGTCC-
T ss_pred             HHhccHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHHHHHHHH--hC----CCeEEEecchhhc-
Confidence            466889988888877664    1         22566999999999999999999983  32    2244555543211 


Q ss_pred             HHHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCC-----------C-h--H----HHhhhcc-
Q 042541          233 KAIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPG-----------S-E--S----LLQKLGF-  292 (695)
Q Consensus       233 ~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~-----------~-~--~----~~~~l~~-  292 (695)
                                   .     ...+....++.++ ..-...++++++|+++..           + .  .    ++..+.. 
T Consensus       245 -------------~-----~~Ge~e~~ir~lF~~A~~~aP~IifiDEiD~i~~~R~~~~~~~~~~~~r~l~~lL~~ldg~  306 (428)
T 4b4t_K          245 -------------K-----YLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGSDREVQRILIELLTQMDGF  306 (428)
T ss_dssp             -------------S-----SCSHHHHHHHHHHHHHHHTCSEEEEEECTHHHHCSCSSSCSCCCCHHHHHHHHHHHHHHHS
T ss_pred             -------------c-----ccchhHHHHHHHHHHHHHcCCCeeechhhhhhhccccCCCCCCChHHHHHHHHHHHHhhCC
Confidence                         0     1112233444444 233467899999998310           1 1  1    2222221 


Q ss_pred             -CCCCCEEEEEcCCCC------CCCCC---eEecCCCChH-HHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCc
Q 042541          293 -QLPDYKILVTSRSEF------PQFGS---VHYLKPLTYE-AARTLFLHSANLQDGNSYIPDENIVSKILRACKGC  357 (695)
Q Consensus       293 -~~~gs~iivTtR~~~------~~~~~---~~~l~~L~~~-ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~  357 (695)
                       ...+..||.||....      ...|.   .+.++.++.. +-..+|..+..........    -...|++.+.|+
T Consensus       307 ~~~~~v~vI~aTN~~~~LD~AllRpGRfd~~I~~p~lPd~~~R~~Il~~~~~~~~l~~~~----dl~~lA~~t~G~  378 (428)
T 4b4t_K          307 DQSTNVKVIMATNRADTLDPALLRPGRLDRKIEFPSLRDRRERRLIFGTIASKMSLAPEA----DLDSLIIRNDSL  378 (428)
T ss_dssp             CSSCSEEEEEEESCSSSCCHHHHSSSSEEEEEECCSSCCHHHHHHHHHHHHHSSCBCTTC----CHHHHHHHTTTC
T ss_pred             CCCCCEEEEEecCChhhcChhhhcCCcceEEEEcCCCCCHHHHHHHHHHHhcCCCCCccc----CHHHHHHHCCCC
Confidence             223445666665542      12232   5677666544 4455665554322211111    146777888775

>3sb4_A Hypothetical leucine rich repeat protein; LRR, right-handed beta-alpha superhelix, leucine-rich repeat structural genomics; HET: MSE PG4; 1.99A {Bacteroides thetaiotaomicron}

Probab=97.68  E-value=5.6e-05  Score=77.71  Aligned_cols=101  Identities=17%  Similarity=0.096  Sum_probs=83.1

Q ss_pred             CCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--ccccccccc-EEeeccccCCcccccchhhhcc
Q 042541          572 KMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNHLQ-KVSLVMCNVGQVFRNSTFRISD  648 (695)
Q Consensus       572 ~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L~-~L~l~~~~i~~~~~~~~~~l~~  648 (695)
                      .+++|+.+++.+|.+.  .++. ..+..+.+|+.|+|.++ +..++  ++.++.+|+ .|++.. .++.+++..|.    
T Consensus       224 ~~~~L~~l~L~~n~i~--~I~~-~aF~~~~~L~~l~l~~n-i~~I~~~aF~~~~~L~~~l~l~~-~l~~I~~~aF~----  294 (329)
T 3sb4_A          224 YMPNLVSLDISKTNAT--TIPD-FTFAQKKYLLKIKLPHN-LKTIGQRVFSNCGRLAGTLELPA-SVTAIEFGAFM----  294 (329)
T ss_dssp             HCTTCCEEECTTBCCC--EECT-TTTTTCTTCCEEECCTT-CCEECTTTTTTCTTCCEEEEECT-TCCEECTTTTT----
T ss_pred             hcCCCeEEECCCCCcc--eecH-hhhhCCCCCCEEECCcc-cceehHHHhhCChhccEEEEEcc-cceEEchhhhh----
Confidence            3789999999987653  2222 23788999999999887 88888  889999999 999988 78888888887    


Q ss_pred             cCCCccEEecccccccccCch-hhcCCCCCceeec
Q 042541          649 AFPNLLEMDIDYCNDLIELPD-GLCDIVSMEKLRI  682 (695)
Q Consensus       649 ~l~~L~~L~l~~c~~l~~lP~-~i~~L~~L~~L~l  682 (695)
                      .+++|+.|+++. +.+..++. .|.++++|+.|+.
T Consensus       295 ~c~~L~~l~l~~-n~i~~I~~~aF~~~~~L~~ly~  328 (329)
T 3sb4_A          295 GCDNLRYVLATG-DKITTLGDELFGNGVPSKLIYK  328 (329)
T ss_dssp             TCTTEEEEEECS-SCCCEECTTTTCTTCCCCEEEC
T ss_pred             CCccCCEEEeCC-CccCccchhhhcCCcchhhhcc
Confidence            899999999987 46788876 4888999998874

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=97.66  E-value=0.00015  Score=83.49  Aligned_cols=140  Identities=11%  Similarity=0.092  Sum_probs=80.3

Q ss_pred             CCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccc-----c-CCCcEEEEEeCCCCCHHHHHHHH
Q 042541          166 VISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQG-----K-FKDDIFYVTVSKNPNVKAIVQKV  239 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~-----~-f~~~~~wv~~~~~~~~~~~~~~i  239 (695)
                      +.+|||+.+++++...|......-+.++|++|+|||++|+.+++  .+..     . ....++.++.             
T Consensus       180 d~iiG~~~~i~~l~~~l~~~~~~~vLL~G~pGtGKT~la~~la~--~l~~~~~p~~l~~~~~~~~~~-------------  244 (758)
T 3pxi_A          180 DPVIGRSKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQ--QIINNEVPEILRDKRVMTLDM-------------  244 (758)
T ss_dssp             CCCCCCHHHHHHHHHHHHCSSSCEEEEESCTTTTTHHHHHHHHH--HHHSSCSCTTTSSCCEECC---------------
T ss_pred             CCccCchHHHHHHHHHHhCCCCCCeEEECCCCCCHHHHHHHHHH--HHhcCCCChhhcCCeEEEecc-------------
Confidence            45899999999999999866666688999999999999999987  3311     1 1222323322             


Q ss_pred             HHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCChHHHhhhccC--CCCCEEEEEcCCCC-----CCCC
Q 042541          240 LHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGSESLLQKLGFQ--LPDYKILVTSRSEF-----PQFG  311 (695)
Q Consensus       240 ~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~~~~~~~l~~~--~~gs~iivTtR~~~-----~~~~  311 (695)
                          +...     ..+....+..++ .....++.+|++|.-.+    ....+...  ....++|.||....     ....
T Consensus       245 ----g~~~-----~G~~e~~l~~~~~~~~~~~~~iLfiD~~~~----~~~~L~~~l~~~~v~~I~at~~~~~~~~~~~d~  311 (758)
T 3pxi_A          245 ----GTKY-----RGEFEDRLKKVMDEIRQAGNIILFIDAAID----ASNILKPSLARGELQCIGATTLDEYRKYIEKDA  311 (758)
T ss_dssp             -----------------CTTHHHHHHHHHTCCCCEEEECC------------CCCTTSSSCEEEEECCTTTTHHHHTTCS
T ss_pred             ----cccc-----cchHHHHHHHHHHHHHhcCCEEEEEcCchh----HHHHHHHHHhcCCEEEEeCCChHHHHHHhhccH
Confidence                0000     000111233333 22246788999992111    11222221  22356666665442     1111


Q ss_pred             ------CeEecCCCChHHHHHHHHHhcc
Q 042541          312 ------SVHYLKPLTYEAARTLFLHSAN  333 (695)
Q Consensus       312 ------~~~~l~~L~~~ea~~Lf~~~~~  333 (695)
                            ..+.+++.+.++..+++.....
T Consensus       312 al~rRf~~i~v~~p~~~~~~~il~~~~~  339 (758)
T 3pxi_A          312 ALERRFQPIQVDQPSVDESIQILQGLRD  339 (758)
T ss_dssp             HHHHSEEEEECCCCCHHHHHHHHHHTTT
T ss_pred             HHHhhCcEEEeCCCCHHHHHHHHHHHHH
Confidence                  2689999999999999986553

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A*

Probab=97.63  E-value=0.00064  Score=73.30  Aligned_cols=170  Identities=11%  Similarity=0.116  Sum_probs=99.8

Q ss_pred             CCCCCCcchHHHHHHHHHc-------------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCH
Q 042541          166 VISPGLDVPLKELKMELFK-------------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNV  232 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~-------------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~  232 (695)
                      ..++|.+..+++|.+++..             ...+-|.|+|++|+|||++|+.+++  ..    ....+.++++.    
T Consensus       204 ~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~--~~----~~~fv~vn~~~----  273 (489)
T 3hu3_A          204 DDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVAN--ET----GAFFFLINGPE----  273 (489)
T ss_dssp             GGCCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHH--HC----SSEEEEEEHHH----
T ss_pred             HHcCCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHH--Hh----CCCEEEEEchH----
Confidence            3579999999998887652             3356799999999999999999987  33    22234444321    


Q ss_pred             HHHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCC--------Ch-------HHHhhhccC--C
Q 042541          233 KAIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPG--------SE-------SLLQKLGFQ--L  294 (695)
Q Consensus       233 ~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~--------~~-------~~~~~l~~~--~  294 (695)
                            +...+.         ......+...+ ....+++.+|+||+++..        .+       .++..+...  .
T Consensus       274 ------l~~~~~---------g~~~~~~~~~f~~A~~~~p~iLfLDEId~l~~~~~~~~~~~~~~~~~~LL~~ld~~~~~  338 (489)
T 3hu3_A          274 ------IMSKLA---------GESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQR  338 (489)
T ss_dssp             ------HHTSCT---------THHHHHHHHHHHHHHHTCSEEEEEESHHHHCBCTTSCCCHHHHHHHHHHHHHHHHSCTT
T ss_pred             ------hhhhhc---------chhHHHHHHHHHHHHhcCCcEEEecchhhhccccccccchHHHHHHHHHHHHhhccccC
Confidence                  111111         11222334444 333567899999998311        11       122222221  2


Q ss_pred             CCCEEEEEcCCCC------C---CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCc-hhHHHHH
Q 042541          295 PDYKILVTSRSEF------P---QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGC-PLALKVV  364 (695)
Q Consensus       295 ~gs~iivTtR~~~------~---~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~-PLai~~~  364 (695)
                      .+..||.||....      .   .....+.+...+.++-.+++..++.......    .....++++.+.|. +-.+..+
T Consensus       339 ~~v~vIaaTn~~~~Ld~al~r~gRf~~~i~i~~P~~~eR~~IL~~~~~~~~l~~----~~~l~~la~~t~g~s~~dL~~L  414 (489)
T 3hu3_A          339 AHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLAD----DVDLEQVANETHGHVGADLAAL  414 (489)
T ss_dssp             SCEEEEEEESCGGGBCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHTTTSCBCT----TCCHHHHHHTCTTCCHHHHHHH
T ss_pred             CceEEEEecCCccccCHHHhCCCcCceEEEeCCCCHHHHHHHHHHHHhcCCCcc----hhhHHHHHHHccCCcHHHHHHH
Confidence            2345555665441      1   2333788999999999999988764322211    11246677788775 5445544

>2ra8_A Uncharacterized protein Q64V53_bacfr; WGR domain, LRR domain, leucine rich repeats, BFR43, structural genomics, PSI-2; 1.95A {Bacteroides fragilis}

Probab=97.62  E-value=6.9e-05  Score=77.71  Aligned_cols=115  Identities=20%  Similarity=0.222  Sum_probs=75.9

Q ss_pred             cCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--ccc--ccccccEEeeccc--cCC--
Q 042541          565 VLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATV--RMNHLQKVSLVMC--NVG--  636 (695)
Q Consensus       565 ~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~--~l~~L~~L~l~~~--~i~--  636 (695)
                      .++..+..+++|+.|.+++|..  ..++.   + .+++|+.|+|..+.++.-.  .++  .+++|++|+|+.+  ...  
T Consensus       163 ~L~~ll~~~P~L~~L~L~g~~~--l~l~~---~-~~~~L~~L~L~~~~l~~~~l~~l~~~~lp~L~~L~L~~~~~~~~~~  236 (362)
T 2ra8_A          163 DLSPVLDAMPLLNNLKIKGTNN--LSIGK---K-PRPNLKSLEIISGGLPDSVVEDILGSDLPNLEKLVLYVGVEDYGFD  236 (362)
T ss_dssp             BCHHHHHTCTTCCEEEEECCBT--CBCCS---C-BCTTCSEEEEECSBCCHHHHHHHHHSBCTTCCEEEEECBCGGGTCC
T ss_pred             CHHHHHhcCCCCcEEEEeCCCC--ceecc---c-cCCCCcEEEEecCCCChHHHHHHHHccCCCCcEEEEeccccccccc
Confidence            3556778899999999998631  12221   3 3789999999998887322  443  7999999999642  111  


Q ss_pred             ----cccccchhhhcccCCCccEEecccccccccCchhh---cCCCCCceeecccccCCC
Q 042541          637 ----QVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGL---CDIVSMEKLRITNCHRLS  689 (695)
Q Consensus       637 ----~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i---~~L~~L~~L~l~~~~~l~  689 (695)
                          .+-+....   ..+++|++|+|++|......+..+   +.+++|++|+|+.|. ++
T Consensus       237 ~~~~~l~~~l~~---~~~p~Lr~L~L~~~~i~~~~~~~la~a~~~~~L~~LdLs~n~-L~  292 (362)
T 2ra8_A          237 GDMNVFRPLFSK---DRFPNLKWLGIVDAEEQNVVVEMFLESDILPQLETMDISAGV-LT  292 (362)
T ss_dssp             SCGGGTGGGSCT---TTCTTCCEEEEESCTTHHHHHHHHHHCSSGGGCSEEECCSSC-CB
T ss_pred             hhHHHHHHHHhc---CCCCCcCEEeCCCCCCchHHHHHHHhCccCCCCCEEECCCCC-CC
Confidence                11111110   158999999999886543333333   358899999998864 54

>3rw6_A Nuclear RNA export factor 1; retroviral constitutive transport element (CTE), RNA recogni motif (RRM); HET: GTP CCC; 2.30A {Homo sapiens} PDB: 3rw7_A 1koo_A 1koh_A 1ft8_A 1fo1_A

Probab=97.61  E-value=5.2e-05  Score=74.59  Aligned_cols=82  Identities=13%  Similarity=0.027  Sum_probs=51.0

Q ss_pred             ccCCCCcEEEeccCCCCCc---c-cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCch----
Q 042541          598 SALSKLKKIRLEHVSLPNS---L-ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPD----  669 (695)
Q Consensus       598 ~~l~~L~~L~L~~~~l~~l---p-~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~----  669 (695)
                      .++++|+.|+|++|.+..+   | .++.+++|++|+|++|.|+.+.. . ..+. .+ +|++|+|++|.....+|.    
T Consensus       167 ~~l~~L~~L~Ls~N~l~~l~~l~~~~~~l~~L~~L~Ls~N~i~~~~~-l-~~l~-~l-~L~~L~L~~Npl~~~~~~~~~y  242 (267)
T 3rw6_A          167 ENIPELLSLNLSNNRLYRLDDMSSIVQKAPNLKILNLSGNELKSERE-L-DKIK-GL-KLEELWLDGNSLCDTFRDQSTY  242 (267)
T ss_dssp             HHCTTCCEEECTTSCCCCCGGGTTHHHHSTTCCEEECTTSCCCSGGG-G-GGGT-TS-CCSEEECTTSTTGGGCSSHHHH
T ss_pred             hhCCCCCEEECCCCCCCCCccchhHHhhCCCCCEEECCCCccCCchh-h-hhcc-cC-CcceEEccCCcCccccCcchhH
Confidence            3466777777777777643   3 44577777777777777776521 1 1111 23 777777777665445552    


Q ss_pred             ---hhcCCCCCceeecc
Q 042541          670 ---GLCDIVSMEKLRIT  683 (695)
Q Consensus       670 ---~i~~L~~L~~L~l~  683 (695)
                         -+..+++|+.||-.
T Consensus       243 ~~~il~~~P~L~~LDg~  259 (267)
T 3rw6_A          243 ISAIRERFPKLLRLDGH  259 (267)
T ss_dssp             HHHHHHHCTTCCEESSC
T ss_pred             HHHHHHHCcccCeECCc
Confidence               25677788777753

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=97.60  E-value=0.00059  Score=78.53  Aligned_cols=150  Identities=11%  Similarity=0.073  Sum_probs=86.9

Q ss_pred             CCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhcccc---ccc-cCCCcEEEEEeCCCCCHHHHHHHHHH
Q 042541          166 VISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQ---VQG-KFKDDIFYVTVSKNPNVKAIVQKVLH  241 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~---~~~-~f~~~~~wv~~~~~~~~~~~~~~i~~  241 (695)
                      +.++||+.+++++.+.|......-+.|+|++|+|||++|+.+++...   +.. .....++.++++.-            
T Consensus       186 d~~iGr~~~i~~l~~~l~~~~~~~vlL~G~~GtGKT~la~~la~~l~~~~v~~~~~~~~~~~~~~~~l------------  253 (758)
T 1r6b_X          186 DPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSL------------  253 (758)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC--------------
T ss_pred             CCccCCHHHHHHHHHHHhccCCCCeEEEcCCCCCHHHHHHHHHHHHHhCCCChhhcCCEEEEEcHHHH------------
Confidence            46799999999999999866667789999999999999999987311   111 12332322222211            


Q ss_pred             hcCCCCCCCCChHHHHHHHHHHHHhc-CCCcEEEEEeCCCCCC--------h-HHHhhhccC--CCCCEEEEEcCCC---
Q 042541          242 HKGYPVPEFQTDEAAINDLERFFKQM-RIEAILLVLDDVWPGS--------E-SLLQKLGFQ--LPDYKILVTSRSE---  306 (695)
Q Consensus       242 ~l~~~~~~~~~~~~~~~~l~~~~~~l-~~~~~LlVlDdv~~~~--------~-~~~~~l~~~--~~gs~iivTtR~~---  306 (695)
                       +....    ........+..+++.+ ..++.+|++||+....        . .....+...  ..+..+|.+|...   
T Consensus       254 -~~~~~----~~g~~e~~l~~~~~~~~~~~~~iL~IDEi~~l~~~~~~~~~~~~~~~~L~~~l~~~~~~~I~at~~~~~~  328 (758)
T 1r6b_X          254 -LAGTK----YRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSGKIRVIGSTTYQEFS  328 (758)
T ss_dssp             --CCCC----CSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSSSCCCEEEEEECHHHHH
T ss_pred             -hcccc----ccchHHHHHHHHHHHHHhcCCeEEEEechHHHhhcCCCCcchHHHHHHHHHHHhCCCeEEEEEeCchHHh
Confidence             00000    0111223444555333 3457999999997551        1 122223222  2345666655432   


Q ss_pred             --C---CCCC---CeEecCCCChHHHHHHHHHhc
Q 042541          307 --F---PQFG---SVHYLKPLTYEAARTLFLHSA  332 (695)
Q Consensus       307 --~---~~~~---~~~~l~~L~~~ea~~Lf~~~~  332 (695)
                        .   ....   ..+.+++.+.++..+++....
T Consensus       329 ~~~~~d~aL~~Rf~~i~v~~p~~~e~~~il~~l~  362 (758)
T 1r6b_X          329 NIFEKDRALARRFQKIDITEPSIEETVQIINGLK  362 (758)
T ss_dssp             CCCCCTTSSGGGEEEEECCCCCHHHHHHHHHHHH
T ss_pred             hhhhcCHHHHhCceEEEcCCCCHHHHHHHHHHHH
Confidence              1   1111   168899999999988887654

>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase, winged-helix domain, ATP hydrolysis, walker A, walker B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A* 1in8_A* 1in7_A* 1j7k_A*

Probab=97.56  E-value=0.0045  Score=63.42  Aligned_cols=164  Identities=18%  Similarity=0.242  Sum_probs=92.4

Q ss_pred             CCCCCCcchHHHHHHHHHc-----CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHH
Q 042541          166 VISPGLDVPLKELKMELFK-----DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVL  240 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~-----~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~  240 (695)
                      +.++|.+..++.+...+..     .....+.|+|++|+||||||+.+++.  ....    +...+.+-.....       
T Consensus        25 ~~~~g~~~~~~~l~~~i~~~~~~~~~~~~~ll~Gp~G~GKTTLa~~ia~~--l~~~----~~~~sg~~~~~~~-------   91 (334)
T 1in4_A           25 DEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASE--LQTN----IHVTSGPVLVKQG-------   91 (334)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHH--HTCC----EEEEETTTCCSHH-------
T ss_pred             HHccCcHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHHH--hCCC----EEEEechHhcCHH-------
Confidence            4568988777777666653     23467999999999999999999873  3211    1111111100111       


Q ss_pred             HhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhccC--------C----------CCCE
Q 042541          241 HHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGFQ--------L----------PDYK  298 (695)
Q Consensus       241 ~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~--------~----------~gs~  298 (695)
                                        .+...+..+ .++.++++|++......    +...+...        .          +...
T Consensus        92 ------------------~l~~~~~~~-~~~~v~~iDE~~~l~~~~~e~L~~~~~~~~~~i~~~~~~~~~~i~~~l~~~~  152 (334)
T 1in4_A           92 ------------------DMAAILTSL-ERGDVLFIDEIHRLNKAVEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPFT  152 (334)
T ss_dssp             ------------------HHHHHHHHC-CTTCEEEEETGGGCCHHHHHHHHHHHHTSCCCC---------------CCCE
T ss_pred             ------------------HHHHHHHHc-cCCCEEEEcchhhcCHHHHHHHHHHHHhcccceeeccCcccccccccCCCeE
Confidence                              111222222 23456778887554322    11111110        0          1122


Q ss_pred             EEE-EcCCCC------CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHH
Q 042541          299 ILV-TSRSEF------PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVV  364 (695)
Q Consensus       299 iiv-TtR~~~------~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~  364 (695)
                      ++- |++...      ...+....+++.+.++-.+++.+.+.....   .-..+.+..|++.++|.|..+..+
T Consensus       153 li~at~~~~~Ls~~l~sR~~l~~~Ld~~~~~~l~~iL~~~~~~~~~---~~~~~~~~~ia~~~~G~~R~a~~l  222 (334)
T 1in4_A          153 LVGATTRSGLLSSPLRSRFGIILELDFYTVKELKEIIKRAASLMDV---EIEDAAAEMIAKRSRGTPRIAIRL  222 (334)
T ss_dssp             EEEEESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHTTC---CBCHHHHHHHHHTSTTCHHHHHHH
T ss_pred             EEEecCCcccCCHHHHHhcCceeeCCCCCHHHHHHHHHHHHHHcCC---CcCHHHHHHHHHhcCCChHHHHHH
Confidence            332 333221      122336889999999999999887643221   224678999999999999765443

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=97.55  E-value=0.0013  Score=64.76  Aligned_cols=169  Identities=12%  Similarity=0.091  Sum_probs=90.5

Q ss_pred             CCCCCCcchHHHHHHHHH---cC---------CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHH
Q 042541          166 VISPGLDVPLKELKMELF---KD---------GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVK  233 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~---~~---------~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~  233 (695)
                      +.++|.+..++++.+.+.   ..         ..+-+.|+|++|+||||||+.+++.  ...    ..+.++.+.-.+  
T Consensus        12 ~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~--~~~----~~~~i~~~~~~~--   83 (257)
T 1lv7_A           12 ADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGE--AKV----PFFTISGSDFVE--   83 (257)
T ss_dssp             GGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHH--HTC----CEEEECSCSSTT--
T ss_pred             HHhcCcHHHHHHHHHHHHHHhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHHH--cCC----CEEEEeHHHHHH--
Confidence            467999887777765443   21         1345889999999999999999873  221    133443332111  


Q ss_pred             HHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCC------------Ch--H----HHhhhcc--
Q 042541          234 AIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPG------------SE--S----LLQKLGF--  292 (695)
Q Consensus       234 ~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~------------~~--~----~~~~l~~--  292 (695)
                              ...    .  ...   ..+..++ ......+.++++|+++..            ..  .    ++..+..  
T Consensus        84 --------~~~----~--~~~---~~~~~~~~~a~~~~~~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~  146 (257)
T 1lv7_A           84 --------MFV----G--VGA---SRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFE  146 (257)
T ss_dssp             --------SCC----C--CCH---HHHHHHHHHHHTTCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCC
T ss_pred             --------Hhh----h--hhH---HHHHHHHHHHHHcCCeeehhhhhhhhccCCCCCcCCCchHHHHHHHHHHHHhhCcc
Confidence                    000    0  111   2233334 223456789999998211            00  1    1222221  


Q ss_pred             CCCCCEEEEEcCCCC------C---CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCC-chhHHH
Q 042541          293 QLPDYKILVTSRSEF------P---QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKG-CPLALK  362 (695)
Q Consensus       293 ~~~gs~iivTtR~~~------~---~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G-~PLai~  362 (695)
                      ...+..||.||....      .   .....+.++..+.++-.+++..........  .  ......++..+.| .+--|.
T Consensus       147 ~~~~~~vI~~tn~~~~l~~~l~r~~rf~~~i~i~~P~~~~r~~il~~~~~~~~l~--~--~~~~~~la~~~~G~~~~dl~  222 (257)
T 1lv7_A          147 GNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLA--P--DIDAAIIARGTPGFSGADLA  222 (257)
T ss_dssp             SSSCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBC--T--TCCHHHHHHTCTTCCHHHHH
T ss_pred             cCCCEEEEEeeCCchhCCHHHcCCCcCCeEEEeCCCCHHHHHHHHHHHHhcCCCC--c--cccHHHHHHHcCCCCHHHHH
Confidence            123445666665441      1   122367788888888888887665332111  1  1124567777888 665444


Q ss_pred             H
Q 042541          363 V  363 (695)
Q Consensus       363 ~  363 (695)
                      .
T Consensus       223 ~  223 (257)
T 1lv7_A          223 N  223 (257)
T ss_dssp             H
T ss_pred             H
Confidence            3

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A*

Probab=97.55  E-value=7.9e-05  Score=74.07  Aligned_cols=44  Identities=18%  Similarity=0.130  Sum_probs=34.7

Q ss_pred             CCCCCCcchHHHHHHHHH---c---------CCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          166 VISPGLDVPLKELKMELF---K---------DGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~---~---------~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +.++|.+..++.+.+.+.   .         ...+-+.|+|++|+|||+||+.+++
T Consensus        11 ~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~   66 (268)
T 2r62_A           11 KDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAG   66 (268)
T ss_dssp             TTSSSCTTTHHHHHHHHHHHHCHHHHHHHSCCCCSCCCCBCSSCSSHHHHHHHHHH
T ss_pred             HHhCCcHHHHHHHHHHHHHHHChHHHHHCCCCCCceEEEECCCCCcHHHHHHHHHH
Confidence            468999998888877654   1         1134478999999999999999987

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=97.52  E-value=0.00091  Score=75.78  Aligned_cols=164  Identities=10%  Similarity=0.112  Sum_probs=97.7

Q ss_pred             CCCCCCcchHHHHHHHHH----cC---------CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCH
Q 042541          166 VISPGLDVPLKELKMELF----KD---------GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNV  232 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~----~~---------~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~  232 (695)
                      +.+.|.++.+++|.+.+.    .+         .++-|.++|++|+|||+||+++++  ...    ...+.++.++    
T Consensus       204 ~dIgGl~~~~~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LAraiA~--elg----~~~~~v~~~~----  273 (806)
T 3cf2_A          204 DDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVAN--ETG----AFFFLINGPE----  273 (806)
T ss_dssp             GGCCSCCTTHHHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHHHT--TTT----CEEEEEEHHH----
T ss_pred             hhhcCHHHHHHHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHH--HhC----CeEEEEEhHH----
Confidence            356889998888887654    11         256799999999999999999998  332    2244554331    


Q ss_pred             HHHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCC-----------hHHHhhhc----c--CC
Q 042541          233 KAIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGS-----------ESLLQKLG----F--QL  294 (695)
Q Consensus       233 ~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~-----------~~~~~~l~----~--~~  294 (695)
                            ++..         ...+....++.++ ......+++|++|+++...           ......+.    .  ..
T Consensus       274 ------l~sk---------~~gese~~lr~lF~~A~~~~PsIIfIDEiDal~~~r~~~~~~~~~riv~~LL~~mdg~~~~  338 (806)
T 3cf2_A          274 ------IMSK---------LAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQR  338 (806)
T ss_dssp             ------HHSS---------CTTHHHHHHHHHHHHHTTSCSEEEEEESGGGTCCTTTTCCCTTHHHHHHHHHTHHHHCCGG
T ss_pred             ------hhcc---------cchHHHHHHHHHHHHHHHcCCeEEEEehhcccccccCCCCChHHHHHHHHHHHHHhccccc
Confidence                  1111         1122344566666 4556789999999985432           01122221    1  11


Q ss_pred             CCCEEEEEcCCCC------C---CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCch
Q 042541          295 PDYKILVTSRSEF------P---QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCP  358 (695)
Q Consensus       295 ~gs~iivTtR~~~------~---~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~P  358 (695)
                      .+..||.||....      .   .....+.++..+.++-.++|..+........    ......|++.+.|.-
T Consensus       339 ~~V~VIaaTN~~d~LD~ALrR~GRFd~~I~i~~Pd~~~R~~IL~~~l~~~~~~~----dvdl~~lA~~T~Gfs  407 (806)
T 3cf2_A          339 AHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLAD----DVDLEQVANETHGHV  407 (806)
T ss_dssp             GCEEEEEECSSTTTSCTTTTSTTSSCEEEECCCCCHHHHHHHHHHTCSSSEECT----TCCHHHHHHHCCSCC
T ss_pred             CCEEEEEecCChhhcCHHHhCCcccceEEecCCCCHHHHHHHHHHHhcCCCCCc----ccCHHHHHHhcCCCC
Confidence            2334555655441      1   2233788888888888888887653322211    112567888888874

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=97.51  E-value=0.00018  Score=73.14  Aligned_cols=61  Identities=15%  Similarity=0.208  Sum_probs=43.4

Q ss_pred             CCCCCcchHHHHHHHHHcC---------CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC
Q 042541          167 ISPGLDVPLKELKMELFKD---------GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP  230 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~~~---------~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~  230 (695)
                      .++|.+..++.+...+...         ....+.|+|++|+|||++|+.+++  .....-. .++.++++...
T Consensus        18 ~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~ll~G~~GtGKt~la~~la~--~~~~~~~-~~~~~~~~~~~   87 (311)
T 4fcw_A           18 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAA--TLFDTEE-AMIRIDMTEYM   87 (311)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHTCSCTTSCSEEEEEESCSSSSHHHHHHHHHH--HHHSCGG-GEEEEEGGGCC
T ss_pred             hcCCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCcCHHHHHHHHHH--HHcCCCc-ceEEeeccccc
Confidence            4689999999988887732         135899999999999999999987  3322111 25567766543

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=97.41  E-value=9.9e-05  Score=65.98  Aligned_cols=58  Identities=21%  Similarity=0.206  Sum_probs=35.7

Q ss_pred             CCCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCC
Q 042541          165 PVISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSK  228 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~  228 (695)
                      ..+++|...+   ....|..-....++|+|+.|+|||||++.++..  .... ...+++++..+
T Consensus        17 ~~f~~g~n~~---~~~~l~~~~g~~~~l~G~~G~GKTtL~~~i~~~--~~~~-g~~~~~~~~~~   74 (149)
T 2kjq_A           17 DKFLGTENAE---LVYVLRHKHGQFIYVWGEEGAGKSHLLQAWVAQ--ALEA-GKNAAYIDAAS   74 (149)
T ss_dssp             CCCCSCCTHH---HHHHCCCCCCSEEEEESSSTTTTCHHHHHHHHH--HHTT-TCCEEEEETTT
T ss_pred             hhcCcCccHH---HHHHHHhcCCCEEEEECCCCCCHHHHHHHHHHH--HHhc-CCcEEEEcHHH
Confidence            3444554433   233333224578999999999999999999873  2221 11256776554

>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A {Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB: 2cea_A* 3kds_E*

Probab=97.41  E-value=0.0026  Score=67.91  Aligned_cols=164  Identities=13%  Similarity=0.117  Sum_probs=93.4

Q ss_pred             CCCCCCcchHHHHHHHHH---cC---------CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHH
Q 042541          166 VISPGLDVPLKELKMELF---KD---------GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVK  233 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~---~~---------~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~  233 (695)
                      +.++|.++.++++.+.+.   ..         -.+-|.|+|++|+|||+||+.+++.  ..    ...+.++.++.... 
T Consensus        16 ~di~G~~~~~~~l~e~v~~l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~~--~~----~~f~~is~~~~~~~-   88 (476)
T 2ce7_A           16 KDVGGAEEAIEELKEVVEFLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGE--AN----VPFFHISGSDFVEL-   88 (476)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHHH--HT----CCEEEEEGGGTTTC-
T ss_pred             HHhCCcHHHHHHHHHHHHHhhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHH--cC----CCeeeCCHHHHHHH-
Confidence            457999988777766543   21         1345889999999999999999873  22    22345554432210 


Q ss_pred             HHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCCh--------------H----HHhhhcc--
Q 042541          234 AIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGSE--------------S----LLQKLGF--  292 (695)
Q Consensus       234 ~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~~--------------~----~~~~l~~--  292 (695)
                               +         .......++.++ ......+.+|++|+++....              .    ++..+..  
T Consensus        89 ---------~---------~g~~~~~~r~lf~~A~~~~p~ILfIDEid~l~~~r~~~~~g~~~~~~~~l~~LL~~ld~~~  150 (476)
T 2ce7_A           89 ---------F---------VGVGAARVRDLFAQAKAHAPCIVFIDEIDAVGRHRGAGLGGGHDEREQTLNQLLVEMDGFD  150 (476)
T ss_dssp             ---------C---------TTHHHHHHHHHHHHHHHTCSEEEEEETGGGTCCC---------CHHHHHHHHHHHHHHHSC
T ss_pred             ---------H---------hcccHHHHHHHHHHHHhcCCCEEEEechhhhhhhcccccCcCcHHHHHHHHHHHHHHhccC
Confidence                     0         001123344444 33356789999999854210              1    1222211  


Q ss_pred             CCCCCEEEEEcCCCC------CC---CCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCch
Q 042541          293 QLPDYKILVTSRSEF------PQ---FGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCP  358 (695)
Q Consensus       293 ~~~gs~iivTtR~~~------~~---~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~P  358 (695)
                      ...+..||.||....      ..   ....+.++..+.++-.+++..++......  ..  .....|++.+.|..
T Consensus       151 ~~~~viVIaaTn~~~~Ld~allR~gRFd~~i~i~~Pd~~~R~~Il~~~~~~~~l~--~~--v~l~~la~~t~G~s  221 (476)
T 2ce7_A          151 SKEGIIVMAATNRPDILDPALLRPGRFDKKIVVDPPDMLGRKKILEIHTRNKPLA--ED--VNLEIIAKRTPGFV  221 (476)
T ss_dssp             GGGTEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBC--TT--CCHHHHHHTCTTCC
T ss_pred             CCCCEEEEEecCChhhhchhhcccCcceeEeecCCCCHHHHHHHHHHHHHhCCCc--ch--hhHHHHHHhcCCCc
Confidence            123455666665541      11   22377888888888888887665432211  11  11455888998877

>3rw6_A Nuclear RNA export factor 1; retroviral constitutive transport element (CTE), RNA recogni motif (RRM); HET: GTP CCC; 2.30A {Homo sapiens} PDB: 3rw7_A 1koo_A 1koh_A 1ft8_A 1fo1_A

Probab=97.38  E-value=0.00019  Score=70.51  Aligned_cols=87  Identities=22%  Similarity=0.347  Sum_probs=62.3

Q ss_pred             cCCCCCcEEEEcccCCCCcccCcc-cccccCCCCcEEEeccCCCCCcccccccc--cccEEeeccccCCcccccch---h
Q 042541          571 QKMDELKVLIVTNYGFSPAELNNF-RVLSALSKLKKIRLEHVSLPNSLATVRMN--HLQKVSLVMCNVGQVFRNST---F  644 (695)
Q Consensus       571 ~~l~~Lr~L~l~~~~~~~~~~~~~-~~l~~l~~L~~L~L~~~~l~~lp~i~~l~--~L~~L~l~~~~i~~~~~~~~---~  644 (695)
                      .++++|++|+|++|.+..  +..+ ..+..+++|++|+|++|.+..+..++.+.  +|++|+|++|++....|...   .
T Consensus       167 ~~l~~L~~L~Ls~N~l~~--l~~l~~~~~~l~~L~~L~Ls~N~i~~~~~l~~l~~l~L~~L~L~~Npl~~~~~~~~~y~~  244 (267)
T 3rw6_A          167 ENIPELLSLNLSNNRLYR--LDDMSSIVQKAPNLKILNLSGNELKSERELDKIKGLKLEELWLDGNSLCDTFRDQSTYIS  244 (267)
T ss_dssp             HHCTTCCEEECTTSCCCC--CGGGTTHHHHSTTCCEEECTTSCCCSGGGGGGGTTSCCSEEECTTSTTGGGCSSHHHHHH
T ss_pred             hhCCCCCEEECCCCCCCC--CccchhHHhhCCCCCEEECCCCccCCchhhhhcccCCcceEEccCCcCccccCcchhHHH
Confidence            568899999999998743  2222 23568999999999999999776445555  99999999999876443210   0


Q ss_pred             hhcccCCCccEEecc
Q 042541          645 RISDAFPNLLEMDID  659 (695)
Q Consensus       645 ~l~~~l~~L~~L~l~  659 (695)
                      .+-..+++|+.||-.
T Consensus       245 ~il~~~P~L~~LDg~  259 (267)
T 3rw6_A          245 AIRERFPKLLRLDGH  259 (267)
T ss_dssp             HHHHHCTTCCEESSC
T ss_pred             HHHHHCcccCeECCc
Confidence            111178999998754

>1io0_A Tropomodulin; LRR protein, right-handed super-helix, protein binding; 1.45A {Gallus gallus} SCOP: c.10.1.1

Probab=97.36  E-value=5.5e-05  Score=70.54  Aligned_cols=115  Identities=13%  Similarity=0.133  Sum_probs=79.4

Q ss_pred             CCCceEEEEEEcc-Ccc----ccCChhhcCCCCCcEEEEcccCCCCcccCcc-cccccCCCCcEEEeccCCCCC-----c
Q 042541          548 QGPEVKVVVLNIR-TKK----YVLPDFLQKMDELKVLIVTNYGFSPAELNNF-RVLSALSKLKKIRLEHVSLPN-----S  616 (695)
Q Consensus       548 ~~~~l~~L~l~~~-~~~----~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~-~~l~~l~~L~~L~L~~~~l~~-----l  616 (695)
                      ..+.|+.|.|+.+ ...    ..+...+...++|++|+|++|.+.......+ ..+...++|++|+|++|.+..     +
T Consensus        34 ~~~~L~~L~L~~n~~i~~~g~~~l~~~L~~~~~L~~L~Ls~n~i~~~g~~~l~~~L~~n~~L~~L~L~~N~i~~~g~~~l  113 (185)
T 1io0_A           34 NDPDLEEVNLNNIMNIPVPTLKACAEALKTNTYVKKFSIVGTRSNDPVAFALAEMLKVNNTLKSLNVESNFISGSGILAL  113 (185)
T ss_dssp             TCTTCCEEECTTCTTCCHHHHHHHHHHHTTCCSCCEEECTTSCCCHHHHHHHHHHHHHCSSCCEEECCSSCCCHHHHHHH
T ss_pred             cCCCCCEEEecCCCCCCHHHHHHHHHHHHhCCCcCEEECcCCCCChHHHHHHHHHHHhCCCcCEEECcCCcCCHHHHHHH
Confidence            3566777877766 433    2355667788999999999998754332221 235566889999999999973     4


Q ss_pred             c-cccccccccEEee--ccccCCcccccchhhhcccCCCccEEeccccc
Q 042541          617 L-ATVRMNHLQKVSL--VMCNVGQVFRNSTFRISDAFPNLLEMDIDYCN  662 (695)
Q Consensus       617 p-~i~~l~~L~~L~l--~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~  662 (695)
                      . .+...++|++|+|  ++|.++..-...+...-...++|+.|+|++|.
T Consensus       114 ~~~L~~n~~L~~L~L~~~~N~i~~~g~~~l~~~L~~n~~L~~L~L~~n~  162 (185)
T 1io0_A          114 VEALQSNTSLIELRIDNQSQPLGNNVEMEIANMLEKNTTLLKFGYHFTQ  162 (185)
T ss_dssp             HHGGGGCSSCCEEECCCCSSCCCHHHHHHHHHHHHHCSSCCEEECCCSS
T ss_pred             HHHHHhCCCceEEEecCCCCCCCHHHHHHHHHHHHhCCCcCEEeccCCC
Confidence            5 7777889999999  88988753211111111156899999999874

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=97.28  E-value=0.0025  Score=63.95  Aligned_cols=23  Identities=13%  Similarity=0.164  Sum_probs=21.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ++.+.++|++|+|||+||+.+++
T Consensus        36 p~~lLl~GppGtGKT~la~aiA~   58 (293)
T 3t15_A           36 PLILGIWGGKGQGKSFQCELVFR   58 (293)
T ss_dssp             CSEEEEEECTTSCHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            46788999999999999999998

>4fdw_A Leucine rich hypothetical protein; putative cell surface protein, BIG3 domain, LRR domain, STRU genomics; 2.05A {Bacteroides ovatus} PDB: 4fd0_A

Probab=97.22  E-value=0.0018  Score=68.12  Aligned_cols=87  Identities=3%  Similarity=0.015  Sum_probs=60.8

Q ss_pred             cccCCCCcEEEeccCCCC-----Ccc--cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCch
Q 042541          597 LSALSKLKKIRLEHVSLP-----NSL--ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPD  669 (695)
Q Consensus       597 l~~l~~L~~L~L~~~~l~-----~lp--~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~  669 (695)
                      +..+.+|+.+.+.++.+.     .++  .+.++.+|+.+.|. +.++.+....+.    .+++|+.+.|..  ++..++.
T Consensus       267 F~~c~~L~~l~l~~~~~~~~~~~~I~~~aF~~c~~L~~l~l~-~~i~~I~~~aF~----~c~~L~~l~lp~--~l~~I~~  339 (401)
T 4fdw_A          267 FYYCPELAEVTTYGSTFNDDPEAMIHPYCLEGCPKLARFEIP-ESIRILGQGLLG----GNRKVTQLTIPA--NVTQINF  339 (401)
T ss_dssp             TTTCTTCCEEEEESSCCCCCTTCEECTTTTTTCTTCCEECCC-TTCCEECTTTTT----TCCSCCEEEECT--TCCEECT
T ss_pred             hhCCCCCCEEEeCCccccCCcccEECHHHhhCCccCCeEEeC-CceEEEhhhhhc----CCCCccEEEECc--cccEEcH
Confidence            566777888888776554     465  67778888888887 347777777765    778888888864  3666654


Q ss_pred             h-hcCCCCCceeecccccCCCCCC
Q 042541          670 G-LCDIVSMEKLRITNCHRLSALP  692 (695)
Q Consensus       670 ~-i~~L~~L~~L~l~~~~~l~~lP  692 (695)
                      + |.++ +|+.|++.+|. +..++
T Consensus       340 ~aF~~~-~L~~l~l~~n~-~~~l~  361 (401)
T 4fdw_A          340 SAFNNT-GIKEVKVEGTT-PPQVF  361 (401)
T ss_dssp             TSSSSS-CCCEEEECCSS-CCBCC
T ss_pred             HhCCCC-CCCEEEEcCCC-Ccccc
Confidence            4 6677 88888888754 44444

>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase, nucleotide-binding, Pro serine protease, stress response; HET: ADP; 3.40A {Bacillus subtilis} PDB: 1x37_A

Probab=97.11  E-value=0.0037  Score=68.47  Aligned_cols=44  Identities=23%  Similarity=0.299  Sum_probs=34.4

Q ss_pred             CCCCCCcchHHHHHHHHH------cCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          166 VISPGLDVPLKELKMELF------KDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~------~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..++|.+...+.+.+.+.      ......+.|+|++|+||||||+.++.
T Consensus        81 ~di~G~~~vk~~i~~~~~l~~~~~~~~g~~vll~Gp~GtGKTtlar~ia~  130 (543)
T 3m6a_A           81 EEHHGLEKVKERILEYLAVQKLTKSLKGPILCLAGPPGVGKTSLAKSIAK  130 (543)
T ss_dssp             HHCSSCHHHHHHHHHHHHHHHHSSSCCSCEEEEESSSSSSHHHHHHHHHH
T ss_pred             HHhccHHHHHHHHHHHHHHHHhcccCCCCEEEEECCCCCCHHHHHHHHHH
Confidence            346888887777765544      12356899999999999999999987

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=97.09  E-value=0.002  Score=65.02  Aligned_cols=43  Identities=16%  Similarity=0.224  Sum_probs=36.5

Q ss_pred             CCCCCcchHHHHHHHHH--cCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          167 ISPGLDVPLKELKMELF--KDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~--~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .++|++..++++.+.+.  ......|.|+|.+|+|||++|+.+++
T Consensus         3 ~iig~s~~~~~~~~~~~~~a~~~~~vLi~Ge~GtGKt~lAr~i~~   47 (304)
T 1ojl_A            3 HMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHA   47 (304)
T ss_dssp             CCCCCSHHHHHHHHHHHHHCSTTSCEEEESCTTSCHHHHHHHHHH
T ss_pred             CcEECCHHHHHHHHHHHHHhCCCCcEEEECCCCchHHHHHHHHHH
Confidence            57999999999988876  23445678999999999999999987

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=97.09  E-value=0.008  Score=64.43  Aligned_cols=45  Identities=16%  Similarity=0.214  Sum_probs=34.9

Q ss_pred             CCCCCCcchHHHHHHHHH---cCC--ceEEEEEcCCCCcHHHHHHHHhcc
Q 042541          166 VISPGLDVPLKELKMELF---KDG--RQFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~---~~~--~~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      +.++|.++.++.+..++.   .+.  .+-+.++|++|+|||++|+.+++.
T Consensus        37 ~~iiG~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~   86 (456)
T 2c9o_A           37 SGLVGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQE   86 (456)
T ss_dssp             TTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHHHHhCCCCCCeEEEECCCcCCHHHHHHHHHHH
Confidence            568999988776655443   332  357889999999999999999873

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=96.99  E-value=0.0023  Score=73.52  Aligned_cols=141  Identities=14%  Similarity=0.170  Sum_probs=79.9

Q ss_pred             CCCCCCcchHHHHHHHHHcC---------CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHH
Q 042541          166 VISPGLDVPLKELKMELFKD---------GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIV  236 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~---------~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~  236 (695)
                      ..++|.+..++.+...+...         ....+.++|++|+|||++|+.+++  .....-.. .+.++++........ 
T Consensus       491 ~~viGq~~a~~~l~~~i~~~~~~~~~~~~p~~~~Ll~Gp~GtGKT~lA~ala~--~l~~~~~~-~i~i~~s~~~~~~~~-  566 (758)
T 3pxi_A          491 SRVIGQDEAVVAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAE--SIFGDEES-MIRIDMSEYMEKHST-  566 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHTTTCSCTTSCSEEEEEESCTTSSHHHHHHHHHH--HHHSCTTC-EEEEEGGGGCSSCCC-
T ss_pred             CcCcChHHHHHHHHHHHHHHHcccCCCCCCceEEEEECCCCCCHHHHHHHHHH--HhcCCCcc-eEEEechhccccccc-
Confidence            45799999999988887721         123699999999999999999987  33222122 556766543210000 


Q ss_pred             HHHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChHHH----hhhcc-----------CCCCCEEEE
Q 042541          237 QKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSESLL----QKLGF-----------QLPDYKILV  301 (695)
Q Consensus       237 ~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~~~----~~l~~-----------~~~gs~iiv  301 (695)
                                     .    ...+...++  .....+|+||++........    ..+..           ...+..||+
T Consensus       567 ---------------~----~~~l~~~~~--~~~~~vl~lDEi~~~~~~~~~~Ll~~le~g~~~~~~g~~~~~~~~~iI~  625 (758)
T 3pxi_A          567 ---------------S----GGQLTEKVR--RKPYSVVLLDAIEKAHPDVFNILLQVLEDGRLTDSKGRTVDFRNTILIM  625 (758)
T ss_dssp             ---------------C-------CHHHHH--HCSSSEEEEECGGGSCHHHHHHHHHHHHHSBCC-----CCBCTTCEEEE
T ss_pred             ---------------c----cchhhHHHH--hCCCeEEEEeCccccCHHHHHHHHHHhccCeEEcCCCCEeccCCeEEEE
Confidence                           0    001111111  13345999999987765422    22221           113568888


Q ss_pred             EcCCCC-------------------CCCCCeEecCCCChHHHHHHHHHh
Q 042541          302 TSRSEF-------------------PQFGSVHYLKPLTYEAARTLFLHS  331 (695)
Q Consensus       302 TtR~~~-------------------~~~~~~~~l~~L~~~ea~~Lf~~~  331 (695)
                      ||....                   ......+.+.+++.++-..++...
T Consensus       626 ttn~~~~~~~~~~~~~~~~f~p~l~~Rl~~~i~~~~l~~~~~~~i~~~~  674 (758)
T 3pxi_A          626 TSNVGASEKDKVMGELKRAFRPEFINRIDEIIVFHSLEKKHLTEIVSLM  674 (758)
T ss_dssp             EESSSTTCCHHHHHHHHHHSCHHHHTTSSEEEECC--CHHHHHHHHHHH
T ss_pred             eCCCChhhHHHHHHHHHhhCCHHHHhhCCeEEecCCCCHHHHHHHHHHH
Confidence            887421                   112236677777777666666543

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=96.84  E-value=0.00063  Score=68.83  Aligned_cols=51  Identities=10%  Similarity=0.070  Sum_probs=33.5

Q ss_pred             hHHHHHHHHHcC---CceEEEEEcCCCCcHHHHHHHHhcccccc-ccCCCcEEEEEeC
Q 042541          174 PLKELKMELFKD---GRQFIVVSAPGGYGKTTLVQRLCKDDQVQ-GKFKDDIFYVTVS  227 (695)
Q Consensus       174 ~~~~l~~~L~~~---~~~vv~I~G~gGiGKTtLa~~~~~~~~~~-~~f~~~~~wv~~~  227 (695)
                      ..+.+.+++...   ....+.|+|++|+|||+||..+++.  .. ..- ..+.+++++
T Consensus       136 ~~~~~~~~i~~~~~~~~~~lll~G~~GtGKT~La~aia~~--~~~~~g-~~v~~~~~~  190 (308)
T 2qgz_A          136 AFSAILDFVEQYPSAEQKGLYLYGDMGIGKSYLLAAMAHE--LSEKKG-VSTTLLHFP  190 (308)
T ss_dssp             HHHHHHHHHHHCSCSSCCEEEEECSTTSSHHHHHHHHHHH--HHHHSC-CCEEEEEHH
T ss_pred             HHHHHHHHHHhccccCCceEEEECCCCCCHHHHHHHHHHH--HHHhcC-CcEEEEEHH
Confidence            344455555532   2478899999999999999999983  33 221 225566654

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=96.77  E-value=0.034  Score=59.69  Aligned_cols=165  Identities=12%  Similarity=0.094  Sum_probs=91.1

Q ss_pred             CCCCCCCcchHHHHHHHHH---cC---------CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCH
Q 042541          165 PVISPGLDVPLKELKMELF---KD---------GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNV  232 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~---~~---------~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~  232 (695)
                      -+.++|.++.++++.+...   ..         -.+-|.|+|++|+||||||+.++..  ..    ...+.++.+.-.. 
T Consensus        30 f~dv~G~~~~k~~l~~lv~~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~~--~~----~~~i~i~g~~~~~-  102 (499)
T 2dhr_A           30 FKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGE--AR----VPFITASGSDFVE-  102 (499)
T ss_dssp             TTSSCSCHHHHHHHHHHHHHHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHHH--TT----CCEEEEEGGGGTS-
T ss_pred             HHHcCCcHHHHHHHHHHHHHhhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHHH--hC----CCEEEEehhHHHH-
Confidence            3467999987777665543   21         1234899999999999999999873  22    2244555443110 


Q ss_pred             HHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhc-CCCcEEEEEeCCCCCC-----------h-------HHHhhhccC
Q 042541          233 KAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQM-RIEAILLVLDDVWPGS-----------E-------SLLQKLGFQ  293 (695)
Q Consensus       233 ~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l-~~~~~LlVlDdv~~~~-----------~-------~~~~~l~~~  293 (695)
                                   .     ........+..+++.. ...+.++++|+++...           +       .++..+...
T Consensus       103 -------------~-----~~g~~~~~v~~lfq~a~~~~p~il~IDEId~l~~~r~~~~~~~~~e~~~~l~~LL~~Ldg~  164 (499)
T 2dhr_A          103 -------------M-----FVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGF  164 (499)
T ss_dssp             -------------S-----CTTHHHHHHHHHTTTSSSSSSCEEEEECGGGTCCCSSSSTTTSSHHHHHHHHHHHHHGGGC
T ss_pred             -------------h-----hhhhHHHHHHHHHHHHHhcCCCEEEEehHHHHHHhhccCcCCCcHHHHHHHHHHHHHhccc
Confidence                         0     0011122334444332 2356899999984321           1       122222211


Q ss_pred             CC--CCEEEEEcCCCC------C---CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCch
Q 042541          294 LP--DYKILVTSRSEF------P---QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCP  358 (695)
Q Consensus       294 ~~--gs~iivTtR~~~------~---~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~P  358 (695)
                      ..  +..++.||....      .   .....+.++..+.++-.+++..++.....    ........|+..+.|+.
T Consensus       165 ~~~~~viviAatn~p~~LD~aLlr~gRfdr~i~i~~Pd~~~R~~IL~~~~~~~~l----~~dv~l~~lA~~t~G~~  236 (499)
T 2dhr_A          165 EKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPL----AEDVDLALLAKRTPGFV  236 (499)
T ss_dssp             CSSCCCEEEECCSCGGGSCTTTSSTTSSCCEEECCCCCHHHHHHHHHHTTSSSCC----CCSSTTHHHHTTSCSCC
T ss_pred             ccCccEEEEEecCChhhcCcccccccccceEEecCCCCHHHHHHHHHHHHhcCCC----ChHHHHHHHHHhcCCCC
Confidence            11  234444554431      1   23347888888988888888876532211    11122556888888875

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=96.76  E-value=0.05  Score=53.83  Aligned_cols=165  Identities=12%  Similarity=0.104  Sum_probs=86.7

Q ss_pred             CCCCCCCcchHHHHHHHHH---cC---------CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCH
Q 042541          165 PVISPGLDVPLKELKMELF---KD---------GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNV  232 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~---~~---------~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~  232 (695)
                      -+.++|.+..++++.+...   ..         -.+-+.|+|++|+|||||++.++..  ..    .+.+.++..     
T Consensus        39 ~~~i~g~~~~~~~l~~l~~~~~~~~~l~~~~~~~~~gvll~Gp~GtGKTtl~~~i~~~--~~----~~~i~~~~~-----  107 (278)
T 1iy2_A           39 FKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGE--AR----VPFITASGS-----  107 (278)
T ss_dssp             GGGSSSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCCEEEEECCTTSSHHHHHHHHHHH--TT----CCEEEEEHH-----
T ss_pred             HHHhCChHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCcChHHHHHHHHHHH--cC----CCEEEecHH-----
Confidence            3567898887766655433   10         0123899999999999999999873  32    223344322     


Q ss_pred             HHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhc-CCCcEEEEEeCCCCC-----------Ch---H----HHhhhccC
Q 042541          233 KAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQM-RIEAILLVLDDVWPG-----------SE---S----LLQKLGFQ  293 (695)
Q Consensus       233 ~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l-~~~~~LlVlDdv~~~-----------~~---~----~~~~l~~~  293 (695)
                       ++    .....         ......+..+++.. ...+.++++||+...           ..   .    ++..+...
T Consensus       108 -~~----~~~~~---------~~~~~~i~~~~~~~~~~~~~i~~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~lsgg  173 (278)
T 1iy2_A          108 -DF----VEMFV---------GVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGF  173 (278)
T ss_dssp             -HH----HHSTT---------THHHHHHHHHHHHHHTSCSEEEEEETHHHHHCC--------CHHHHHHHHHHHHHHTTC
T ss_pred             -HH----HHHHh---------hHHHHHHHHHHHHHHhcCCcEEehhhhHhhhcccccccCCcchHHHHHHHHHHHHHhCC
Confidence             11    11110         01122333444322 345789999998311           11   1    12222211


Q ss_pred             CC-CC-EEEEEcCCCC---------CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCch
Q 042541          294 LP-DY-KILVTSRSEF---------PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCP  358 (695)
Q Consensus       294 ~~-gs-~iivTtR~~~---------~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~P  358 (695)
                      .. .. .++.||....         ......+.++..+.++-.+++...+......    .......+++.+.|..
T Consensus       174 ~~~~~~i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~~~~~~----~~~~~~~la~~~~G~~  245 (278)
T 1iy2_A          174 EKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLA----EDVDLALLAKRTPGFV  245 (278)
T ss_dssp             CTTCCEEEEEEESCTTSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSCBC----TTCCHHHHHHTCTTCC
T ss_pred             CCCCCEEEEEecCCchhCCHhHcCCCcCCeEEEeCCcCHHHHHHHHHHHHccCCCC----cccCHHHHHHHcCCCC
Confidence            11 12 3333444431         1234478888888888888887665322111    1112456777777754

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=96.73  E-value=0.0053  Score=58.47  Aligned_cols=44  Identities=23%  Similarity=0.185  Sum_probs=33.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIV  236 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~  236 (695)
                      ..++.|+|++|+|||||+..++.    .  -...++|++.....+...+.
T Consensus        20 G~~~~i~G~~GsGKTtl~~~l~~----~--~~~~v~~i~~~~~~~~~~~~   63 (220)
T 2cvh_A           20 GVLTQVYGPYASGKTTLALQTGL----L--SGKKVAYVDTEGGFSPERLV   63 (220)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHH----H--HCSEEEEEESSCCCCHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH----H--cCCcEEEEECCCCCCHHHHH
Confidence            47999999999999999999886    1  12347899887766665544

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=96.64  E-value=0.0038  Score=71.76  Aligned_cols=106  Identities=15%  Similarity=0.164  Sum_probs=60.7

Q ss_pred             CCCCCCcchHHHHHHHHHc---------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHH
Q 042541          166 VISPGLDVPLKELKMELFK---------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIV  236 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~---------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~  236 (695)
                      ..++|.+..++.+...+..         .....+.++|++|+|||++|+.+++  ..    ....+.++++.......  
T Consensus       458 ~~v~g~~~~~~~l~~~i~~~~~g~~~~~~p~~~~ll~G~~GtGKT~la~~la~--~l----~~~~~~i~~s~~~~~~~--  529 (758)
T 1r6b_X          458 MLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSK--AL----GIELLRFDMSEYMERHT--  529 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHH--HH----TCEEEEEEGGGCSSSSC--
T ss_pred             hhccCHHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCcHHHHHHHHHH--Hh----cCCEEEEechhhcchhh--
Confidence            4578999998888877761         1134799999999999999999987  33    22245666654322100  


Q ss_pred             HHHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH
Q 042541          237 QKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES  285 (695)
Q Consensus       237 ~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~  285 (695)
                         ...+-+..+.. ...+....+...++  +....+|+||++......
T Consensus       530 ---~~~l~g~~~g~-~g~~~~~~l~~~~~--~~~~~vl~lDEi~~~~~~  572 (758)
T 1r6b_X          530 ---VSRLIGAPPGY-VGFDQGGLLTDAVI--KHPHAVLLLDEIEKAHPD  572 (758)
T ss_dssp             ---CSSSCCCCSCS-HHHHHTTHHHHHHH--HCSSEEEEEETGGGSCHH
T ss_pred             ---HhhhcCCCCCC-cCccccchHHHHHH--hCCCcEEEEeCccccCHH
Confidence               00111111111 11111112222232  244689999999877654

>4fdw_A Leucine rich hypothetical protein; putative cell surface protein, BIG3 domain, LRR domain, STRU genomics; 2.05A {Bacteroides ovatus} PDB: 4fd0_A

Probab=96.54  E-value=0.015  Score=61.19  Aligned_cols=126  Identities=10%  Similarity=0.018  Sum_probs=89.4

Q ss_pred             CceEEEEEEccCccccC-ChhhcCCCCCcEEEEcccCCCCccc--CcccccccCCCCcEEEeccCCCCCcc--ccccccc
Q 042541          550 PEVKVVVLNIRTKKYVL-PDFLQKMDELKVLIVTNYGFSPAEL--NNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNH  624 (695)
Q Consensus       550 ~~l~~L~l~~~~~~~~~-p~~~~~l~~Lr~L~l~~~~~~~~~~--~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~  624 (695)
                      .+|+.+.+..+  ...+ +..|.++++|+.+.+.++.......  -....+..|.+|+.+.|. +++..++  .+.++.+
T Consensus       248 ~~L~~i~lp~~--i~~I~~~aF~~c~~L~~l~l~~~~~~~~~~~~I~~~aF~~c~~L~~l~l~-~~i~~I~~~aF~~c~~  324 (401)
T 4fdw_A          248 SGITTVKLPNG--VTNIASRAFYYCPELAEVTTYGSTFNDDPEAMIHPYCLEGCPKLARFEIP-ESIRILGQGLLGGNRK  324 (401)
T ss_dssp             CCCSEEEEETT--CCEECTTTTTTCTTCCEEEEESSCCCCCTTCEECTTTTTTCTTCCEECCC-TTCCEECTTTTTTCCS
T ss_pred             CCccEEEeCCC--ccEEChhHhhCCCCCCEEEeCCccccCCcccEECHHHhhCCccCCeEEeC-CceEEEhhhhhcCCCC
Confidence            56777777432  2233 3478899999999998765431111  111237789999999998 4688888  8889999


Q ss_pred             ccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCch-hhcCCC-CCceeecccc
Q 042541          625 LQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPD-GLCDIV-SMEKLRITNC  685 (695)
Q Consensus       625 L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~-~i~~L~-~L~~L~l~~~  685 (695)
                      |+.+.|..+ ++.+.+..|.    .+ +|+.+++.++. +..++. .+..++ +++.|++..+
T Consensus       325 L~~l~lp~~-l~~I~~~aF~----~~-~L~~l~l~~n~-~~~l~~~~F~~~~~~l~~l~vp~~  380 (401)
T 4fdw_A          325 VTQLTIPAN-VTQINFSAFN----NT-GIKEVKVEGTT-PPQVFEKVWYGFPDDITVIRVPAE  380 (401)
T ss_dssp             CCEEEECTT-CCEECTTSSS----SS-CCCEEEECCSS-CCBCCCSSCCCSCTTCCEEEECGG
T ss_pred             ccEEEECcc-ccEEcHHhCC----CC-CCCEEEEcCCC-CcccccccccCCCCCccEEEeCHH
Confidence            999999554 7777777776    78 99999999864 445543 356664 7888888763

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=96.52  E-value=0.015  Score=59.56  Aligned_cols=58  Identities=16%  Similarity=0.184  Sum_probs=40.4

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhcccccccc---CCCcEEEEEeCCCCCHHHHHHHHHHhcCC
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGK---FKDDIFYVTVSKNPNVKAIVQKVLHHKGY  245 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~---f~~~~~wv~~~~~~~~~~~~~~i~~~l~~  245 (695)
                      ..++.|+|.+|+||||||..++........   -...++|++....++...+.. ++..++.
T Consensus       122 G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~~~~~~~l~~-~~~~~g~  182 (343)
T 1v5w_A          122 MAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRD-IADRFNV  182 (343)
T ss_dssp             SEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHHHH-HHHHTTC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHH-HHHHcCC
Confidence            579999999999999999988763222111   234588999988877766544 3444443

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=96.46  E-value=0.0074  Score=61.44  Aligned_cols=58  Identities=19%  Similarity=0.230  Sum_probs=40.6

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhcccccccc---CCCcEEEEEeCCCCCHHHHHHHHHHhcCC
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGK---FKDDIFYVTVSKNPNVKAIVQKVLHHKGY  245 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~---f~~~~~wv~~~~~~~~~~~~~~i~~~l~~  245 (695)
                      ..++.|+|.+|+||||||..++........   ....++|++....++...+.. +++.++.
T Consensus       107 G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~~~~~~l~~-~~~~~g~  167 (324)
T 2z43_A          107 RTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIEN-MAKALGL  167 (324)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHHHHH-HHHHTTC
T ss_pred             CcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHH-HHHHhCC
Confidence            479999999999999999988763221111   134588999988877766653 3455543

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=96.43  E-value=0.0076  Score=58.35  Aligned_cols=58  Identities=14%  Similarity=0.105  Sum_probs=38.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccc---cCCCcEEEEEeCCCCCHHHHHHHHHHhcCC
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQG---KFKDDIFYVTVSKNPNVKAIVQKVLHHKGY  245 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~---~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~  245 (695)
                      ..++.|+|++|+|||||+..++.......   ....+++|++....++...+. ++++.++.
T Consensus        24 G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~~~~~~~~~~-~~~~~~g~   84 (243)
T 1n0w_A           24 GSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERLL-AVAERYGL   84 (243)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHHH-HHHHHTTC
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECCCCcCHHHHH-HHHHHcCC
Confidence            47999999999999999998876311111   013458899887765555443 34444443

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=96.34  E-value=0.0067  Score=56.05  Aligned_cols=118  Identities=18%  Similarity=0.144  Sum_probs=62.8

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCC---CCHHHHHHHHHH---hcCCCCC-CCCCh----HH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKN---PNVKAIVQKVLH---HKGYPVP-EFQTD----EA  255 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~---~~~~~~~~~i~~---~l~~~~~-~~~~~----~~  255 (695)
                      ...|.|++..|.||||+|-...-  +...+ ..+|..+.+-..   .....++..+.-   ..+.... .....    ..
T Consensus        28 ~g~i~v~tG~GkGKTTaA~Glal--RA~g~-G~rV~~vQF~Kg~~~~gE~~~l~~L~v~~~~~g~gf~~~~~~~~~~~~~  104 (196)
T 1g5t_A           28 RGIIIVFTGNGKGKTTAAFGTAA--RAVGH-GKNVGVVQFIKGTWPNGERNLLEPHGVEFQVMATGFTWETQNREADTAA  104 (196)
T ss_dssp             CCCEEEEESSSSCHHHHHHHHHH--HHHHT-TCCEEEEESSCCSSCCHHHHHHGGGTCEEEECCTTCCCCGGGHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHHHHH--HHHHC-CCeEEEEEeeCCCCCccHHHHHHhCCcEEEEcccccccCCCCcHHHHHH
Confidence            35677777777999999987765  33333 223667765442   234444444310   0111000 01111    11


Q ss_pred             HHHHHHHHHHhcCC-CcEEEEEeCCCC------CC-hHHHhhhccCCCCCEEEEEcCCCC
Q 042541          256 AINDLERFFKQMRI-EAILLVLDDVWP------GS-ESLLQKLGFQLPDYKILVTSRSEF  307 (695)
Q Consensus       256 ~~~~l~~~~~~l~~-~~~LlVlDdv~~------~~-~~~~~~l~~~~~gs~iivTtR~~~  307 (695)
                      ....+....+.+.+ +-=|||||++..      .. +.+++.+.....+..||+|+|...
T Consensus       105 a~~~l~~a~~~l~~~~yDlvILDEi~~al~~g~l~~~ev~~~l~~Rp~~~~vIlTGr~ap  164 (196)
T 1g5t_A          105 CMAVWQHGKRMLADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGCH  164 (196)
T ss_dssp             HHHHHHHHHHHTTCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSCC
T ss_pred             HHHHHHHHHHHHhcCCCCEEEEeCCCccccCCCCCHHHHHHHHHhCcCCCEEEEECCCCc
Confidence            22233333345544 445999999721      11 335555555556789999999873

>2vhj_A Ntpase P4, P4; non- hydrolysable ATP analogue, hydrolase, virus dsRNA, molecular motor, packaging ATPase, hexameric helicase; HET: ADP; 1.80A {Pseudomonas phage PHI12} PDB: 2vhq_A* 1w44_A* 1w46_A* 1w47_A* 1w48_A* 1w49_A* 1w4a_A* 1w4b_A* 1w4c_A 2vht_A* 2vhu_A* 2vhc_A*

Probab=96.30  E-value=0.0033  Score=62.82  Aligned_cols=34  Identities=32%  Similarity=0.357  Sum_probs=26.4

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEe
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTV  226 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~  226 (695)
                      .+++.|+|++|+|||+||.+++..    ...  .++|+++
T Consensus       123 gsviLI~GpPGsGKTtLAlqlA~~----~G~--~VlyIs~  156 (331)
T 2vhj_A          123 SGMVIVTGKGNSGKTPLVHALGEA----LGG--KDKYATV  156 (331)
T ss_dssp             SEEEEEECSCSSSHHHHHHHHHHH----HHT--TSCCEEE
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHh----CCC--CEEEEEe
Confidence            467889999999999999999873    112  2558887

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=96.30  E-value=0.013  Score=58.04  Aligned_cols=43  Identities=23%  Similarity=0.314  Sum_probs=31.3

Q ss_pred             CCCCCcchHHHHHHHHH----c---------CCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          167 ISPGLDVPLKELKMELF----K---------DGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~----~---------~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+.|.++.+++|.+.+.    .         .-.+=+.|+|++|+||||||+.++.
T Consensus        11 di~g~~~~~~~l~~~i~~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtLakala~   66 (274)
T 2x8a_A           11 DIGALEDIREELTMAILAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAKAVAN   66 (274)
T ss_dssp             -CCHHHHHHHHHHHHHTHHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHHHHHHHH
T ss_pred             HhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHHHHHHHH
Confidence            45777777777766542    1         1122399999999999999999987

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=96.29  E-value=0.0089  Score=60.82  Aligned_cols=58  Identities=19%  Similarity=0.241  Sum_probs=40.4

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccc---------cCC----CcEEEEEeCCCCCHHHHHHHHHHhcCC
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQG---------KFK----DDIFYVTVSKNPNVKAIVQKVLHHKGY  245 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~---------~f~----~~~~wv~~~~~~~~~~~~~~i~~~l~~  245 (695)
                      ..++.|+|.+|+|||+||..++.......         ...    ..++|++....++...+... ++.++.
T Consensus        98 g~i~~i~G~~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~~~~~~l~~~-~~~~g~  168 (322)
T 2i1q_A           98 QSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQM-AEHAGI  168 (322)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHHHHHHH-HHHHTC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEECCCCCCHHHHHHH-HHHcCC
Confidence            57999999999999999998876322211         111    45889999988777766543 445543

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=96.23  E-value=0.0054  Score=60.46  Aligned_cols=60  Identities=12%  Similarity=0.040  Sum_probs=40.4

Q ss_pred             CCCCCcchHHHHHHHHH--cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCC
Q 042541          167 ISPGLDVPLKELKMELF--KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKN  229 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~--~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~  229 (695)
                      .++|.+..+.++.+.+.  ......|.|+|.+|+|||++|+.+++.  .... ....+.++++..
T Consensus         7 ~~ig~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKt~la~~i~~~--~~~~-~~~~~~v~~~~~   68 (265)
T 2bjv_A            7 NLLGEANSFLEVLEQVSHLAPLDKPVLIIGERGTGKELIASRLHYL--SSRW-QGPFISLNCAAL   68 (265)
T ss_dssp             ---CCCHHHHHHHHHHHHHTTSCSCEEEECCTTSCHHHHHHHHHHT--STTT-TSCEEEEEGGGS
T ss_pred             cceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHh--cCcc-CCCeEEEecCCC
Confidence            47999999998887765  233456789999999999999999873  2211 112446666654

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=96.19  E-value=0.015  Score=59.58  Aligned_cols=86  Identities=15%  Similarity=0.141  Sum_probs=53.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCC-----CCChHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPE-----FQTDEAAINDLE  261 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~-----~~~~~~~~~~l~  261 (695)
                      ..++.|+|++|+||||||..++..  .... ...++|++....++..     .+++++.....     ....++....+.
T Consensus        61 G~i~~I~GppGsGKSTLal~la~~--~~~~-gg~VlyId~E~s~~~~-----ra~rlgv~~~~l~i~~~~~~e~~l~~~~  132 (356)
T 3hr8_A           61 GRIVEIFGQESSGKTTLALHAIAE--AQKM-GGVAAFIDAEHALDPV-----YAKNLGVDLKSLLISQPDHGEQALEIVD  132 (356)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHH--HHHT-TCCEEEEESSCCCCHH-----HHHHHTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH--HHhc-CCeEEEEecccccchH-----HHHHcCCchhhhhhhhccCHHHHHHHHH
Confidence            479999999999999999998863  2221 2237899888777654     34444433211     122333333333


Q ss_pred             HHHHhcCCCcEEEEEeCCCCC
Q 042541          262 RFFKQMRIEAILLVLDDVWPG  282 (695)
Q Consensus       262 ~~~~~l~~~~~LlVlDdv~~~  282 (695)
                      .+++  ..+.-++|+|.+...
T Consensus       133 ~l~~--~~~~dlvVIDSi~~l  151 (356)
T 3hr8_A          133 ELVR--SGVVDLIVVDSVAAL  151 (356)
T ss_dssp             HHHH--TSCCSEEEEECTTTC
T ss_pred             HHhh--hcCCCeEEehHhhhh
Confidence            3332  245668999997543

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=96.18  E-value=0.014  Score=58.02  Aligned_cols=87  Identities=11%  Similarity=0.158  Sum_probs=54.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhccccccccC-CCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCC-----CChHHH-HHHH
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKDDQVQGKF-KDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEF-----QTDEAA-INDL  260 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f-~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~-----~~~~~~-~~~l  260 (695)
                      .++-|.|++|+|||||+.+++.  .....+ ...++|++..+.++..     .+++++......     .+.++. .. +
T Consensus        29 GiteI~G~pGsGKTtL~Lq~~~--~~~~~g~g~~vlyId~E~s~~~~-----ra~~lGvd~d~llv~~~~~~E~~~l~-i  100 (333)
T 3io5_A           29 GLLILAGPSKSFKSNFGLTMVS--SYMRQYPDAVCLFYDSEFGITPA-----YLRSMGVDPERVIHTPVQSLEQLRID-M  100 (333)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHH--HHHHHCTTCEEEEEESSCCCCHH-----HHHHTTCCGGGEEEEECSBHHHHHHH-H
T ss_pred             CeEEEECCCCCCHHHHHHHHHH--HHHhcCCCceEEEEeccchhhHH-----HHHHhCCCHHHeEEEcCCCHHHHHHH-H
Confidence            4789999999999999988876  333322 3458899998888764     366676543211     122222 22 1


Q ss_pred             HHHHHhc-CCCcEEEEEeCCCCC
Q 042541          261 ERFFKQM-RIEAILLVLDDVWPG  282 (695)
Q Consensus       261 ~~~~~~l-~~~~~LlVlDdv~~~  282 (695)
                      .+.+..+ .++.-++|+|-+...
T Consensus       101 ~~~l~~i~~~~~~lvVIDSI~aL  123 (333)
T 3io5_A          101 VNQLDAIERGEKVVVFIDSLGNL  123 (333)
T ss_dssp             HHHHHTCCTTCCEEEEEECSTTC
T ss_pred             HHHHHHhhccCceEEEEeccccc
Confidence            1222212 467889999998543

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=96.09  E-value=0.0024  Score=60.86  Aligned_cols=111  Identities=11%  Similarity=0.136  Sum_probs=61.0

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFF-  264 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-  264 (695)
                      ...++.|+|..|+||||++..+++  +...+-.. ++.+.......   ....+.+.++...+... .. ....+.+.+ 
T Consensus        11 ~G~i~litG~mGsGKTT~ll~~~~--r~~~~g~k-Vli~~~~~d~r---~~~~i~srlG~~~~~~~-~~-~~~~i~~~i~   82 (223)
T 2b8t_A           11 IGWIEFITGPMFAGKTAELIRRLH--RLEYADVK-YLVFKPKIDTR---SIRNIQSRTGTSLPSVE-VE-SAPEILNYIM   82 (223)
T ss_dssp             CCEEEEEECSTTSCHHHHHHHHHH--HHHHTTCC-EEEEEECCCGG---GCSSCCCCCCCSSCCEE-ES-STHHHHHHHH
T ss_pred             CcEEEEEECCCCCcHHHHHHHHHH--HHHhcCCE-EEEEEeccCch---HHHHHHHhcCCCccccc-cC-CHHHHHHHHH
Confidence            357899999999999999988877  44333222 55555443221   22244555554322211 00 112233333 


Q ss_pred             HhcCC-CcEEEEEeCCCCCChHH---HhhhccCCCCCEEEEEcCCC
Q 042541          265 KQMRI-EAILLVLDDVWPGSESL---LQKLGFQLPDYKILVTSRSE  306 (695)
Q Consensus       265 ~~l~~-~~~LlVlDdv~~~~~~~---~~~l~~~~~gs~iivTtR~~  306 (695)
                      +.+.+ +.-+||+|.+.......   +..+..  .|..||+|-+..
T Consensus        83 ~~~~~~~~dvViIDEaQ~l~~~~ve~l~~L~~--~gi~Vil~Gl~~  126 (223)
T 2b8t_A           83 SNSFNDETKVIGIDEVQFFDDRICEVANILAE--NGFVVIISGLDK  126 (223)
T ss_dssp             STTSCTTCCEEEECSGGGSCTHHHHHHHHHHH--TTCEEEEECCSB
T ss_pred             HHhhCCCCCEEEEecCccCcHHHHHHHHHHHh--CCCeEEEEeccc
Confidence            22333 34599999986554332   333322  378899988854

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=96.08  E-value=0.022  Score=54.51  Aligned_cols=47  Identities=23%  Similarity=0.354  Sum_probs=31.5

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQK  238 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~  238 (695)
                      ..+++|+|++|+|||||++.++..  .... ...++|+....  ....+...
T Consensus        23 G~~~~i~G~~GsGKTtl~~~l~~~--~~~~-~~~v~~~~~~~--~~~~~~~~   69 (235)
T 2w0m_A           23 GFFIALTGEPGTGKTIFSLHFIAK--GLRD-GDPCIYVTTEE--SRDSIIRQ   69 (235)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHH--HHHH-TCCEEEEESSS--CHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHH--HHHC-CCeEEEEEccc--CHHHHHHH
Confidence            478999999999999999998853  2111 22377776544  34444443

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=96.00  E-value=0.0042  Score=72.21  Aligned_cols=43  Identities=21%  Similarity=0.281  Sum_probs=35.6

Q ss_pred             CCCCCcchHHHHHHHHHcC---------CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          167 ISPGLDVPLKELKMELFKD---------GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~~~---------~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .++|.+..++.+...+...         ....+.|+|+.|+|||++|+.+++
T Consensus       559 ~viG~~~a~~~l~~~i~~~~~g~~~~~~p~~~vLl~Gp~GtGKT~lA~~la~  610 (854)
T 1qvr_A          559 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAA  610 (854)
T ss_dssp             HSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHH
T ss_pred             ccCCcHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCCHHHHHHHHHH
Confidence            4799999999888877621         125789999999999999999987

>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus}

Probab=95.93  E-value=0.066  Score=56.25  Aligned_cols=24  Identities=29%  Similarity=0.451  Sum_probs=21.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+.+|.++|.+|+||||++..++.
T Consensus        99 ~p~vIlivG~~G~GKTTt~~kLA~  122 (443)
T 3dm5_A           99 KPTILLMVGIQGSGKTTTVAKLAR  122 (443)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHH
Confidence            368999999999999999988876

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=95.83  E-value=0.0066  Score=57.07  Aligned_cols=39  Identities=26%  Similarity=0.330  Sum_probs=31.4

Q ss_pred             CcchHHHHHHHHHc---CCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          171 LDVPLKELKMELFK---DGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       171 r~~~~~~l~~~L~~---~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      |+..++++.+.+..   ....+|+|+|+.|+||||+++.+..
T Consensus         3 ~~~~~~~l~~~~~~~~~~~~~~i~i~G~~GsGKstl~~~l~~   44 (201)
T 1rz3_A            3 LRDRIDFLCKTILAIKTAGRLVLGIDGLSRSGKTTLANQLSQ   44 (201)
T ss_dssp             HHHHHHHHHHHHHTSCCSSSEEEEEEECTTSSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            45567777777763   3468999999999999999998876

>1sky_E F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alpha3BETA3 SUBC F1-ATPase, hydrolase; 3.20A {Bacillus SP} SCOP: a.69.1.1 b.49.1.1 c.37.1.11

Probab=95.76  E-value=0.02  Score=60.37  Aligned_cols=101  Identities=14%  Similarity=0.125  Sum_probs=56.4

Q ss_pred             HHHHHH-cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC-CHHHHHHHHHHhcCC-------CCC
Q 042541          178 LKMELF-KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKGY-------PVP  248 (695)
Q Consensus       178 l~~~L~-~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~~-------~~~  248 (695)
                      .++.|. -...+.++|+|.+|+|||||+..+...  ....+..-++++-+++.. ...++..++...-..       ...
T Consensus       141 ~ID~L~pi~kGq~~~i~G~sGvGKTtL~~~l~~~--~~~~~~~i~V~~~iGerttev~el~~~l~~~~~l~~tvvv~~~~  218 (473)
T 1sky_E          141 VVDLLAPYIKGGKIGLFGGAGVGKTVLIQELIHN--IAQEHGGISVFAGVGERTREGNDLYHEMKDSGVISKTAMVFGQM  218 (473)
T ss_dssp             HHHHHSCEETTCEEEEECCSSSCHHHHHHHHHHH--HHHHTCCCEEEEEESSCHHHHHHHHHHHHHTSGGGGEEEEEECT
T ss_pred             HHHHHhhhccCCEEEEECCCCCCccHHHHHHHhh--hhhccCcEEEEeeeccCchHHHHHHHHhhhcCCcceeEEEEEcC
Confidence            345554 122356899999999999999998873  332233224566676654 345555555443000       000


Q ss_pred             CCCChHHH-----HHHHHHHHHhcCCCcEEEEEeCCC
Q 042541          249 EFQTDEAA-----INDLERFFKQMRIEAILLVLDDVW  280 (695)
Q Consensus       249 ~~~~~~~~-----~~~l~~~~~~l~~~~~LlVlDdv~  280 (695)
                      ........     .-.+.+.+...+++++|+++||+.
T Consensus       219 ~d~pg~r~~~~~~~ltiAEyFrd~~G~~VLl~~D~it  255 (473)
T 1sky_E          219 NEPPGARMRVALTGLTMAEYFRDEQGQDGLLFIDNIF  255 (473)
T ss_dssp             TSCHHHHHHHHHHHHHHHHHHHHHSCCEEEEEEECTH
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHhcCCcEEEEeccHH
Confidence            11111111     113444443336899999999983

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=95.68  E-value=0.031  Score=57.58  Aligned_cols=84  Identities=18%  Similarity=0.184  Sum_probs=50.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCC-----CCChHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPE-----FQTDEAAINDLE  261 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~-----~~~~~~~~~~l~  261 (695)
                      ..++.|+|.+|+||||||.+++..  .... ...++|++....++..     ..+.++.....     ....++..+.+.
T Consensus        74 G~li~I~G~pGsGKTtlal~la~~--~~~~-g~~vlyi~~E~s~~~~-----~a~~~g~d~~~l~i~~~~~~e~~l~~l~  145 (366)
T 1xp8_A           74 GRITEIYGPESGGKTTLALAIVAQ--AQKA-GGTCAFIDAEHALDPV-----YARALGVNTDELLVSQPDNGEQALEIME  145 (366)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHH--HHHT-TCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             CcEEEEEcCCCCChHHHHHHHHHH--HHHC-CCeEEEEECCCChhHH-----HHHHcCCCHHHceeecCCcHHHHHHHHH
Confidence            468999999999999999888763  2211 2248899998877654     24445432110     112233333333


Q ss_pred             HHHHhcCCCcEEEEEeCCC
Q 042541          262 RFFKQMRIEAILLVLDDVW  280 (695)
Q Consensus       262 ~~~~~l~~~~~LlVlDdv~  280 (695)
                      .+.+  ..+.-+||+|.+.
T Consensus       146 ~l~~--~~~~~lVVIDsl~  162 (366)
T 1xp8_A          146 LLVR--SGAIDVVVVDSVA  162 (366)
T ss_dssp             HHHT--TTCCSEEEEECTT
T ss_pred             HHHh--cCCCCEEEEeChH
Confidence            2221  2456699999974

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=95.66  E-value=0.029  Score=57.52  Aligned_cols=85  Identities=16%  Similarity=0.189  Sum_probs=51.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCC-----CCChHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPE-----FQTDEAAINDLE  261 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~-----~~~~~~~~~~l~  261 (695)
                      ..++.|+|++|+||||||.+++..  .... ...++|++....++..     ..+.++.....     ..+.++....+.
T Consensus        61 G~iv~I~G~pGsGKTtLal~la~~--~~~~-g~~vlyi~~E~~~~~~-----~a~~lG~~~~~l~i~~~~~~e~~l~~~~  132 (349)
T 2zr9_A           61 GRVIEIYGPESSGKTTVALHAVAN--AQAA-GGIAAFIDAEHALDPE-----YAKKLGVDTDSLLVSQPDTGEQALEIAD  132 (349)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHH--HHHT-TCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH--HHhC-CCeEEEEECCCCcCHH-----HHHHcCCCHHHeEEecCCCHHHHHHHHH
Confidence            579999999999999999988763  2221 2348899998777653     24445533211     112222222222


Q ss_pred             HHHHhcCCCcEEEEEeCCCC
Q 042541          262 RFFKQMRIEAILLVLDDVWP  281 (695)
Q Consensus       262 ~~~~~l~~~~~LlVlDdv~~  281 (695)
                      .+..  ..+.-+||+|.+..
T Consensus       133 ~l~~--~~~~~lIVIDsl~~  150 (349)
T 2zr9_A          133 MLVR--SGALDIIVIDSVAA  150 (349)
T ss_dssp             HHHT--TTCCSEEEEECGGG
T ss_pred             HHHh--cCCCCEEEEcChHh
Confidence            2221  34567999999743

>1u94_A RECA protein, recombinase A; homologous recombination, ATPase, DNA repair, DNA binding protein; 1.90A {Escherichia coli} SCOP: c.37.1.11 d.48.1.1 PDB: 1u98_A 1u99_A 1xms_A* 1xmv_A* 2rec_A 2reb_A 1n03_A* 1rea_A 1aa3_A

Probab=95.62  E-value=0.025  Score=58.12  Aligned_cols=84  Identities=17%  Similarity=0.203  Sum_probs=50.4

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCC-----CCChHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPE-----FQTDEAAINDLE  261 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~-----~~~~~~~~~~l~  261 (695)
                      ..++.|.|.+|+||||||.+++..  .... ...++|++....++...     ...++.....     ....++..+.+.
T Consensus        63 G~ii~I~G~pGsGKTtLal~la~~--~~~~-g~~vlyid~E~s~~~~~-----a~~~g~~~~~l~i~~~~~~e~~~~~~~  134 (356)
T 1u94_A           63 GRIVEIYGPESSGKTTLTLQVIAA--AQRE-GKTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEICD  134 (356)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHH--HHHT-TCCEEEEESSCCCCHHH-----HHHTTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH--HHHC-CCeEEEEeCCCCccHHH-----HHHcCCChhheeeeCCCCHHHHHHHHH
Confidence            579999999999999999988763  2221 22488999988776442     3445432211     012222222232


Q ss_pred             HHHHhcCCCcEEEEEeCCC
Q 042541          262 RFFKQMRIEAILLVLDDVW  280 (695)
Q Consensus       262 ~~~~~l~~~~~LlVlDdv~  280 (695)
                      .+.+  ..+.-+||+|.+.
T Consensus       135 ~l~~--~~~~~lVVIDsl~  151 (356)
T 1u94_A          135 ALAR--SGAVDVIVVDSVA  151 (356)
T ss_dssp             HHHH--HTCCSEEEEECGG
T ss_pred             HHHh--ccCCCEEEEcCHH
Confidence            2222  2456699999974

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=95.56  E-value=0.022  Score=57.08  Aligned_cols=39  Identities=23%  Similarity=0.260  Sum_probs=28.5

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeC
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVS  227 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~  227 (695)
                      ...+|.|+|++|+||||++..++..  .... ...+.++...
T Consensus       103 ~~~vi~ivG~~GsGKTTl~~~LA~~--l~~~-g~kV~lv~~D  141 (306)
T 1vma_A          103 PPFVIMVVGVNGTGKTTSCGKLAKM--FVDE-GKSVVLAAAD  141 (306)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHH--HHHT-TCCEEEEEEC
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHHH--HHhc-CCEEEEEccc
Confidence            3579999999999999999998873  3222 2336666654

>4a74_A DNA repair and recombination protein RADA; hydrolase, recombinase; HET: DNA ANP; 1.48A {Pyrococcus furiosus} PDB: 4a6x_A* 4a6p_A* 4a7o_A*

Probab=95.53  E-value=0.044  Score=52.35  Aligned_cols=47  Identities=19%  Similarity=0.271  Sum_probs=32.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccc---cccCCCcEEEEEeCCCCCHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQV---QGKFKDDIFYVTVSKNPNVK  233 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~---~~~f~~~~~wv~~~~~~~~~  233 (695)
                      ..+++|+|+.|+|||||++.++.....   ......+++|++-.......
T Consensus        25 G~~~~l~G~nGsGKSTll~~l~g~~~~~~~~g~~~~~~i~~~~~~~~~~~   74 (231)
T 4a74_A           25 QAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPE   74 (231)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCEEEEEECCCCCCHH
Confidence            479999999999999999998752111   11234457788876554433

>1jr3_D DNA polymerase III, delta subunit; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1jqj_C* 1xxh_A* 1xxi_A* 3glf_A* 3glg_A* 3glh_A* 3gli_A*

Probab=95.48  E-value=0.18  Score=51.47  Aligned_cols=159  Identities=13%  Similarity=0.013  Sum_probs=95.9

Q ss_pred             HHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHH
Q 042541          177 ELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAA  256 (695)
Q Consensus       177 ~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~  256 (695)
                      ++.+.|...-.++..++|+.|.||++.+..+.... ....|+. ...+.+....++.++...+-.               
T Consensus         8 ~l~~~l~~~~~~~yl~~G~e~~~~~~~~~~l~~~~-~~~~~~~-~~~~~~~~~~~~~~l~~~~~~---------------   70 (343)
T 1jr3_D            8 QLRAQLNEGLRAAYLLLGNDPLLLQESQDAVRQVA-AAQGFEE-HHTFSIDPNTDWNAIFSLCQA---------------   70 (343)
T ss_dssp             THHHHHHHCCCSEEEEEESCHHHHHHHHHHHHHHH-HHHTCCE-EEEEECCTTCCHHHHHHHHHH---------------
T ss_pred             HHHHHHhcCCCcEEEEECCcHHHHHHHHHHHHHHH-HhCCCCe-eEEEEecCCCCHHHHHHHhcC---------------
Confidence            34444543446799999999999999998887621 1123432 112233333333333222110               


Q ss_pred             HHHHHHHHHhcCCCcEEEEEeCCCC-CCh----HHHhhhccCCCCCEEEEEcCCC-C-----------CCCCCeEecCCC
Q 042541          257 INDLERFFKQMRIEAILLVLDDVWP-GSE----SLLQKLGFQLPDYKILVTSRSE-F-----------PQFGSVHYLKPL  319 (695)
Q Consensus       257 ~~~l~~~~~~l~~~~~LlVlDdv~~-~~~----~~~~~l~~~~~gs~iivTtR~~-~-----------~~~~~~~~l~~L  319 (695)
                              ..+-+++-++|+|++.. ...    .++..+....+++.+|+++... .           ...+..++..++
T Consensus        71 --------~plf~~~kvvii~~~~~kl~~~~~~aLl~~le~p~~~~~~il~~~~~~~~~~~~k~~~~i~sr~~~~~~~~l  142 (343)
T 1jr3_D           71 --------MSLFASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTCQTP  142 (343)
T ss_dssp             --------HHHCCSCEEEEEECCSSCCCTTHHHHHHHHHTTCBTTEEEEEEESCCCTTTTTSHHHHHHTTTCEEEEECCC
T ss_pred             --------cCCccCCeEEEEECCCCCCChHHHHHHHHHHhcCCCCeEEEEEcCCCChhhHhhHHHHHHHhCceEEEeeCC
Confidence                    12246678899999866 332    1444454445577777665431 0           123347899999


Q ss_pred             ChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHH
Q 042541          320 TYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKV  363 (695)
Q Consensus       320 ~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~  363 (695)
                      +.++-...+...+...+.   .-..+.+..+++.++|.+..+..
T Consensus       143 ~~~~l~~~l~~~~~~~g~---~i~~~a~~~l~~~~~gdl~~~~~  183 (343)
T 1jr3_D          143 EQAQLPRWVAARAKQLNL---ELDDAANQVLCYCYEGNLLALAQ  183 (343)
T ss_dssp             CTTHHHHHHHHHHHHTTC---EECHHHHHHHHHSSTTCHHHHHH
T ss_pred             CHHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHhchHHHHHHH
Confidence            999998888776643322   12367788999999998877664

>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase, antibiotic resistance, phosphorylation, mononucleoti binding fold; HET: ATP; 2.50A {Streptomyces venezuelae} SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A* 1qhy_A*

Probab=95.47  E-value=0.0067  Score=55.59  Aligned_cols=22  Identities=23%  Similarity=0.422  Sum_probs=20.5

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+|.|+|++|+||||+|+.+.+
T Consensus         4 ~~i~l~G~~GsGKST~a~~La~   25 (178)
T 1qhx_A            4 RMIILNGGSSAGKSGIVRCLQS   25 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5799999999999999999987

>3ice_A Transcription termination factor RHO; transcription, ATPase, hexamer, helicase, RNA, RECA, OB fold ATP-binding, hydrolase; HET: MSE ADP SPD; 2.80A {Escherichia coli k-12} PDB: 1pv4_A 1pvo_A* 1xpo_A* 1xpr_A* 1xpu_A* 2ht1_A

Probab=95.46  E-value=0.012  Score=60.04  Aligned_cols=101  Identities=13%  Similarity=0.123  Sum_probs=52.7

Q ss_pred             HHHHHHH-cCCceEEEEEcCCCCcHHHHHHHHhccccccc-cCCCcEEEEEeCCCCC-HHHHHHHHHHhcCCCCCCCCCh
Q 042541          177 ELKMELF-KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQG-KFKDDIFYVTVSKNPN-VKAIVQKVLHHKGYPVPEFQTD  253 (695)
Q Consensus       177 ~l~~~L~-~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~-~f~~~~~wv~~~~~~~-~~~~~~~i~~~l~~~~~~~~~~  253 (695)
                      ++++.+. -.....++|+|++|+|||||++.+.+  .+.. +-+..++++-+++... +.++.+.+-..+-....+.+..
T Consensus       163 raID~~~pi~rGQr~~IvG~sG~GKTtLl~~Iar--~i~~~~~~v~~I~~lIGER~~Ev~~~~~~~~~~vV~atadep~~  240 (422)
T 3ice_A          163 RVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQ--SIAYNHPDCVLMVLLIDERPEEVTEMQRLVKGEVVASTFDEPAS  240 (422)
T ss_dssp             HHHHHHSCCBTTCEEEEECCSSSSHHHHHHHHHH--HHHHHCTTSEEEEEEESSCHHHHHHHHTTCSSEEEEECTTSCHH
T ss_pred             eeeeeeeeecCCcEEEEecCCCCChhHHHHHHHH--HHhhcCCCeeEEEEEecCChHHHHHHHHHhCeEEEEeCCCCCHH
Confidence            3445444 33457899999999999999998876  3322 2232345677776542 2333222200010011111111


Q ss_pred             HH-----HHHHHHHHHHhcCCCcEEEEEeCCC
Q 042541          254 EA-----AINDLERFFKQMRIEAILLVLDDVW  280 (695)
Q Consensus       254 ~~-----~~~~l~~~~~~l~~~~~LlVlDdv~  280 (695)
                      ..     ..-.+.+.+.. .++.+|+++||+.
T Consensus       241 ~r~~~a~~alt~AEyfrd-~G~dVLil~DslT  271 (422)
T 3ice_A          241 RHVQVAEMVIEKAKRLVE-HKKDVIILLDSIT  271 (422)
T ss_dssp             HHHHHHHHHHHHHHHHHH-TSCEEEEEEECHH
T ss_pred             HHHHHHHHHHHHHHHHHh-cCCCEEEEEeCch
Confidence            11     11112233322 6999999999983

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=95.45  E-value=0.036  Score=57.77  Aligned_cols=58  Identities=16%  Similarity=0.170  Sum_probs=37.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhcccccc---ccCCCcEEEEEeCCCCCHHHHHHHHHHhcCC
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQ---GKFKDDIFYVTVSKNPNVKAIVQKVLHHKGY  245 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~---~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~  245 (695)
                      ..++.|+|++|+|||||+..++-.....   ..-..+++|++....+....+. .+.+.++.
T Consensus       178 Gei~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~E~~~~~~rl~-~~a~~~gl  238 (400)
T 3lda_A          178 GSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPVRLV-SIAQRFGL  238 (400)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHHH-HHHHHTTC
T ss_pred             CcEEEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEeCCCccCHHHHH-HHHHHcCC
Confidence            4799999999999999999765311111   1123347899887766655443 35555554

>2px0_A Flagellar biosynthesis protein FLHF; SRP GTPase, flagellum, protein transport, biosynthetic protein; HET: GNP; 3.00A {Bacillus subtilis} PDB: 2px3_A* 3syn_A*

Probab=95.38  E-value=0.053  Score=54.12  Aligned_cols=86  Identities=16%  Similarity=0.165  Sum_probs=47.8

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCC-CCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKN-PNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFK  265 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~-~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~  265 (695)
                      ..+++|+|++|+||||++..++..  ....-...+..+..... ....+.+....+..+.+.......    ..+...+.
T Consensus       105 g~vi~lvG~~GsGKTTl~~~LA~~--l~~~~G~~V~lv~~D~~r~~a~eqL~~~~~~~gl~~~~~~~~----~~l~~al~  178 (296)
T 2px0_A          105 SKYIVLFGSTGAGKTTTLAKLAAI--SMLEKHKKIAFITTDTYRIAAVEQLKTYAELLQAPLEVCYTK----EEFQQAKE  178 (296)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHHHH--HHHTTCCCEEEEECCCSSTTHHHHHHHHHTTTTCCCCBCSSH----HHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH--HHHhcCCEEEEEecCcccchHHHHHHHHHHhcCCCeEecCCH----HHHHHHHH
Confidence            579999999999999999988763  32111223666665432 233344444444444332111111    22344444


Q ss_pred             hcCCCcEEEEEeCC
Q 042541          266 QMRIEAILLVLDDV  279 (695)
Q Consensus       266 ~l~~~~~LlVlDdv  279 (695)
                      .+ .+.=++|+|-.
T Consensus       179 ~~-~~~dlvIiDT~  191 (296)
T 2px0_A          179 LF-SEYDHVFVDTA  191 (296)
T ss_dssp             HG-GGSSEEEEECC
T ss_pred             Hh-cCCCEEEEeCC
Confidence            44 44568889954

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=95.33  E-value=0.01  Score=56.13  Aligned_cols=35  Identities=31%  Similarity=0.413  Sum_probs=26.8

Q ss_pred             HHHHHHHHHc--CCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          175 LKELKMELFK--DGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       175 ~~~l~~~L~~--~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +++|.+.+..  ....+|+|+|+.|+|||||++.+..
T Consensus         8 ~~~~~~~~~~~~~~g~~v~I~G~sGsGKSTl~~~l~~   44 (208)
T 3c8u_A            8 CQGVLERLDPRQPGRQLVALSGAPGSGKSTLSNPLAA   44 (208)
T ss_dssp             HHHHHHHSCTTCCSCEEEEEECCTTSCTHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            3444454442  4568999999999999999999876

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=95.31  E-value=0.038  Score=58.32  Aligned_cols=41  Identities=27%  Similarity=0.364  Sum_probs=30.0

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCC
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSK  228 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~  228 (695)
                      ..++|.|+|.+|+||||++..++.  .........+..++...
T Consensus        99 ~~~vI~ivG~~GvGKTT~a~~LA~--~l~~~~G~kVllvd~D~  139 (433)
T 2xxa_A           99 PPAVVLMAGLQGAGKTTSVGKLGK--FLREKHKKKVLVVSADV  139 (433)
T ss_dssp             SSEEEEEECSTTSSHHHHHHHHHH--HHHHTSCCCEEEEECCC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH--HHHHhcCCeEEEEecCC
Confidence            368999999999999999998886  33332233476777753

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=95.25  E-value=0.0089  Score=54.45  Aligned_cols=20  Identities=25%  Similarity=0.497  Sum_probs=18.7

Q ss_pred             eEEEEEcCCCCcHHHHHHHH
Q 042541          188 QFIVVSAPGGYGKTTLVQRL  207 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~  207 (695)
                      .+|+|.|++|+||||+|+.+
T Consensus         2 ~~I~l~G~~GsGKsT~a~~L   21 (179)
T 3lw7_A            2 KVILITGMPGSGKSEFAKLL   21 (179)
T ss_dssp             CEEEEECCTTSCHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHH
Confidence            47999999999999999998

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=95.23  E-value=0.1  Score=52.68  Aligned_cols=52  Identities=17%  Similarity=0.298  Sum_probs=37.6

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHK  243 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l  243 (695)
                      ..++.|.|.+|+||||||..++.+...++   ..++|++..  .+...+...++...
T Consensus        68 G~l~li~G~pG~GKTtl~l~ia~~~a~~g---~~vl~~slE--~s~~~l~~R~~~~~  119 (315)
T 3bh0_A           68 RNFVLIAARPSMGKTAFALKQAKNMSDND---DVVNLHSLE--MGKKENIKRLIVTA  119 (315)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHHHHHTTT---CEEEEEESS--SCHHHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHHcC---CeEEEEECC--CCHHHHHHHHHHHH
Confidence            47999999999999999998876422222   347788776  45677777776553

>3rfe_A Platelet glycoprotein IB beta chain; platelet surface receptor, GPIX, cell adhesion; HET: NAG; 1.25A {Homo sapiens} PDB: 3rez_A*

Probab=95.21  E-value=0.027  Score=48.62  Aligned_cols=35  Identities=11%  Similarity=-0.034  Sum_probs=24.7

Q ss_pred             CCcEEEeccCCCCCcc--cccccccccEEeeccccCC
Q 042541          602 KLKKIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVG  636 (695)
Q Consensus       602 ~L~~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~  636 (695)
                      +|++|+|++|.|+.+|  .+..+++|++|+|++|++.
T Consensus        32 ~l~~L~Ls~N~l~~l~~~~f~~l~~L~~L~L~~NP~~   68 (130)
T 3rfe_A           32 DTTELVLTGNNLTALPPGLLDALPALRTAHLGANPWR   68 (130)
T ss_dssp             TCSEEECTTSCCSSCCTTTGGGCTTCCEEECCSSCCB
T ss_pred             CCCEEECCCCcCCccChhhhhhccccCEEEecCCCee
Confidence            5777777777777777  5666777777777777543

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=95.20  E-value=0.01  Score=60.56  Aligned_cols=142  Identities=14%  Similarity=0.151  Sum_probs=80.9

Q ss_pred             CCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCC
Q 042541          167 ISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYP  246 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~  246 (695)
                      .++|++..++.+...+..+  .-+.++|++|+|||+||+.+.+  ....    ....+.++......++.....  .. .
T Consensus        28 ~i~g~~~~~~~l~~~l~~~--~~vll~G~pGtGKT~la~~la~--~~~~----~~~~i~~~~~~~~~~l~g~~~--~~-~   96 (331)
T 2r44_A           28 VVVGQKYMINRLLIGICTG--GHILLEGVPGLAKTLSVNTLAK--TMDL----DFHRIQFTPDLLPSDLIGTMI--YN-Q   96 (331)
T ss_dssp             TCCSCHHHHHHHHHHHHHT--CCEEEESCCCHHHHHHHHHHHH--HTTC----CEEEEECCTTCCHHHHHEEEE--EE-T
T ss_pred             ceeCcHHHHHHHHHHHHcC--CeEEEECCCCCcHHHHHHHHHH--HhCC----CeEEEecCCCCChhhcCCcee--ec-C
Confidence            5799999998888887764  3588999999999999999987  3322    234555544444443321110  00 0


Q ss_pred             CCCCCChHHHHHHHHHHHHhcC-C--CcEEEEEeCCCCCChHHH----hhhcc-----------CCCCCEEEEEcCCCC-
Q 042541          247 VPEFQTDEAAINDLERFFKQMR-I--EAILLVLDDVWPGSESLL----QKLGF-----------QLPDYKILVTSRSEF-  307 (695)
Q Consensus       247 ~~~~~~~~~~~~~l~~~~~~l~-~--~~~LlVlDdv~~~~~~~~----~~l~~-----------~~~gs~iivTtR~~~-  307 (695)
                      ...  .           + ... +  ...++++|+++.......    ..+..           ......||.|+.... 
T Consensus        97 ~~~--~-----------~-~~~~g~l~~~vl~iDEi~~~~~~~~~~Ll~~l~~~~~~~~g~~~~~~~~~~viat~np~~~  162 (331)
T 2r44_A           97 HKG--N-----------F-EVKKGPVFSNFILADEVNRSPAKVQSALLECMQEKQVTIGDTTYPLDNPFLVLATQNPVEQ  162 (331)
T ss_dssp             TTT--E-----------E-EEEECTTCSSEEEEETGGGSCHHHHHHHHHHHHHSEEEETTEEEECCSSCEEEEEECTTCC
T ss_pred             CCC--c-----------e-EeccCcccccEEEEEccccCCHHHHHHHHHHHhcCceeeCCEEEECCCCEEEEEecCCCcc
Confidence            000  0           0 001 1  135899999977664322    22211           112345555655221 


Q ss_pred             -----------CCCCCeEecCCCChHHHHHHHHHhcc
Q 042541          308 -----------PQFGSVHYLKPLTYEAARTLFLHSAN  333 (695)
Q Consensus       308 -----------~~~~~~~~l~~L~~~ea~~Lf~~~~~  333 (695)
                                 ......+.+++.+.++-.+++.....
T Consensus       163 ~~~~~l~~~l~~Rf~~~i~i~~p~~~~~~~il~~~~~  199 (331)
T 2r44_A          163 EGTYPLPEAQVDRFMMKIHLTYLDKESELEVMRRVSN  199 (331)
T ss_dssp             SCCCCCCHHHHTTSSEEEECCCCCHHHHHHHHHHHHC
T ss_pred             cCcccCCHHHHhheeEEEEcCCCCHHHHHHHHHhccc
Confidence                       01112578888888888888877654

>3kb2_A SPBC2 prophage-derived uncharacterized protein YORR; alpha-beta protein., structural genomics, PSI-2, protein structure initiative; HET: G3D; 2.20A {Bacillus subtilis} SCOP: c.37.1.1 PDB: 2axp_A*

Probab=95.19  E-value=0.0092  Score=54.23  Aligned_cols=22  Identities=27%  Similarity=0.463  Sum_probs=20.2

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+|+|.|+.|+||||+|+.+..
T Consensus         2 ~~i~l~G~~GsGKsT~~~~L~~   23 (173)
T 3kb2_A            2 TLIILEGPDCCFKSTVAAKLSK   23 (173)
T ss_dssp             CEEEEECSSSSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            4789999999999999999876

>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural genomics, PSI, protein struc initiative; 3.20A {Agrobacterium tumefaciens str} SCOP: c.37.1.25

Probab=95.15  E-value=0.012  Score=54.65  Aligned_cols=24  Identities=29%  Similarity=0.577  Sum_probs=21.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+++|+|++|+|||||++.+..
T Consensus         8 ~g~~i~l~G~~GsGKSTl~~~La~   31 (191)
T 1zp6_A            8 GGNILLLSGHPGSGKSTIAEALAN   31 (191)
T ss_dssp             TTEEEEEEECTTSCHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHh
Confidence            347899999999999999999986

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=95.09  E-value=0.012  Score=54.03  Aligned_cols=22  Identities=23%  Similarity=0.344  Sum_probs=20.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+|.|.|++|+||||+|+.+..
T Consensus         3 ~~I~i~G~~GsGKST~a~~L~~   24 (181)
T 1ly1_A            3 KIILTIGCPGSGKSTWAREFIA   24 (181)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEecCCCCCHHHHHHHHHh
Confidence            5799999999999999999876

>3uie_A Adenylyl-sulfate kinase 1, chloroplastic; rossmann fold, transferase-transferase complex; HET: ADX ANP; 1.79A {Arabidopsis thaliana} SCOP: c.37.1.0 PDB: 4fxp_A*

Probab=95.08  E-value=0.014  Score=54.74  Aligned_cols=27  Identities=30%  Similarity=0.337  Sum_probs=23.7

Q ss_pred             HcCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          183 FKDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       183 ~~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ......+|+|+|++|+||||+++.+..
T Consensus        21 ~~~~g~~i~l~G~sGsGKSTl~~~La~   47 (200)
T 3uie_A           21 LDQKGCVIWVTGLSGSGKSTLACALNQ   47 (200)
T ss_dssp             HTSCCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             cCCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            345568999999999999999999987

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=95.07  E-value=0.011  Score=54.47  Aligned_cols=23  Identities=22%  Similarity=0.410  Sum_probs=21.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .++++|+|+.|+|||||++.+..
T Consensus         5 g~~i~i~GpsGsGKSTL~~~L~~   27 (180)
T 1kgd_A            5 RKTLVLLGAHGVGRRHIKNTLIT   27 (180)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHh
Confidence            36899999999999999999876

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=95.06  E-value=0.018  Score=61.93  Aligned_cols=41  Identities=12%  Similarity=0.117  Sum_probs=35.5

Q ss_pred             CCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          167 ISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .++|.+..++.+...+..+  .-|.|+|++|+|||+||+.+++
T Consensus        23 ~ivGq~~~i~~l~~al~~~--~~VLL~GpPGtGKT~LAraLa~   63 (500)
T 3nbx_X           23 GLYERSHAIRLCLLAALSG--ESVFLLGPPGIAKSLIARRLKF   63 (500)
T ss_dssp             TCSSCHHHHHHHHHHHHHT--CEEEEECCSSSSHHHHHHHGGG
T ss_pred             hhHHHHHHHHHHHHHHhcC--CeeEeecCchHHHHHHHHHHHH
Confidence            4699999998888777655  4688999999999999999987

>2ck3_D ATP synthase subunit beta\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1cow_D* 1bmf_D* 1e1q_D* 1e1r_D* 1efr_D* 1e79_D* 1h8h_D* 1ohh_D* 1qo1_D 1w0j_D* 1w0k_D* 1h8e_D* 2jdi_D* 2jiz_D* 2jj1_D* 2jj2_D* 2v7q_D* 2wss_D* 2w6j_D 2w6e_D ...

Probab=95.03  E-value=0.14  Score=53.88  Aligned_cols=102  Identities=13%  Similarity=0.145  Sum_probs=61.2

Q ss_pred             HHHHHHH-cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC-CHHHHHHHHHHhcCCC--------
Q 042541          177 ELKMELF-KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKGYP--------  246 (695)
Q Consensus       177 ~l~~~L~-~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~~~--------  246 (695)
                      ++++.|. -...+-++|.|.+|+|||+|+..+.+.. .+.+-+. ++++-+++.. ...++.+++...=...        
T Consensus       142 r~ID~l~pigkGQr~~Ifgg~G~GKT~L~~~i~~~~-~~~~~~v-~V~~~iGER~rEv~e~~~~~~~~~~l~~~~~~~rt  219 (482)
T 2ck3_D          142 KVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNV-AKAHGGY-SVFAGVGERTREGNDLYHEMIESGVINLKDATSKV  219 (482)
T ss_dssp             HHHHHHSCEETTCEEEEEECTTSSHHHHHHHHHHHT-TTTCSSE-EEEEEESCCHHHHHHHHHHHHHHTSSCSSSSCCCE
T ss_pred             EEEecccccccCCeeeeecCCCCChHHHHHHHHHhh-HhhCCCE-EEEEECCCcchHHHHHHHHhhhccccccccCCceE
Confidence            4556555 3345789999999999999999988731 1222233 5577777665 4667777777652211        


Q ss_pred             -----CCCCCCh-----HHHHHHHHHHHHhcCCCcEEEEEeCCC
Q 042541          247 -----VPEFQTD-----EAAINDLERFFKQMRIEAILLVLDDVW  280 (695)
Q Consensus       247 -----~~~~~~~-----~~~~~~l~~~~~~l~~~~~LlVlDdv~  280 (695)
                           ..+.+..     ....-.+.+.+..-+++.+||++||+.
T Consensus       220 vvV~~t~d~p~~~r~~~~~~a~tiAEyfrd~~G~dVLll~Dsit  263 (482)
T 2ck3_D          220 ALVYGQMNEPPGARARVALTGLTVAEYFRDQEGQDVLLFIDNIF  263 (482)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHHHHHHHHTTCSCEEEEEECTH
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHHHHHHhcCCcEEEEeccHH
Confidence                 0111111     111223344443336899999999983

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=95.02  E-value=0.016  Score=54.93  Aligned_cols=24  Identities=29%  Similarity=0.373  Sum_probs=21.9

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..++|.|.|++|+||||.|+.+++
T Consensus        28 k~kiI~llGpPGsGKgTqa~~L~~   51 (217)
T 3umf_A           28 KAKVIFVLGGPGSGKGTQCEKLVQ   51 (217)
T ss_dssp             SCEEEEEECCTTCCHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            468999999999999999998876

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=95.01  E-value=0.04  Score=57.83  Aligned_cols=93  Identities=13%  Similarity=0.050  Sum_probs=49.2

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC-CHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHH
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFF  264 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~  264 (695)
                      ...+|.++|++|+||||++..++..  .... ...+..++..... ...+-+.......+.+........+........+
T Consensus        96 ~~~vI~lvG~~GsGKTTt~~kLA~~--l~~~-G~kVllv~~D~~r~~a~eqL~~~~~~~gv~~~~~~~~~dp~~i~~~al  172 (433)
T 3kl4_A           96 LPFIIMLVGVQGSGKTTTAGKLAYF--YKKR-GYKVGLVAADVYRPAAYDQLLQLGNQIGVQVYGEPNNQNPIEIAKKGV  172 (433)
T ss_dssp             SSEEEEECCCTTSCHHHHHHHHHHH--HHHT-TCCEEEEEECCSCHHHHHHHHHHHHTTTCCEECCTTCSCHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH--HHHc-CCeEEEEecCccchhHHHHHHHHHHhcCCceeeccccCCHHHHHHHHH
Confidence            3589999999999999999988863  3222 2336566654321 2333344444555443221111111222223334


Q ss_pred             HhcC-CCcEEEEEeCCCC
Q 042541          265 KQMR-IEAILLVLDDVWP  281 (695)
Q Consensus       265 ~~l~-~~~~LlVlDdv~~  281 (695)
                      .... ...=++|+|-...
T Consensus       173 ~~a~~~~~DvvIIDTaGr  190 (433)
T 3kl4_A          173 DIFVKNKMDIIIVDTAGR  190 (433)
T ss_dssp             HHTTTTTCSEEEEEECCC
T ss_pred             HHHHhcCCCEEEEECCCC
Confidence            3333 3344667887653

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G

Probab=94.98  E-value=0.0097  Score=61.23  Aligned_cols=44  Identities=23%  Similarity=0.184  Sum_probs=32.9

Q ss_pred             CCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          166 VISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +.++|.+..++.+...+..+...-|.|+|++|+|||++|+.+++
T Consensus        24 ~~i~G~~~~~~~l~~~~~~~~~~~vLl~G~~GtGKT~la~~la~   67 (350)
T 1g8p_A           24 SAIVGQEDMKLALLLTAVDPGIGGVLVFGDRGTGKSTAVRALAA   67 (350)
T ss_dssp             GGSCSCHHHHHHHHHHHHCGGGCCEEEECCGGGCTTHHHHHHHH
T ss_pred             hhccChHHHHHHHHHHhhCCCCceEEEECCCCccHHHHHHHHHH
Confidence            45799888666554444433334589999999999999999987

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=94.96  E-value=0.012  Score=55.20  Aligned_cols=23  Identities=30%  Similarity=0.304  Sum_probs=21.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+|.|+|++|+||||+++.+..
T Consensus        25 ~~~i~l~G~~GsGKsTl~~~La~   47 (199)
T 3vaa_A           25 MVRIFLTGYMGAGKTTLGKAFAR   47 (199)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHH
Confidence            46899999999999999999986

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A*

Probab=94.88  E-value=0.03  Score=54.66  Aligned_cols=164  Identities=12%  Similarity=0.111  Sum_probs=84.4

Q ss_pred             CCCCCCcchHHHHHHHHH---cC---------CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHH
Q 042541          166 VISPGLDVPLKELKMELF---KD---------GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVK  233 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~---~~---------~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~  233 (695)
                      +.++|.+....++.+...   ..         -.+-+.|+|++|+|||||++.++..  ..    .+.+.++..      
T Consensus        16 ~~i~g~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~g~ll~G~~G~GKTtl~~~i~~~--~~----~~~i~~~~~------   83 (254)
T 1ixz_A           16 KDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGE--AR----VPFITASGS------   83 (254)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHH--TT----CCEEEEEHH------
T ss_pred             HHhCCcHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCCCCHHHHHHHHHHH--hC----CCEEEeeHH------
Confidence            457898876666654432   10         0223899999999999999999873  22    223344321      


Q ss_pred             HHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhc-CCCcEEEEEeCCCCC-----------Ch-------HHHhhhccCC
Q 042541          234 AIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQM-RIEAILLVLDDVWPG-----------SE-------SLLQKLGFQL  294 (695)
Q Consensus       234 ~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l-~~~~~LlVlDdv~~~-----------~~-------~~~~~l~~~~  294 (695)
                      +    +....         .......+..+++.. ...+.++++|++...           ..       .++..+....
T Consensus        84 ~----~~~~~---------~~~~~~~i~~~~~~~~~~~~~i~~~Deid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~g~~  150 (254)
T 1ixz_A           84 D----FVEMF---------VGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFE  150 (254)
T ss_dssp             H----HHHSC---------TTHHHHHHHHHHHHHTTSSSEEEEEETHHHHHC---------CHHHHHHHHHHHHHHHTCC
T ss_pred             H----HHHHH---------hhHHHHHHHHHHHHHHhcCCeEEEehhhhhhhcccCccccccchHHHHHHHHHHHHHhCCC
Confidence            1    11111         001123344444333 345789999998311           11       1122222111


Q ss_pred             C-CCEEEE-EcCCCC------C---CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCch
Q 042541          295 P-DYKILV-TSRSEF------P---QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCP  358 (695)
Q Consensus       295 ~-gs~iiv-TtR~~~------~---~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~P  358 (695)
                      . ...+++ ||....      .   .....+.++..+.++-.+++...+......    .......|++.+.|.-
T Consensus       151 ~~~~~i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~~~~~~----~~~~~~~la~~~~G~~  221 (254)
T 1ixz_A          151 KDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLA----EDVDLALLAKRTPGFV  221 (254)
T ss_dssp             TTCCEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBC----TTCCHHHHHHTCTTCC
T ss_pred             CCCCEEEEEccCCchhCCHHHcCCCcCCeEEeeCCcCHHHHHHHHHHHHcCCCCC----cccCHHHHHHHcCCCC
Confidence            2 223333 444331      1   233467888888888888887655321110    1111445777777653

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=94.87  E-value=0.037  Score=55.31  Aligned_cols=92  Identities=16%  Similarity=0.115  Sum_probs=48.5

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC-CHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFK  265 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~  265 (695)
                      ..+++++|.+|+||||++..++..  .... ...+.+++..... ...+.+....+..+.+.-......+..+.+...++
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~--~~~~-g~~v~l~~~D~~r~~a~~ql~~~~~~~~v~v~~~~~~~~p~~~~~~~l~  174 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYF--YKKK-GFKVGLVGADVYRPAALEQLQQLGQQIGVPVYGEPGEKDVVGIAKRGVE  174 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHH--HHHT-TCCEEEEECCCSSSHHHHHHHHHHHHHTCCEECCTTCCCHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH--HHHC-CCeEEEEecCCCCHHHHHHHHHHhccCCeEEEecCCCCCHHHHHHHHHH
Confidence            578999999999999999988863  3222 2347677765332 23333444455444321111000111122233444


Q ss_pred             hcC-CCcEEEEEeCCCC
Q 042541          266 QMR-IEAILLVLDDVWP  281 (695)
Q Consensus       266 ~l~-~~~~LlVlDdv~~  281 (695)
                      .++ .+-=++|+|-.-.
T Consensus       175 ~~~~~~~D~ViIDTpg~  191 (297)
T 1j8m_F          175 KFLSEKMEIIIVDTAGR  191 (297)
T ss_dssp             HHHHTTCSEEEEECCCS
T ss_pred             HHHhCCCCEEEEeCCCC
Confidence            443 3334788887543

>1ex7_A Guanylate kinase; substrate-induced FIT, domain movement, GMP, ATP, substrate specificity, X-RAY diffraction, transferase; HET: 5GP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1ex6_A* 1gky_A* 3sqk_A 4f4j_A

Probab=94.86  E-value=0.011  Score=54.63  Aligned_cols=22  Identities=45%  Similarity=0.761  Sum_probs=19.9

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +.|.|+|++|+|||||++.+..
T Consensus         2 RpIVi~GPSG~GK~Tl~~~L~~   23 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKKLFA   23 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
Confidence            5688999999999999999876

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=94.86  E-value=0.011  Score=53.84  Aligned_cols=22  Identities=32%  Similarity=0.525  Sum_probs=20.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+|+|+|+.|+||||+++.+..
T Consensus         5 ~~i~l~G~~GsGKSTl~~~La~   26 (173)
T 1kag_A            5 RNIFLVGPMGAGKSTIGRQLAQ   26 (173)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHH
Confidence            5799999999999999999886

>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerizat motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11

Probab=94.86  E-value=0.094  Score=53.71  Aligned_cols=56  Identities=16%  Similarity=0.224  Sum_probs=36.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccC---CCcEEEEEeCCCCCHHHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKF---KDDIFYVTVSKNPNVKAIVQKVLHHK  243 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f---~~~~~wv~~~~~~~~~~~~~~i~~~l  243 (695)
                      ..++.|+|+.|+|||||+..++.........   ...++|++....+....+ ..+.+..
T Consensus       131 G~i~~I~G~~GsGKTTL~~~l~~~~~~~~~~Gg~~G~vi~i~~e~~~~~~~i-~~i~q~~  189 (349)
T 1pzn_A          131 QAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERI-REIAQNR  189 (349)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHHH-HHHHHTT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhccchhcCCCCCeEEEEeCCCCCCHHHH-HHHHHHc
Confidence            5899999999999999999988632111111   234579988766544333 3344443

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=94.81  E-value=0.014  Score=53.92  Aligned_cols=23  Identities=30%  Similarity=0.268  Sum_probs=20.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+.|.|+|+.|+||||+|+.+..
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La~   27 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLAK   27 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            46789999999999999999986

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=94.80  E-value=0.015  Score=54.52  Aligned_cols=25  Identities=28%  Similarity=0.472  Sum_probs=22.0

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ....+|+|+|+.|+|||||++.+..
T Consensus        27 ~~g~~i~l~G~~GsGKSTl~~~L~~   51 (200)
T 4eun_A           27 EPTRHVVVMGVSGSGKTTIAHGVAD   51 (200)
T ss_dssp             -CCCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHH
Confidence            3467999999999999999999986

>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M domain, RNA-binding, signal sequence-binding, helix-turn-helix, protein targeting; 3.20A {Thermus aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB: 2iy3_A

Probab=94.80  E-value=0.033  Score=58.36  Aligned_cols=38  Identities=26%  Similarity=0.322  Sum_probs=27.6

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeC
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVS  227 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~  227 (695)
                      ..+|.|+|++|+||||++..++..  .... ...+..+...
T Consensus        98 ~~vi~i~G~~GsGKTT~~~~LA~~--l~~~-g~~Vllvd~D  135 (425)
T 2ffh_A           98 RNLWFLVGLQGSGKTTTAAKLALY--YKGK-GRRPLLVAAD  135 (425)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHH--HHTT-TCCEEEEECC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH--HHHc-CCeEEEeecc
Confidence            478999999999999999988863  3322 3336666653

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=94.78  E-value=0.022  Score=54.36  Aligned_cols=36  Identities=25%  Similarity=0.254  Sum_probs=28.2

Q ss_pred             HHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhcc
Q 042541          175 LKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       175 ~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      .+.+...+.......|+|+|.+|+|||||+..+...
T Consensus        26 a~~~r~~~~~~~~~~i~ivG~~gvGKTtl~~~l~~~   61 (226)
T 2hf9_A           26 ADKNRKLLNKHGVVAFDFMGAIGSGKTLLIEKLIDN   61 (226)
T ss_dssp             HHHHHHHHHHTTCEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCeEEEEEcCCCCCHHHHHHHHHHH
Confidence            344445455556789999999999999999998873

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=94.73  E-value=0.058  Score=61.14  Aligned_cols=91  Identities=19%  Similarity=0.254  Sum_probs=54.7

Q ss_pred             CCCCCCcchHHHHHHHHHc-------------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCH
Q 042541          166 VISPGLDVPLKELKMELFK-------------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNV  232 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~-------------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~  232 (695)
                      ..+.|.++..++|.+.+.-             ...+-|.++|++|.|||.+|+++++.  ...      -++.++.    
T Consensus       477 ~diggl~~~k~~l~e~v~~p~~~p~~f~~~g~~~~~gvLl~GPPGtGKT~lAkaiA~e--~~~------~f~~v~~----  544 (806)
T 3cf2_A          477 EDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANE--CQA------NFISIKG----  544 (806)
T ss_dssp             TTCCSCHHHHHHHTTTTTTTTTCSGGGSSSCCCCCSCCEEESSTTSSHHHHHHHHHHT--TTC------EEEECCH----
T ss_pred             HHhCCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEecCCCCCchHHHHHHHHH--hCC------ceEEecc----
Confidence            4557777777777666541             11355889999999999999999982  222      2333331    


Q ss_pred             HHHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCC
Q 042541          233 KAIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWP  281 (695)
Q Consensus       233 ~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~  281 (695)
                          .+++....+      ..+   ..++.++ ..-+..+++|++|+++.
T Consensus       545 ----~~l~s~~vG------ese---~~vr~lF~~Ar~~~P~IifiDEiDs  581 (806)
T 3cf2_A          545 ----PELLTMWFG------ESE---ANVREIFDKARQAAPCVLFFDELDS  581 (806)
T ss_dssp             ----HHHHTTTCS------SCH---HHHHHHHHHHHTTCSEEEECSCGGG
T ss_pred             ----chhhccccc------hHH---HHHHHHHHHHHHcCCceeechhhhH
Confidence                122222111      112   3345555 33356789999999853

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=94.71  E-value=0.017  Score=54.52  Aligned_cols=24  Identities=38%  Similarity=0.558  Sum_probs=21.9

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+|+|+|+.|+|||||++.+..
T Consensus         7 ~g~~i~l~GpsGsGKsTl~~~L~~   30 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTVREAVFK   30 (208)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCcEEEEECcCCCCHHHHHHHHHh
Confidence            457899999999999999999986

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=94.70  E-value=0.02  Score=59.33  Aligned_cols=43  Identities=28%  Similarity=0.436  Sum_probs=35.1

Q ss_pred             CCCCCcchHHHHHHHHH-------------c--CCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          167 ISPGLDVPLKELKMELF-------------K--DGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~-------------~--~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .++|.+..++.+...+.             .  .....|.++|++|+|||++|+.+++
T Consensus        16 ~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~la~~ia~   73 (363)
T 3hws_A           16 YVIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLAR   73 (363)
T ss_dssp             HCCSCHHHHHHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHHHHHHHH
T ss_pred             hccCHHHHHHHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHHHHHHHH
Confidence            36999998888888773             0  1246789999999999999999987

>1odf_A YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser2 intergenic region; yeast protein, ATP binding protein; 2.25A {Saccharomyces cerevisiae} SCOP: c.37.1.6

Probab=94.69  E-value=0.024  Score=56.40  Aligned_cols=24  Identities=29%  Similarity=0.421  Sum_probs=21.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+|+|+|..|+||||||+.+..
T Consensus        30 ~~~ii~I~G~sGsGKSTla~~L~~   53 (290)
T 1odf_A           30 CPLFIFFSGPQGSGKSFTSIQIYN   53 (290)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            467999999999999999998876

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=94.66  E-value=0.023  Score=59.17  Aligned_cols=44  Identities=25%  Similarity=0.371  Sum_probs=34.6

Q ss_pred             CCCCCCcchHHHHHHHHH------------------------------cCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          166 VISPGLDVPLKELKMELF------------------------------KDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~------------------------------~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..++|.+..++.|...+.                              ......+.++|++|+|||++|+.+++
T Consensus        21 ~~viGq~~ak~~l~~~~~~~~~~~~~g~~~~~~~~~~~~~p~~~~~~~~~~~~~ill~Gp~GtGKT~la~~la~   94 (376)
T 1um8_A           21 NYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAK   94 (376)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHH
T ss_pred             hHccCcHHHHHHHHHHHHHHHHHHHhhhhhhhccccccccccccccccccCCCCEEEECCCCCCHHHHHHHHHH
Confidence            356899888888877662                              01235688999999999999999987

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=94.60  E-value=0.019  Score=53.86  Aligned_cols=23  Identities=48%  Similarity=0.806  Sum_probs=21.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|+|||||++.+..
T Consensus         7 g~ii~l~Gp~GsGKSTl~~~L~~   29 (205)
T 3tr0_A            7 ANLFIISAPSGAGKTSLVRALVK   29 (205)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CcEEEEECcCCCCHHHHHHHHHh
Confidence            46899999999999999999876

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=94.60  E-value=0.018  Score=52.39  Aligned_cols=23  Identities=26%  Similarity=0.481  Sum_probs=20.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|+|||||++.++.
T Consensus         9 gei~~l~G~nGsGKSTl~~~~~~   31 (171)
T 4gp7_A            9 LSLVVLIGSSGSGKSTFAKKHFK   31 (171)
T ss_dssp             SEEEEEECCTTSCHHHHHHHHSC
T ss_pred             CEEEEEECCCCCCHHHHHHHHcc
Confidence            47899999999999999997653

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=94.58  E-value=0.017  Score=53.46  Aligned_cols=22  Identities=23%  Similarity=0.424  Sum_probs=20.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+|.|.|+.|+||||+|+.+..
T Consensus         2 ~~I~i~G~~GsGKsT~~~~L~~   23 (194)
T 1nks_A            2 KIGIVTGIPGVGKSTVLAKVKE   23 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            4789999999999999999987

>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate hydrolases fold, S genomics, joint center for structural genomics, JCSG; HET: MSE; 1.70A {Chloroflexus aurantiacus}

Probab=94.58  E-value=0.019  Score=53.21  Aligned_cols=23  Identities=39%  Similarity=0.491  Sum_probs=21.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+|.|.|++|+||||+|+.+..
T Consensus         5 ~~~I~l~G~~GsGKST~~~~L~~   27 (193)
T 2rhm_A            5 PALIIVTGHPATGKTTLSQALAT   27 (193)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999876

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=94.53  E-value=0.014  Score=54.69  Aligned_cols=23  Identities=26%  Similarity=0.369  Sum_probs=21.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+|+|.|+.|+||||+|+.+..
T Consensus        18 ~~~I~l~G~~GsGKSTla~~L~~   40 (202)
T 3t61_A           18 PGSIVVMGVSGSGKSSVGEAIAE   40 (202)
T ss_dssp             SSCEEEECSTTSCHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999876

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=94.49  E-value=0.019  Score=52.30  Aligned_cols=23  Identities=17%  Similarity=0.392  Sum_probs=21.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+|+|+|+.|+||||+++.+..
T Consensus         8 g~~i~l~G~~GsGKSTl~~~l~~   30 (175)
T 1knq_A            8 HHIYVLMGVSGSGKSAVASEVAH   30 (175)
T ss_dssp             SEEEEEECSTTSCHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHH
Confidence            46899999999999999999876

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=94.46  E-value=0.024  Score=53.87  Aligned_cols=38  Identities=21%  Similarity=0.232  Sum_probs=29.3

Q ss_pred             chHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhcc
Q 042541          173 VPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       173 ~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      +..+.+...+.....++|+|+|.+|+|||||+..+...
T Consensus        16 ~~~~~~~~~~~~~~~~~i~i~G~~g~GKTTl~~~l~~~   53 (221)
T 2wsm_A           16 RLAEKNREALRESGTVAVNIMGAIGSGKTLLIERTIER   53 (221)
T ss_dssp             HHHHHHHHHHHHHTCEEEEEEECTTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHhhcccCceEEEEEcCCCCCHHHHHHHHHHH
Confidence            34455555555556789999999999999999998873

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=94.44  E-value=0.019  Score=53.14  Aligned_cols=22  Identities=32%  Similarity=0.351  Sum_probs=20.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+|.|.|++|+||||+++.+..
T Consensus         4 ~~I~i~G~~GsGKsT~~~~L~~   25 (192)
T 1kht_A            4 KVVVVTGVPGVGSTTSSQLAMD   25 (192)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5799999999999999999987

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=94.39  E-value=0.032  Score=56.58  Aligned_cols=41  Identities=20%  Similarity=0.316  Sum_probs=30.1

Q ss_pred             CCCcchHHHHHHHHH----cCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          169 PGLDVPLKELKMELF----KDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       169 vGr~~~~~~l~~~L~----~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      |+.+.-.+++.+.+.    .+....|.|+|+.|+||||+++.++.
T Consensus         2 ~~~~~L~~~il~~l~~~i~~g~~~~i~l~G~~G~GKTTl~~~la~   46 (359)
T 2ga8_A            2 VDTHKLADDVLQLLDNRIEDNYRVCVILVGSPGSGKSTIAEELCQ   46 (359)
T ss_dssp             CCHHHHHHHHHHHHHHTTTTCSCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHhccCCeeEEEEECCCCCcHHHHHHHHHH
Confidence            344445566666654    34456799999999999999998876

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=94.39  E-value=0.018  Score=53.14  Aligned_cols=24  Identities=29%  Similarity=0.398  Sum_probs=21.8

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+|.|.|++|+||||+++.+..
T Consensus        12 ~~~~i~l~G~~GsGKsT~~~~L~~   35 (186)
T 2yvu_A           12 KGIVVWLTGLPGSGKTTIATRLAD   35 (186)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHH
Confidence            357899999999999999999987

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=94.39  E-value=0.018  Score=54.20  Aligned_cols=23  Identities=35%  Similarity=0.583  Sum_probs=21.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+|+|+|++|+|||||++.+..
T Consensus        12 ~~~i~l~G~sGsGKsTl~~~L~~   34 (204)
T 2qor_A           12 IPPLVVCGPSGVGKGTLIKKVLS   34 (204)
T ss_dssp             CCCEEEECCTTSCHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            57899999999999999999876

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=94.36  E-value=0.023  Score=53.70  Aligned_cols=24  Identities=33%  Similarity=0.349  Sum_probs=21.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+|+|+|+.|+|||||++.+..
T Consensus         5 ~~~~i~i~G~~GsGKSTl~~~l~~   28 (211)
T 3asz_A            5 KPFVIGIAGGTASGKTTLAQALAR   28 (211)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHH
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHH
Confidence            457899999999999999999876

>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein struct initiative, northeast structural genomics consortium, NESG, function; 2.40A {Bacillus halodurans} SCOP: c.37.1.25

Probab=94.34  E-value=0.022  Score=52.69  Aligned_cols=22  Identities=32%  Similarity=0.718  Sum_probs=20.1

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+++|+|+.|+|||||++.+..
T Consensus         3 ~ii~l~G~~GaGKSTl~~~L~~   24 (189)
T 2bdt_A            3 KLYIITGPAGVGKSTTCKRLAA   24 (189)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHhc
Confidence            5789999999999999999975

>4fs7_A Uncharacterized protein; leucine-rich repeats, protein binding, extracellular protein structural genomics; HET: MSE; 1.19A {Bacteroides ovatus}

Probab=94.33  E-value=0.27  Score=51.30  Aligned_cols=122  Identities=12%  Similarity=0.141  Sum_probs=70.1

Q ss_pred             CCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--cccccccc
Q 042541          548 QGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNHL  625 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L  625 (695)
                      .+..++.+.+..+.. ..-...+..+..+..+.......     .. ..+..+.+|+.+.+.. ++..++  ++.++.+|
T Consensus       251 ~~~~l~~~~~~~~~~-~i~~~~F~~~~~l~~~~~~~~~i-----~~-~~F~~~~~L~~i~l~~-~i~~I~~~aF~~c~~L  322 (394)
T 4fs7_A          251 GCTDLESISIQNNKL-RIGGSLFYNCSGLKKVIYGSVIV-----PE-KTFYGCSSLTEVKLLD-SVKFIGEEAFESCTSL  322 (394)
T ss_dssp             TCSSCCEEEECCTTC-EECSCTTTTCTTCCEEEECSSEE-----CT-TTTTTCTTCCEEEECT-TCCEECTTTTTTCTTC
T ss_pred             ccccceeEEcCCCcc-eeeccccccccccceeccCceee-----cc-cccccccccccccccc-ccceechhhhcCCCCC
Confidence            455555555543311 11122455556666555543211     11 1145666777777754 356666  66677778


Q ss_pred             cEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchh-hcCCCCCceeeccc
Q 042541          626 QKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDG-LCDIVSMEKLRITN  684 (695)
Q Consensus       626 ~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~-i~~L~~L~~L~l~~  684 (695)
                      +.++|..+ ++.+....+.    .+++|+.+.+..  ++..++.. |.++.+|+.+++..
T Consensus       323 ~~i~lp~~-v~~I~~~aF~----~c~~L~~i~lp~--~l~~I~~~aF~~C~~L~~i~lp~  375 (394)
T 4fs7_A          323 VSIDLPYL-VEEIGKRSFR----GCTSLSNINFPL--SLRKIGANAFQGCINLKKVELPK  375 (394)
T ss_dssp             CEECCCTT-CCEECTTTTT----TCTTCCEECCCT--TCCEECTTTBTTCTTCCEEEEEG
T ss_pred             CEEEeCCc-ccEEhHHhcc----CCCCCCEEEECc--cccEehHHHhhCCCCCCEEEECC
Confidence            87777543 6666666665    677777777764  25666543 66777777777754

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=94.33  E-value=0.023  Score=53.36  Aligned_cols=23  Identities=39%  Similarity=0.655  Sum_probs=21.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+|+|+|+.|+||||+++.+..
T Consensus         6 g~~i~l~G~~GsGKSTl~~~L~~   28 (207)
T 2j41_A            6 GLLIVLSGPSGVGKGTVRKRIFE   28 (207)
T ss_dssp             CCEEEEECSTTSCHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999876

>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins (A/B), protein binding, transferase, phosphotransferase; HET: ADP; 1.76A {Homo sapiens} SCOP: c.37.1.1 PDB: 3iik_A 3iil_A* 3iim_A* 1rkb_A

Probab=94.32  E-value=0.017  Score=52.99  Aligned_cols=23  Identities=35%  Similarity=0.437  Sum_probs=20.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .++|.|+|++|+||||+++.+..
T Consensus        11 ~~~i~i~G~~GsGKst~~~~l~~   33 (180)
T 3iij_A           11 LPNILLTGTPGVGKTTLGKELAS   33 (180)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHH
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHH
Confidence            46789999999999999999886

>3fwy_A Light-independent protochlorophyllide reductase I ATP-binding protein; BCHL, electron donor, DPOR, Fe protein, nitrogenase; HET: ADP; 1.63A {Rhodobacter sphaeroides 2}

Probab=94.32  E-value=0.023  Score=57.29  Aligned_cols=41  Identities=20%  Similarity=0.329  Sum_probs=30.1

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCC
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSK  228 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~  228 (695)
                      ++.+||+|+|-|||||||.+..+.-  -+.. ...+|.-+++..
T Consensus        46 ~~aKVIAIaGKGGVGKTTtavNLA~--aLA~-~GkkVllID~Dp   86 (314)
T 3fwy_A           46 TGAKVFAVYGKGGIGKSTTSSNLSA--AFSI-LGKRVLQIGCDP   86 (314)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHHH--HHHH-TTCCEEEEEESS
T ss_pred             CCceEEEEECCCccCHHHHHHHHHH--HHHH-CCCeEEEEecCC
Confidence            4579999999999999999987765  2322 233477888763

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=94.29  E-value=0.022  Score=51.58  Aligned_cols=23  Identities=35%  Similarity=0.362  Sum_probs=20.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+|+|.|+.|+||||+|+.+..
T Consensus         7 ~~~i~l~G~~GsGKSTva~~La~   29 (168)
T 1zuh_A            7 MQHLVLIGFMGSGKSSLAQELGL   29 (168)
T ss_dssp             -CEEEEESCTTSSHHHHHHHHHH
T ss_pred             cceEEEECCCCCCHHHHHHHHHH
Confidence            47899999999999999999876

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=94.25  E-value=0.023  Score=55.51  Aligned_cols=22  Identities=18%  Similarity=0.363  Sum_probs=20.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+|.|.|+.|+||||||+.++.
T Consensus         2 ~li~I~G~~GSGKSTla~~La~   23 (253)
T 2ze6_A            2 LLHLIYGPTCSGKTDMAIQIAQ   23 (253)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHh
Confidence            4789999999999999999876

>1fx0_B ATP synthase beta chain; latent ATPase, thermal stability, potential tentoxin binding hydrolase; 3.20A {Spinacia oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_B*

Probab=94.23  E-value=0.11  Score=54.87  Aligned_cols=101  Identities=13%  Similarity=0.124  Sum_probs=60.9

Q ss_pred             HHHHHH-cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC-CHHHHHHHHHHhcCCC-------C-
Q 042541          178 LKMELF-KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKGYP-------V-  247 (695)
Q Consensus       178 l~~~L~-~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~~~-------~-  247 (695)
                      +++.|. -...+-++|.|.+|+|||+|+..+.+.. .+.+-+. ++++-+++.. ...++.+++...=...       . 
T Consensus       155 vID~l~pigkGqr~gIfgg~GvGKT~L~~~l~~~~-a~~~~~v-~V~~~iGER~rEv~e~~~~~~~~~~l~~~~l~~~rt  232 (498)
T 1fx0_B          155 VVNLLAPYRRGGKIGLFGGAGVGKTVLIMELINNI-AKAHGGV-SVFGGVGERTREGNDLYMEMKESGVINEQNIAESKV  232 (498)
T ss_dssp             THHHHSCCCTTCCEEEEECSSSSHHHHHHHHHHHT-TTTCSSC-EEEEEESCCSHHHHHHHHHHHHTTSSCSSTTCCCCE
T ss_pred             EeeeecccccCCeEEeecCCCCCchHHHHHHHHHH-HhhCCCE-EEEEEcccCcHHHHHHHHhhhcccccccccccccce
Confidence            445555 3345779999999999999999888731 1223344 6688888765 5677777777642211       0 


Q ss_pred             ------CCCCC-----hHHHHHHHHHHHHhcCCCcEEEEEeCCC
Q 042541          248 ------PEFQT-----DEAAINDLERFFKQMRIEAILLVLDDVW  280 (695)
Q Consensus       248 ------~~~~~-----~~~~~~~l~~~~~~l~~~~~LlVlDdv~  280 (695)
                            .+.+.     .....-.+.+.+..-+++.+|+++||+.
T Consensus       233 vvV~~t~d~p~~~R~~~~~~altiAEyfrd~~G~dVLl~~Dsit  276 (498)
T 1fx0_B          233 ALVYGQMNEPPGARMRVGLTALTMAEYFRDVNEQDVLLFIDNIF  276 (498)
T ss_dssp             EEEEECTTSCHHHHTTHHHHHHHTHHHHTTTSCCEEEEEEECSH
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhcCCcEEEEeccHH
Confidence                  01010     1111222334443335799999999983

>1y63_A LMAJ004144AAA protein; structural genomics, protein structure initiative, PSI, SGPP structural genomics of pathogenic protozoa consortium; HET: ADP; 1.70A {Leishmania major} SCOP: c.37.1.1

Probab=94.22  E-value=0.025  Score=52.13  Aligned_cols=23  Identities=22%  Similarity=0.403  Sum_probs=21.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...|+|+|+.|+||||+++.+..
T Consensus        10 ~~~I~l~G~~GsGKSTv~~~La~   32 (184)
T 1y63_A           10 GINILITGTPGTGKTSMAEMIAA   32 (184)
T ss_dssp             SCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999876

>1uf9_A TT1252 protein; P-loop, nucleotide binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; HET: ATP; 2.80A {Thermus thermophilus} SCOP: c.37.1.1

Probab=94.22  E-value=0.026  Score=52.72  Aligned_cols=25  Identities=24%  Similarity=0.236  Sum_probs=22.3

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ....+|+|+|+.|+||||+++.+..
T Consensus         6 ~~~~~I~i~G~~GsGKST~~~~La~   30 (203)
T 1uf9_A            6 KHPIIIGITGNIGSGKSTVAALLRS   30 (203)
T ss_dssp             CCCEEEEEEECTTSCHHHHHHHHHH
T ss_pred             cCceEEEEECCCCCCHHHHHHHHHH
Confidence            3467899999999999999999986

>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292; mixed alpha-beta protein, rossman fold, signaling protein, transferase; 1.40A {Aquifex aeolicus} SCOP: c.37.1.11

Probab=94.22  E-value=0.024  Score=51.97  Aligned_cols=22  Identities=36%  Similarity=0.643  Sum_probs=19.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHhcc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      .++|+|+.|+|||||++.++..
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~   23 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVER   23 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999988763

>3ney_A 55 kDa erythrocyte membrane protein; structural genomics consortium, SGC, 55 kDa erythrocyte MEMB protein; 2.26A {Homo sapiens} SCOP: c.37.1.0

Probab=94.18  E-value=0.025  Score=52.51  Aligned_cols=24  Identities=25%  Similarity=0.526  Sum_probs=21.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..++|+|+|+.|+|||||++.+..
T Consensus        18 ~g~~ivl~GPSGaGKsTL~~~L~~   41 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSHIKNALLS   41 (197)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCCEEEEECcCCCCHHHHHHHHHh
Confidence            357899999999999999999886

>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A* 1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E* 1ht1_E* 1ht2_E*

Probab=94.18  E-value=0.027  Score=59.27  Aligned_cols=44  Identities=25%  Similarity=0.310  Sum_probs=35.0

Q ss_pred             CCCCCCcchHHHHHHHHHc--------------CCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          166 VISPGLDVPLKELKMELFK--------------DGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~--------------~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+++|-++.++.+...+..              ...+-|.++|++|+||||+|+.++.
T Consensus        15 ~~IvGqe~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GppGtGKT~lar~lA~   72 (444)
T 1g41_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAK   72 (444)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhhhccccccccccCCceEEEEcCCCCCHHHHHHHHHH
Confidence            4679988888888766632              1245689999999999999999987

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=94.18  E-value=0.02  Score=53.62  Aligned_cols=23  Identities=39%  Similarity=0.706  Sum_probs=20.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .++++|+|+.|+|||||++.+..
T Consensus         4 g~~i~lvGpsGaGKSTLl~~L~~   26 (198)
T 1lvg_A            4 PRPVVLSGPSGAGKSTLLKKLFQ   26 (198)
T ss_dssp             -CCEEEECCTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHh
Confidence            36799999999999999999876

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=94.18  E-value=0.026  Score=52.39  Aligned_cols=23  Identities=26%  Similarity=0.319  Sum_probs=20.8

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+|+|.|+.|+||||+|+.+..
T Consensus         3 ~~~I~l~G~~GsGKsT~a~~L~~   25 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGTQCARIVE   25 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999998876

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=94.18  E-value=0.028  Score=52.92  Aligned_cols=23  Identities=39%  Similarity=0.375  Sum_probs=21.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+|+|+|++|+||||+|+.+..
T Consensus        21 ~~~i~i~G~~GsGKSTl~~~L~~   43 (207)
T 2qt1_A           21 TFIIGISGVTNSGKTTLAKNLQK   43 (207)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            47899999999999999999876

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=94.17  E-value=0.023  Score=53.15  Aligned_cols=21  Identities=29%  Similarity=0.393  Sum_probs=19.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .|+|.|+.|+||||+++.+..
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~   22 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISK   22 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEECCCccCHHHHHHHHHH
Confidence            689999999999999999987

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=94.16  E-value=0.038  Score=54.96  Aligned_cols=23  Identities=22%  Similarity=0.346  Sum_probs=21.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+|.|.|++|+||||+|+.+..
T Consensus        33 ~~livl~G~sGsGKSTla~~L~~   55 (287)
T 1gvn_B           33 PTAFLLGGQPGSGKTSLRSAIFE   55 (287)
T ss_dssp             CEEEEEECCTTSCTHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            57899999999999999999876

>3rfe_A Platelet glycoprotein IB beta chain; platelet surface receptor, GPIX, cell adhesion; HET: NAG; 1.25A {Homo sapiens} PDB: 3rez_A*

Probab=94.15  E-value=0.063  Score=46.22  Aligned_cols=53  Identities=13%  Similarity=-0.007  Sum_probs=44.6

Q ss_pred             cEEEeccCCCC--Ccc-cccccccccEEeeccccCCcccccchhhhcccCCCccEEeccccc
Q 042541          604 KKIRLEHVSLP--NSL-ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCN  662 (695)
Q Consensus       604 ~~L~L~~~~l~--~lp-~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~  662 (695)
                      ..++-++++++  .+| .+  -.+|++|+|++|.|+.+++..+.    .+++|++|+|++|.
T Consensus        11 ~~v~Cs~~~L~~~~vP~~l--p~~l~~L~Ls~N~l~~l~~~~f~----~l~~L~~L~L~~NP   66 (130)
T 3rfe_A           11 TLVDCGRRGLTWASLPTAF--PVDTTELVLTGNNLTALPPGLLD----ALPALRTAHLGANP   66 (130)
T ss_dssp             TEEECCSSCCCTTTSCSCC--CTTCSEEECTTSCCSSCCTTTGG----GCTTCCEEECCSSC
T ss_pred             CEEEeCCCCCccccCCCCC--CcCCCEEECCCCcCCccChhhhh----hccccCEEEecCCC
Confidence            46788888888  888 43  34799999999999999998887    89999999999864

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=94.15  E-value=0.02  Score=52.27  Aligned_cols=22  Identities=41%  Similarity=0.433  Sum_probs=19.9

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +.|.|.|++|+||||+|+.+..
T Consensus         5 ~~i~i~G~~GsGKsTla~~La~   26 (175)
T 1via_A            5 KNIVFIGFMGSGKSTLARALAK   26 (175)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHH
Confidence            3589999999999999999986

>1uj2_A Uridine-cytidine kinase 2; alpha/beta mononucleotide-binding HOLD, transferase; HET: C5P ADP; 1.80A {Homo sapiens} SCOP: c.37.1.6 PDB: 1uei_A* 1uej_A* 1udw_A 1ufq_A* 1xrj_A*

Probab=94.10  E-value=0.027  Score=54.94  Aligned_cols=25  Identities=20%  Similarity=0.294  Sum_probs=21.7

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ....+|+|.|+.|+||||+|+.+..
T Consensus        20 ~~~~iI~I~G~~GSGKST~a~~L~~   44 (252)
T 1uj2_A           20 GEPFLIGVSGGTASGKSSVCAKIVQ   44 (252)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCcEEEEEECCCCCCHHHHHHHHHH
Confidence            3467899999999999999998876

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=94.10  E-value=0.099  Score=52.92  Aligned_cols=57  Identities=14%  Similarity=0.164  Sum_probs=35.8

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCC-CCHHHHHHHHHHhcC
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKN-PNVKAIVQKVLHHKG  244 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~-~~~~~~~~~i~~~l~  244 (695)
                      ....+++|+|+.|+||||+++.++..  .+.. ...+.++...-. ....+-+....+.++
T Consensus       127 ~~g~vi~lvG~nGaGKTTll~~Lag~--l~~~-~g~V~l~g~D~~r~~a~eql~~~~~~~g  184 (328)
T 3e70_C          127 EKPYVIMFVGFNGSGKTTTIAKLANW--LKNH-GFSVVIAASDTFRAGAIEQLEEHAKRIG  184 (328)
T ss_dssp             CSSEEEEEECCTTSSHHHHHHHHHHH--HHHT-TCCEEEEEECCSSTTHHHHHHHHHHHTT
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHH--HHhc-CCEEEEEeecccccchHHHHHHHHHHcC
Confidence            45789999999999999999998863  2221 233655544321 233444455555555

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=94.09  E-value=0.027  Score=52.33  Aligned_cols=24  Identities=25%  Similarity=0.379  Sum_probs=21.5

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+|+|.|+.|+||||+|+.+.+
T Consensus         8 ~~~~I~l~G~~GsGKsT~~~~La~   31 (196)
T 2c95_A            8 KTNIIFVVGGPGSGKGTQCEKIVQ   31 (196)
T ss_dssp             TSCEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHH
Confidence            357899999999999999999876

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=94.08  E-value=0.03  Score=52.48  Aligned_cols=24  Identities=33%  Similarity=0.357  Sum_probs=21.5

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+|+|.|+.|+||||+|+.+.+
T Consensus        14 ~~~~I~l~G~~GsGKsT~~~~L~~   37 (203)
T 1ukz_A           14 QVSVIFVLGGPGAGKGTQCEKLVK   37 (203)
T ss_dssp             TCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            357899999999999999999876

>2if2_A Dephospho-COA kinase; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 3.00A {Aquifex aeolicus}

Probab=94.07  E-value=0.024  Score=53.13  Aligned_cols=22  Identities=27%  Similarity=0.323  Sum_probs=19.9

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+|+|+|+.|+||||+++.+..
T Consensus         2 ~~i~i~G~~GsGKSTl~~~L~~   23 (204)
T 2if2_A            2 KRIGLTGNIGCGKSTVAQMFRE   23 (204)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHH
Confidence            3699999999999999999875

>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide monophosphate kinase,, transferase; 1.75A {Escherichia coli} SCOP: c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A* 1kdt_A* 2cmk_A* 2fem_A 2feo_A*

Probab=94.05  E-value=0.025  Score=54.05  Aligned_cols=22  Identities=32%  Similarity=0.622  Sum_probs=20.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+|+|+|+.|+||||+++.+..
T Consensus         6 ~~i~i~G~~GsGKSTl~~~L~~   27 (227)
T 1cke_A            6 PVITIDGPSGAGKGTLCKAMAE   27 (227)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5899999999999999999876

>1jjv_A Dephospho-COA kinase; P-loop nucleotide-binding fold, structure 2 function project, S2F, structural genomics, transferase; HET: ATP; 2.00A {Haemophilus influenzae} SCOP: c.37.1.1

Probab=94.01  E-value=0.028  Score=52.78  Aligned_cols=22  Identities=23%  Similarity=0.300  Sum_probs=20.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+|+|+|+.|+||||+++.+..
T Consensus         3 ~~i~l~G~~GsGKST~~~~La~   24 (206)
T 1jjv_A            3 YIVGLTGGIGSGKTTIANLFTD   24 (206)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHT
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            4799999999999999999865

>2iyv_A Shikimate kinase, SK; transferase, aromatic amino acid biosynthesis, P-loop kinase, metal- binding, shikimate pathway; HET: ADP; 1.35A {Mycobacterium tuberculosis} SCOP: c.37.1.2 PDB: 2iyr_A* 2iyq_A* 2iyt_A 2iyu_A* 2iys_A* 2iyw_A* 2iyx_A* 2iyy_A* 2iyz_A* 2g1k_A* 1l4y_A* 1u8a_A* 1we2_A* 1zyu_A* 2dfn_A* 2dft_A* 2g1j_A 1l4u_A* 3baf_A*

Probab=93.99  E-value=0.02  Score=52.70  Aligned_cols=22  Identities=36%  Similarity=0.431  Sum_probs=20.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+|.|+|++|+||||+|+.+..
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~   24 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIGRRLAK   24 (184)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHH
Confidence            4689999999999999999876

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=93.95  E-value=0.15  Score=54.00  Aligned_cols=51  Identities=18%  Similarity=0.316  Sum_probs=35.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHh
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHH  242 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~  242 (695)
                      ..++.|.|.+|+||||||..++.+...+   ...++|++...  +...+...++..
T Consensus       197 G~liiIaG~pG~GKTtlal~ia~~~a~~---g~~vl~fSlEm--s~~ql~~R~~~~  247 (444)
T 3bgw_A          197 RNFVLIAARPSMGKTAFALKQAKNMSDN---DDVVNLHSLEM--GKKENIKRLIVT  247 (444)
T ss_dssp             SCEEEEEECSSSSHHHHHHHHHHHHHHT---TCEEEEECSSS--CTTHHHHHHHHH
T ss_pred             CcEEEEEeCCCCChHHHHHHHHHHHHHc---CCEEEEEECCC--CHHHHHHHHHHH
Confidence            4689999999999999999888742222   33477776654  344555555543

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=93.95  E-value=0.027  Score=52.44  Aligned_cols=23  Identities=26%  Similarity=0.391  Sum_probs=21.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+|+|.|+.|+||||+|+.+..
T Consensus        12 ~~~I~l~G~~GsGKsT~a~~L~~   34 (199)
T 2bwj_A           12 CKIIFIIGGPGSGKGTQCEKLVE   34 (199)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999886

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=93.93  E-value=0.03  Score=51.55  Aligned_cols=23  Identities=35%  Similarity=0.509  Sum_probs=20.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...|+|.|+.|+||||+++.+.+
T Consensus         4 g~~I~l~G~~GsGKST~~~~La~   26 (186)
T 3cm0_A            4 GQAVIFLGPPGAGKGTQASRLAQ   26 (186)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            35799999999999999999876

>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima}

Probab=93.92  E-value=0.021  Score=58.28  Aligned_cols=52  Identities=15%  Similarity=0.134  Sum_probs=34.9

Q ss_pred             HHHHHHHH-cCCceEEEEEcCCCCcHHHHHHHHhccccccc-cCCCcEEEEEeCCC
Q 042541          176 KELKMELF-KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQG-KFKDDIFYVTVSKN  229 (695)
Q Consensus       176 ~~l~~~L~-~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~-~f~~~~~wv~~~~~  229 (695)
                      -++++.+. -...+-++|+|.+|+|||+|+..+.+.  +.. +-+..++++-+++.
T Consensus       163 iraID~l~PigrGQR~lIfg~~g~GKT~Ll~~Ia~~--i~~~~~dv~~V~~lIGER  216 (427)
T 3l0o_A          163 TRLIDLFAPIGKGQRGMIVAPPKAGKTTILKEIANG--IAENHPDTIRIILLIDER  216 (427)
T ss_dssp             HHHHHHHSCCBTTCEEEEEECTTCCHHHHHHHHHHH--HHHHCTTSEEEEEECSCC
T ss_pred             chhhhhcccccCCceEEEecCCCCChhHHHHHHHHH--HhhcCCCeEEEEEEeccC
Confidence            35556665 234578899999999999999988873  322 22333456666654

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=93.92  E-value=0.068  Score=53.35  Aligned_cols=38  Identities=26%  Similarity=0.322  Sum_probs=27.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeC
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVS  227 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~  227 (695)
                      ..+++|+|.+|+||||++..++..  .... ...+.++...
T Consensus        98 ~~~i~i~g~~G~GKTT~~~~la~~--~~~~-~~~v~l~~~d  135 (295)
T 1ls1_A           98 RNLWFLVGLQGSGKTTTAAKLALY--YKGK-GRRPLLVAAD  135 (295)
T ss_dssp             SEEEEEECCTTTTHHHHHHHHHHH--HHHT-TCCEEEEECC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH--HHHc-CCeEEEecCC
Confidence            478999999999999999998873  3222 3346666654

>1e6c_A Shikimate kinase; phosphoryl transfer, ADP, shikimate pathway, P-loop protein, transferase; 1.8A {Erwinia chrysanthemi} SCOP: c.37.1.2 PDB: 1shk_A 2shk_A*

Probab=93.90  E-value=0.024  Score=51.50  Aligned_cols=22  Identities=27%  Similarity=0.400  Sum_probs=20.1

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+|.|.|+.|+||||+|+.+..
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~   24 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGRELAR   24 (173)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHH
Confidence            4689999999999999999876

>1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase, TR; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A

Probab=93.87  E-value=0.031  Score=52.61  Aligned_cols=24  Identities=33%  Similarity=0.515  Sum_probs=21.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+++|+|+.|+|||||++.+..
T Consensus        19 ~Gei~~l~GpnGsGKSTLl~~l~g   42 (207)
T 1znw_A           19 VGRVVVLSGPSAVGKSTVVRCLRE   42 (207)
T ss_dssp             CCCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHh
Confidence            347999999999999999999876

>3a4m_A L-seryl-tRNA(SEC) kinase; P-loop motif, walker A motif, ATP binding motif, ATP- binding, nucleotide-binding, transferase; HET: ADP; 1.79A {Methanocaldococcus jannaschii} PDB: 3a4l_A* 3a4n_A 3am1_A* 3add_A* 3adc_A* 3adb_A*

Probab=93.87  E-value=0.032  Score=54.68  Aligned_cols=23  Identities=30%  Similarity=0.514  Sum_probs=21.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+|.|.|++|+||||+|+.+..
T Consensus         4 ~~lIvl~G~pGSGKSTla~~La~   26 (260)
T 3a4m_A            4 IMLIILTGLPGVGKSTFSKNLAK   26 (260)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHH
Confidence            46899999999999999999986

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=93.82  E-value=0.13  Score=55.20  Aligned_cols=38  Identities=24%  Similarity=0.219  Sum_probs=26.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeC
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVS  227 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~  227 (695)
                      .++|.|+|.+|+||||++..++..  .... ...+..|+..
T Consensus       101 ~~vI~ivG~~GvGKTTl~~kLA~~--l~~~-G~kVllVd~D  138 (504)
T 2j37_W          101 QNVIMFVGLQGSGKTTTCSKLAYY--YQRK-GWKTCLICAD  138 (504)
T ss_dssp             -EEEEEECSTTSSHHHHHHHHHHH--HHHT-TCCEEEEEEC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH--HHhC-CCeEEEEecc
Confidence            579999999999999999988863  2221 2235556553

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=93.82  E-value=0.045  Score=50.78  Aligned_cols=35  Identities=23%  Similarity=0.260  Sum_probs=26.5

Q ss_pred             HHHHHHHHHc-CCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          175 LKELKMELFK-DGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       175 ~~~l~~~L~~-~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +..+..++.. +....+.|+|++|+||||+|..+++
T Consensus        45 ~~~l~~~~~~iPkkn~ili~GPPGtGKTt~a~ala~   80 (212)
T 1tue_A           45 LGALKSFLKGTPKKNCLVFCGPANTGKSYFGMSFIH   80 (212)
T ss_dssp             HHHHHHHHHTCTTCSEEEEESCGGGCHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCcccEEEEECCCCCCHHHHHHHHHH
Confidence            5556555553 2234799999999999999998887

>3aez_A Pantothenate kinase; transferase, homodimer, COA biosynthesis, nucleotide binding binding, cytoplasm, nucleotide-binding; HET: GDP PAZ; 2.20A {Mycobacterium tuberculosis} PDB: 2ges_A* 2geu_A* 2gev_A* 2zs7_A* 2zs8_A* 2zs9_A* 2zsa_A* 2zsb_A* 2zsd_A* 2zse_A* 2zsf_A* 2get_A* 3af0_A* 3af1_A* 3af2_A* 3af3_A* 3af4_A* 3avp_A* 3avo_A* 3avq_A*

Probab=93.81  E-value=0.035  Score=55.89  Aligned_cols=24  Identities=25%  Similarity=0.137  Sum_probs=21.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+|+|+|+.|+|||||++.+..
T Consensus        89 ~g~ivgI~G~sGsGKSTL~~~L~g  112 (312)
T 3aez_A           89 VPFIIGVAGSVAVGKSTTARVLQA  112 (312)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCEEEEEECCCCchHHHHHHHHHh
Confidence            357999999999999999998876

>2bbw_A Adenylate kinase 4, AK4; nucleotide kinase, nucleotide binding, human, structura genomics, structural genomics consortium, SGC, transferase; HET: GP5; 2.05A {Homo sapiens} PDB: 2ar7_A* 3ndp_A

Probab=93.79  E-value=0.031  Score=54.24  Aligned_cols=23  Identities=35%  Similarity=0.479  Sum_probs=21.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+|+|+|+.|+|||||++.+..
T Consensus        27 ~~~i~l~G~~GsGKSTl~k~La~   49 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVCQRIAQ   49 (246)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999999985

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=93.79  E-value=0.033  Score=52.43  Aligned_cols=23  Identities=22%  Similarity=0.254  Sum_probs=21.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+|+|.|+.|+||||+|+.+..
T Consensus         4 ~~~I~i~G~~GsGKsT~~~~L~~   26 (213)
T 2plr_A            4 GVLIAFEGIDGSGKSSQATLLKD   26 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHH
Confidence            36899999999999999999987

>1s96_A Guanylate kinase, GMP kinase; E.coli, dimer, SAD, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.1 PDB: 2an9_A* 2anb_A* 2anc_A 2f3r_A* 2f3t_A*

Probab=93.78  E-value=0.034  Score=52.85  Aligned_cols=24  Identities=46%  Similarity=0.701  Sum_probs=21.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+++|+|+.|+|||||.+.+..
T Consensus        15 ~G~ii~l~GpsGsGKSTLlk~L~g   38 (219)
T 1s96_A           15 QGTLYIVSAPSGAGKSSLIQALLK   38 (219)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhc
Confidence            357999999999999999999876

>1xjc_A MOBB protein homolog; structural genomics, midwest center for structural GEN PSI, protein structure initiative, MCSG; 2.10A {Geobacillus stearothermophilus} SCOP: c.37.1.10

Probab=93.77  E-value=0.034  Score=50.23  Aligned_cols=23  Identities=26%  Similarity=0.218  Sum_probs=21.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .++++|+|..|+|||||+..+..
T Consensus         4 ~~~i~i~G~sGsGKTTl~~~L~~   26 (169)
T 1xjc_A            4 MNVWQVVGYKHSGKTTLMEKWVA   26 (169)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH
Confidence            57899999999999999999887

>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate kinase); nucleoside monophosphate kinase, NMP kinase; HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP: c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*

Probab=93.76  E-value=0.033  Score=51.53  Aligned_cols=23  Identities=22%  Similarity=0.315  Sum_probs=21.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+|+|.|+.|+||||+|+.+..
T Consensus         6 ~~~I~l~G~~GsGKsT~~~~L~~   28 (194)
T 1qf9_A            6 PNVVFVLGGPGSGKGTQCANIVR   28 (194)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999876

>1htw_A HI0065; nucleotide-binding fold, structural genomics, structure 2 function project, S2F, unknown function; HET: ADP; 1.70A {Haemophilus influenzae} SCOP: c.37.1.18 PDB: 1fl9_A

Probab=93.74  E-value=0.04  Score=49.31  Aligned_cols=25  Identities=24%  Similarity=0.365  Sum_probs=22.3

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ....+++|+|+.|.|||||++.++.
T Consensus        31 ~~Ge~v~L~G~nGaGKTTLlr~l~g   55 (158)
T 1htw_A           31 EKAIMVYLNGDLGAGKTTLTRGMLQ   55 (158)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHH
Confidence            4457999999999999999999886

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=93.72  E-value=0.028  Score=53.40  Aligned_cols=23  Identities=35%  Similarity=0.599  Sum_probs=21.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|+|||||++.+..
T Consensus        23 G~~~~lvGpsGsGKSTLl~~L~g   45 (218)
T 1z6g_A           23 IYPLVICGPSGVGKGTLIKKLLN   45 (218)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHh
Confidence            46899999999999999999876

>2cdn_A Adenylate kinase; phosphoryl transfer, associative mechanism, ATP-binding, nucleotide biosynthesis, nucleotide-binding, transferase; HET: ADP; 1.9A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1p4s_A

Probab=93.72  E-value=0.036  Score=51.81  Aligned_cols=23  Identities=26%  Similarity=0.414  Sum_probs=20.8

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+|+|+|+.|+||||+|+.+..
T Consensus        20 ~~~I~l~G~~GsGKST~a~~La~   42 (201)
T 2cdn_A           20 HMRVLLLGPPGAGKGTQAVKLAE   42 (201)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            45899999999999999999876

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=93.70  E-value=0.034  Score=50.22  Aligned_cols=21  Identities=24%  Similarity=0.099  Sum_probs=19.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .|+|.|+.|+||||+|+.+.+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~   22 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSR   22 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHH
Confidence            589999999999999999876

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=93.66  E-value=0.039  Score=53.48  Aligned_cols=25  Identities=24%  Similarity=0.272  Sum_probs=22.0

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ....+|+|.|+.|+|||||++.+..
T Consensus        23 ~~g~iigI~G~~GsGKSTl~k~L~~   47 (245)
T 2jeo_A           23 MRPFLIGVSGGTASGKSTVCEKIME   47 (245)
T ss_dssp             CCSEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            3457999999999999999998876

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=93.64  E-value=0.035  Score=55.88  Aligned_cols=40  Identities=15%  Similarity=0.134  Sum_probs=27.7

Q ss_pred             CCcchHHHHHHHHHc----CCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          170 GLDVPLKELKMELFK----DGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       170 Gr~~~~~~l~~~L~~----~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      |-...+..+...+..    ..+.+|+|.|+.|+|||||++.+..
T Consensus        71 ~~~~~l~~~~~~~l~~~~~~~p~iigI~GpsGSGKSTl~~~L~~  114 (321)
T 3tqc_A           71 TARQTLQQATYQFLGKPEPKVPYIIGIAGSVAVGKSTTSRVLKA  114 (321)
T ss_dssp             HHHHHHHHHHHHHHTCCCCCCCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHhccCCCCCCEEEEEECCCCCCHHHHHHHHHH
Confidence            333344444444432    2356999999999999999998865

>3tlx_A Adenylate kinase 2; structural genomics, structural genomics consortium, SGC, RO fold, transferase, ATP binding, phosphorylation; HET: ADP ATP AMP; 2.75A {Plasmodium falciparum}

Probab=93.63  E-value=0.057  Score=52.25  Aligned_cols=25  Identities=24%  Similarity=0.141  Sum_probs=22.2

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ....+|+|.|++|+||||+|+.+.+
T Consensus        27 ~~~~~I~l~G~~GsGKsT~a~~L~~   51 (243)
T 3tlx_A           27 KPDGRYIFLGAPGSGKGTQSLNLKK   51 (243)
T ss_dssp             SCCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHH
Confidence            3567899999999999999999876

>1pgv_A TMD-1, tropomodulin TMD-1; structural genomics, PSI, protein structure initiative, southeast collaboratory for structural genomics secsg; 1.80A {Caenorhabditis elegans} SCOP: c.10.1.1

Probab=93.61  E-value=0.042  Score=50.88  Aligned_cols=117  Identities=11%  Similarity=0.130  Sum_probs=65.7

Q ss_pred             hhcCCCCCcEEEEccc-CCCCcccCc-ccccccCCCCcEEEeccCCCC-----Ccc-cccccccccEEeeccccCCcccc
Q 042541          569 FLQKMDELKVLIVTNY-GFSPAELNN-FRVLSALSKLKKIRLEHVSLP-----NSL-ATVRMNHLQKVSLVMCNVGQVFR  640 (695)
Q Consensus       569 ~~~~l~~Lr~L~l~~~-~~~~~~~~~-~~~l~~l~~L~~L~L~~~~l~-----~lp-~i~~l~~L~~L~l~~~~i~~~~~  640 (695)
                      .+..-+.|+.|+|+++ .+....... ...+..-..|+.|+|++|.+.     .+- .+..=+.|++|+|++|.|...--
T Consensus        36 ll~~n~~L~~L~L~~nn~igd~ga~~la~aL~~N~~L~~L~L~~n~igd~ga~alA~aL~~N~tL~~L~L~~N~Ig~~Ga  115 (197)
T 1pgv_A           36 LREDDTDLKEVNINNMKRVSKERIRSLIEAACNSKHIEKFSLANTAISDSEARGLIELIETSPSLRVLNVESNFLTPELL  115 (197)
T ss_dssp             HHTTCSSCCEEECTTCCSSCHHHHHHHHHHHTTCSCCCEEECTTSCCBHHHHTTHHHHHHHCSSCCEEECCSSBCCHHHH
T ss_pred             HHhcCCCccEEECCCCCCCCHHHHHHHHHHHhhCCCcCEEEccCCCCChHHHHHHHHHHhcCCccCeEecCCCcCCHHHH
Confidence            3445567888888764 442222111 122444566888888888876     233 34445678888888888764211


Q ss_pred             cchhhhcccCCCccEEecccccc--cc-----cCchhhcCCCCCceeecccc
Q 042541          641 NSTFRISDAFPNLLEMDIDYCND--LI-----ELPDGLCDIVSMEKLRITNC  685 (695)
Q Consensus       641 ~~~~~l~~~l~~L~~L~l~~c~~--l~-----~lP~~i~~L~~L~~L~l~~~  685 (695)
                      ..+...-..-+.|+.|+|++|.+  ++     .+-..+..=++|+.|+++.|
T Consensus       116 ~ala~aL~~N~tL~~L~L~n~~~~~ig~~g~~~ia~aL~~N~tL~~L~l~~~  167 (197)
T 1pgv_A          116 ARLLRSTLVTQSIVEFKADNQRQSVLGNQVEMDMMMAIEENESLLRVGISFA  167 (197)
T ss_dssp             HHHHHHTTTTCCCSEEECCCCSSCCCCHHHHHHHHHHHHHCSSCCEEECCCC
T ss_pred             HHHHHHHhhCCceeEEECCCCcCcCcCHHHHHHHHHHHHhCCCcCeEeccCC
Confidence            11100000234588888876532  22     23344555678888888764

>2grj_A Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosphocoenzyme kinase, structural genomics, joint center for structural GE JCSG; HET: ADP COD; 2.60A {Thermotoga maritima}

Probab=93.59  E-value=0.035  Score=51.53  Aligned_cols=24  Identities=29%  Similarity=0.292  Sum_probs=21.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+|+|+|+.|+||||+++.+..
T Consensus        11 ~~~iIgltG~~GSGKSTva~~L~~   34 (192)
T 2grj_A           11 HHMVIGVTGKIGTGKSTVCEILKN   34 (192)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHHHH
T ss_pred             cceEEEEECCCCCCHHHHHHHHHH
Confidence            357899999999999999999876

>3zvl_A Bifunctional polynucleotide phosphatase/kinase; hydrolase-transferase complex, base excision repair, BER, non-homologous END-joining, NHEJ; 1.65A {Mus musculus} PDB: 3zvm_A* 3zvn_A* 1yj5_A 3u7e_B* 3u7f_B* 3u7h_B* 3u7g_A*

Probab=93.58  E-value=0.11  Score=54.76  Aligned_cols=25  Identities=24%  Similarity=0.303  Sum_probs=22.4

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ....+|.|+|++|+||||+|+.++.
T Consensus       256 ~~~~lIil~G~pGSGKSTla~~L~~  280 (416)
T 3zvl_A          256 PNPEVVVAVGFPGAGKSTFIQEHLV  280 (416)
T ss_dssp             SSCCEEEEESCTTSSHHHHHHHHTG
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            3468999999999999999999886

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=93.54  E-value=0.025  Score=51.87  Aligned_cols=23  Identities=30%  Similarity=0.437  Sum_probs=16.8

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+|.|.|+.|+||||+|+.+..
T Consensus         5 ~~~I~l~G~~GsGKST~a~~La~   27 (183)
T 2vli_A            5 SPIIWINGPFGVGKTHTAHTLHE   27 (183)
T ss_dssp             CCEEEEECCC----CHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999876

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=93.54  E-value=0.035  Score=51.38  Aligned_cols=21  Identities=33%  Similarity=0.498  Sum_probs=19.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +|+|.|+.|+||||+|+.+.+
T Consensus         2 ~I~l~G~~GsGKsT~~~~L~~   22 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKKLYE   22 (195)
T ss_dssp             EEEEECSTTSCHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            689999999999999999987

>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer, nucleotide twinning, protein complex, protein transport; HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D 2iyl_D* 2cnw_D* 2j7p_D*

Probab=93.49  E-value=0.039  Score=55.29  Aligned_cols=24  Identities=29%  Similarity=0.490  Sum_probs=21.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+|+|+|++|+||||+++.++.
T Consensus       101 ~g~vi~lvG~nGsGKTTll~~Lag  124 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTTIAKLGR  124 (304)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHH
Confidence            357999999999999999999886

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=93.44  E-value=0.27  Score=52.22  Aligned_cols=52  Identities=10%  Similarity=0.128  Sum_probs=37.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHh
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHH  242 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~  242 (695)
                      ..++.|.|.+|+||||||..++.+  ........++|++..  .+...+...++..
T Consensus       200 G~l~ii~G~pg~GKT~lal~ia~~--~a~~~g~~vl~~slE--~~~~~l~~R~~~~  251 (444)
T 2q6t_A          200 GSLNIIAARPAMGKTAFALTIAQN--AALKEGVGVGIYSLE--MPAAQLTLRMMCS  251 (444)
T ss_dssp             TCEEEEEECTTSCHHHHHHHHHHH--HHHTTCCCEEEEESS--SCHHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHH--HHHhCCCeEEEEECC--CCHHHHHHHHHHH
Confidence            468999999999999999988874  222123347787775  3566777776654

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=93.43  E-value=0.046  Score=53.29  Aligned_cols=23  Identities=30%  Similarity=0.312  Sum_probs=21.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+|.|+|++|+||||+|+.+..
T Consensus        32 ~~~i~l~G~~GsGKSTla~~L~~   54 (253)
T 2p5t_B           32 PIAILLGGQSGAGKTTIHRIKQK   54 (253)
T ss_dssp             CEEEEEESCGGGTTHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            57899999999999999999876

>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding, signal recognition particle, GTP-binding, RNA-binding; 2.50A {Methanocaldococcus jannaschii} PDB: 3ndb_B

Probab=93.41  E-value=0.052  Score=57.24  Aligned_cols=24  Identities=29%  Similarity=0.432  Sum_probs=21.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhcc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      ..+|.|+|.+|+||||++..++..
T Consensus        99 ~~vI~ivG~~GvGKTTla~~La~~  122 (432)
T 2v3c_C           99 QNVILLVGIQGSGKTTTAAKLARY  122 (432)
T ss_dssp             CCCEEEECCSSSSTTHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999888763

>1aky_A Adenylate kinase; ATP:AMP phosphotransferase, myokinase, transferase (phosphotransferase); HET: AP5; 1.63A {Saccharomyces cerevisiae} SCOP: c.37.1.1 g.41.2.1 PDB: 2aky_A* 3aky_A* 1dvr_A*

Probab=93.41  E-value=0.041  Score=52.29  Aligned_cols=23  Identities=30%  Similarity=0.351  Sum_probs=20.8

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...|.|.|+.|+||||+|+.+..
T Consensus         4 ~~~I~l~G~~GsGKsT~a~~La~   26 (220)
T 1aky_A            4 SIRMVLIGPPGAGKGTQAPNLQE   26 (220)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46799999999999999999876

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=93.41  E-value=0.038  Score=52.09  Aligned_cols=23  Identities=30%  Similarity=0.382  Sum_probs=21.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+|+|.|+.|+||||+++.+..
T Consensus        10 ~~~I~l~G~~GsGKST~~~~L~~   32 (212)
T 2wwf_A           10 GKFIVFEGLDRSGKSTQSKLLVE   32 (212)
T ss_dssp             SCEEEEEESTTSSHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHH
Confidence            46899999999999999999987

>1nn5_A Similar to deoxythymidylate kinase (thymidylate K; P-loop, D4TMP, transferase; HET: 2DT ANP; 1.50A {Homo sapiens} SCOP: c.37.1.1 PDB: 1e2e_A* 1e2d_A* 1e2g_A* 1e2q_A* 1e99_A* 1e9a_A* 1e9b_A* 1nmx_A* 1nmz_A* 1nn0_A* 1nn1_A* 1e2f_A* 1nn3_A* 2xx3_A* 1e9c_A* 1e9d_A* 1e9e_A* 1e98_A* 1nmy_A* 1e9f_A*

Probab=93.41  E-value=0.041  Score=51.90  Aligned_cols=23  Identities=26%  Similarity=0.384  Sum_probs=21.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+|+|.|+.|+||||+|+.+.+
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~L~~   31 (215)
T 1nn5_A            9 GALIVLEGVDRAGKSTQSRKLVE   31 (215)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999987

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=93.36  E-value=0.04  Score=53.72  Aligned_cols=24  Identities=38%  Similarity=0.520  Sum_probs=21.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+|+|+|+.|+||||+++.+..
T Consensus        26 ~g~~I~I~G~~GsGKSTl~k~La~   49 (252)
T 4e22_A           26 IAPVITVDGPSGAGKGTLCKALAE   49 (252)
T ss_dssp             TSCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            346899999999999999999985

>2pez_A Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (PAPS synthetase...; NMP-kinase fold, protein in complex with nucleic acid; HET: GGZ DAT; 1.40A {Homo sapiens} PDB: 2pey_A* 2ax4_A*

Probab=93.18  E-value=0.052  Score=49.61  Aligned_cols=23  Identities=26%  Similarity=0.254  Sum_probs=21.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+|+|+|+.|+||||+++.+..
T Consensus         5 g~~i~l~G~~GsGKST~~~~L~~   27 (179)
T 2pez_A            5 GCTVWLTGLSGAGKTTVSMALEE   27 (179)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999986

>2v54_A DTMP kinase, thymidylate kinase; nucleotide biosynthesis, ATP-binding, nucleotide-binding, poxvirus, transferase; HET: TYD POP; 2.4A {Vaccinia virus copenhagen} PDB: 2w0s_A*

Probab=93.17  E-value=0.045  Score=51.15  Aligned_cols=23  Identities=26%  Similarity=0.283  Sum_probs=21.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+|+|.|+.|+||||+++.+.+
T Consensus         4 ~~~I~l~G~~GsGKsT~~~~L~~   26 (204)
T 2v54_A            4 GALIVFEGLDKSGKTTQCMNIME   26 (204)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHH
Confidence            46899999999999999999987

>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2

Probab=93.15  E-value=0.32  Score=52.60  Aligned_cols=53  Identities=11%  Similarity=0.185  Sum_probs=37.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHK  243 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l  243 (695)
                      ..++.|.|.+|+||||||..++.+  ........++|++...  +...+...++...
T Consensus       242 G~l~li~G~pG~GKT~lal~~a~~--~a~~~g~~vl~~s~E~--s~~~l~~r~~~~~  294 (503)
T 1q57_A          242 GEVIMVTSGSGMVMSTFVRQQALQ--WGTAMGKKVGLAMLEE--SVEETAEDLIGLH  294 (503)
T ss_dssp             TCEEEEEESSCHHHHHHHHHHHHH--HTTTSCCCEEEEESSS--CHHHHHHHHHHHH
T ss_pred             CeEEEEeecCCCCchHHHHHHHHH--HHHhcCCcEEEEeccC--CHHHHHHHHHHHH
Confidence            478999999999999999988873  3222233477887755  4667777766543

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=93.15  E-value=0.34  Score=49.04  Aligned_cols=52  Identities=12%  Similarity=0.205  Sum_probs=37.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHK  243 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l  243 (695)
                      ..++.|.|.+|+||||||..++.+...   ....++|++..  -+...+...++...
T Consensus        46 G~LiiIaG~pG~GKTt~al~ia~~~a~---~g~~Vl~fSlE--ms~~ql~~Rlls~~   97 (338)
T 4a1f_A           46 GSLVIIGARPSMGKTSLMMNMVLSALN---DDRGVAVFSLE--MSAEQLALRALSDL   97 (338)
T ss_dssp             TCEEEEEECTTSCHHHHHHHHHHHHHH---TTCEEEEEESS--SCHHHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHH---cCCeEEEEeCC--CCHHHHHHHHHHHh
Confidence            468999999999999999988874222   23346777664  45677777776543

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=93.12  E-value=0.043  Score=52.45  Aligned_cols=23  Identities=26%  Similarity=0.299  Sum_probs=20.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...|.|.|+.|+||||+|+.+..
T Consensus         7 ~~~I~l~G~~GsGKsT~a~~La~   29 (227)
T 1zd8_A            7 LLRAVIMGAPGSGKGTVSSRITT   29 (227)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46799999999999999999876

>1m7g_A Adenylylsulfate kinase; APS kinase, transferase, sulfate Met nucleotide 2 kinase; HET: AV2 ADX ADP; 1.43A {Penicillium chrysogenum} SCOP: c.37.1.4 PDB: 1d6j_A* 1m7h_A* 3cr7_A*

Probab=93.11  E-value=0.07  Score=50.31  Aligned_cols=26  Identities=23%  Similarity=0.210  Sum_probs=22.8

Q ss_pred             cCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          184 KDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       184 ~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .....+|.|.|+.|+||||+++.+..
T Consensus        22 ~~~~~~i~~~G~~GsGKsT~~~~l~~   47 (211)
T 1m7g_A           22 NQRGLTIWLTGLSASGKSTLAVELEH   47 (211)
T ss_dssp             TSSCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHH
Confidence            34468999999999999999999886

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=93.05  E-value=0.046  Score=51.71  Aligned_cols=21  Identities=29%  Similarity=0.343  Sum_probs=19.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .|+|.|++|+||||+|+.+..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~   22 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAEQIIE   22 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            478999999999999999876

>1gtv_A TMK, thymidylate kinase; transferase, transferase (ATP:TMP phosphotransferase); HET: TYD TMP; 1.55A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1g3u_A* 1gsi_A* 1mrn_A* 1mrs_A* 1n5i_A* 1n5j_A* 1n5k_A* 1n5l_A* 1w2g_A* 1w2h_A*

Probab=93.03  E-value=0.025  Score=53.44  Aligned_cols=22  Identities=36%  Similarity=0.584  Sum_probs=20.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+|+|.|+.|+||||+++.+..
T Consensus         1 ~~I~i~G~~GsGKsTl~~~L~~   22 (214)
T 1gtv_A            1 MLIAIEGVDGAGKRTLVEKLSG   22 (214)
T ss_dssp             CEEEEEEEEEEEHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHH
Confidence            3789999999999999999876

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=93.01  E-value=0.19  Score=62.36  Aligned_cols=85  Identities=16%  Similarity=0.187  Sum_probs=54.1

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCC-----CCChHHHHHHH
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPE-----FQTDEAAINDL  260 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~-----~~~~~~~~~~l  260 (695)
                      ..+.|.|+|++|+|||+||.++...  ...+ ...++|+++.+.++...     ++.++.+...     ....+.....+
T Consensus      1426 ~g~~vll~GppGtGKT~LA~ala~e--a~~~-G~~v~Fi~~e~~~~~l~-----a~~~G~dl~~l~v~~~~~~E~~l~~~ 1497 (2050)
T 3cmu_A         1426 MGRIVEIYGPESSGKTTLTLQVIAA--AQRE-GKTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEIC 1497 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHH--HHTT-TCCEEEECTTSCCCHHH-----HHHTTCCTTTCEEECCSSHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH--HHHc-CCcEEEEEcccccCHHH-----HHHcCCCchhceeecCChHHHHHHHH
Confidence            3689999999999999999998873  2222 23477999988877666     3444422111     11223333333


Q ss_pred             HHHHHhcCCCcEEEEEeCCC
Q 042541          261 ERFFKQMRIEAILLVLDDVW  280 (695)
Q Consensus       261 ~~~~~~l~~~~~LlVlDdv~  280 (695)
                      ..+.+  ..+..+||+|.+.
T Consensus      1498 ~~lvr--~~~~~lVVIDsi~ 1515 (2050)
T 3cmu_A         1498 DALAR--SGAVDVIVVDSVA 1515 (2050)
T ss_dssp             HHHHH--HTCCSEEEESCGG
T ss_pred             HHHHh--cCCCCEEEEcChh
Confidence            33332  3567899999984

>1vht_A Dephospho-COA kinase; structural genomics, transferase; HET: BA3; 1.59A {Escherichia coli} SCOP: c.37.1.1 PDB: 1vhl_A* 1viy_A 1t3h_A 1n3b_A

Probab=93.00  E-value=0.058  Score=51.11  Aligned_cols=23  Identities=22%  Similarity=0.413  Sum_probs=20.6

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+|+|.|+.|+||||+++.+..
T Consensus         4 ~~~I~i~G~~GSGKST~~~~L~~   26 (218)
T 1vht_A            4 RYIVALTGGIGSGKSTVANAFAD   26 (218)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999864

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=92.96  E-value=0.044  Score=52.17  Aligned_cols=23  Identities=17%  Similarity=0.164  Sum_probs=20.8

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...|.|.|+.|+||||+++.+..
T Consensus         5 ~~~I~l~G~~GsGKsT~~~~La~   27 (222)
T 1zak_A            5 PLKVMISGAPASGKGTQCELIKT   27 (222)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            45799999999999999999986

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=92.96  E-value=0.031  Score=50.73  Aligned_cols=22  Identities=27%  Similarity=0.462  Sum_probs=20.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ++++|+|..|+|||||++.+..
T Consensus         3 ~~v~IvG~SGsGKSTL~~~L~~   24 (171)
T 2f1r_A            3 LILSIVGTSDSGKTTLITRMMP   24 (171)
T ss_dssp             CEEEEEESCHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5799999999999999998876

>2f6r_A COA synthase, bifunctional coenzyme A synthase; 18044849, bifunctional coenzyme A synthase (COA synthase), S genomics; HET: ACO UNL; 1.70A {Mus musculus}

Probab=92.95  E-value=0.057  Score=53.51  Aligned_cols=24  Identities=29%  Similarity=0.455  Sum_probs=21.2

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+|+|.|+.|+||||+|+.+..
T Consensus        74 ~~~iI~I~G~~GSGKSTva~~La~   97 (281)
T 2f6r_A           74 GLYVLGLTGISGSGKSSVAQRLKN   97 (281)
T ss_dssp             TCEEEEEEECTTSCHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            357899999999999999999873

>3tif_A Uncharacterized ABC transporter ATP-binding prote; nucleotide-binding domain, ABC transporter ATPase; HET: ADP; 1.80A {Methanocaldococcus jannaschii dsm 2661ORGANISM_TAXID} PDB: 1l2t_A* 1f3o_A*

Probab=92.94  E-value=0.056  Score=51.97  Aligned_cols=23  Identities=26%  Similarity=0.572  Sum_probs=21.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|+|||||.+.+..
T Consensus        31 Ge~~~iiG~nGsGKSTLl~~l~G   53 (235)
T 3tif_A           31 GEFVSIMGPSGSGKSTMLNIIGC   53 (235)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhc
Confidence            47899999999999999999875

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=92.89  E-value=0.046  Score=50.58  Aligned_cols=23  Identities=30%  Similarity=0.622  Sum_probs=20.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhcc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      .+++|+|+.|+|||||++.++..
T Consensus         2 ~~i~i~G~nG~GKTTll~~l~g~   24 (189)
T 2i3b_A            2 RHVFLTGPPGVGKTTLIHKASEV   24 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHH
T ss_pred             CEEEEECCCCChHHHHHHHHHhh
Confidence            36899999999999999988763

>3dl0_A Adenylate kinase; phosphotransferase, zinc coordination, ATP-binding, binding, nucleotide biosynthesis, nucleotide-binding, trans; HET: AP5; 1.58A {Bacillus subtilis} PDB: 1p3j_A* 2ori_A* 2eu8_A* 2oo7_A* 2p3s_A* 2qaj_A* 2osb_A* 3dkv_A* 1zin_A* 1zio_A* 1zip_A* 1s3g_A*

Probab=92.88  E-value=0.05  Score=51.45  Aligned_cols=21  Identities=29%  Similarity=0.338  Sum_probs=19.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .|+|.|++|+||||+|+.+..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~   22 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGERIVE   22 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            478999999999999999875

>4eaq_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, MTBI, transferase; HET: ATM; 1.85A {Staphylococcus aureus subsp} PDB: 4dwj_A* 4f4i_A

Probab=92.87  E-value=0.1  Score=49.87  Aligned_cols=23  Identities=35%  Similarity=0.661  Sum_probs=21.4

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+|+|.|+.|+||||+++.+..
T Consensus        26 g~~i~i~G~~GsGKsT~~~~l~~   48 (229)
T 4eaq_A           26 SAFITFEGPEGSGKTTVINEVYH   48 (229)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHH
Confidence            47899999999999999999987

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=92.84  E-value=0.053  Score=51.74  Aligned_cols=23  Identities=30%  Similarity=0.471  Sum_probs=21.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|+|||||.+.++.
T Consensus        30 Ge~~~iiG~nGsGKSTLl~~l~G   52 (224)
T 2pcj_A           30 GEFVSIIGASGSGKSTLLYILGL   52 (224)
T ss_dssp             TCEEEEEECTTSCHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            46899999999999999999885

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=92.82  E-value=0.036  Score=53.22  Aligned_cols=23  Identities=43%  Similarity=0.720  Sum_probs=16.5

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHh-c
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLC-K  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~-~  209 (695)
                      ..+++|+|+.|+|||||++.+. .
T Consensus        27 G~ii~l~Gp~GsGKSTl~~~L~~~   50 (231)
T 3lnc_A           27 GVILVLSSPSGCGKTTVANKLLEK   50 (231)
T ss_dssp             CCEEEEECSCC----CHHHHHHC-
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhc
Confidence            4689999999999999999988 5

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=92.81  E-value=0.14  Score=51.17  Aligned_cols=53  Identities=17%  Similarity=0.313  Sum_probs=34.2

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHh
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHH  242 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~  242 (695)
                      ...+++|.|++|+|||||++.++..  ........++|++...  +...+...+...
T Consensus        34 ~G~~~~i~G~~G~GKTTl~~~ia~~--~~~~~G~~v~~~~~e~--~~~~~~~r~~~~   86 (296)
T 1cr0_A           34 GGEVIMVTSGSGMGKSTFVRQQALQ--WGTAMGKKVGLAMLEE--SVEETAEDLIGL   86 (296)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHHH--HHHTSCCCEEEEESSS--CHHHHHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHH--HHHHcCCeEEEEeCcC--CHHHHHHHHHHH
Confidence            3479999999999999999998863  2222122376776543  344454444443

>1np6_A Molybdopterin-guanine dinucleotide biosynthesis protein B; mixed alpha-beta fold, elongated beta-sheet, walker A motif, P-loop structural motif; 1.90A {Escherichia coli} SCOP: c.37.1.10 PDB: 1p9n_A

Probab=92.78  E-value=0.059  Score=49.04  Aligned_cols=23  Identities=35%  Similarity=0.481  Sum_probs=21.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .++++|+|+.|+|||||+..+..
T Consensus         6 ~~~i~i~G~sGsGKTTl~~~l~~   28 (174)
T 1np6_A            6 IPLLAFAAWSGTGKTTLLKKLIP   28 (174)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHH
T ss_pred             ceEEEEEeCCCCCHHHHHHHHHH
Confidence            57899999999999999999886

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=92.76  E-value=0.063  Score=53.74  Aligned_cols=23  Identities=30%  Similarity=0.432  Sum_probs=21.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|+||||+++.++.
T Consensus       100 g~vi~lvG~nGsGKTTll~~Lag  122 (302)
T 3b9q_A          100 PAVIMIVGVNGGGKTTSLGKLAH  122 (302)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHH
Confidence            47999999999999999999887

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=92.72  E-value=0.06  Score=51.92  Aligned_cols=22  Identities=23%  Similarity=0.549  Sum_probs=20.7

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+++|+|+.|+|||||.+.++.
T Consensus        25 e~~~liG~nGsGKSTLl~~l~G   46 (240)
T 2onk_A           25 DYCVLLGPTGAGKSVFLELIAG   46 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHhC
Confidence            7899999999999999999886

>4gt6_A Cell surface protein; leucine rich repeats, putative protein binding, extracellula protein, structural genomics; HET: MSE; 1.80A {Faecalibacterium prausnitzii a2-165}

Probab=92.71  E-value=0.34  Score=50.45  Aligned_cols=79  Identities=11%  Similarity=0.211  Sum_probs=34.2

Q ss_pred             cccCCCCcEEEeccCCCCCcc--cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCC
Q 042541          597 LSALSKLKKIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDI  674 (695)
Q Consensus       597 l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L  674 (695)
                      +..+.+|+.+.|.. +++.++  ++.++.+|+.+.|..+ ++.+....|.    ++++|+.+++.++..  .+ ..+...
T Consensus       307 F~~c~~L~~i~lp~-~v~~I~~~aF~~C~~L~~i~ip~s-v~~I~~~aF~----~C~~L~~i~~~~~~~--~~-~~~~~~  377 (394)
T 4gt6_A          307 FAGCISLKSIDIPE-GITQILDDAFAGCEQLERIAIPSS-VTKIPESAFS----NCTALNNIEYSGSRS--QW-NAISTD  377 (394)
T ss_dssp             TTTCTTCCEEECCT-TCCEECTTTTTTCTTCCEEEECTT-CCBCCGGGGT----TCTTCCEEEESSCHH--HH-HTCBCC
T ss_pred             ecCCCCcCEEEeCC-cccEehHhHhhCCCCCCEEEECcc-cCEEhHhHhh----CCCCCCEEEECCcee--eh-hhhhcc
Confidence            44455555555543 244444  4555555555555332 4444444444    555555555554311  11 234444


Q ss_pred             CCCceeeccc
Q 042541          675 VSMEKLRITN  684 (695)
Q Consensus       675 ~~L~~L~l~~  684 (695)
                      .+|+.|.+..
T Consensus       378 ~~L~~i~i~~  387 (394)
T 4gt6_A          378 SGLQNLPVAP  387 (394)
T ss_dssp             CCC-------
T ss_pred             CCCCEEEeCC
Confidence            4555554443

>1sq5_A Pantothenate kinase; P-loop, transferase; HET: PAU ADP; 2.20A {Escherichia coli} SCOP: c.37.1.6 PDB: 1esm_A* 1esn_A*

Probab=92.67  E-value=0.065  Score=53.94  Aligned_cols=42  Identities=14%  Similarity=0.061  Sum_probs=28.9

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccc-cCCCcEEEEEeCCC
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQG-KFKDDIFYVTVSKN  229 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~-~f~~~~~wv~~~~~  229 (695)
                      ...+|+|+|+.|+|||||++.+..  .... .....+.+++....
T Consensus        79 ~g~iigI~G~~GsGKSTl~~~L~~--~l~~~~~~G~i~vi~~d~~  121 (308)
T 1sq5_A           79 IPYIISIAGSVAVGKSTTARVLQA--LLSRWPEHRRVELITTDGF  121 (308)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHH--HHTTSTTCCCEEEEEGGGG
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH--HHhhCCCCCeEEEEecCCc
Confidence            457999999999999999999876  2221 12233656665543

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=92.66  E-value=0.046  Score=53.01  Aligned_cols=23  Identities=22%  Similarity=0.257  Sum_probs=21.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+|+|+|+.|+||||+++.+..
T Consensus        48 g~~i~l~G~~GsGKSTl~~~La~   70 (250)
T 3nwj_A           48 GRSMYLVGMMGSGKTTVGKIMAR   70 (250)
T ss_dssp             TCCEEEECSTTSCHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            36899999999999999999986

>2cbz_A Multidrug resistance-associated protein 1; ABC proteins, MRP1/ABCC1, nucleotide-binding domain, ATP- binding, hydrolysis, transport; HET: ATP; 1.5A {Homo sapiens}

Probab=92.64  E-value=0.065  Score=51.58  Aligned_cols=23  Identities=26%  Similarity=0.433  Sum_probs=21.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|+|||||++.++.
T Consensus        31 Ge~~~i~G~nGsGKSTLl~~l~G   53 (237)
T 2cbz_A           31 GALVAVVGQVGCGKSSLLSALLA   53 (237)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            47899999999999999999876

>3io3_A DEHA2D07832P; chaperone, membrane traffic, ATPase; HET: ADP; 1.80A {Debaryomyces hansenii}

Probab=92.60  E-value=0.11  Score=53.11  Aligned_cols=51  Identities=22%  Similarity=0.356  Sum_probs=35.6

Q ss_pred             HHcCCceEEEEEcCCCCcHHHHHHHHhccccccc-cCCCcEEEEEeCCCCCHHH
Q 042541          182 LFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQG-KFKDDIFYVTVSKNPNVKA  234 (695)
Q Consensus       182 L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~-~f~~~~~wv~~~~~~~~~~  234 (695)
                      +.....+++.+.|.||+||||+|..++.  .... ....+++-++.....+...
T Consensus        13 l~~~~~~i~~~~gkGGvGKTt~a~~lA~--~la~~~~g~~vllid~D~~~~l~~   64 (348)
T 3io3_A           13 VQHDSLKWIFVGGKGGVGKTTTSSSVAV--QLALAQPNEQFLLISTDPAHNLSD   64 (348)
T ss_dssp             HTCTTCSEEEEECSTTSSHHHHHHHHHH--HHHHHCTTSCEEEEECCSSCHHHH
T ss_pred             hcCCCcEEEEEeCCCCCcHHHHHHHHHH--HHHHhcCCCeEEEEECCCCCChHH
Confidence            4455578999999999999999998876  3331 2334477888775544443

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=92.59  E-value=0.06  Score=54.43  Aligned_cols=22  Identities=36%  Similarity=0.511  Sum_probs=20.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+|+|.|+.|+||||||+.++.
T Consensus         8 ~lI~I~GptgSGKTtla~~La~   29 (340)
T 3d3q_A            8 FLIVIVGPTASGKTELSIEVAK   29 (340)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             ceEEEECCCcCcHHHHHHHHHH
Confidence            5899999999999999999886

>3gqb_B V-type ATP synthase beta chain; A3B3, V-ATPase, ATP synthesis, ATP-binding, hydrogen ION TRA hydrolase, ION transport; 2.80A {Thermus thermophilus HB8} PDB: 3a5c_D* 3a5d_D 3j0j_D*

Probab=92.56  E-value=0.088  Score=55.05  Aligned_cols=103  Identities=9%  Similarity=0.065  Sum_probs=57.6

Q ss_pred             HHHHHH-cCCceEEEEEcCCCCcHHHHHHHHhcccccc--------ccCCCcEEEEEeCCCC-CHHHHHHHHHHh--cC-
Q 042541          178 LKMELF-KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQ--------GKFKDDIFYVTVSKNP-NVKAIVQKVLHH--KG-  244 (695)
Q Consensus       178 l~~~L~-~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~--------~~f~~~~~wv~~~~~~-~~~~~~~~i~~~--l~-  244 (695)
                      .++.|. -...+-++|.|.+|+|||+|+.++++.....        ++-+..++++-+++.. ...++.+++...  +. 
T Consensus       137 aID~l~pigrGQr~~Ifgg~G~GKt~L~~~Ia~~~~a~~~~~~~~~d~~~~~~V~~~iGeR~~Ev~e~~~~l~~~g~~~r  216 (464)
T 3gqb_B          137 TIDVMNTLVRGQKLPIFSGSGLPANEIAAQIARQATVRPDLSGEGEKEEPFAVVFAAMGITQRELSYFIQEFERTGALSR  216 (464)
T ss_dssp             HHHTTSCCBTTCBCCEEEETTSCHHHHHHHHHHHCBCCHHHHCCCSTTCCEEEEEEEEEECHHHHHHHHHHHHHTSGGGG
T ss_pred             eeecccccccCCEEEEecCCCCCchHHHHHHHHHHHhcccccccccCCCceEEEEEEecCchHHHHHHHHHhhhcccccc
Confidence            334444 2234667899999999999999998754331        1222235577777654 556666666543  10 


Q ss_pred             ----CCCCCCCChHH-----HHHHHHHHHHhcCCCcEEEEEeCCC
Q 042541          245 ----YPVPEFQTDEA-----AINDLERFFKQMRIEAILLVLDDVW  280 (695)
Q Consensus       245 ----~~~~~~~~~~~-----~~~~l~~~~~~l~~~~~LlVlDdv~  280 (695)
                          ....+.+....     ..-.+.+.+..-.++.+|+++||+-
T Consensus       217 tvvv~~t~d~p~~~r~~~~~~a~tiAEyfrd~~G~~VLl~~DdlT  261 (464)
T 3gqb_B          217 SVLFLNKADDPTIERILTPRMALTVAEYLAFEHDYHVLVILTDMT  261 (464)
T ss_dssp             EEEEEEETTSCTHHHHHHHHHHHHHHHHHHHTTCCEEEEEEETHH
T ss_pred             eEEEEECCCCCHHHHHHHHHHHHHHHHHHHHhcCCeEEEEEcChH
Confidence                01111111111     1122334443324899999999973

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=92.55  E-value=0.077  Score=58.92  Aligned_cols=42  Identities=17%  Similarity=0.234  Sum_probs=35.6

Q ss_pred             CCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          166 VISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +.++|.+..++.+...+..+  ..+.|+|++|+||||||+.++.
T Consensus        41 ~~i~G~~~~l~~l~~~i~~g--~~vll~Gp~GtGKTtlar~ia~   82 (604)
T 3k1j_A           41 DQVIGQEHAVEVIKTAANQK--RHVLLIGEPGTGKSMLGQAMAE   82 (604)
T ss_dssp             HHCCSCHHHHHHHHHHHHTT--CCEEEECCTTSSHHHHHHHHHH
T ss_pred             ceEECchhhHhhccccccCC--CEEEEEeCCCCCHHHHHHHHhc
Confidence            45799888888887777655  5789999999999999999987

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=92.52  E-value=0.069  Score=52.26  Aligned_cols=24  Identities=21%  Similarity=0.354  Sum_probs=21.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+++|+|+.|+|||||.+.++.
T Consensus        31 ~Ge~~~liG~nGsGKSTLlk~l~G   54 (262)
T 1b0u_A           31 AGDVISIIGSSGSGKSTFLRCINF   54 (262)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhc
Confidence            347899999999999999999886

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=92.50  E-value=0.058  Score=54.34  Aligned_cols=23  Identities=26%  Similarity=0.449  Sum_probs=21.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .++|+|+|+.|+||||||..++.
T Consensus        40 ~~lIvI~GPTgsGKTtLa~~LA~   62 (339)
T 3a8t_A           40 EKLLVLMGATGTGKSRLSIDLAA   62 (339)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHT
T ss_pred             CceEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999987

>3ake_A Cytidylate kinase; CMP kinase, CMP complex, open conformation, nucleotide metab transferase; HET: C5P; 1.50A {Thermus thermophilus} PDB: 3akc_A* 3akd_A*

Probab=92.48  E-value=0.062  Score=50.36  Aligned_cols=22  Identities=18%  Similarity=0.555  Sum_probs=20.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ++|+|.|+.|+||||+++.+..
T Consensus         3 ~~i~i~G~~GsGKst~~~~la~   24 (208)
T 3ake_A            3 GIVTIDGPSASGKSSVARRVAA   24 (208)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            3899999999999999999876

>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics, cell membrane, cobalt transport, hydrolase, ION transport; 2.30A {Clostridium perfringens atcc 13124}

Probab=92.47  E-value=0.063  Score=52.86  Aligned_cols=23  Identities=26%  Similarity=0.380  Sum_probs=21.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|+|||||++.+..
T Consensus        34 Ge~~~iiGpnGsGKSTLl~~l~G   56 (275)
T 3gfo_A           34 GEVTAILGGNGVGKSTLFQNFNG   56 (275)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHc
Confidence            47899999999999999999875

>3vr4_D V-type sodium ATPase subunit D; V-ATPase, rotary motor, P-loop, hydrolas ATPase, ATP binding; HET: MSE B3P; 2.17A {Enterococcus hirae} PDB: 3vr3_D* 3vr2_D* 3vr5_D 3vr6_D*

Probab=92.47  E-value=0.09  Score=54.96  Aligned_cols=103  Identities=9%  Similarity=0.055  Sum_probs=57.3

Q ss_pred             HHHHHH-cCCceEEEEEcCCCCcHHHHHHHHhcccccc-ccCCCcEEEEEeCCCC-CHHHHHHHHHHh--cC-----CCC
Q 042541          178 LKMELF-KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQ-GKFKDDIFYVTVSKNP-NVKAIVQKVLHH--KG-----YPV  247 (695)
Q Consensus       178 l~~~L~-~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~-~~f~~~~~wv~~~~~~-~~~~~~~~i~~~--l~-----~~~  247 (695)
                      .++.|. -...+-++|.|..|+|||+|+.++.+..... ++-+..++++-+++.. ...++.+++...  +.     ...
T Consensus       141 aID~l~pigrGQr~~Ifgg~G~GKt~L~~~Ia~~~~~~~d~~~~~~V~~~iGeR~~Ev~e~~~~~~~~g~~~rtvvV~at  220 (465)
T 3vr4_D          141 AIDHLNTLVRGQKLPVFSGSGLPHKELAAQIARQATVLDSSDDFAVVFAAIGITFEEAEFFMEDFRQTGAIDRSVMFMNL  220 (465)
T ss_dssp             HHHTTSCCBTTCBCCEEECTTSCHHHHHHHHHHHCBCSSCSSCEEEEEEEEEECHHHHHHHHHHHHHHTGGGGEEEEEEE
T ss_pred             EEecccccccCCEEEEeCCCCcChHHHHHHHHHHHHhccCCCceEEEEEEecCCcHHHHHHHHHHhhcCCccceEEEEEC
Confidence            334444 2234557899999999999999998843331 1122235577777554 566677766553  11     011


Q ss_pred             CCCCChHH-----HHHHHHHHHHhcCCCcEEEEEeCCC
Q 042541          248 PEFQTDEA-----AINDLERFFKQMRIEAILLVLDDVW  280 (695)
Q Consensus       248 ~~~~~~~~-----~~~~l~~~~~~l~~~~~LlVlDdv~  280 (695)
                      .+.+....     ..-.+.+.+..-.++.+|+++||+-
T Consensus       221 sd~p~~~r~~a~~~a~tiAEyfrd~~G~~VLl~~DslT  258 (465)
T 3vr4_D          221 ANDPAIERIATPRMALTAAEYLAYEKGMHVLVIMTDMT  258 (465)
T ss_dssp             TTSCHHHHHHHHHHHHHHHHHHHHTTCCEEEEEEECHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHhcCCeEEEEEcChH
Confidence            11111111     1122334443224899999999973

>3p32_A Probable GTPase RV1496/MT1543; structural genomics, seattle structural genomics center for infectious disease, ssgcid, MEAB, MMAA; HET: GDP PGE; 1.90A {Mycobacterium tuberculosis} PDB: 3md0_A* 4gt1_A* 3nxs_A* 3tk1_A*

Probab=92.37  E-value=0.11  Score=53.43  Aligned_cols=35  Identities=20%  Similarity=0.339  Sum_probs=27.2

Q ss_pred             HHHHHHHHH--cCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          175 LKELKMELF--KDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       175 ~~~l~~~L~--~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..++...+.  .+...+|+|+|.+|+|||||+..+..
T Consensus        65 ~~~~~~~~~~~~~~~~~I~i~G~~G~GKSTl~~~L~~  101 (355)
T 3p32_A           65 AQQLLLRLLPDSGNAHRVGITGVPGVGKSTAIEALGM  101 (355)
T ss_dssp             HHHHHHHHGGGCCCSEEEEEECCTTSSHHHHHHHHHH
T ss_pred             HHHHHHHhHhhcCCceEEEEECCCCCCHHHHHHHHHH
Confidence            344455554  45678999999999999999998876

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=92.36  E-value=0.052  Score=51.04  Aligned_cols=23  Identities=26%  Similarity=0.320  Sum_probs=20.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|+|||||++.++.
T Consensus        22 Ge~~~liG~nGsGKSTLl~~l~G   44 (208)
T 3b85_A           22 NTIVFGLGPAGSGKTYLAMAKAV   44 (208)
T ss_dssp             CSEEEEECCTTSSTTHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            36899999999999999998875

>3r20_A Cytidylate kinase; structural genomics, seattle structural genomics center for infectious disease, ssgcid, ADP, DCMP, D transferase; 2.00A {Mycobacterium smegmatis} SCOP: c.37.1.0 PDB: 3r8c_A 4die_A*

Probab=92.36  E-value=0.067  Score=51.12  Aligned_cols=23  Identities=26%  Similarity=0.580  Sum_probs=20.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+|+|.|++|+||||+++.+..
T Consensus         9 ~~~i~i~G~~GsGKsTla~~la~   31 (233)
T 3r20_A            9 SLVVAVDGPAGTGKSSVSRGLAR   31 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999876

>2olj_A Amino acid ABC transporter; ABC domain, ATPase, hydrolase; HET: ADP; 2.05A {Geobacillus stearothermophilus} PDB: 2olk_A* 2ouk_A 2q0h_A* 3c4j_A* 3c41_J*

Probab=92.35  E-value=0.075  Score=51.96  Aligned_cols=24  Identities=33%  Similarity=0.533  Sum_probs=21.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+++|+|+.|+|||||++.++.
T Consensus        49 ~Gei~~liG~NGsGKSTLlk~l~G   72 (263)
T 2olj_A           49 EGEVVVVIGPSGSGKSTFLRCLNL   72 (263)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCCEEEEEcCCCCcHHHHHHHHHc
Confidence            357999999999999999999886

>4h09_A Hypothetical leucine rich repeat protein; two LRR_5 domains, PF13306 family, structural genomics, JOIN for structural genomics, JCSG; 2.50A {Eubacterium ventriosum}

Probab=92.33  E-value=0.84  Score=47.07  Aligned_cols=79  Identities=10%  Similarity=0.075  Sum_probs=40.7

Q ss_pred             cccCCCCcEEEeccCCCCCcc--cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchh-hcC
Q 042541          597 LSALSKLKKIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDG-LCD  673 (695)
Q Consensus       597 l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~-i~~  673 (695)
                      +..+.+|+.+.+.. ++..++  .+.++.+|+.+.+.++.++.+.+..+.    .+++|+.+.|..  .+..++.. |.+
T Consensus       259 F~~~~~l~~i~l~~-~i~~i~~~aF~~c~~L~~i~l~~~~i~~I~~~aF~----~c~~L~~i~lp~--~l~~I~~~aF~~  331 (379)
T 4h09_A          259 LQNCTALKTLNFYA-KVKTVPYLLCSGCSNLTKVVMDNSAIETLEPRVFM----DCVKLSSVTLPT--ALKTIQVYAFKN  331 (379)
T ss_dssp             TTTCTTCCEEEECC-CCSEECTTTTTTCTTCCEEEECCTTCCEECTTTTT----TCTTCCEEECCT--TCCEECTTTTTT
T ss_pred             cceeehhccccccc-cceeccccccccccccccccccccccceehhhhhc----CCCCCCEEEcCc--cccEEHHHHhhC
Confidence            34445555555532 244444  455556666666655555555555554    555566665542  24444432 445


Q ss_pred             CCCCceeec
Q 042541          674 IVSMEKLRI  682 (695)
Q Consensus       674 L~~L~~L~l  682 (695)
                      +.+|+.+.+
T Consensus       332 C~~L~~i~i  340 (379)
T 4h09_A          332 CKALSTISY  340 (379)
T ss_dssp             CTTCCCCCC
T ss_pred             CCCCCEEEE
Confidence            555555554

>4gzl_A RAS-related C3 botulinum toxin substrate 1; rossmann fold, GTP binding, membrane, hydrolase; HET: GNP; 2.00A {Homo sapiens} PDB: 3th5_A* 4gzm_A*

Probab=92.32  E-value=0.071  Score=49.88  Aligned_cols=36  Identities=22%  Similarity=0.230  Sum_probs=21.0

Q ss_pred             HHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhcc
Q 042541          175 LKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       175 ~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      .+.+.........--|+|+|.+|+|||||+..+.+.
T Consensus        18 ~~~m~~~~~~~~~~ki~vvG~~~~GKSsLi~~l~~~   53 (204)
T 4gzl_A           18 GSHMENLYFQGQAIKCVVVGDGAVGKTCLLISYTTN   53 (204)
T ss_dssp             ------------CEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             hhHHHhHhhcCCeEEEEEECcCCCCHHHHHHHHHhC
Confidence            344434343444567899999999999999888764

>1mv5_A LMRA, multidrug resistance ABC transporter ATP-binding and permease protein; asymmetric dimer, tetramer, P-glycoprotein; HET: ATP ADP; 3.10A {Lactococcus lactis} SCOP: c.37.1.12

Probab=92.32  E-value=0.082  Score=51.12  Aligned_cols=24  Identities=29%  Similarity=0.483  Sum_probs=21.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+++|+|+.|+|||||.+.++.
T Consensus        27 ~Ge~~~i~G~nGsGKSTLl~~l~G   50 (243)
T 1mv5_A           27 PNSIIAFAGPSGGGKSTIFSLLER   50 (243)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhc
Confidence            357999999999999999999875

>2ck3_A ATP synthase subunit alpha\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1bmf_A* 1e1q_A* 1e1r_A* 1e79_A* 1h8h_A* 1nbm_A* 1ohh_A* 1qo1_A 1w0j_A* 1w0k_A* 1h8e_A* 2jdi_A* 2wss_A* 2w6j_A 2w6e_A 2w6g_A 2w6f_A 2w6h_A 2w6i_A 1cow_A* ...

Probab=92.31  E-value=0.27  Score=52.16  Aligned_cols=102  Identities=15%  Similarity=0.214  Sum_probs=58.5

Q ss_pred             HHHHHHH-cCCceEEEEEcCCCCcHHHHH-HHHhccccc----cccCCCcEEEEEeCCCC-CHHHHHHHHHHhcCC----
Q 042541          177 ELKMELF-KDGRQFIVVSAPGGYGKTTLV-QRLCKDDQV----QGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKGY----  245 (695)
Q Consensus       177 ~l~~~L~-~~~~~vv~I~G~gGiGKTtLa-~~~~~~~~~----~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~~----  245 (695)
                      +.++.+. -...+-++|.|..|+|||+|| ..+.+....    .++-+..++++-+++.. ...++.+.+...=..    
T Consensus       151 raID~l~PigrGQR~~I~g~~g~GKT~Lal~~I~~q~~~~~~~~~~~d~~~V~~~IGeR~~Ev~~~~~~~~~~g~m~~tv  230 (510)
T 2ck3_A          151 KAVDSLVPIGRGQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTI  230 (510)
T ss_dssp             HHHHHHSCCBTTCBCEEEESTTSSHHHHHHHHHHHTHHHHTSCCTTTCCEEEEEEESCCHHHHHHHHHHHHHTTCGGGEE
T ss_pred             eeeccccccccCCEEEEecCCCCCchHHHHHHHHHHHhhccccccCCCeEEEEEECCCCcHHHHHHHHHHHhcCCcccce
Confidence            3445555 334567899999999999995 466663221    01234336688888765 456677777653111    


Q ss_pred             ---CCCCCCChHH-----HHHHHHHHHHhcCCCcEEEEEeCC
Q 042541          246 ---PVPEFQTDEA-----AINDLERFFKQMRIEAILLVLDDV  279 (695)
Q Consensus       246 ---~~~~~~~~~~-----~~~~l~~~~~~l~~~~~LlVlDdv  279 (695)
                         ...+.+....     ..-.+.+.+.. .++.+|+++||+
T Consensus       231 vV~atad~p~~~r~~a~~~a~tiAEyfrd-~G~dVLli~Dsl  271 (510)
T 2ck3_A          231 VVSATASDAAPLQYLAPYSGCSMGEYFRD-NGKHALIIYDDL  271 (510)
T ss_dssp             EEEECTTSCHHHHHHHHHHHHHHHHHHHT-TTCEEEEEEETH
T ss_pred             EEEECCCCCHHHHHHHHHHHHHHHHHHHH-cCCcEEEEEcCH
Confidence               1111111111     12234444433 699999999997

>3exa_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.30A {Bacillus halodurans} PDB: 2qgn_A

Probab=92.30  E-value=0.072  Score=52.99  Aligned_cols=23  Identities=26%  Similarity=0.439  Sum_probs=21.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .++|+|+|+.|+||||||..++.
T Consensus         3 ~~~i~i~GptgsGKt~la~~La~   25 (322)
T 3exa_A            3 EKLVAIVGPTAVGKTKTSVMLAK   25 (322)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CcEEEEECCCcCCHHHHHHHHHH
Confidence            46899999999999999999886

>4g1u_C Hemin import ATP-binding protein HMUV; membrane transporter, type II ABC importer, HMUT, plasma MEM transport protein-hydrolase complex; 3.01A {Yersinia pestis}

Probab=92.26  E-value=0.07  Score=52.33  Aligned_cols=23  Identities=30%  Similarity=0.595  Sum_probs=21.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|+|||||++.+..
T Consensus        37 Ge~~~liG~nGsGKSTLl~~l~G   59 (266)
T 4g1u_C           37 GEMVAIIGPNGAGKSTLLRLLTG   59 (266)
T ss_dssp             TCEEEEECCTTSCHHHHHHHHTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhc
Confidence            47899999999999999999986

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=92.24  E-value=0.072  Score=53.47  Aligned_cols=23  Identities=30%  Similarity=0.381  Sum_probs=21.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .++|.|+|+.|+||||||+.++.
T Consensus         5 ~~~i~i~GptGsGKTtla~~La~   27 (323)
T 3crm_A            5 PPAIFLMGPTAAGKTDLAMALAD   27 (323)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            36899999999999999999886

>1ji0_A ABC transporter; ATP binding protein, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: ATP; 2.00A {Thermotoga maritima} SCOP: c.37.1.12

Probab=92.24  E-value=0.07  Score=51.47  Aligned_cols=23  Identities=26%  Similarity=0.414  Sum_probs=21.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|+|||||.+.++.
T Consensus        32 Ge~~~l~G~nGsGKSTLl~~l~G   54 (240)
T 1ji0_A           32 GQIVTLIGANGAGKTTTLSAIAG   54 (240)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            46899999999999999999986

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=92.18  E-value=0.073  Score=50.92  Aligned_cols=23  Identities=30%  Similarity=0.479  Sum_probs=21.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|+|||||.+.++.
T Consensus        34 Ge~~~i~G~nGsGKSTLl~~l~G   56 (229)
T 2pze_A           34 GQLLAVAGSTGAGKTSLLMMIMG   56 (229)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            46899999999999999999986

>1sgw_A Putative ABC transporter; structural genomics, P protein structure initiative, southeast collaboratory for S genomics, secsg; 1.70A {Pyrococcus furiosus} SCOP: c.37.1.12

Probab=92.18  E-value=0.062  Score=50.74  Aligned_cols=23  Identities=30%  Similarity=0.579  Sum_probs=20.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|+|||||.+.++.
T Consensus        35 Ge~~~iiG~NGsGKSTLlk~l~G   57 (214)
T 1sgw_A           35 GNVVNFHGPNGIGKTTLLKTIST   57 (214)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            46899999999999999999875

>4hlc_A DTMP kinase, thymidylate kinase; TMK, MRSA, pipiridine, transfera transferase inhibitor complex; HET: T05; 1.55A {Staphylococcus aureus subsp} PDB: 2cck_A 4gfd_A* 4gsy_A* 4hdc_A* 4hej_A* 2ccj_A* 4hld_A* 2ccg_A*

Probab=92.17  E-value=0.22  Score=46.65  Aligned_cols=50  Identities=18%  Similarity=0.391  Sum_probs=33.2

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHH
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLH  241 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~  241 (695)
                      +.|+|-|.-|+||||+++.+.+  .+...++  ++...-.......+.+++++.
T Consensus         3 kFI~~EG~dGsGKsTq~~~L~~--~L~~~~~--v~~~~eP~~t~~g~~ir~~l~   52 (205)
T 4hlc_A            3 AFITFEGPEGSGKTTVINEVYH--RLVKDYD--VIMTREPGGVPTGEEIRKIVL   52 (205)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH--HHTTTSC--EEEEESSTTCHHHHHHHHHHH
T ss_pred             CEEEEECCCCCcHHHHHHHHHH--HHHCCCC--EEEeeCCCCChHHHHHHHHHh
Confidence            5789999999999999999987  4444443  444444444444455555554

>1g6h_A High-affinity branched-chain amino acid transport ATP-binding protein; beta-core domain; HET: ADP; 1.60A {Methanocaldococcus jannaschii} SCOP: c.37.1.12 PDB: 1gaj_A 1g9x_A*

Probab=92.16  E-value=0.072  Score=52.00  Aligned_cols=23  Identities=26%  Similarity=0.530  Sum_probs=21.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|+|||||.+.++.
T Consensus        33 Ge~~~liG~nGsGKSTLlk~l~G   55 (257)
T 1g6h_A           33 GDVTLIIGPNGSGKSTLINVITG   55 (257)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            46899999999999999999876

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=92.15  E-value=0.073  Score=50.71  Aligned_cols=21  Identities=29%  Similarity=0.327  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .|.|.|+.|+||||+|+.+..
T Consensus         2 ~I~l~G~~GsGKsT~a~~La~   22 (223)
T 2xb4_A            2 NILIFGPNGSGKGTQGNLVKD   22 (223)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            588999999999999999876

>3iqw_A Tail-anchored protein targeting factor GET3; ATPase, Zn binding, protein transport; HET: ANP; 3.00A {Chaetomium thermophilum} PDB: 3iqx_A* 3ibg_A*

Probab=92.12  E-value=0.17  Score=51.27  Aligned_cols=52  Identities=23%  Similarity=0.318  Sum_probs=35.9

Q ss_pred             HHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHH
Q 042541          181 ELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAI  235 (695)
Q Consensus       181 ~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~  235 (695)
                      .+.+...+++.+.|-||+||||+|..++.  ..... ..+++-|+.....+....
T Consensus        10 ~l~~~~~~i~~~sgkGGvGKTt~a~~lA~--~la~~-g~~vllid~D~~~~l~~~   61 (334)
T 3iqw_A           10 ILDQRSLRWIFVGGKGGVGKTTTSCSLAI--QLAKV-RRSVLLLSTDPAHNLSDA   61 (334)
T ss_dssp             HHHCTTCCEEEEECSTTSSHHHHHHHHHH--HHTTS-SSCEEEEECCSSCHHHHH
T ss_pred             HhcCCCeEEEEEeCCCCccHHHHHHHHHH--HHHhC-CCcEEEEECCCCCChhHH
Confidence            34455578899999999999999988876  33322 334778887755544433

>1vpl_A ABC transporter, ATP-binding protein; TM0544, structural GENO joint center for structural genomics, JCSG, protein structu initiative, PSI; 2.10A {Thermotoga maritima} SCOP: c.37.1.12

Probab=92.10  E-value=0.084  Score=51.41  Aligned_cols=24  Identities=25%  Similarity=0.403  Sum_probs=21.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+++|+|+.|+|||||.+.++.
T Consensus        40 ~Gei~~l~G~NGsGKSTLlk~l~G   63 (256)
T 1vpl_A           40 EGEIFGLIGPNGAGKTTTLRIIST   63 (256)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhc
Confidence            347899999999999999999876

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=92.09  E-value=0.043  Score=54.65  Aligned_cols=24  Identities=21%  Similarity=0.362  Sum_probs=18.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+|+|.|+.|+||||+|+.+.+
T Consensus         4 ~~~iIgItG~sGSGKSTva~~L~~   27 (290)
T 1a7j_A            4 KHPIISVTGSSGAGTSTVKHTFDQ   27 (290)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHH
T ss_pred             CceEEEEECCCCCCHHHHHHHHHH
Confidence            456899999999999999999876

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=92.07  E-value=0.12  Score=52.12  Aligned_cols=39  Identities=13%  Similarity=0.200  Sum_probs=28.5

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeC
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVS  227 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~  227 (695)
                      ...+|+|+|.+|+||||++..++.  ..... ...++++...
T Consensus       104 ~~~vI~ivG~~G~GKTT~~~~LA~--~l~~~-g~kVllid~D  142 (320)
T 1zu4_A          104 RLNIFMLVGVNGTGKTTSLAKMAN--YYAEL-GYKVLIAAAD  142 (320)
T ss_dssp             SCEEEEEESSTTSSHHHHHHHHHH--HHHHT-TCCEEEEECC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH--HHHHC-CCeEEEEeCC
Confidence            358999999999999999998886  33322 3346666654

>2ff7_A Alpha-hemolysin translocation ATP-binding protein HLYB; ABC-transporter, transport protein; HET: ADP; 1.60A {Escherichia coli} SCOP: c.37.1.12 PDB: 2ffb_A* 2fgk_A* 2ffa_A* 2fgj_A* 2pmk_A* 3b5j_A* 1mt0_A 1xef_A*

Probab=92.05  E-value=0.076  Score=51.46  Aligned_cols=23  Identities=26%  Similarity=0.414  Sum_probs=21.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|+|||||++.++.
T Consensus        35 Ge~~~i~G~nGsGKSTLl~~l~G   57 (247)
T 2ff7_A           35 GEVIGIVGRSGSGKSTLTKLIQR   57 (247)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            46899999999999999999876

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}

Probab=92.05  E-value=0.2  Score=53.41  Aligned_cols=42  Identities=19%  Similarity=0.242  Sum_probs=28.6

Q ss_pred             CCCCCcchHHHHHH----HHHcCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          167 ISPGLDVPLKELKM----ELFKDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       167 ~~vGr~~~~~~l~~----~L~~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .|-+-..+-++.+.    .+..++ +.+.|.|.+|+||||++..+..
T Consensus        22 ~~~~Ln~~Q~~av~~~~~~i~~~~-~~~li~G~aGTGKT~ll~~~~~   67 (459)
T 3upu_A           22 TFDDLTEGQKNAFNIVMKAIKEKK-HHVTINGPAGTGATTLTKFIIE   67 (459)
T ss_dssp             CSSCCCHHHHHHHHHHHHHHHSSS-CEEEEECCTTSCHHHHHHHHHH
T ss_pred             ccccCCHHHHHHHHHHHHHHhcCC-CEEEEEeCCCCCHHHHHHHHHH
Confidence            34444444444444    333333 4899999999999999998877

>2zej_A Dardarin, leucine-rich repeat kinase 2; parkinson'S disease, LRRK2, ROC, GTPase, ROCO, ATP-B disease mutation, GTP-binding, GTPase activation; HET: GDP; 2.00A {Homo sapiens} PDB: 3d6t_B*

Probab=92.03  E-value=0.075  Score=48.71  Aligned_cols=22  Identities=41%  Similarity=0.569  Sum_probs=19.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHhcc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      -|+|+|.+|+|||||+..+...
T Consensus         4 kv~ivG~~gvGKStLl~~l~~~   25 (184)
T 2zej_A            4 KLMIVGNTGSGKTTLLQQLMKT   25 (184)
T ss_dssp             EEEEESCTTSSHHHHHHHHTCC
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4789999999999999998863

>3foz_A TRNA delta(2)-isopentenylpyrophosphate transferas; nucleoside modification, isopentenyl-tRNA transferase, transferase-RNA complex; 2.50A {Escherichia coli k-12} PDB: 2zxu_A* 2zm5_A

Probab=92.03  E-value=0.083  Score=52.43  Aligned_cols=24  Identities=33%  Similarity=0.342  Sum_probs=21.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..++|.|+|+.|+||||||..++.
T Consensus         9 ~~~~i~i~GptgsGKt~la~~La~   32 (316)
T 3foz_A            9 LPKAIFLMGPTASGKTALAIELRK   32 (316)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCcEEEEECCCccCHHHHHHHHHH
Confidence            357899999999999999999986

>4fs7_A Uncharacterized protein; leucine-rich repeats, protein binding, extracellular protein structural genomics; HET: MSE; 1.19A {Bacteroides ovatus}

Probab=92.02  E-value=0.59  Score=48.61  Aligned_cols=118  Identities=11%  Similarity=0.120  Sum_probs=81.8

Q ss_pred             CCCCceEEEEEEccCccccCC-hhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--cccccc
Q 042541          547 MQGPEVKVVVLNIRTKKYVLP-DFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMN  623 (695)
Q Consensus       547 ~~~~~l~~L~l~~~~~~~~~p-~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~  623 (695)
                      ..++.++.+.+...    .++ ..+..+.+|..+.+.++ .  ..+.. ..+..+.+|+.+.+.. +++.++  ++.++.
T Consensus       273 ~~~~~l~~~~~~~~----~i~~~~F~~~~~L~~i~l~~~-i--~~I~~-~aF~~c~~L~~i~lp~-~v~~I~~~aF~~c~  343 (394)
T 4fs7_A          273 YNCSGLKKVIYGSV----IVPEKTFYGCSSLTEVKLLDS-V--KFIGE-EAFESCTSLVSIDLPY-LVEEIGKRSFRGCT  343 (394)
T ss_dssp             TTCTTCCEEEECSS----EECTTTTTTCTTCCEEEECTT-C--CEECT-TTTTTCTTCCEECCCT-TCCEECTTTTTTCT
T ss_pred             ccccccceeccCce----eeccccccccccccccccccc-c--ceech-hhhcCCCCCCEEEeCC-cccEEhHHhccCCC
Confidence            35666666655332    233 35778899999988653 1  11111 1267888999999964 477887  888999


Q ss_pred             cccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCcee
Q 042541          624 HLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKL  680 (695)
Q Consensus       624 ~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L  680 (695)
                      +|+.+.+..+ ++.+....+.    .+++|+.+++..  .+..+...+.+.++|+.+
T Consensus       344 ~L~~i~lp~~-l~~I~~~aF~----~C~~L~~i~lp~--~~~~~~~~F~~c~~L~~I  393 (394)
T 4fs7_A          344 SLSNINFPLS-LRKIGANAFQ----GCINLKKVELPK--RLEQYRYDFEDTTKFKWI  393 (394)
T ss_dssp             TCCEECCCTT-CCEECTTTBT----TCTTCCEEEEEG--GGGGGGGGBCTTCEEEEE
T ss_pred             CCCEEEECcc-ccEehHHHhh----CCCCCCEEEECC--CCEEhhheecCCCCCcEE
Confidence            9999999776 7777777776    899999999875  355555556666666543

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=92.01  E-value=0.085  Score=51.53  Aligned_cols=24  Identities=21%  Similarity=0.310  Sum_probs=21.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+++|+|+.|+|||||++.+..
T Consensus        45 ~Ge~~~i~G~nGsGKSTLl~~l~G   68 (260)
T 2ghi_A           45 SGTTCALVGHTGSGKSTIAKLLYR   68 (260)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhc
Confidence            347899999999999999999986

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=92.01  E-value=0.088  Score=53.91  Aligned_cols=23  Identities=30%  Similarity=0.432  Sum_probs=21.4

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|+||||+++.++.
T Consensus       157 g~vi~lvG~nGsGKTTll~~Lag  179 (359)
T 2og2_A          157 PAVIMIVGVNGGGKTTSLGKLAH  179 (359)
T ss_dssp             SEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CeEEEEEcCCCChHHHHHHHHHh
Confidence            57999999999999999999887

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=91.99  E-value=0.076  Score=50.33  Aligned_cols=22  Identities=23%  Similarity=0.292  Sum_probs=20.1

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..|.|.|+.|+||||+|+.+..
T Consensus         6 ~~I~l~G~~GsGKsT~a~~La~   27 (217)
T 3be4_A            6 HNLILIGAPGSGKGTQCEFIKK   27 (217)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            4689999999999999999876

>1e4v_A Adenylate kinase; transferase(phosphotransferase); HET: AP5; 1.85A {Escherichia coli} SCOP: c.37.1.1 g.41.2.1 PDB: 1e4y_A* 1ake_A* 1ank_A* 2eck_A* 3hpq_A* 4ake_A 3hpr_A*

Probab=91.99  E-value=0.074  Score=50.22  Aligned_cols=21  Identities=24%  Similarity=0.154  Sum_probs=19.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .|+|.|+.|+||||+|+.+..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~   22 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQAQFIME   22 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            478999999999999999876

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=91.98  E-value=0.11  Score=49.94  Aligned_cols=47  Identities=21%  Similarity=0.282  Sum_probs=31.6

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQK  238 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~  238 (695)
                      ..++.|.|++|+||||||..++..  .... ...++|++....  ...+...
T Consensus        23 G~~~~i~G~~GsGKTtl~~~~~~~--~~~~-~~~v~~~~~e~~--~~~~~~~   69 (247)
T 2dr3_A           23 RNVVLLSGGPGTGKTIFSQQFLWN--GLKM-GEPGIYVALEEH--PVQVRQN   69 (247)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHHHH--HHHT-TCCEEEEESSSC--HHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH--HHhc-CCeEEEEEccCC--HHHHHHH
Confidence            468999999999999999877652  2111 334778876553  3444433

>2d2e_A SUFC protein; ABC-ATPase, SUF protein, 310-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics, binding; 1.70A {Thermus thermophilus} PDB: 2d2f_A*

Probab=91.98  E-value=0.078  Score=51.51  Aligned_cols=23  Identities=30%  Similarity=0.421  Sum_probs=21.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|+|||||++.++.
T Consensus        29 Ge~~~l~G~nGsGKSTLlk~l~G   51 (250)
T 2d2e_A           29 GEVHALMGPNGAGKSTLGKILAG   51 (250)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            46899999999999999999986

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=91.94  E-value=0.087  Score=51.80  Aligned_cols=24  Identities=25%  Similarity=0.393  Sum_probs=21.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+++|+|+.|+|||||++.++.
T Consensus        44 ~Ge~~~i~G~nGsGKSTLlk~l~G   67 (271)
T 2ixe_A           44 PGKVTALVGPNGSGKSTVAALLQN   67 (271)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhc
Confidence            357899999999999999999876

>2zu0_C Probable ATP-dependent transporter SUFC; iron-sulfur cluster, ABC-ATPase, ATP-binding, cytoplasm, nucleotide-binding; HET: MES; 2.20A {Escherichia coli} PDB: 2d3w_A

Probab=91.91  E-value=0.09  Score=51.61  Aligned_cols=24  Identities=29%  Similarity=0.443  Sum_probs=21.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+++|+|+.|+|||||++.++.
T Consensus        45 ~Ge~~~l~G~NGsGKSTLlk~l~G   68 (267)
T 2zu0_C           45 PGEVHAIMGPNGSGKSTLSATLAG   68 (267)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhC
Confidence            347899999999999999999986

>1ltq_A Polynucleotide kinase; phosphatase, alpha/beta, P-loop, transferase; HET: ADP; 2.33A {Enterobacteria phage T4} SCOP: c.108.1.9 c.37.1.1 PDB: 1rc8_A* 1rpz_A* 1rrc_A* 2ia5_A

Probab=91.86  E-value=0.085  Score=52.79  Aligned_cols=22  Identities=23%  Similarity=0.344  Sum_probs=20.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+|.|.|++|+||||+|+.+..
T Consensus         3 ~~I~l~G~~GsGKST~a~~L~~   24 (301)
T 1ltq_A            3 KIILTIGCPGSGKSTWAREFIA   24 (301)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5799999999999999999876

>2qi9_C Vitamin B12 import ATP-binding protein BTUD; inner membrane, membrane, transmembrane, transport, ATP- binding, hydrolase, nucleotide-binding, periplasm; HET: 1PE; 2.60A {Escherichia coli} PDB: 1l7v_C* 4dbl_C

Probab=91.85  E-value=0.084  Score=51.16  Aligned_cols=23  Identities=30%  Similarity=0.616  Sum_probs=21.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|+|||||.+.++.
T Consensus        26 Ge~~~liG~NGsGKSTLlk~l~G   48 (249)
T 2qi9_C           26 GEILHLVGPNGAGKSTLLARMAG   48 (249)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhC
Confidence            46899999999999999999986

>1oix_A RAS-related protein RAB-11A; small G protein, intracellular trafficking, GTP-binding, lipoprotein, prenylation, protein transport; HET: GDP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1oiw_A* 1oiv_A* 3rwo_B* 3rwm_B*

Probab=91.84  E-value=0.082  Score=48.86  Aligned_cols=24  Identities=25%  Similarity=0.459  Sum_probs=21.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhcc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      .-.|+|+|..|+|||||++.+...
T Consensus        29 ~~kv~lvG~~g~GKSTLl~~l~~~   52 (191)
T 1oix_A           29 LFKVVLIGDSGVGKSNLLSRFTRN   52 (191)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcC
Confidence            357899999999999999998764

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=91.84  E-value=0.12  Score=49.22  Aligned_cols=23  Identities=39%  Similarity=0.638  Sum_probs=18.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...|.|.|+.|+||||+++.+.+
T Consensus        25 g~~I~~eG~~GsGKsT~~~~l~~   47 (227)
T 3v9p_A           25 GKFITFEGIDGAGKTTHLQWFCD   47 (227)
T ss_dssp             CCEEEEECCC---CHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999987

>2qe7_A ATP synthase subunit alpha; blockage of ATP hydrolysis, F1-ATPase, single analysis, thermoalkaliphilic, hydrolase; 3.06A {Bacillus SP} PDB: 1sky_B

Probab=91.82  E-value=0.27  Score=51.96  Aligned_cols=97  Identities=16%  Similarity=0.184  Sum_probs=57.0

Q ss_pred             HHHHHH-cCCceEEEEEcCCCCcHHHHH-HHHhccccccccCCCcEEEEEeCCCC-CHHHHHHHHHHhcCCC-------C
Q 042541          178 LKMELF-KDGRQFIVVSAPGGYGKTTLV-QRLCKDDQVQGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKGYP-------V  247 (695)
Q Consensus       178 l~~~L~-~~~~~vv~I~G~gGiGKTtLa-~~~~~~~~~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~~~-------~  247 (695)
                      .++.+. -...+-++|.|..|+|||+|| ..+.+.  .  .-+..++++-+++.. ...++.+.+...=...       .
T Consensus       152 aID~l~PigrGQR~~Ifg~~g~GKT~Lal~~I~~~--~--~~dv~~V~~~iGeR~~Ev~~~~~~~~~~g~m~~tvvV~at  227 (502)
T 2qe7_A          152 AIDSMIPIGRGQRELIIGDRQTGKTTIAIDTIINQ--K--GQDVICIYVAIGQKQSTVAGVVETLRQHDALDYTIVVTAS  227 (502)
T ss_dssp             HHHHSSCCBTTCBCEEEECSSSCHHHHHHHHHHGG--G--SCSEEEEEEEESCCHHHHHHHHHHHHHTTCSTTEEEEEEC
T ss_pred             ecccccccccCCEEEEECCCCCCchHHHHHHHHHh--h--cCCcEEEEEECCCcchHHHHHHHHHhhCCCcceeEEEEEC
Confidence            345544 233567899999999999996 466663  2  233224677788765 4566777776532111       1


Q ss_pred             CCCCChHH-----HHHHHHHHHHhcCCCcEEEEEeCC
Q 042541          248 PEFQTDEA-----AINDLERFFKQMRIEAILLVLDDV  279 (695)
Q Consensus       248 ~~~~~~~~-----~~~~l~~~~~~l~~~~~LlVlDdv  279 (695)
                      .+.+....     ..-.+.+.+.. .++.+|+++||+
T Consensus       228 ad~p~~~r~~a~~~a~tiAEyfrd-~G~dVLl~~Dsl  263 (502)
T 2qe7_A          228 ASEPAPLLYLAPYAGCAMGEYFMY-KGKHALVVYDDL  263 (502)
T ss_dssp             TTSCHHHHHHHHHHHHHHHHHHHT-TTCEEEEEEECH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHH-cCCcEEEEEecH
Confidence            11111111     11234444533 699999999997

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=91.76  E-value=0.1  Score=50.99  Aligned_cols=25  Identities=28%  Similarity=0.504  Sum_probs=22.2

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ....+++|+|+.|+|||||++.+..
T Consensus        23 ~~g~~v~i~Gp~GsGKSTll~~l~g   47 (261)
T 2eyu_A           23 RKMGLILVTGPTGSGKSTTIASMID   47 (261)
T ss_dssp             CSSEEEEEECSTTCSHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCccHHHHHHHHHH
Confidence            4458999999999999999998876

>1ak2_A Adenylate kinase isoenzyme-2; nucleoside monophosphate kinase, phosphotransferase; 1.92A {Bos taurus} SCOP: c.37.1.1 g.41.2.1 PDB: 2ak2_A 2c9y_A*

Probab=91.74  E-value=0.096  Score=50.22  Aligned_cols=23  Identities=35%  Similarity=0.398  Sum_probs=20.8

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...|.|.|+.|+||||+|+.+.+
T Consensus        16 ~~~I~l~G~~GsGKsT~a~~La~   38 (233)
T 1ak2_A           16 GVRAVLLGPPGAGKGTQAPKLAK   38 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            35799999999999999999986

>4edh_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology; HET: TMP ADP; 1.32A {Pseudomonas aeruginosa PAO1} PDB: 4e5u_A* 4esh_A* 4gmd_A* 3uwk_A* 3uwo_A* 3uxm_A*

Probab=91.73  E-value=0.25  Score=46.55  Aligned_cols=23  Identities=30%  Similarity=0.505  Sum_probs=21.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...|+|.|+.|+||||+++.+.+
T Consensus         6 g~~i~~eG~~gsGKsT~~~~l~~   28 (213)
T 4edh_A            6 GLFVTLEGPEGAGKSTNRDYLAE   28 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHH
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHH
Confidence            46899999999999999999987

>2v9p_A Replication protein E1; AAA+ molecular motor, DNA replication, DNA translocation, nucleotide-binding, DNA-binding; 3.00A {Bovine papillomavirus type 1} PDB: 2gxa_A*

Probab=91.73  E-value=0.092  Score=52.40  Aligned_cols=25  Identities=20%  Similarity=0.344  Sum_probs=22.2

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +...+++|+|+.|+|||||++.+..
T Consensus       124 ~~Ge~vaIvGpsGsGKSTLl~lL~g  148 (305)
T 2v9p_A          124 PKKNCLAFIGPPNTGKSMLCNSLIH  148 (305)
T ss_dssp             TTCSEEEEECSSSSSHHHHHHHHHH
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhh
Confidence            4457999999999999999999876

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=91.72  E-value=0.096  Score=51.38  Aligned_cols=23  Identities=30%  Similarity=0.483  Sum_probs=21.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|+|||||.+.++.
T Consensus        33 Ge~~~liG~nGsGKSTLl~~i~G   55 (266)
T 2yz2_A           33 GECLLVAGNTGSGKSTLLQIVAG   55 (266)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhC
Confidence            47899999999999999999875

>3sr0_A Adenylate kinase; phosphoryl transfer analogue, ALF4, transferase (phosphotran phosphoryl transfer, nucleotide-binding; HET: ADP AMP; 1.56A {Aquifex aeolicus} PDB: 2rh5_A 2rgx_A*

Probab=91.71  E-value=0.088  Score=49.39  Aligned_cols=21  Identities=43%  Similarity=0.631  Sum_probs=19.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +|.|.|++|+||+|.|+.++.
T Consensus         2 ~Iil~GpPGsGKgTqa~~La~   22 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLAK   22 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            578999999999999998876

>2wji_A Ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GNP; 1.90A {Methanocaldococcus jannaschii} PDB: 2wjj_A* 2wjh_A*

Probab=91.66  E-value=0.1  Score=46.84  Aligned_cols=23  Identities=22%  Similarity=0.258  Sum_probs=20.5

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhcc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      ..|+|+|.+|+|||||...+...
T Consensus         4 ~~v~lvG~~gvGKStL~~~l~~~   26 (165)
T 2wji_A            4 YEIALIGNPNVGKSTIFNALTGE   26 (165)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHCC
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            46899999999999999998763

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=91.65  E-value=0.09  Score=51.10  Aligned_cols=23  Identities=30%  Similarity=0.459  Sum_probs=21.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|+|||||.+.++.
T Consensus        31 Ge~~~l~G~nGsGKSTLl~~l~G   53 (253)
T 2nq2_C           31 GDILAVLGQNGCGKSTLLDLLLG   53 (253)
T ss_dssp             TCEEEEECCSSSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            46899999999999999999886

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=91.64  E-value=0.09  Score=51.93  Aligned_cols=23  Identities=30%  Similarity=0.313  Sum_probs=21.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|+|||||.+.++.
T Consensus        47 Ge~~~liG~NGsGKSTLlk~l~G   69 (279)
T 2ihy_A           47 GDKWILYGLNGAGKTTLLNILNA   69 (279)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhC
Confidence            46899999999999999999986

>2qmh_A HPR kinase/phosphorylase; V267F mutation, ATP-binding, carbohydrate metabolism, magnesium, metal-binding, multifunctional enzyme; 2.60A {Lactobacillus casei} PDB: 1jb1_A 1kkl_A 1kkm_A*

Probab=91.63  E-value=0.097  Score=48.25  Aligned_cols=23  Identities=17%  Similarity=0.316  Sum_probs=20.8

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+.|.|.|+.|+||||||..+..
T Consensus        34 g~~ilI~GpsGsGKStLA~~La~   56 (205)
T 2qmh_A           34 GLGVLITGDSGVGKSETALELVQ   56 (205)
T ss_dssp             TEEEEEECCCTTTTHHHHHHHHT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH
Confidence            46789999999999999999876

>2vp4_A Deoxynucleoside kinase; ATP-binding, DNA synthesis, phosphoprotein, feedback inhibition, deoxyribonucleoside kinase, salvage pathway; HET: DCP; 2.20A {Drosophila melanogaster} SCOP: c.37.1.1 PDB: 1j90_A* 2jj8_A* 2vp2_A* 1oe0_A* 2vp5_A* 2vp6_A* 2vp9_A* 2vpp_A* 2vqs_A* 2vp0_A* 1ot3_A* 2jcs_A* 1zm7_A* 1zmx_A*

Probab=91.63  E-value=0.092  Score=50.25  Aligned_cols=24  Identities=25%  Similarity=0.299  Sum_probs=21.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+|+|.|+.|+||||+++.+..
T Consensus        19 ~g~~i~i~G~~GsGKSTl~~~L~~   42 (230)
T 2vp4_A           19 QPFTVLIEGNIGSGKTTYLNHFEK   42 (230)
T ss_dssp             CCEEEEEECSTTSCHHHHHHTTGG
T ss_pred             CceEEEEECCCCCCHHHHHHHHHh
Confidence            357999999999999999999886

>4dzz_A Plasmid partitioning protein PARF; deviant walker BOX, DNA segregation, unknown function; HET: ADP; 1.80A {Escherichia coli} PDB: 4e03_A* 4e07_A* 4e09_A*

Probab=91.59  E-value=0.13  Score=47.90  Aligned_cols=86  Identities=17%  Similarity=0.089  Sum_probs=47.7

Q ss_pred             eEEEEE-cCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHh
Q 042541          188 QFIVVS-APGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQ  266 (695)
Q Consensus       188 ~vv~I~-G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~  266 (695)
                      ++|+|+ +-||+||||+|..++.  .... ...+++.++.....+....+.       .......-.......+.+.++.
T Consensus         2 ~vi~v~s~kgG~GKTt~a~~la~--~la~-~g~~vlliD~D~~~~~~~~~~-------~~~~~~~~~~~~~~~l~~~l~~   71 (206)
T 4dzz_A            2 KVISFLNPKGGSGKTTAVINIAT--ALSR-SGYNIAVVDTDPQMSLTNWSK-------AGKAAFDVFTAASEKDVYGIRK   71 (206)
T ss_dssp             EEEEECCSSTTSSHHHHHHHHHH--HHHH-TTCCEEEEECCTTCHHHHHHT-------TSCCSSEEEECCSHHHHHTHHH
T ss_pred             eEEEEEeCCCCccHHHHHHHHHH--HHHH-CCCeEEEEECCCCCCHHHHHh-------cCCCCCcEEecCcHHHHHHHHH
Confidence            577887 6899999999998876  3332 233478888875554443322       1111000000000345555555


Q ss_pred             cCCCcEEEEEeCCCCCC
Q 042541          267 MRIEAILLVLDDVWPGS  283 (695)
Q Consensus       267 l~~~~~LlVlDdv~~~~  283 (695)
                      ++++-=++|+|---...
T Consensus        72 l~~~yD~viiD~~~~~~   88 (206)
T 4dzz_A           72 DLADYDFAIVDGAGSLS   88 (206)
T ss_dssp             HTTTSSEEEEECCSSSS
T ss_pred             hcCCCCEEEEECCCCCC
Confidence            55554578888754443

>1yrb_A ATP(GTP)binding protein; GTPase, P-loop, rossman fold, GDP, HYDR; HET: GDP; 1.75A {Pyrococcus abyssi} SCOP: c.37.1.10 PDB: 1yr6_A* 1yr8_A* 1yr9_A* 1yra_A* 1yr7_A* 2oxr_A*

Probab=91.58  E-value=0.098  Score=51.06  Aligned_cols=23  Identities=30%  Similarity=0.466  Sum_probs=21.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..++.+.|.||+||||++..++.
T Consensus        14 ~~i~~~~GkgGvGKTTl~~~La~   36 (262)
T 1yrb_A           14 SMIVVFVGTAGSGKTTLTGEFGR   36 (262)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEEeCCCCCCHHHHHHHHHH
Confidence            57889999999999999999886

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=91.48  E-value=0.17  Score=47.39  Aligned_cols=108  Identities=15%  Similarity=0.185  Sum_probs=52.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCC--CCChHHHHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPE--FQTDEAAINDLERFF  264 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~--~~~~~~~~~~l~~~~  264 (695)
                      ..+..++|.-|.||||.+...+..  ...+-.. ++.+....+.  ..-...+...++.....  ....       ..++
T Consensus        28 G~l~vitG~MgsGKTT~lL~~a~r--~~~~g~k-Vli~k~~~d~--R~ge~~i~s~~g~~~~a~~~~~~-------~~~~   95 (214)
T 2j9r_A           28 GWIEVICGSMFSGKSEELIRRVRR--TQFAKQH-AIVFKPCIDN--RYSEEDVVSHNGLKVKAVPVSAS-------KDIF   95 (214)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHH--HHHTTCC-EEEEECC-------------------CCEEECSSG-------GGGG
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHH--HHHCCCE-EEEEEeccCC--cchHHHHHhhcCCeeEEeecCCH-------HHHH
Confidence            478899999999999999877763  3222222 5455433221  11122344444332221  1111       1223


Q ss_pred             HhcCCCcEEEEEeCCCCCChHHHhhhcc-CCCCCEEEEEcCCC
Q 042541          265 KQMRIEAILLVLDDVWPGSESLLQKLGF-QLPDYKILVTSRSE  306 (695)
Q Consensus       265 ~~l~~~~~LlVlDdv~~~~~~~~~~l~~-~~~gs~iivTtR~~  306 (695)
                      +.+.++--+|++|.+.-.....++.+.. ...|..||+|-++.
T Consensus        96 ~~~~~~~dvViIDEaQF~~~~~V~~l~~l~~~~~~Vi~~Gl~~  138 (214)
T 2j9r_A           96 KHITEEMDVIAIDEVQFFDGDIVEVVQVLANRGYRVIVAGLDQ  138 (214)
T ss_dssp             GGCCSSCCEEEECCGGGSCTTHHHHHHHHHHTTCEEEEEECSB
T ss_pred             HHHhcCCCEEEEECcccCCHHHHHHHHHHhhCCCEEEEEeccc
Confidence            3334434499999986543332333322 12478999998854

>4h09_A Hypothetical leucine rich repeat protein; two LRR_5 domains, PF13306 family, structural genomics, JOIN for structural genomics, JCSG; 2.50A {Eubacterium ventriosum}

Probab=91.42  E-value=1.1  Score=46.00  Aligned_cols=109  Identities=12%  Similarity=0.085  Sum_probs=73.9

Q ss_pred             CCCCceEEEEEEccCccccCC-hhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--cccccc
Q 042541          547 MQGPEVKVVVLNIRTKKYVLP-DFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMN  623 (695)
Q Consensus       547 ~~~~~l~~L~l~~~~~~~~~p-~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~  623 (695)
                      ..+..|+.+.+..+  ...++ ..+.++.+|..+.+..+ .  ..+. ...+..+.+|+.+.+.++.++.++  .+.++.
T Consensus       237 ~~~~~L~~i~lp~~--v~~I~~~aF~~~~~l~~i~l~~~-i--~~i~-~~aF~~c~~L~~i~l~~~~i~~I~~~aF~~c~  310 (379)
T 4h09_A          237 YGMKALDEIAIPKN--VTSIGSFLLQNCTALKTLNFYAK-V--KTVP-YLLCSGCSNLTKVVMDNSAIETLEPRVFMDCV  310 (379)
T ss_dssp             TTCSSCCEEEECTT--CCEECTTTTTTCTTCCEEEECCC-C--SEEC-TTTTTTCTTCCEEEECCTTCCEECTTTTTTCT
T ss_pred             cCCccceEEEcCCC--ccEeCccccceeehhcccccccc-c--eecc-ccccccccccccccccccccceehhhhhcCCC
Confidence            35667777766443  22232 35777888888888542 1  1111 122678899999999998899888  888999


Q ss_pred             cccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCc
Q 042541          624 HLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELP  668 (695)
Q Consensus       624 ~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP  668 (695)
                      +|+.+.|..+ ++.+....|.    ++++|+.+.+..  .+..+.
T Consensus       311 ~L~~i~lp~~-l~~I~~~aF~----~C~~L~~i~ip~--~v~~I~  348 (379)
T 4h09_A          311 KLSSVTLPTA-LKTIQVYAFK----NCKALSTISYPK--SITLIE  348 (379)
T ss_dssp             TCCEEECCTT-CCEECTTTTT----TCTTCCCCCCCT--TCCEEC
T ss_pred             CCCEEEcCcc-ccEEHHHHhh----CCCCCCEEEECC--ccCEEc
Confidence            9999999654 6777776665    778888777753  244443

>2f9l_A RAB11B, member RAS oncogene family; RAB11B GTPase, vesicle transport, hydrolase; HET: GDP; 1.55A {Homo sapiens} SCOP: c.37.1.8 PDB: 2f9m_A* 1yzk_A* 2hv8_A* 2gzd_A* 2gzh_A* 2d7c_A* 3bfk_A*

Probab=91.35  E-value=0.092  Score=48.80  Aligned_cols=23  Identities=26%  Similarity=0.511  Sum_probs=20.5

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhcc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      -.|+|+|..|+|||||.+.+...
T Consensus         6 ~kv~lvG~~g~GKSTLl~~l~~~   28 (199)
T 2f9l_A            6 FKVVLIGDSGVGKSNLLSRFTRN   28 (199)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECcCCCCHHHHHHHHhcC
Confidence            46899999999999999998864

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=91.34  E-value=0.056  Score=49.98  Aligned_cols=108  Identities=12%  Similarity=0.141  Sum_probs=53.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCC--CCChHHHHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPE--FQTDEAAINDLERFF  264 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~--~~~~~~~~~~l~~~~  264 (695)
                      .++..++|..|.||||.+....+....++ +.  ++.+......  ..-...+...++...+.  ....       ..++
T Consensus         8 g~i~v~~G~mgsGKTT~ll~~a~r~~~~g-~k--V~v~k~~~d~--r~~~~~i~s~~g~~~~a~~~~~~-------~~i~   75 (191)
T 1xx6_A            8 GWVEVIVGPMYSGKSEELIRRIRRAKIAK-QK--IQVFKPEIDN--RYSKEDVVSHMGEKEQAVAIKNS-------REIL   75 (191)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHTT-CC--EEEEEEC---------CEEECTTSCEEECEEESSS-------THHH
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHHCC-CE--EEEEEeccCc--cchHHHHHhhcCCceeeEeeCCH-------HHHH
Confidence            47899999999999999988777322222 22  4444422111  10111223333321110  0111       1233


Q ss_pred             HhcCCCcEEEEEeCCCCCChHHHhhhcc-CCCCCEEEEEcCCC
Q 042541          265 KQMRIEAILLVLDDVWPGSESLLQKLGF-QLPDYKILVTSRSE  306 (695)
Q Consensus       265 ~~l~~~~~LlVlDdv~~~~~~~~~~l~~-~~~gs~iivTtR~~  306 (695)
                      +.+.++--+|++|.+.......+..+.. ...|..||+|.++.
T Consensus        76 ~~~~~~~dvViIDEaqfl~~~~v~~l~~l~~~~~~Vi~~Gl~~  118 (191)
T 1xx6_A           76 KYFEEDTEVIAIDEVQFFDDEIVEIVNKIAESGRRVICAGLDM  118 (191)
T ss_dssp             HHCCTTCSEEEECSGGGSCTHHHHHHHHHHHTTCEEEEEECSB
T ss_pred             HHHhccCCEEEEECCCCCCHHHHHHHHHHHhCCCEEEEEeccc
Confidence            3444433499999975543332333222 12378999988754

>2c61_A A-type ATP synthase non-catalytic subunit B; hydrolase, H+ ATPase, A1AO, ATP synthesis, hydrogen ION transport, ION transport; 1.5A {Methanosarcina mazei GO1} PDB: 3dsr_A* 3b2q_A* 2rkw_A* 3eiu_A*

Probab=91.31  E-value=0.17  Score=53.18  Aligned_cols=102  Identities=8%  Similarity=0.081  Sum_probs=57.3

Q ss_pred             HHHHHH-cCCceEEEEEcCCCCcHHHHHHHHhccccccccC-CCcEEEEEeCCCC-CHHHHHHHHHHhcCC-------CC
Q 042541          178 LKMELF-KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKF-KDDIFYVTVSKNP-NVKAIVQKVLHHKGY-------PV  247 (695)
Q Consensus       178 l~~~L~-~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f-~~~~~wv~~~~~~-~~~~~~~~i~~~l~~-------~~  247 (695)
                      .++.|. -...+-++|.|.+|+|||+|+.+++++......- +..++++-+++.. ...++.+++...=..       ..
T Consensus       142 ~ID~l~pigrGQr~~Ifgg~G~GKt~Ll~~Ia~~~~~n~~~~~~~~V~~~iGER~~Ev~e~~~~~~~~g~m~rtvvV~~t  221 (469)
T 2c61_A          142 TIDGTNTLVRGQKLPIFSASGLPHNEIALQIARQASVPGSESAFAVVFAAMGITNEEAQYFMSDFEKTGALERAVVFLNL  221 (469)
T ss_dssp             HHHTTSCCBTTCBCCEEECTTSCHHHHHHHHHHHCBCTTCSSCEEEEEEEEEECHHHHHHHHHHHHHHSGGGGEEEEEEE
T ss_pred             eeeeeeccccCCEEEEECCCCCCHHHHHHHHHHHHhhccCCCCcEEEEEEccCCcHHHHHHHHHHHhccCccceEEEEEC
Confidence            345444 2334667889999999999999998854432211 1225577777654 566777777654111       11


Q ss_pred             CCCCChH-----HHHHHHHHHHHhcCCCcEEEEEeCC
Q 042541          248 PEFQTDE-----AAINDLERFFKQMRIEAILLVLDDV  279 (695)
Q Consensus       248 ~~~~~~~-----~~~~~l~~~~~~l~~~~~LlVlDdv  279 (695)
                      .+.+...     ...-.+.+.+..-+++.+|+++||+
T Consensus       222 sd~p~~~r~~~~~~a~tiAEyfrdd~G~dVLl~~Dsl  258 (469)
T 2c61_A          222 ADDPAVERIVTPRMALTAAEYLAYEHGMHVLVILTDI  258 (469)
T ss_dssp             TTSCHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEECH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHhcCCeEEEEEeCH
Confidence            1111111     1112233333212489999999996

>2yhs_A FTSY, cell division protein FTSY; cell cycle, protein targeting, simibi class GTPase, GTP-BIND membrane, nucleotide-binding; 1.60A {Escherichia coli} PDB: 2qy9_A 2xxa_B* 1fts_A

Probab=91.30  E-value=0.11  Score=55.02  Aligned_cols=23  Identities=30%  Similarity=0.481  Sum_probs=21.4

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|..|+|||||++.++.
T Consensus       293 GeVI~LVGpNGSGKTTLl~~LAg  315 (503)
T 2yhs_A          293 PFVILMVGVNGVGKTTTIGKLAR  315 (503)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCcccHHHHHHHHHH
Confidence            57999999999999999999886

>1p9r_A General secretion pathway protein E; bacterial type II secretion system cytoplasmic protein - GSPE, putative ATPase/ ATP binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11 PDB: 1p9w_A*

Probab=91.28  E-value=0.2  Score=52.43  Aligned_cols=41  Identities=24%  Similarity=0.292  Sum_probs=28.6

Q ss_pred             CCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          169 PGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       169 vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +|.......+...+......+++|+|+.|+|||||.+.+..
T Consensus       149 Lg~~~~~~~~L~~l~~~~ggii~I~GpnGSGKTTlL~allg  189 (418)
T 1p9r_A          149 LGMTAHNHDNFRRLIKRPHGIILVTGPTGSGKSTTLYAGLQ  189 (418)
T ss_dssp             SCCCHHHHHHHHHHHTSSSEEEEEECSTTSCHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHh
Confidence            34443333333333445568999999999999999999876

>1fx0_A ATP synthase alpha chain; latent ATPase, thermal stability, potential tentoxin binding hydrolase; 3.20A {Spinacia oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_A*

Probab=91.15  E-value=0.17  Score=53.52  Aligned_cols=88  Identities=16%  Similarity=0.210  Sum_probs=52.9

Q ss_pred             ceEEEEEcCCCCcHHHHH-HHHhccccccccCCCcEEEEEeCCCC-CHHHHHHHHHHhcC-------CCCCCCCC-----
Q 042541          187 RQFIVVSAPGGYGKTTLV-QRLCKDDQVQGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKG-------YPVPEFQT-----  252 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa-~~~~~~~~~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~-------~~~~~~~~-----  252 (695)
                      .+-++|.|..|+|||+|| ..+.+.  ..  -+..++++-+++.. ...++.+.+...=.       ....+.+.     
T Consensus       163 GQR~~Ifg~~g~GKT~Lal~~I~~~--~~--~dv~~V~~~iGeR~~Ev~~~~~~~~~~g~m~rtvvV~atad~p~~~r~~  238 (507)
T 1fx0_A          163 GQRELIIGDRQTGKTAVATDTILNQ--QG--QNVICVYVAIGQKASSVAQVVTNFQERGAMEYTIVVAETADSPATLQYL  238 (507)
T ss_dssp             TCBCBEEESSSSSHHHHHHHHHHTC--CT--TTCEEEEEEESCCHHHHHHHHHHTGGGTGGGSEEEEEECTTSCGGGTTH
T ss_pred             CCEEEEecCCCCCccHHHHHHHHHh--hc--CCcEEEEEEcCCCchHHHHHHHHHHhcCccccceEEEECCCCCHHHHHH
Confidence            467899999999999996 577663  22  34335678888765 45566666554210       01111111     


Q ss_pred             hHHHHHHHHHHHHhcCCCcEEEEEeCC
Q 042541          253 DEAAINDLERFFKQMRIEAILLVLDDV  279 (695)
Q Consensus       253 ~~~~~~~l~~~~~~l~~~~~LlVlDdv  279 (695)
                      .....-.+.+.+.. .++.+|+++||+
T Consensus       239 a~~~a~tiAEyfrd-~G~dVLli~Dsl  264 (507)
T 1fx0_A          239 APYTGAALAEYFMY-RERHTLIIYDDL  264 (507)
T ss_dssp             HHHHHHHHHHHHHH-TTCEEEEEEECH
T ss_pred             HHHHHHHHHHHHHH-cCCcEEEEEecH
Confidence            12223345555533 699999999997

>2r9v_A ATP synthase subunit alpha; TM1612, structural genomics, JOI for structural genomics, JCSG, protein structure initiative ATP synthesis; HET: ATP PG4; 2.10A {Thermotoga maritima MSB8}

Probab=91.06  E-value=0.24  Score=52.49  Aligned_cols=98  Identities=14%  Similarity=0.137  Sum_probs=57.4

Q ss_pred             HHHHHHH-cCCceEEEEEcCCCCcHHHHH-HHHhccccccccCCCcEEEEEeCCCC-CHHHHHHHHHHhcC-------CC
Q 042541          177 ELKMELF-KDGRQFIVVSAPGGYGKTTLV-QRLCKDDQVQGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKG-------YP  246 (695)
Q Consensus       177 ~l~~~L~-~~~~~vv~I~G~gGiGKTtLa-~~~~~~~~~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~-------~~  246 (695)
                      +.++.+. -...+-++|.|..|+|||+|| ..+.+.  .  .-+..++++-+++.. ...++.+.+...=.       ..
T Consensus       164 raID~l~PigrGQR~~I~g~~g~GKT~Lal~~I~~~--~--~~dv~~V~~~IGeR~~Ev~e~~~~~~~~g~m~rtvvV~a  239 (515)
T 2r9v_A          164 KAIDSMIPIGRGQRELIIGDRQTGKTAIAIDTIINQ--K--GQGVYCIYVAIGQKKSAIARIIDKLRQYGAMEYTTVVVA  239 (515)
T ss_dssp             HHHHHHSCEETTCBEEEEEETTSSHHHHHHHHHHTT--T--TTTEEEEEEEESCCHHHHHHHHHHHHHTTGGGGEEEEEE
T ss_pred             cccccccccccCCEEEEEcCCCCCccHHHHHHHHHh--h--cCCcEEEEEEcCCCcHHHHHHHHHHHhCCCcceeEEEEE
Confidence            3445554 234467899999999999996 467663  2  233224677788765 45667777765311       11


Q ss_pred             CCCCCChH-----HHHHHHHHHHHhcCCCcEEEEEeCC
Q 042541          247 VPEFQTDE-----AAINDLERFFKQMRIEAILLVLDDV  279 (695)
Q Consensus       247 ~~~~~~~~-----~~~~~l~~~~~~l~~~~~LlVlDdv  279 (695)
                      ..+.+...     ...-.+.+.+.. .++.+|+++||+
T Consensus       240 tad~p~~~r~~a~~~a~tiAEyfrd-~G~dVLli~Dsl  276 (515)
T 2r9v_A          240 SASDPASLQYIAPYAGCAMGEYFAY-SGRDALVVYDDL  276 (515)
T ss_dssp             CTTSCHHHHHHHHHHHHHHHHHHHT-TTCEEEEEEETH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHH-cCCcEEEEeccH
Confidence            11111111     112234444433 689999999997

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=91.04  E-value=0.13  Score=45.54  Aligned_cols=23  Identities=30%  Similarity=0.469  Sum_probs=20.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhcc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      +-|+|+|.+|+|||||+..+...
T Consensus         2 ~ki~v~G~~~~GKSsli~~l~~~   24 (161)
T 2dyk_A            2 HKVVIVGRPNVGKSSLFNRLLKK   24 (161)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            46899999999999999998764

>1tq4_A IIGP1, interferon-inducible GTPase; interferon gamma, dimer, immunology, signaling protein; HET: GDP; 1.95A {Mus musculus} SCOP: c.37.1.8 PDB: 1tqd_A* 1tq6_A* 1tpz_A* 1tq2_A*

Probab=91.02  E-value=0.15  Score=53.16  Aligned_cols=24  Identities=21%  Similarity=0.342  Sum_probs=21.8

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+++|+|+.|+|||||.+.+..
T Consensus        68 ~~~~valvG~nGaGKSTLln~L~G   91 (413)
T 1tq4_A           68 SVLNVAVTGETGSGKSSFINTLRG   91 (413)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCcHHHHHHHHhC
Confidence            457999999999999999999876

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=90.97  E-value=0.12  Score=50.59  Aligned_cols=23  Identities=30%  Similarity=0.596  Sum_probs=21.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|+|||||.+.++.
T Consensus        30 Ge~~~i~G~NGsGKSTLlk~l~G   52 (263)
T 2pjz_A           30 GEKVIILGPNGSGKTTLLRAISG   52 (263)
T ss_dssp             SSEEEEECCTTSSHHHHHHHHTT
T ss_pred             CEEEEEECCCCCCHHHHHHHHhC
Confidence            46899999999999999999986

>2afh_E Nitrogenase iron protein 1; nitrogen fixation, iron-sulfur, metal-binding, molybdenum, oxidoreductase; HET: HCA CFN CLF PGE PG4 P6G 1PE; 2.10A {Azotobacter vinelandii} SCOP: c.37.1.10 PDB: 1g1m_A 1g5p_A 1m1y_E* 1m34_E* 1n2c_E* 1nip_A* 1fp6_A* 2afi_E* 2afk_E* 2nip_A 1de0_A 1xcp_A* 1xdb_A 1xd8_A 1xd9_A* 1g20_E* 1g21_E* 2c8v_A* 1rw4_A

Probab=90.96  E-value=0.2  Score=49.78  Aligned_cols=39  Identities=21%  Similarity=0.315  Sum_probs=29.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCC
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKN  229 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~  229 (695)
                      ++|+|.|-||+||||+|..++.  ..... ..+++.|+....
T Consensus         3 kvIavs~KGGvGKTT~a~nLA~--~La~~-G~rVlliD~D~q   41 (289)
T 2afh_E            3 RQCAIYGKGGIGKSTTTQNLVA--ALAEM-GKKVMIVGCDPK   41 (289)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHH--HHHHT-TCCEEEEEECSS
T ss_pred             eEEEEeCCCcCcHHHHHHHHHH--HHHHC-CCeEEEEecCCC
Confidence            6788899999999999998886  33222 334778887643

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A

Probab=90.95  E-value=0.11  Score=51.51  Aligned_cols=23  Identities=30%  Similarity=0.494  Sum_probs=21.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..++.|+|++|+|||||+..++.
T Consensus        30 G~i~~i~G~~GsGKTtl~~~l~~   52 (279)
T 1nlf_A           30 GTVGALVSPGGAGKSMLALQLAA   52 (279)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHH
Confidence            47999999999999999998875

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=90.90  E-value=0.2  Score=46.02  Aligned_cols=24  Identities=33%  Similarity=0.571  Sum_probs=21.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhcc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      ...|+|+|.+|+|||||+..+...
T Consensus        48 ~~~i~vvG~~g~GKSsll~~l~~~   71 (193)
T 2ged_A           48 QPSIIIAGPQNSGKTSLLTLLTTD   71 (193)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            457999999999999999998764

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=90.88  E-value=0.3  Score=45.30  Aligned_cols=51  Identities=22%  Similarity=0.321  Sum_probs=34.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHh
Q 042541          189 FIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHH  242 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~  242 (695)
                      .|+|-|.-|+||||.++.+++  .+...-.. +.+..-.......+.++.++..
T Consensus         2 fI~~EG~DGsGKsTq~~~L~~--~L~~~g~~-v~~treP~~t~~~~~ir~~l~~   52 (197)
T 3hjn_A            2 FITFEGIDGSGKSTQIQLLAQ--YLEKRGKK-VILKREPGGTETGEKIRKILLE   52 (197)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH--HHHHTTCC-EEEEESSCSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH--HHHHCCCc-EEEEECCCCCcHHHHHHHHhhc
Confidence            478899999999999999987  45443333 5455555554555555555543

>4gt6_A Cell surface protein; leucine rich repeats, putative protein binding, extracellula protein, structural genomics; HET: MSE; 1.80A {Faecalibacterium prausnitzii a2-165}

Probab=90.84  E-value=0.53  Score=48.97  Aligned_cols=105  Identities=8%  Similarity=0.170  Sum_probs=78.7

Q ss_pred             hhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--cccccccccEEeeccccCCcccccchhhh
Q 042541          569 FLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFRNSTFRI  646 (695)
Q Consensus       569 ~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~~~~l  646 (695)
                      .|.++.+|+.+.+.++..   .+.. ..+.++.+|+.+.+. +.+..++  .+.++.+|+.+.|..+ ++.+....|.  
T Consensus       260 aF~~c~~L~~i~lp~~~~---~I~~-~aF~~c~~L~~i~l~-~~i~~I~~~aF~~c~~L~~i~lp~~-v~~I~~~aF~--  331 (394)
T 4gt6_A          260 AFDSCAYLASVKMPDSVV---SIGT-GAFMNCPALQDIEFS-SRITELPESVFAGCISLKSIDIPEG-ITQILDDAFA--  331 (394)
T ss_dssp             TTTTCSSCCEEECCTTCC---EECT-TTTTTCTTCCEEECC-TTCCEECTTTTTTCTTCCEEECCTT-CCEECTTTTT--
T ss_pred             eeeecccccEEecccccc---eecC-cccccccccccccCC-CcccccCceeecCCCCcCEEEeCCc-ccEehHhHhh--
Confidence            577888899888765322   1111 125678889999885 5677788  8888999999999754 6777777776  


Q ss_pred             cccCCCccEEecccccccccCchh-hcCCCCCceeecccc
Q 042541          647 SDAFPNLLEMDIDYCNDLIELPDG-LCDIVSMEKLRITNC  685 (695)
Q Consensus       647 ~~~l~~L~~L~l~~c~~l~~lP~~-i~~L~~L~~L~l~~~  685 (695)
                        .+++|+.+.+..  .+..++.. |.++.+|+.+++.++
T Consensus       332 --~C~~L~~i~ip~--sv~~I~~~aF~~C~~L~~i~~~~~  367 (394)
T 4gt6_A          332 --GCEQLERIAIPS--SVTKIPESAFSNCTALNNIEYSGS  367 (394)
T ss_dssp             --TCTTCCEEEECT--TCCBCCGGGGTTCTTCCEEEESSC
T ss_pred             --CCCCCCEEEECc--ccCEEhHhHhhCCCCCCEEEECCc
Confidence              899999999964  47778654 889999999998764

>1svm_A Large T antigen; AAA+ fold, viral protein; HET: ATP; 1.94A {Simian virus 40} SCOP: c.37.1.20 PDB: 1svl_A* 1svo_A 1n25_A 2h1l_A

Probab=90.84  E-value=0.12  Score=53.21  Aligned_cols=25  Identities=28%  Similarity=0.418  Sum_probs=22.4

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +...+++|+|+.|+|||||++.+..
T Consensus       167 ~~~~~i~l~G~~GsGKSTl~~~l~~  191 (377)
T 1svm_A          167 PKKRYWLFKGPIDSGKTTLAAALLE  191 (377)
T ss_dssp             TTCCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHh
Confidence            4457999999999999999999986

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=90.82  E-value=0.074  Score=58.75  Aligned_cols=21  Identities=19%  Similarity=0.395  Sum_probs=19.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      -|.++|++|+|||+||+.+++
T Consensus       329 ~vLL~GppGtGKT~LAr~la~  349 (595)
T 3f9v_A          329 HILIIGDPGTAKSQMLQFISR  349 (595)
T ss_dssp             CEEEEESSCCTHHHHHHSSST
T ss_pred             ceEEECCCchHHHHHHHHHHH
Confidence            589999999999999999886

>1cp2_A CP2, nitrogenase iron protein; oxidoreductase; 1.93A {Clostridium pasteurianum} SCOP: c.37.1.10

Probab=90.79  E-value=0.24  Score=48.45  Aligned_cols=39  Identities=23%  Similarity=0.367  Sum_probs=28.8

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCC
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKN  229 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~  229 (695)
                      ++|+|.|-||+||||+|..++.  ..... ..+++.|+....
T Consensus         2 ~vI~vs~KGGvGKTT~a~nLA~--~la~~-G~~VlliD~D~q   40 (269)
T 1cp2_A            2 RQVAIYGKGGIGKSTTTQNLTS--GLHAM-GKTIMVVGCDPK   40 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHH--HHHTT-TCCEEEEEECTT
T ss_pred             cEEEEecCCCCcHHHHHHHHHH--HHHHC-CCcEEEEcCCCC
Confidence            5788899999999999988886  33322 334778887643

>3oaa_A ATP synthase subunit alpha; rossmann fold, hydrolase, hydrolase-transport PROT complex; HET: ANP ADP; 3.26A {Escherichia coli DH1} PDB: 2a7u_A

Probab=90.77  E-value=0.58  Score=49.36  Aligned_cols=98  Identities=17%  Similarity=0.229  Sum_probs=57.6

Q ss_pred             HHHHHH-cCCceEEEEEcCCCCcHHHHH-HHHhccccccccCCCcEEEEEeCCCC-CHHHHHHHHHHhcCCC-------C
Q 042541          178 LKMELF-KDGRQFIVVSAPGGYGKTTLV-QRLCKDDQVQGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKGYP-------V  247 (695)
Q Consensus       178 l~~~L~-~~~~~vv~I~G~gGiGKTtLa-~~~~~~~~~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~~~-------~  247 (695)
                      .++.|. -...+-++|.|..|+|||+|+ ..+.+.    ..-+..++++-+++.. ...++.+.+...=...       .
T Consensus       152 aID~l~PigrGQR~~Ifg~~g~GKT~l~l~~I~n~----~~~dv~~V~~~IGeR~~ev~e~~~~l~~~g~m~~tvvV~at  227 (513)
T 3oaa_A          152 AVDSMIPIGRGQRELIIGDRQTGKTALAIDAIINQ----RDSGIKCIYVAIGQKASTISNVVRKLEEHGALANTIVVVAT  227 (513)
T ss_dssp             HHHHHSCCBTTCBCEEEESSSSSHHHHHHHHHHTT----SSSSCEEEEEEESCCHHHHHHHHHHHHHHSCSTTEEEEEEC
T ss_pred             eeccccccccCCEEEeecCCCCCcchHHHHHHHhh----ccCCceEEEEEecCChHHHHHHHHHHhhcCcccceEEEEEC
Confidence            445554 334567899999999999996 566652    2233335688888765 4567777765541111       1


Q ss_pred             CCCCChH-----HHHHHHHHHHHhcCCCcEEEEEeCCC
Q 042541          248 PEFQTDE-----AAINDLERFFKQMRIEAILLVLDDVW  280 (695)
Q Consensus       248 ~~~~~~~-----~~~~~l~~~~~~l~~~~~LlVlDdv~  280 (695)
                      .+.+...     ...-.+.+.+.. +++.+|+++||+.
T Consensus       228 ad~p~~~r~~a~~~a~tiAEyfrd-~G~dVLli~Dslt  264 (513)
T 3oaa_A          228 ASESAALQYLAPYAGCAMGEYFRD-RGEDALIIYDDLS  264 (513)
T ss_dssp             TTSCHHHHHHHHHHHHHHHHHHHH-TTCEEEEEEETHH
T ss_pred             CCCChHHHHHHHHHHHHHHHHHHh-cCCCEEEEecChH
Confidence            1111111     112234444432 6999999999973

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=90.75  E-value=0.13  Score=49.28  Aligned_cols=23  Identities=26%  Similarity=0.456  Sum_probs=21.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+|+|.|+.|+||||+++.+..
T Consensus        16 ~~~i~i~G~~gsGKst~~~~l~~   38 (236)
T 1q3t_A           16 TIQIAIDGPASSGKSTVAKIIAK   38 (236)
T ss_dssp             CCEEEEECSSCSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999999876

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=90.74  E-value=0.24  Score=46.79  Aligned_cols=38  Identities=16%  Similarity=0.247  Sum_probs=26.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCC
Q 042541          189 FIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKN  229 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~  229 (695)
                      .|.+.|.||+||||+|..+.... ....++  +..+.+...
T Consensus         8 ~I~~~~kgGvGKTt~a~~la~~l-~~~G~~--V~v~d~D~q   45 (228)
T 2r8r_A            8 KVFLGAAPGVGKTYAMLQAAHAQ-LRQGVR--VMAGVVETH   45 (228)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHH-HHTTCC--EEEEECCCT
T ss_pred             EEEEECCCCCcHHHHHHHHHHHH-HHCCCC--EEEEEeCCC
Confidence            48889999999999998887732 222233  656666543

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=90.73  E-value=0.49  Score=58.76  Aligned_cols=85  Identities=16%  Similarity=0.202  Sum_probs=54.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCC-----CCChHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPE-----FQTDEAAINDLE  261 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~-----~~~~~~~~~~l~  261 (695)
                      ..++.|+|++|+||||||.+++..  .... ...++|++.....+...     ++.++.....     ..+.++..+.+.
T Consensus       383 G~lilI~G~pGsGKTtLaLqia~~--~a~~-G~~vlyis~E~s~~~~~-----a~~lGvd~~~L~I~~~~~~e~il~~~~  454 (2050)
T 3cmu_A          383 GRIVEIYGPESSGKTTLTLQVIAA--AQRE-GKTCAFIDAEHALDPIY-----ARKLGVDIDNLLCSQPDTGEQALEICD  454 (2050)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHHH--HHTT-TCCEEEECTTSCCCHHH-----HHHTTCCTTTCEEECCSSHHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHH--HHhc-CCeEEEEEcCCCHHHHH-----HHHcCCCHHHeEEeCCCCHHHHHHHHH
Confidence            579999999999999999998873  3222 23488999888777542     4556543221     123333334443


Q ss_pred             HHHHhcCCCcEEEEEeCCCC
Q 042541          262 RFFKQMRIEAILLVLDDVWP  281 (695)
Q Consensus       262 ~~~~~l~~~~~LlVlDdv~~  281 (695)
                      .+.+  ..+.-+||+|.+..
T Consensus       455 ~lv~--~~~~~lIVIDSL~a  472 (2050)
T 3cmu_A          455 ALAR--SGAVDVIVVDSVAA  472 (2050)
T ss_dssp             HHHH--HTCCSEEEESCGGG
T ss_pred             HHHH--hcCCcEEEECCHHH
Confidence            3332  24567999999743

>3nh6_A ATP-binding cassette SUB-family B member 6, mitoc; ABC-transporter, ABCB6, nucleotide binding domain, heme BIOS transport protein; 2.00A {Homo sapiens} PDB: 3nh9_A* 3nha_A* 3nhb_A*

Probab=90.71  E-value=0.1  Score=52.10  Aligned_cols=24  Identities=29%  Similarity=0.530  Sum_probs=21.5

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+++|+|+.|+|||||++.+..
T Consensus        79 ~Ge~vaivG~sGsGKSTLl~ll~g  102 (306)
T 3nh6_A           79 PGQTLALVGPSGAGKSTILRLLFR  102 (306)
T ss_dssp             TTCEEEEESSSCHHHHHHHHHHTT
T ss_pred             CCCEEEEECCCCchHHHHHHHHHc
Confidence            357999999999999999999875

>2bbs_A Cystic fibrosis transmembrane conductance regulator; ATP binding cassette, transport protein; HET: ATP; 2.05A {Homo sapiens} PDB: 2bbt_A* 1xmi_A* 1xmj_A* 2bbo_A* 3si7_A* 1r0w_A 1q3h_A 1r0x_A* 1r0y_A* 1r0z_A* 1r10_A* 1xf9_A* 1xfa_A*

Probab=90.67  E-value=0.14  Score=50.92  Aligned_cols=24  Identities=29%  Similarity=0.445  Sum_probs=21.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+++|+|+.|+|||||.+.+..
T Consensus        63 ~Ge~~~i~G~NGsGKSTLlk~l~G   86 (290)
T 2bbs_A           63 RGQLLAVAGSTGAGKTSLLMMIMG   86 (290)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhc
Confidence            357999999999999999999876

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=90.66  E-value=0.12  Score=50.72  Aligned_cols=21  Identities=48%  Similarity=0.640  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .++|+|+.|+|||||.+.++.
T Consensus         4 ~v~lvG~nGaGKSTLln~L~g   24 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVNTLFK   24 (270)
T ss_dssp             EEEEEESSSSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            589999999999999999886

>2ce2_X GTPase HRAS; signaling protein, guanine nucleotide binding protein, fluor membrane, lipoprotein, palmitate, prenylation; HET: GDP XY2; 1.0A {Homo sapiens} PDB: 2cl0_X* 2cl6_X* 2cl7_X* 2clc_X* 2evw_X* 2cld_X* 1aa9_A* 1ioz_A* 1q21_A* 6q21_A* 3k9l_A* 3k9n_A* 1ctq_A* 1bkd_R 1crp_A* 1crq_A* 1crr_A* 121p_A* 1gnp_A* 1gnq_A* ...

Probab=90.57  E-value=0.12  Score=45.85  Aligned_cols=22  Identities=36%  Similarity=0.611  Sum_probs=19.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHhcc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      -|.|+|.+|+|||||+..+...
T Consensus         5 ~i~v~G~~~~GKssl~~~l~~~   26 (166)
T 2ce2_X            5 KLVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4889999999999999998764

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=90.57  E-value=0.14  Score=49.23  Aligned_cols=23  Identities=26%  Similarity=0.323  Sum_probs=21.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...|+|.|..|+||||+++.+.+
T Consensus         2 ~~~i~~~G~~g~GKtt~~~~l~~   24 (241)
T 2ocp_A            2 PRRLSIEGNIAVGKSTFVKLLTK   24 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHH
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHH
Confidence            46899999999999999999987

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=90.56  E-value=0.15  Score=46.71  Aligned_cols=23  Identities=22%  Similarity=0.258  Sum_probs=20.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhcc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      ..|+|+|.+|+|||||...+...
T Consensus         8 ~~i~lvG~~gvGKStL~~~l~~~   30 (188)
T 2wjg_A            8 YEIALIGNPNVGKSTIFNALTGE   30 (188)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            56899999999999999999863

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=90.54  E-value=0.15  Score=49.16  Aligned_cols=49  Identities=14%  Similarity=0.253  Sum_probs=31.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKV  239 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i  239 (695)
                      ..++.|.|.+|+|||+||.+++.+. ....-. .+++++...  +...+...+
T Consensus        30 G~l~~i~G~pG~GKT~l~l~~~~~~-~~~~~~-~v~~~s~E~--~~~~~~~~~   78 (251)
T 2zts_A           30 GTTVLLTGGTGTGKTTFAAQFIYKG-AEEYGE-PGVFVTLEE--RARDLRREM   78 (251)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHHHH-HHHHCC-CEEEEESSS--CHHHHHHHH
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHH-HHhcCC-CceeecccC--CHHHHHHHH
Confidence            4789999999999999998876421 222122 266776654  345554443

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=90.54  E-value=1  Score=42.85  Aligned_cols=32  Identities=22%  Similarity=0.390  Sum_probs=22.9

Q ss_pred             HHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHh
Q 042541          175 LKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLC  208 (695)
Q Consensus       175 ~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~  208 (695)
                      .++++..+..+  +.+.|+|+.|+||||+.....
T Consensus        66 q~~~i~~i~~g--~~~~i~g~TGsGKTt~~~~~~   97 (235)
T 3llm_A           66 ESEILEAISQN--SVVIIRGATGCGKTTQVPQFI   97 (235)
T ss_dssp             HHHHHHHHHHC--SEEEEECCTTSSHHHHHHHHH
T ss_pred             HHHHHHHHhcC--CEEEEEeCCCCCcHHhHHHHH
Confidence            34555555543  689999999999998765543

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=90.48  E-value=0.21  Score=45.07  Aligned_cols=25  Identities=20%  Similarity=0.260  Sum_probs=21.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhcc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      ....|+|+|.+|+|||||+..+.+.
T Consensus         7 ~~~~i~v~G~~~~GKssl~~~l~~~   31 (178)
T 2lkc_A            7 RPPVVTIMGHVDHGKTTLLDAIRHS   31 (178)
T ss_dssp             CCCEEEEESCTTTTHHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3567899999999999999998764

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=90.46  E-value=0.33  Score=45.61  Aligned_cols=51  Identities=18%  Similarity=0.360  Sum_probs=33.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhccccccc-cCCCcEEEEEeCCCCCHHHHHHHHHH
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKDDQVQG-KFKDDIFYVTVSKNPNVKAIVQKVLH  241 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~~~~~~-~f~~~~~wv~~~~~~~~~~~~~~i~~  241 (695)
                      ..|.|.|+.|+||||+++.+.+  .... .+.. +....-.....+.+.+++++.
T Consensus         4 ~~i~~eG~~gsGKsT~~~~l~~--~l~~~~~~~-v~~~rep~~t~~g~~ir~~l~   55 (213)
T 4tmk_A            4 KYIVIEGLEGAGKTTARNVVVE--TLEQLGIRD-MVFTREPGGTQLAEKLRSLLL   55 (213)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHH--HHHHTTCCC-EEEEESSCSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH--HHHHcCCCc-ceeeeCCCCCHHHHHHHHHHh
Confidence            5799999999999999999987  3332 2323 434443333344555666665

>1z2a_A RAS-related protein RAB-23; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 1.90A {Mus musculus} SCOP: c.37.1.8 PDB: 1z22_A*

Probab=90.42  E-value=0.13  Score=45.88  Aligned_cols=23  Identities=39%  Similarity=0.719  Sum_probs=20.2

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhcc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      --|.|+|.+|+|||||+..+.+.
T Consensus         6 ~~i~v~G~~~~GKssl~~~l~~~   28 (168)
T 1z2a_A            6 IKMVVVGNGAVGKSSMIQRYCKG   28 (168)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEEECcCCCCHHHHHHHHHcC
Confidence            45889999999999999998764

>2nzj_A GTP-binding protein REM 1; GDP/GTP binding, GTP hydrolysis, RAD and GEM like GTP protein 1, structural genomics; HET: GDP; 2.50A {Homo sapiens}

Probab=90.40  E-value=0.14  Score=46.15  Aligned_cols=23  Identities=26%  Similarity=0.332  Sum_probs=20.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhcc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      --|+|+|.+|+|||||+..+...
T Consensus         5 ~ki~i~G~~~vGKSsl~~~l~~~   27 (175)
T 2nzj_A            5 YRVVLLGDPGVGKTSLASLFAGK   27 (175)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEEEECCCCccHHHHHHHHhcC
Confidence            45899999999999999998764

>3eph_A TRNA isopentenyltransferase; transferase, alternative initiation, ATP-binding, cytoplasm, mitochondrion, nucleotide-binding, nucleus; 2.95A {Saccharomyces cerevisiae} PDB: 3epj_A 3epk_A* 3epl_A*

Probab=90.38  E-value=0.14  Score=52.90  Aligned_cols=22  Identities=32%  Similarity=0.578  Sum_probs=20.5

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ++|+|.|+.|+||||||..++.
T Consensus         3 ~~i~i~GptgsGKttla~~La~   24 (409)
T 3eph_A            3 KVIVIAGTTGVGKSQLSIQLAQ   24 (409)
T ss_dssp             EEEEEEECSSSSHHHHHHHHHH
T ss_pred             cEEEEECcchhhHHHHHHHHHH
Confidence            6899999999999999999886

>3fvq_A Fe(3+) IONS import ATP-binding protein FBPC; nucleotide binding domain, ABC motor domain, ferric iron TRA ATP-binding, cell inner membrane; HET: ATP; 1.90A {Neisseria gonorrhoeae}

Probab=90.37  E-value=0.15  Score=52.16  Aligned_cols=23  Identities=30%  Similarity=0.530  Sum_probs=21.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|+|||||.+.++-
T Consensus        30 Ge~~~llGpsGsGKSTLLr~iaG   52 (359)
T 3fvq_A           30 GEILFIIGASGCGKTTLLRCLAG   52 (359)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCchHHHHHHHHhc
Confidence            47899999999999999999886

>1zj6_A ADP-ribosylation factor-like protein 5; ARL, GTP-binding, transport protein; HET: G3D; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=90.36  E-value=0.26  Score=44.99  Aligned_cols=34  Identities=18%  Similarity=0.340  Sum_probs=26.3

Q ss_pred             HHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhcc
Q 042541          176 KELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       176 ~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      ..+.+ +......-|+|+|.+|+|||||...+.+.
T Consensus         6 ~~~~~-~~~~~~~~i~v~G~~~~GKssl~~~l~~~   39 (187)
T 1zj6_A            6 TRIWR-LFNHQEHKVIIVGLDNAGKTTILYQFSMN   39 (187)
T ss_dssp             HHHHH-HHTTSCEEEEEEESTTSSHHHHHHHHHTT
T ss_pred             HHHHH-hcCCCccEEEEECCCCCCHHHHHHHHhcC
Confidence            34445 44555677999999999999999998853

>1u0j_A DNA replication protein; AAA+ protein, P-loop atpases, helicase; HET: DNA ADP; 2.10A {Adeno-associated virus - 2} SCOP: c.37.1.20 PDB: 1s9h_A

Probab=90.33  E-value=0.24  Score=48.07  Aligned_cols=34  Identities=21%  Similarity=0.192  Sum_probs=25.9

Q ss_pred             HHHHHHHHcC--CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          176 KELKMELFKD--GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       176 ~~l~~~L~~~--~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+..+|...  ....|.++|++|.|||.+|..+++
T Consensus        91 ~~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~ala~  126 (267)
T 1u0j_A           91 SVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAH  126 (267)
T ss_dssp             HHHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHH
T ss_pred             HHHHHHHhCCCCCCcEEEEECCCCCCHHHHHHHHHh
Confidence            3355555532  245799999999999999999987

---

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	695
d2a5yb3	277	c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenor	6e-21
d1kgda_	178	c.37.1.1 (A:) Guanylate kinase-like domain of Cask	0.001

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]} Length = 277

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

 Score = 91.4 bits (226), Expect = 6e-21
 Identities = 35/254 (13%), Positives = 70/254 (27%), Gaps = 24/254 (9%)

Query: 175 LKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLC-KDDQVQGKFKDDIFYVTVSKNPNVK 233
           + +   E+      F+ +    G GK+ +  +   K DQ+ G   D I ++  S      
Sbjct: 32  VIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKS 91

Query: 234 AIVQKVLHHKG-YPVPEFQTDEAAINDLERFFKQMRIEAIL------LVLDDVWPGSESL 286
                           +     +  +      K+M   A++       V DDV       
Sbjct: 92  TFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVV----QE 147

Query: 287 LQKLGFQLPDYKILVTSRSEFPQFG-----SVHYLKPLTYEAARTLFLHSANLQDGNSYI 341
                 Q    + LVT+R                +  L  +                   
Sbjct: 148 ETIRWAQELRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDECYDFLEAYG--MPMPVGE 205

Query: 342 PDENIVSKILRACKGCPLALKVVGGSLCGKHEVFWQRMVKECSRGESVFQSKNDILDCLG 401
            +E++++K +    G P  L +   S   K      ++  +        +    +     
Sbjct: 206 KEEDVLNKTIELSSGNPATLMMFFKSCEPKTFEKMAQLNNKLES-----RGLVGVECITP 260

Query: 402 SSLDVLNNEVKECY 415
            S   L   ++ C 
Sbjct: 261 YSYKSLAMALQRCV 274

>d1kgda_ c.37.1.1 (A:) Guanylate kinase-like domain of Cask {Human (Homo sapiens) [TaxId: 9606]} Length = 178

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase-like domain of Cask
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.9 bits (87), Expect = 0.001
 Identities = 8/45 (17%), Positives = 16/45 (35%), Gaps = 2/45 (4%)

Query: 187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPN 231
           R+ +V+    G G+  +   L        +F   I + T     +
Sbjct: 3   RKTLVLLGAHGVGRRHIKNTLITKH--PDRFAYPIPHTTRPPKKD 45

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	695
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	100.0
d1p9ag_	266	von Willebrand factor binding domain of glycoprote	99.31
d1ogqa_	313	Polygalacturonase inhibiting protein PGIP {Kidney	99.28
d1dcea3	124	Rab geranylgeranyltransferase alpha-subunit, C-ter	99.27
d1p9ag_	266	von Willebrand factor binding domain of glycoprote	99.27
d1a9na_	162	Splicesomal U2A' protein {Human (Homo sapiens) [Ta	99.26
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	99.2
d1ozna_	284	Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Huma	99.15
d1w8aa_	192	Slit {Fruit fly (Drosophila melanogaster) [TaxId:	99.14
d1a9na_	162	Splicesomal U2A' protein {Human (Homo sapiens) [Ta	99.13
d1xkua_	305	Decorin {Cow (Bos taurus) [TaxId: 9913]}	99.13
d2omxa2	199	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.12
d1h6ta2	210	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.09
d1ozna_	284	Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Huma	99.08
d1h6ta2	210	Internalin B {Listeria monocytogenes [TaxId: 1639]	99.08
d1ogqa_	313	Polygalacturonase inhibiting protein PGIP {Kidney	99.07
d1w8aa_	192	Slit {Fruit fly (Drosophila melanogaster) [TaxId:	99.04
d2omxa2	199	Internalin B {Listeria monocytogenes [TaxId: 1639]	98.99
d1m9la_	198	Outer arm dynein light chain 1 {Green algae (Chlam	98.97
d1dcea3	124	Rab geranylgeranyltransferase alpha-subunit, C-ter	98.96
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	98.92
d1h6ua2	227	Internalin H {Listeria monocytogenes [TaxId: 1639]	98.91
d1h6ua2	227	Internalin H {Listeria monocytogenes [TaxId: 1639]	98.9
d2omza2	384	Internalin A {Listeria monocytogenes [TaxId: 1639]	98.84
d2omza2	384	Internalin A {Listeria monocytogenes [TaxId: 1639]	98.81
d1xwdc1	242	Follicle-stimulating hormone receptor {Human (Homo	98.81
d2ifga3	156	High affinity nerve growth factor receptor, N-term	98.8
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	98.78
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	98.78
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	98.76
d1m9la_	198	Outer arm dynein light chain 1 {Green algae (Chlam	98.75
d1xkua_	305	Decorin {Cow (Bos taurus) [TaxId: 9913]}	98.7
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	98.68
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	98.67
d2astb2	284	Cyclin A/CDK2-associated p19, Skp2 {Human (Homo sa	98.62
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	98.52
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	98.47
d1xwdc1	242	Follicle-stimulating hormone receptor {Human (Homo	98.46
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	98.45
d2ifga3	156	High affinity nerve growth factor receptor, N-term	98.44
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	98.42
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	98.39
d2astb2	284	Cyclin A/CDK2-associated p19, Skp2 {Human (Homo sa	98.33
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	98.31
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	98.31
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	98.26
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	98.18
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	98.14
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	98.14
d1jl5a_	353	Leucine rich effector protein YopM {Yersinia pesti	98.13
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	98.1
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	98.01
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	97.97
d1jl5a_	353	Leucine rich effector protein YopM {Yersinia pesti	97.88
d1koha1	162	mRNA export factor tap {Human (Homo sapiens) [TaxI	97.64
d1z7xw1	460	Ribonuclease inhibitor {Human (Homo sapiens) [TaxI	97.6
d2ca6a1	344	Rna1p (RanGAP1), N-terminal domain {Fission yeast	97.56
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	97.45
d2ca6a1	344	Rna1p (RanGAP1), N-terminal domain {Fission yeast	97.44
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	97.35
d1koha1	162	mRNA export factor tap {Human (Homo sapiens) [TaxI	97.28
d1z7xw1	460	Ribonuclease inhibitor {Human (Homo sapiens) [TaxI	97.05
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	96.71
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	96.69
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	96.66
d2qy9a2	211	GTPase domain of the signal recognition particle r	96.61
d1pgva_	167	Tropomodulin C-terminal domain {nematode (Caenorha	96.59
d1okkd2	207	GTPase domain of the signal recognition particle r	96.53
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	96.52
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	96.52
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	96.5
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	96.46
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	96.43
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.4
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	96.35
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	96.35
d1ls1a2	207	GTPase domain of the signal sequence recognition p	96.27
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.25
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	96.25
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	96.23
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	96.15
d1io0a_	166	Tropomodulin C-terminal domain {Chicken (Gallus ga	96.15
d1pgva_	167	Tropomodulin C-terminal domain {nematode (Caenorha	96.09
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	96.09
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	96.08
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	96.05
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	96.05
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	96.05
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	96.04
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	96.0
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	96.0
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	95.99
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	95.9
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	95.89
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	95.85
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	95.85
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	95.81
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	95.79
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	95.78
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	95.72
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	95.72
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	95.64
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	95.63
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	95.6
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	95.5
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	95.49
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	95.42
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	95.29
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	95.18
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	95.1
d1xpua3	289	Transcription termination factor Rho, ATPase domai	94.87
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	94.81
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	94.78
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	94.75
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	94.75
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	94.66
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	94.64
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	94.63
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	94.54
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	94.49
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	94.45
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	94.45
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	94.35
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	94.32
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	94.23
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	94.14
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	94.13
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	94.12
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	94.12
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	93.96
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	93.95
d1io0a_	166	Tropomodulin C-terminal domain {Chicken (Gallus ga	93.86
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	93.83
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	93.82
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	93.8
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	93.79
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	93.65
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	93.63
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	93.58
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	93.58
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	93.48
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	93.48
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	93.46
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	93.34
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	93.17
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	93.17
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	93.13
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	93.09
d1g2912	240	Maltose transport protein MalK, N-terminal domain	93.0
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	92.95
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	92.94
d2awna2	232	Maltose transport protein MalK, N-terminal domain	92.94
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	92.94
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	92.85
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	92.85
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	92.81
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	92.81
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	92.78
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	92.72
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	92.71
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	92.68
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	92.67
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	92.62
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	92.56
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	92.44
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	92.4
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	92.39
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	92.38
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	92.23
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	92.14
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	92.06
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	91.96
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	91.96
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	91.94
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	91.93
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	91.91
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	91.74
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	91.74
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	91.6
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	91.6
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	91.57
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	91.44
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	91.37
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	91.33
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	91.33
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	91.33
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	91.32
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	91.31
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	91.24
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	91.23
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	91.23
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	91.21
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	91.2
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	91.17
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	91.15
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	91.13
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	91.04
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	91.04
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	90.96
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	90.93
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	90.93
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	90.91
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	90.79
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	90.74
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	90.72
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	90.66
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	90.63
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	90.63
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	90.62
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	90.59
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	90.55
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	90.48
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	90.43
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	90.34
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	90.27
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	90.27
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	90.26
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	90.25
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	90.21
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	90.17
d1nrjb_	209	Signal recognition particle receptor beta-subunit	90.08
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	90.06
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	90.06
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	89.96
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	89.93
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	89.84
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	89.8
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	89.79
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	89.76
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	89.72
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	89.66
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	89.6
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	89.56
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	89.52
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	89.41
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	89.39
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	89.31
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	89.3
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	89.25
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	89.16
d2fh5b1	207	Signal recognition particle receptor beta-subunit	89.15
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	88.94
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	88.94
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	88.91
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	88.77
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	88.72
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	88.4
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	88.38
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	88.34
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	88.24
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	88.16
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	88.0
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	87.8
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	87.59
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	87.52
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	87.14
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	87.12
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	87.08
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	86.95
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	86.32
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	86.01
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	85.96
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	84.72
d1tuea_	205	Replication protein E1 helicase domain {Human papi	83.86
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	83.73
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	83.58
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	83.0
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	82.55
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	81.84
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	81.6
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	80.65
d1e2ka_	329	Thymidine kinase {Herpes simplex virus type 1, dif	80.42

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

Probab=100.00  E-value=1.1e-37  Score=312.51  Aligned_cols=247  Identities=12%  Similarity=0.033  Sum_probs=184.6

Q ss_pred             CCCCCCCCCCCCCCcchHHHHHHHHH---cCCceEEEEEcCCCCcHHHHHHHHhcccc--ccccCCCcEEEEEeCCCCCH
Q 042541          158 CCSAPDPPVISPGLDVPLKELKMELF---KDGRQFIVVSAPGGYGKTTLVQRLCKDDQ--VQGKFKDDIFYVTVSKNPNV  232 (695)
Q Consensus       158 ~~~~~~~~~~~vGr~~~~~~l~~~L~---~~~~~vv~I~G~gGiGKTtLa~~~~~~~~--~~~~f~~~~~wv~~~~~~~~  232 (695)
                      .+++|..+. ++||+.++++|+++|.   +.+.++|+|+||||+||||||+++|++..  ...+|++ ++|+++++.++.
T Consensus        13 ~~~~p~~~~-~~gR~~~~~~i~~~L~~~~~~~~~~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~-~~Wv~vs~~~~~   90 (277)
T d2a5yb3          13 LGNVPKQMT-CYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDS-IVWLKDSGTAPK   90 (277)
T ss_dssp             HTTCBCCCC-SCCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSE-EEEEECCCCSTT
T ss_pred             ccCCCCCCc-eeCcHHHHHHHHHHHHhccCCCceEEEEECCCCCCHHHHHHHHHHhhhhhhhhcCce-EEEEEecCCCCH
Confidence            345665555 5799999999999997   34578999999999999999999998643  5666777 899999998887


Q ss_pred             HHHHHHHHH---hcCCCCCC----CCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCChHHHhhhccCCCCCEEEEEcC
Q 042541          233 KAIVQKVLH---HKGYPVPE----FQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGSESLLQKLGFQLPDYKILVTSR  304 (695)
Q Consensus       233 ~~~~~~i~~---~l~~~~~~----~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~~~~~~~l~~~~~gs~iivTtR  304 (695)
                      ..+...+..   .++.....    ....... ......+ +.+.++++|+||||||+...  +..+.  ..||+||||||
T Consensus        91 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~L~~kr~LlVLDDv~~~~~--~~~~~--~~~srilvTTR  165 (277)
T d2a5yb3          91 STFDLFTDILLMLKSEDDLLNFPSVEHVTSV-VLKRMICNALIDRPNTLFVFDDVVQEET--IRWAQ--ELRLRCLVTTR  165 (277)
T ss_dssp             HHHHHHHHHHHHHTTTSCCTTCCCCTTCCHH-HHHHHHHHHHTTSTTEEEEEEEECCHHH--HHHHH--HTTCEEEEEES
T ss_pred             HHHHHHHHHHHHHhcchhhcCCccchhhhhH-HHHHHHHHHHhccCCeeEecchhhHHhh--hhhhc--ccCceEEEEee
Confidence            766555533   33322111    1111111 1122233 67789999999999998654  33332  35799999999


Q ss_pred             CCCCC-----CCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHHHHHhhCCCCHHHHHHH
Q 042541          305 SEFPQ-----FGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKVVGGSLCGKHEVFWQRM  379 (695)
Q Consensus       305 ~~~~~-----~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~~~~~L~~~~~~~w~~~  379 (695)
                      +..+.     ....|++++|+.+|||+||..+++....  ....++++++|+++|+|+||||+++|+.|+.++.+.|...
T Consensus       166 ~~~v~~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~--~~~~~~~~~~iv~~c~GlPLAl~~ig~~l~~k~~~~~~~~  243 (277)
T d2a5yb3         166 DVEISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMPV--GEKEEDVLNKTIELSSGNPATLMMFFKSCEPKTFEKMAQL  243 (277)
T ss_dssp             BGGGGGGCCSCEEEEECCCCCHHHHHHHHHHTSCCCC----CHHHHHHHHHHHHHTTCHHHHHHHHTTCCSSSHHHHHHH
T ss_pred             hHHHHHhcCCCCceEECCCCCHHHHHHHHHHHhCCccC--chhhHHHHHHHHHHhCCCHHHHHHHHHHhccCCHHHHHHH
Confidence            88432     1137999999999999999998875433  2335788999999999999999999999999999999876


Q ss_pred             HHHhcCCCCccCchhhHHHHHHHHHHhccHHHHHHHhhh
Q 042541          380 VKECSRGESVFQSKNDILDCLGSSLDVLNNEVKECYLDL  418 (695)
Q Consensus       380 l~~~~~~~~~~~~~~~i~~~l~~s~~~L~~~~k~cf~~l  418 (695)
                      ...+...     ...++..++.+||+.||+++|+||.++
T Consensus       244 ~~~L~~~-----~~~~v~~il~~sY~~L~~~lk~c~~~l  277 (277)
T d2a5yb3         244 NNKLESR-----GLVGVECITPYSYKSLAMALQRCVEVL  277 (277)
T ss_dssp             HHHHHHH-----CSSTTCCCSSSSSSSHHHHHHHHHHTS
T ss_pred             HHHHhcC-----cHHHHHHHHHHHHhcccHHHHHHHHhC
Confidence            6655321     224677888999999999999999874

>d1p9ag_ c.10.2.7 (G:) von Willebrand factor binding domain of glycoprotein Ib alpha {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: von Willebrand factor binding domain of glycoprotein Ib alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.31  E-value=7.1e-12  Score=123.31  Aligned_cols=158  Identities=16%  Similarity=0.190  Sum_probs=109.2

Q ss_pred             CccceEEeeecCCcccCCCC-CCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCc
Q 042541          526 PNNASLLSISTDETFSSNWP-DMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLK  604 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~~~~~-~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~  604 (695)
                      +..+++|.+..+........ ...+++|+.|.|+.+... .+|. +..+++|++|++++|.+...    ...+..+++|+
T Consensus        30 p~~l~~L~Ls~N~i~~l~~~~f~~l~~L~~L~L~~N~l~-~l~~-~~~l~~L~~L~Ls~N~l~~~----~~~~~~l~~L~  103 (266)
T d1p9ag_          30 PKDTTILHLSENLLYTFSLATLMPYTRLTQLNLDRAELT-KLQV-DGTLPVLGTLDLSHNQLQSL----PLLGQTLPALT  103 (266)
T ss_dssp             CTTCCEEECTTSCCSEEEGGGGTTCTTCCEEECTTSCCC-EEEC-CSCCTTCCEEECCSSCCSSC----CCCTTTCTTCC
T ss_pred             CcCCCEEECcCCcCCCcCHHHhhcccccccccccccccc-cccc-cccccccccccccccccccc----ccccccccccc
Confidence            45677777766543221111 236788888888777443 3442 46788888888888766321    22367788899


Q ss_pred             EEEeccCCCCCcc--cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCch-hhcCCCCCceee
Q 042541          605 KIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPD-GLCDIVSMEKLR  681 (695)
Q Consensus       605 ~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~-~i~~L~~L~~L~  681 (695)
                      +|+++++.+..++  .+..+.+|++|++++|.+..+++..+.    .+++|+.|++++| .+..+|. .++.+++|++|+
T Consensus       104 ~L~l~~~~~~~~~~~~~~~l~~l~~L~l~~n~l~~l~~~~~~----~l~~l~~l~l~~N-~l~~~~~~~~~~l~~L~~L~  178 (266)
T d1p9ag_         104 VLDVSFNRLTSLPLGALRGLGELQELYLKGNELKTLPPGLLT----PTPKLEKLSLANN-NLTELPAGLLNGLENLDTLL  178 (266)
T ss_dssp             EEECCSSCCCCCCSSTTTTCTTCCEEECTTSCCCCCCTTTTT----TCTTCCEEECTTS-CCSCCCTTTTTTCTTCCEEE
T ss_pred             cccccccccceeeccccccccccccccccccccceecccccc----ccccchhcccccc-cccccCccccccccccceee
Confidence            9999888887666  666777888888888877777777665    6788888888875 4555554 467788888888


Q ss_pred             cccccCCCCCCCCC
Q 042541          682 ITNCHRLSALPEGI  695 (695)
Q Consensus       682 l~~~~~l~~lP~~i  695 (695)
                      |++|. +..+|.++
T Consensus       179 Ls~N~-L~~lp~~~  191 (266)
T d1p9ag_         179 LQENS-LYTIPKGF  191 (266)
T ss_dssp             CCSSC-CCCCCTTT
T ss_pred             cccCC-CcccChhH
Confidence            88855 77887653

>d1ogqa_ c.10.2.8 (A:) Polygalacturonase inhibiting protein PGIP {Kidney bean (Phaseolus vulgaris) [TaxId: 3885]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Polygalacturonase inhibiting protein PGIP
domain: Polygalacturonase inhibiting protein PGIP
species: Kidney bean (Phaseolus vulgaris) [TaxId: 3885]

Probab=99.28  E-value=5.2e-12  Score=127.54  Aligned_cols=166  Identities=14%  Similarity=0.116  Sum_probs=106.3

Q ss_pred             cceEEeeecCCccc--CCCC-CCCCCceEEEEEEc-cCccccCChhhcCCCCCcEEEEcccCCCCccc------------
Q 042541          528 NASLLSISTDETFS--SNWP-DMQGPEVKVVVLNI-RTKKYVLPDFLQKMDELKVLIVTNYGFSPAEL------------  591 (695)
Q Consensus       528 ~~r~l~~~~~~~~~--~~~~-~~~~~~l~~L~l~~-~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~------------  591 (695)
                      .+..+.+.+.....  ..+. -..+++|++|.|+. +...+.+|..|+++++|++|++++|.+.....            
T Consensus        51 ~v~~L~L~~~~l~g~~~lp~~l~~L~~L~~L~Ls~~N~l~g~iP~~i~~L~~L~~L~Ls~N~l~~~~~~~~~~~~~L~~l  130 (313)
T d1ogqa_          51 RVNNLDLSGLNLPKPYPIPSSLANLPYLNFLYIGGINNLVGPIPPAIAKLTQLHYLYITHTNVSGAIPDFLSQIKTLVTL  130 (313)
T ss_dssp             CEEEEEEECCCCSSCEECCGGGGGCTTCSEEEEEEETTEESCCCGGGGGCTTCSEEEEEEECCEEECCGGGGGCTTCCEE
T ss_pred             EEEEEECCCCCCCCCCCCChHHhcCccccccccccccccccccccccccccccchhhhccccccccccccccchhhhccc
Confidence            35555665443221  1112 23788999999986 56777899999999999999999886532110            


Q ss_pred             ---------CcccccccCCCCcEEEeccCCCC-Ccc-cccccccc-cEEeeccccCCcccccchhhh-------------
Q 042541          592 ---------NNFRVLSALSKLKKIRLEHVSLP-NSL-ATVRMNHL-QKVSLVMCNVGQVFRNSTFRI-------------  646 (695)
Q Consensus       592 ---------~~~~~l~~l~~L~~L~L~~~~l~-~lp-~i~~l~~L-~~L~l~~~~i~~~~~~~~~~l-------------  646 (695)
                               ..++.++++++|+++++++|.+. .+| .++.+.+| ++++++.|++++.++..+..+             
T Consensus       131 ~l~~N~~~~~~p~~l~~l~~L~~l~l~~n~l~~~ip~~~~~l~~l~~~l~~~~n~l~~~~~~~~~~l~~~~l~l~~~~~~  210 (313)
T d1ogqa_         131 DFSYNALSGTLPPSISSLPNLVGITFDGNRISGAIPDSYGSFSKLFTSMTISRNRLTGKIPPTFANLNLAFVDLSRNMLE  210 (313)
T ss_dssp             ECCSSEEESCCCGGGGGCTTCCEEECCSSCCEEECCGGGGCCCTTCCEEECCSSEEEEECCGGGGGCCCSEEECCSSEEE
T ss_pred             ccccccccccCchhhccCcccceeeccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence                     00123556666666666666555 455 45444443 445554444433222211100             


Q ss_pred             ---------------------------c--ccCCCccEEecccccccccCchhhcCCCCCceeecccccCCCCCCC
Q 042541          647 ---------------------------S--DAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPE  693 (695)
Q Consensus       647 ---------------------------~--~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~~l~~lP~  693 (695)
                                                 +  ..+++|+.|++++|...+.+|.+|++|++|++|+|++|...|.+|+
T Consensus       211 ~~~~~~~~~~~~l~~l~~~~~~l~~~~~~~~~~~~L~~L~Ls~N~l~g~iP~~l~~L~~L~~L~Ls~N~l~g~iP~  286 (313)
T d1ogqa_         211 GDASVLFGSDKNTQKIHLAKNSLAFDLGKVGLSKNLNGLDLRNNRIYGTLPQGLTQLKFLHSLNVSFNNLCGEIPQ  286 (313)
T ss_dssp             ECCGGGCCTTSCCSEEECCSSEECCBGGGCCCCTTCCEEECCSSCCEECCCGGGGGCTTCCEEECCSSEEEEECCC
T ss_pred             ccccccccccccccccccccccccccccccccccccccccCccCeecccCChHHhCCCCCCEEECcCCcccccCCC
Confidence                                       0  0477899999999876668999999999999999999886668886

>d1dcea3 c.10.2.2 (A:444-567) Rab geranylgeranyltransferase alpha-subunit, C-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Rab geranylgeranyltransferase alpha-subunit, C-terminal domain
domain: Rab geranylgeranyltransferase alpha-subunit, C-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.27  E-value=9.1e-12  Score=106.54  Aligned_cols=102  Identities=17%  Similarity=0.141  Sum_probs=77.1

Q ss_pred             cEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc-cccccccccEEeeccccCCcccccchhhhcccCCCccE
Q 042541          577 KVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL-ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLE  655 (695)
Q Consensus       577 r~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp-~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~  655 (695)
                      |+|++++|++.     .++.++.+.+|++|++++|.++.+| .++.+++|++|++++|.++.+++ +.     .+++|++
T Consensus         1 R~L~Ls~n~l~-----~l~~l~~l~~L~~L~ls~N~l~~lp~~~~~l~~L~~L~l~~N~i~~l~~-~~-----~l~~L~~   69 (124)
T d1dcea3           1 RVLHLAHKDLT-----VLCHLEQLLLVTHLDLSHNRLRALPPALAALRCLEVLQASDNALENVDG-VA-----NLPRLQE   69 (124)
T ss_dssp             SEEECTTSCCS-----SCCCGGGGTTCCEEECCSSCCCCCCGGGGGCTTCCEEECCSSCCCCCGG-GT-----TCSSCCE
T ss_pred             CEEEcCCCCCC-----CCcccccCCCCCEEECCCCccCcchhhhhhhhcccccccccccccccCc-cc-----cccccCe
Confidence            67888887763     2233678888888888888888888 88888888888888888887643 33     7888888


Q ss_pred             EecccccccccCc--hhhcCCCCCceeecccccCCCCC
Q 042541          656 MDIDYCNDLIELP--DGLCDIVSMEKLRITNCHRLSAL  691 (695)
Q Consensus       656 L~l~~c~~l~~lP--~~i~~L~~L~~L~l~~~~~l~~l  691 (695)
                      |++++| .+..+|  ..++.+++|++|++++|+ +..+
T Consensus        70 L~l~~N-~i~~~~~~~~l~~~~~L~~L~l~~N~-i~~~  105 (124)
T d1dcea3          70 LLLCNN-RLQQSAAIQPLVSCPRLVLLNLQGNS-LCQE  105 (124)
T ss_dssp             EECCSS-CCCSSSTTGGGGGCTTCCEEECTTSG-GGGS
T ss_pred             EECCCC-ccCCCCCchhhcCCCCCCEEECCCCc-CCcC
Confidence            888885 566665  357888888888888865 5443

>d1p9ag_ c.10.2.7 (G:) von Willebrand factor binding domain of glycoprotein Ib alpha {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: von Willebrand factor binding domain of glycoprotein Ib alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.27  E-value=2.2e-11  Score=119.63  Aligned_cols=152  Identities=18%  Similarity=0.132  Sum_probs=123.9

Q ss_pred             CCccceEEeeecCCcccCCCCCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCc
Q 042541          525 HPNNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLK  604 (695)
Q Consensus       525 ~~~~~r~l~~~~~~~~~~~~~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~  604 (695)
                      .....+.|.+..+... .......+++|+.|.++.+... ..|..+..+++|++|+++++.....  . ...+..+.+|+
T Consensus        53 ~l~~L~~L~L~~N~l~-~l~~~~~l~~L~~L~Ls~N~l~-~~~~~~~~l~~L~~L~l~~~~~~~~--~-~~~~~~l~~l~  127 (266)
T d1p9ag_          53 PYTRLTQLNLDRAELT-KLQVDGTLPVLGTLDLSHNQLQ-SLPLLGQTLPALTVLDVSFNRLTSL--P-LGALRGLGELQ  127 (266)
T ss_dssp             TCTTCCEEECTTSCCC-EEECCSCCTTCCEEECCSSCCS-SCCCCTTTCTTCCEEECCSSCCCCC--C-SSTTTTCTTCC
T ss_pred             cccccccccccccccc-cccccccccccccccccccccc-cccccccccccccccccccccccee--e-ccccccccccc
Confidence            4557888888765432 2223347899999999888543 4566788999999999998866321  1 12367889999


Q ss_pred             EEEeccCCCCCcc--cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeec
Q 042541          605 KIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRI  682 (695)
Q Consensus       605 ~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l  682 (695)
                      +|.+.+|.+..+|  .+..+++|++|++++|+++.+++..+.    .+++|++|+|++| .+..+|.++..+++|++|+|
T Consensus       128 ~L~l~~n~l~~l~~~~~~~l~~l~~l~l~~N~l~~~~~~~~~----~l~~L~~L~Ls~N-~L~~lp~~~~~~~~L~~L~L  202 (266)
T d1p9ag_         128 ELYLKGNELKTLPPGLLTPTPKLEKLSLANNNLTELPAGLLN----GLENLDTLLLQEN-SLYTIPKGFFGSHLLPFAFL  202 (266)
T ss_dssp             EEECTTSCCCCCCTTTTTTCTTCCEEECTTSCCSCCCTTTTT----TCTTCCEEECCSS-CCCCCCTTTTTTCCCSEEEC
T ss_pred             cccccccccceeccccccccccchhcccccccccccCccccc----cccccceeecccC-CCcccChhHCCCCCCCEEEe
Confidence            9999999999888  677899999999999999999998876    8999999999996 58899999999999999999


Q ss_pred             cccc
Q 042541          683 TNCH  686 (695)
Q Consensus       683 ~~~~  686 (695)
                      ++|+
T Consensus       203 ~~Np  206 (266)
T d1p9ag_         203 HGNP  206 (266)
T ss_dssp             CSCC
T ss_pred             cCCC
Confidence            9976

>d1a9na_ c.10.2.4 (A:) Splicesomal U2A' protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: U2A'-like
domain: Splicesomal U2A' protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.26  E-value=6.1e-12  Score=113.27  Aligned_cols=125  Identities=9%  Similarity=0.069  Sum_probs=88.3

Q ss_pred             CCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc-c-ccccccc
Q 042541          548 QGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL-A-TVRMNHL  625 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp-~-i~~l~~L  625 (695)
                      ++.+++.|.|+++.. ..+|..+..+++|++|++++|.+.     .++.+..+++|++|++++|.++.+| . +..+++|
T Consensus        16 n~~~lr~L~L~~n~I-~~i~~~~~~l~~L~~L~Ls~N~i~-----~l~~~~~l~~L~~L~ls~N~i~~l~~~~~~~l~~L   89 (162)
T d1a9na_          16 NAVRDRELDLRGYKI-PVIENLGATLDQFDAIDFSDNEIR-----KLDGFPLLRRLKTLLVNNNRICRIGEGLDQALPDL   89 (162)
T ss_dssp             CTTSCEEEECTTSCC-CSCCCGGGGTTCCSEEECCSSCCC-----EECCCCCCSSCCEEECCSSCCCEECSCHHHHCTTC
T ss_pred             CcCcCcEEECCCCCC-CccCccccccccCCEEECCCCCCC-----ccCCcccCcchhhhhcccccccCCCcccccccccc
Confidence            456778888777643 334555667788888888887653     2233677888888888888888777 4 4568888


Q ss_pred             cEEeeccccCCcccc-cchhhhcccCCCccEEecccccccccCch----hhcCCCCCceeecc
Q 042541          626 QKVSLVMCNVGQVFR-NSTFRISDAFPNLLEMDIDYCNDLIELPD----GLCDIVSMEKLRIT  683 (695)
Q Consensus       626 ~~L~l~~~~i~~~~~-~~~~~l~~~l~~L~~L~l~~c~~l~~lP~----~i~~L~~L~~L~l~  683 (695)
                      ++|++++|.++.++. ..+.    .+++|++|++++| .+..+|.    .+..+++|+.||-.
T Consensus        90 ~~L~L~~N~i~~~~~l~~l~----~l~~L~~L~l~~N-~i~~~~~~r~~~i~~lp~L~~LD~~  147 (162)
T d1a9na_          90 TELILTNNSLVELGDLDPLA----SLKSLTYLCILRN-PVTNKKHYRLYVIYKVPQVRVLDFQ  147 (162)
T ss_dssp             CEEECCSCCCCCGGGGGGGG----GCTTCCEEECCSS-GGGGSTTHHHHHHHHCTTCSEETTE
T ss_pred             ccceeccccccccccccccc----cccccchhhcCCC-ccccccchHHHHHHHCCCcCeeCCC
Confidence            888888888877654 2233    6888888888886 3566663    36778888888754

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.20  E-value=6.8e-11  Score=116.87  Aligned_cols=191  Identities=16%  Similarity=0.115  Sum_probs=112.4

Q ss_pred             CCCCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCC-----CCCHHHHHHH
Q 042541          164 PPVISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSK-----NPNVKAIVQK  238 (695)
Q Consensus       164 ~~~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~-----~~~~~~~~~~  238 (695)
                      .++.||||++++++|.+    ...++|.|+|++|+|||+|++++.+  +...    ...|+++..     ......+...
T Consensus        10 ~~~~f~GR~~el~~l~~----~~~~~i~i~G~~G~GKTsLl~~~~~--~~~~----~~~~i~~~~~~~~~~~~~~~~~~~   79 (283)
T d2fnaa2          10 NRKDFFDREKEIEKLKG----LRAPITLVLGLRRTGKSSIIKIGIN--ELNL----PYIYLDLRKFEERNYISYKDFLLE   79 (283)
T ss_dssp             SGGGSCCCHHHHHHHHH----TCSSEEEEEESTTSSHHHHHHHHHH--HHTC----CEEEEEGGGGTTCSCCCHHHHHHH
T ss_pred             ChhhCCChHHHHHHHHh----ccCCEEEEEcCCCCcHHHHHHHHHH--HCCC----CeEEEEeccccccccccHHHHHHH
Confidence            46789999999998865    3457899999999999999999887  3322    245776532     2234444444


Q ss_pred             HHHhcC--------------CCC------C--CC---CChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCC-------hHH
Q 042541          239 VLHHKG--------------YPV------P--EF---QTDEAAINDLERFFKQMRIEAILLVLDDVWPGS-------ESL  286 (695)
Q Consensus       239 i~~~l~--------------~~~------~--~~---~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~-------~~~  286 (695)
                      +.....              ...      .  ..   .........+-..+....++++++|+|++....       .+.
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~i~id~~~~~~~~~~~~~~~~  159 (283)
T d2fnaa2          80 LQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASKDNVIIVLDEAQELVKLRGVNLLPA  159 (283)
T ss_dssp             HHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCSSCEEEEEETGGGGGGCTTCCCHHH
T ss_pred             HHHHhhhhhhhhHHHHHHHHhhhcccccccccccccchhhhhHHHHHHHHHHhhcccccccccchhhhhcccchHHHHHH
Confidence            333211              000      0  00   000111222223334556889999999974321       112


Q ss_pred             HhhhccCCCCCEEEEEcCCC------C-------CC---CCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHH
Q 042541          287 LQKLGFQLPDYKILVTSRSE------F-------PQ---FGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKI  350 (695)
Q Consensus       287 ~~~l~~~~~gs~iivTtR~~------~-------~~---~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I  350 (695)
                      +.......+....+++.+..      .       ..   ....+.|++++.+++.+++.+........     .+..++|
T Consensus       160 l~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~L~~l~~~e~~~~l~~~~~~~~~~-----~~~~~~i  234 (283)
T d2fnaa2         160 LAYAYDNLKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADID-----FKDYEVV  234 (283)
T ss_dssp             HHHHHHHCTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHHTCC-----CCCHHHH
T ss_pred             HHHHHHhhhhhhhhhccccchHHHHHHHhhhhcchhcccceeEEeeCCCCHHHHHHHHHhhhhhcCCC-----HHHHHHH
Confidence            22222233444555544332      0       01   12368899999999999998765322211     1126799


Q ss_pred             HHhcCCchhHHHHHHHhhC
Q 042541          351 LRACKGCPLALKVVGGSLC  369 (695)
Q Consensus       351 ~~~c~G~PLai~~~~~~L~  369 (695)
                      ++.++|+|..+..++..+.
T Consensus       235 ~~~~~G~P~~L~~~~~~~~  253 (283)
T d2fnaa2         235 YEKIGGIPGWLTYFGFIYL  253 (283)
T ss_dssp             HHHHCSCHHHHHHHHHHHH
T ss_pred             HHHhCCCHHHHHHHHHHHH
Confidence            9999999999999887543

>d1ozna_ c.10.2.7 (A:) Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Reticulon 4 receptor (Nogo-66 receptor, Ngr)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.15  E-value=2.1e-10  Score=113.69  Aligned_cols=113  Identities=13%  Similarity=0.134  Sum_probs=60.5

Q ss_pred             ChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--cccccccccEEeeccccCCcccccchh
Q 042541          567 PDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFRNSTF  644 (695)
Q Consensus       567 p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~~~  644 (695)
                      |..+.++++|++|++.+|......   ...+..+.+|+.+++++|.++.+|  .+..+++|+.|++++|.++.+++..+.
T Consensus        98 ~~~~~~l~~L~~L~l~~n~~~~~~---~~~~~~~~~L~~l~l~~N~l~~i~~~~f~~~~~L~~L~l~~N~l~~l~~~~f~  174 (284)
T d1ozna_          98 PATFHGLGRLHTLHLDRCGLQELG---PGLFRGLAALQYLYLQDNALQALPDDTFRDLGNLTHLFLHGNRISSVPERAFR  174 (284)
T ss_dssp             TTTTTTCTTCCEEECTTSCCCCCC---TTTTTTCTTCCEEECCSSCCCCCCTTTTTTCTTCCEEECCSSCCCEECTTTTT
T ss_pred             chhhcccccCCEEecCCccccccc---ccccchhcccchhhhccccccccChhHhccccchhhcccccCcccccchhhhc
Confidence            345666666666666665442111   111444555566666666555554  445555566666666655555555544


Q ss_pred             hhcccCCCccEEecccccccccCchhhcCCCCCceeeccccc
Q 042541          645 RISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCH  686 (695)
Q Consensus       645 ~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~  686 (695)
                          .+++|+.|++++|......|..|.++++|++|++++|.
T Consensus       175 ----~l~~L~~l~l~~N~l~~i~~~~f~~l~~L~~L~l~~N~  212 (284)
T d1ozna_         175 ----GLHSLDRLLLHQNRVAHVHPHAFRDLGRLMTLYLFANN  212 (284)
T ss_dssp             ----TCTTCCEEECCSSCCCEECTTTTTTCTTCCEEECCSSC
T ss_pred             ----cccccchhhhhhccccccChhHhhhhhhcccccccccc
Confidence                55555555555544333344555555555555555543

>d1w8aa_ c.10.2.7 (A:) Slit {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Slit
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.14  E-value=7.4e-11  Score=109.59  Aligned_cols=85  Identities=15%  Similarity=0.205  Sum_probs=39.8

Q ss_pred             cccCCCCcEEEeccCCCCCcc--cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchh-hcC
Q 042541          597 LSALSKLKKIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDG-LCD  673 (695)
Q Consensus       597 l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~-i~~  673 (695)
                      +..+++|+.|+|++|.+..++  .+..+++|++|+|++|+++.+++..+.    .+++|++|+|++| .+..+|.+ |..
T Consensus        50 f~~l~~L~~L~L~~N~i~~~~~~~~~~~~~L~~L~Ls~N~l~~l~~~~F~----~l~~L~~L~L~~N-~l~~i~~~~f~~  124 (192)
T d1w8aa_          50 FGRLPHLVKLELKRNQLTGIEPNAFEGASHIQELQLGENKIKEISNKMFL----GLHQLKTLNLYDN-QISCVMPGSFEH  124 (192)
T ss_dssp             GGGCTTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSCCCCEECSSSST----TCTTCCEEECCSS-CCCEECTTSSTT
T ss_pred             cCCCceEeeeeccccccccccccccccccccceeeeccccccccCHHHHh----CCCcccccccCCc-cccccCHHHhcC
Confidence            344444555555554444333  444445555555555555544444443    4445555555543 23444332 444


Q ss_pred             CCCCceeeccccc
Q 042541          674 IVSMEKLRITNCH  686 (695)
Q Consensus       674 L~~L~~L~l~~~~  686 (695)
                      +++|++|+|++|+
T Consensus       125 l~~L~~l~L~~N~  137 (192)
T d1w8aa_         125 LNSLTSLNLASNP  137 (192)
T ss_dssp             CTTCCEEECTTCC
T ss_pred             Ccccccccccccc
Confidence            4555555554443

>d1a9na_ c.10.2.4 (A:) Splicesomal U2A' protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: U2A'-like
domain: Splicesomal U2A' protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.13  E-value=5.1e-11  Score=107.06  Aligned_cols=113  Identities=16%  Similarity=0.183  Sum_probs=94.7

Q ss_pred             hcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcccccccccccEEeeccccCCcccccchhhhccc
Q 042541          570 LQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDA  649 (695)
Q Consensus       570 ~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~  649 (695)
                      +.++.+||.|+|++|++..  ++..  ...+++|++|+|++|.+..++.+..+++|++|++++|.++.+++..+.    .
T Consensus        14 ~~n~~~lr~L~L~~n~I~~--i~~~--~~~l~~L~~L~Ls~N~i~~l~~~~~l~~L~~L~ls~N~i~~l~~~~~~----~   85 (162)
T d1a9na_          14 YTNAVRDRELDLRGYKIPV--IENL--GATLDQFDAIDFSDNEIRKLDGFPLLRRLKTLLVNNNRICRIGEGLDQ----A   85 (162)
T ss_dssp             EECTTSCEEEECTTSCCCS--CCCG--GGGTTCCSEEECCSSCCCEECCCCCCSSCCEEECCSSCCCEECSCHHH----H
T ss_pred             ccCcCcCcEEECCCCCCCc--cCcc--ccccccCCEEECCCCCCCccCCcccCcchhhhhcccccccCCCccccc----c
Confidence            5677889999999988742  3332  467899999999999999888788999999999999999999988775    7


Q ss_pred             CCCccEEecccccccccCch--hhcCCCCCceeecccccCCCCCC
Q 042541          650 FPNLLEMDIDYCNDLIELPD--GLCDIVSMEKLRITNCHRLSALP  692 (695)
Q Consensus       650 l~~L~~L~l~~c~~l~~lP~--~i~~L~~L~~L~l~~~~~l~~lP  692 (695)
                      +++|++|++++| .+..+|.  .+..+++|++|++++|+ +..+|
T Consensus        86 l~~L~~L~L~~N-~i~~~~~l~~l~~l~~L~~L~l~~N~-i~~~~  128 (162)
T d1a9na_          86 LPDLTELILTNN-SLVELGDLDPLASLKSLTYLCILRNP-VTNKK  128 (162)
T ss_dssp             CTTCCEEECCSC-CCCCGGGGGGGGGCTTCCEEECCSSG-GGGST
T ss_pred             ccccccceeccc-cccccccccccccccccchhhcCCCc-ccccc
Confidence            999999999996 5677764  58899999999999986 65555

>d1xkua_ c.10.2.7 (A:) Decorin {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Decorin
species: Cow (Bos taurus) [TaxId: 9913]

Probab=99.13  E-value=2.8e-10  Score=114.09  Aligned_cols=163  Identities=17%  Similarity=0.277  Sum_probs=114.0

Q ss_pred             CCccceEEeeecCCcccCCCC-CCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCC--cc-----------
Q 042541          525 HPNNASLLSISTDETFSSNWP-DMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSP--AE-----------  590 (695)
Q Consensus       525 ~~~~~r~l~~~~~~~~~~~~~-~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~--~~-----------  590 (695)
                      .+..+++|.+.++........ ...+++|+.|.++.+......|..|..+++|++|++++|.+..  ..           
T Consensus        29 l~~~l~~L~Ls~N~i~~l~~~~f~~l~~L~~L~l~~n~~~~i~~~~f~~l~~L~~L~l~~n~l~~l~~~~~~~l~~L~~~  108 (305)
T d1xkua_          29 LPPDTALLDLQNNKITEIKDGDFKNLKNLHTLILINNKISKISPGAFAPLVKLERLYLSKNQLKELPEKMPKTLQELRVH  108 (305)
T ss_dssp             CCTTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSSCCCCBCTTTTTTCTTCCEEECCSSCCSBCCSSCCTTCCEEECC
T ss_pred             CCCCCCEEECcCCcCCCcChhHhhccccccccccccccccccchhhhhCCCccCEecccCCccCcCccchhhhhhhhhcc
Confidence            346788888877654322222 2367889999988887766667788899999999988874320  00           


Q ss_pred             ---cCcc----------------------------cccccCCCCcEEEeccCCCCCc----------------------c
Q 042541          591 ---LNNF----------------------------RVLSALSKLKKIRLEHVSLPNS----------------------L  617 (695)
Q Consensus       591 ---~~~~----------------------------~~l~~l~~L~~L~L~~~~l~~l----------------------p  617 (695)
                         +...                            ..+..+++|+++++.+|.+..+                      +
T Consensus       109 ~n~l~~l~~~~~~~~~~~~~l~~~~n~~~~~~~~~~~~~~l~~L~~l~l~~n~l~~l~~~~~~~L~~L~l~~n~~~~~~~  188 (305)
T d1xkua_         109 ENEITKVRKSVFNGLNQMIVVELGTNPLKSSGIENGAFQGMKKLSYIRIADTNITTIPQGLPPSLTELHLDGNKITKVDA  188 (305)
T ss_dssp             SSCCCBBCHHHHTTCTTCCEEECCSSCCCGGGBCTTGGGGCTTCCEEECCSSCCCSCCSSCCTTCSEEECTTSCCCEECT
T ss_pred             ccchhhhhhhhhhccccccccccccccccccCCCccccccccccCccccccCCccccCcccCCccCEEECCCCcCCCCCh
Confidence               0000                            0123344555555555544322                      3


Q ss_pred             -cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccccCCCCCCC
Q 042541          618 -ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALPE  693 (695)
Q Consensus       618 -~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~~l~~lP~  693 (695)
                       .+.+++++++|++++|.+..+++..+.    .+++|++|+|++| .+..+|.++..+++|++|++++|. ++.+|.
T Consensus       189 ~~~~~~~~l~~L~~s~n~l~~~~~~~~~----~l~~L~~L~L~~N-~L~~lp~~l~~l~~L~~L~Ls~N~-i~~i~~  259 (305)
T d1xkua_         189 ASLKGLNNLAKLGLSFNSISAVDNGSLA----NTPHLRELHLNNN-KLVKVPGGLADHKYIQVVYLHNNN-ISAIGS  259 (305)
T ss_dssp             GGGTTCTTCCEEECCSSCCCEECTTTGG----GSTTCCEEECCSS-CCSSCCTTTTTCSSCCEEECCSSC-CCCCCT
T ss_pred             hHhhcccccccccccccccccccccccc----ccccceeeecccc-cccccccccccccCCCEEECCCCc-cCccCh
Confidence             556677788888888888887777665    8999999999997 688999999999999999999965 888865

>d2omxa2 c.10.2.1 (A:37-235) Internalin B {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin B
species: Listeria monocytogenes [TaxId: 1639]

Probab=99.12  E-value=1.7e-10  Score=107.68  Aligned_cols=129  Identities=12%  Similarity=0.260  Sum_probs=99.3

Q ss_pred             CCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcccccccccccE
Q 042541          548 QGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSLATVRMNHLQK  627 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp~i~~l~~L~~  627 (695)
                      .+++|++|.++.+.... +++ ++++++|++|++++|...     ..+.++.+++|++|+++++.+..++.+..+++|++
T Consensus        60 ~l~nL~~L~Ls~N~l~~-~~~-l~~l~~L~~L~l~~n~~~-----~~~~l~~l~~L~~L~l~~~~~~~~~~~~~l~~L~~  132 (199)
T d2omxa2          60 YLNNLTQINFSNNQLTD-ITP-LKNLTKLVDILMNNNQIA-----DITPLANLTNLTGLTLFNNQITDIDPLKNLTNLNR  132 (199)
T ss_dssp             GCTTCCEEECCSSCCCC-CGG-GTTCTTCCEEECCSSCCC-----CCGGGTTCTTCSEEECCSSCCCCCGGGTTCTTCSE
T ss_pred             cCCCcCcCccccccccC-ccc-ccCCcccccccccccccc-----cccccccccccccccccccccccccccchhhhhHH
Confidence            57889999988875433 333 788999999999887652     22337788899999998888876666778899999


Q ss_pred             EeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccccCCCCCC
Q 042541          628 VSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALP  692 (695)
Q Consensus       628 L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~~l~~lP  692 (695)
                      |++++|.+..++ ...     .+++|+.|++.+| .+..+|. ++++++|++|++++|+ +..+|
T Consensus       133 L~l~~n~l~~~~-~l~-----~~~~L~~L~l~~n-~l~~l~~-l~~l~~L~~L~ls~N~-i~~i~  188 (199)
T d2omxa2         133 LELSSNTISDIS-ALS-----GLTSLQQLNFSSN-QVTDLKP-LANLTTLERLDISSNK-VSDIS  188 (199)
T ss_dssp             EECCSSCCCCCG-GGT-----TCTTCSEEECCSS-CCCCCGG-GTTCTTCCEEECCSSC-CCCCG
T ss_pred             hhhhhhhhcccc-ccc-----ccccccccccccc-cccCCcc-ccCCCCCCEEECCCCC-CCCCc
Confidence            999999887654 333     7889999999986 5677764 8899999999999975 77665

>d1h6ta2 c.10.2.1 (A:31-240) Internalin B {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin B
species: Listeria monocytogenes [TaxId: 1639]

Probab=99.09  E-value=3.7e-10  Score=106.35  Aligned_cols=142  Identities=17%  Similarity=0.240  Sum_probs=95.3

Q ss_pred             ccceEEeeecCCcccCCCCCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEE
Q 042541          527 NNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKI  606 (695)
Q Consensus       527 ~~~r~l~~~~~~~~~~~~~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L  606 (695)
                      ...+.|.+.++.... ......+++|+.|.++.+... .+| .+..+++|+.|++.+|...     .++.+..+++|+.+
T Consensus        68 ~~L~~L~L~~n~i~~-l~~~~~l~~L~~L~l~~n~i~-~l~-~l~~l~~L~~L~l~~~~~~-----~~~~l~~l~~l~~l  139 (210)
T d1h6ta2          68 PNVTKLFLNGNKLTD-IKPLANLKNLGWLFLDENKVK-DLS-SLKDLKKLKSLSLEHNGIS-----DINGLVHLPQLESL  139 (210)
T ss_dssp             TTCCEEECCSSCCCC-CGGGTTCTTCCEEECCSSCCC-CGG-GGTTCTTCCEEECTTSCCC-----CCGGGGGCTTCCEE
T ss_pred             CCCCEEeCCCccccC-ccccccCcccccccccccccc-ccc-ccccccccccccccccccc-----cccccccccccccc
Confidence            356666666553321 122235677777777766432 344 4677778888888776542     22346677778888


Q ss_pred             EeccCCCCCcccccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeeccc
Q 042541          607 RLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITN  684 (695)
Q Consensus       607 ~L~~~~l~~lp~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~  684 (695)
                      ++++|.++..+.+.++++|+++++++|.++.+++ ..     .+++|+.|++++| .+..+| ++..|++|++|+|++
T Consensus       140 ~~~~n~l~~~~~~~~l~~L~~l~l~~n~l~~i~~-l~-----~l~~L~~L~Ls~N-~i~~l~-~l~~l~~L~~L~Ls~  209 (210)
T d1h6ta2         140 YLGNNKITDITVLSRLTKLDTLSLEDNQISDIVP-LA-----GLTKLQNLYLSKN-HISDLR-ALAGLKNLDVLELFS  209 (210)
T ss_dssp             ECCSSCCCCCGGGGGCTTCSEEECCSSCCCCCGG-GT-----TCTTCCEEECCSS-CCCBCG-GGTTCTTCSEEEEEE
T ss_pred             cccccccccccccccccccccccccccccccccc-cc-----CCCCCCEEECCCC-CCCCCh-hhcCCCCCCEEEccC
Confidence            8888877765556678888888888888777554 22     6888888888876 567776 488888888888865

>d1ozna_ c.10.2.7 (A:) Reticulon 4 receptor (Nogo-66 receptor, Ngr) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Reticulon 4 receptor (Nogo-66 receptor, Ngr)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.08  E-value=5.7e-10  Score=110.49  Aligned_cols=132  Identities=14%  Similarity=0.146  Sum_probs=110.6

Q ss_pred             CCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--cccccccc
Q 042541          548 QGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNHL  625 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L  625 (695)
                      .+++|+.|.++.+......+..+..+.+|+.+++.+|.+..  ++ ...+..+.+|+.|++++|++..+|  .+.++++|
T Consensus       103 ~l~~L~~L~l~~n~~~~~~~~~~~~~~~L~~l~l~~N~l~~--i~-~~~f~~~~~L~~L~l~~N~l~~l~~~~f~~l~~L  179 (284)
T d1ozna_         103 GLGRLHTLHLDRCGLQELGPGLFRGLAALQYLYLQDNALQA--LP-DDTFRDLGNLTHLFLHGNRISSVPERAFRGLHSL  179 (284)
T ss_dssp             TCTTCCEEECTTSCCCCCCTTTTTTCTTCCEEECCSSCCCC--CC-TTTTTTCTTCCEEECCSSCCCEECTTTTTTCTTC
T ss_pred             ccccCCEEecCCcccccccccccchhcccchhhhccccccc--cC-hhHhccccchhhcccccCcccccchhhhcccccc
Confidence            67899999998886655566678889999999999987742  21 123678889999999999999887  78899999


Q ss_pred             cEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeeccccc
Q 042541          626 QKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCH  686 (695)
Q Consensus       626 ~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~  686 (695)
                      ++|++++|.++.++|..+.    .+++|++|++++|......|..++.+++|++|++++|+
T Consensus       180 ~~l~l~~N~l~~i~~~~f~----~l~~L~~L~l~~N~i~~~~~~~~~~~~~L~~L~l~~N~  236 (284)
T d1ozna_         180 DRLLLHQNRVAHVHPHAFR----DLGRLMTLYLFANNLSALPTEALAPLRALQYLRLNDNP  236 (284)
T ss_dssp             CEEECCSSCCCEECTTTTT----TCTTCCEEECCSSCCSCCCHHHHTTCTTCCEEECCSSC
T ss_pred             chhhhhhccccccChhHhh----hhhhcccccccccccccccccccccccccCEEEecCCC
Confidence            9999999999999888877    89999999999975444444568999999999999976

>d1h6ta2 c.10.2.1 (A:31-240) Internalin B {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin B
species: Listeria monocytogenes [TaxId: 1639]

Probab=99.08  E-value=3.5e-10  Score=106.54  Aligned_cols=129  Identities=19%  Similarity=0.282  Sum_probs=106.5

Q ss_pred             CCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcccccccccccE
Q 042541          548 QGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSLATVRMNHLQK  627 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp~i~~l~~L~~  627 (695)
                      .+++|+.|.++++.... ++ .+..+++|++|++++|.+.     .++.+..+++|+.|++.+|.+..++.+..+++|++
T Consensus        66 ~l~~L~~L~L~~n~i~~-l~-~~~~l~~L~~L~l~~n~i~-----~l~~l~~l~~L~~L~l~~~~~~~~~~l~~l~~l~~  138 (210)
T d1h6ta2          66 YLPNVTKLFLNGNKLTD-IK-PLANLKNLGWLFLDENKVK-----DLSSLKDLKKLKSLSLEHNGISDINGLVHLPQLES  138 (210)
T ss_dssp             GCTTCCEEECCSSCCCC-CG-GGTTCTTCCEEECCSSCCC-----CGGGGTTCTTCCEEECTTSCCCCCGGGGGCTTCCE
T ss_pred             hCCCCCEEeCCCccccC-cc-ccccCcccccccccccccc-----ccccccccccccccccccccccccccccccccccc
Confidence            58899999998885443 44 3678999999999988663     34457889999999999999988777889999999


Q ss_pred             EeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccccCCCCCC
Q 042541          628 VSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCHRLSALP  692 (695)
Q Consensus       628 L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~~l~~lP  692 (695)
                      +++++|.++..+. ..     .+++|+++++++| .+..+|. ++++++|+.|++++|. ++.+|
T Consensus       139 l~~~~n~l~~~~~-~~-----~l~~L~~l~l~~n-~l~~i~~-l~~l~~L~~L~Ls~N~-i~~l~  194 (210)
T d1h6ta2         139 LYLGNNKITDITV-LS-----RLTKLDTLSLEDN-QISDIVP-LAGLTKLQNLYLSKNH-ISDLR  194 (210)
T ss_dssp             EECCSSCCCCCGG-GG-----GCTTCSEEECCSS-CCCCCGG-GTTCTTCCEEECCSSC-CCBCG
T ss_pred             ccccccccccccc-cc-----ccccccccccccc-ccccccc-ccCCCCCCEEECCCCC-CCCCh
Confidence            9999999886443 22     7999999999997 5677764 9999999999999975 77776

>d1ogqa_ c.10.2.8 (A:) Polygalacturonase inhibiting protein PGIP {Kidney bean (Phaseolus vulgaris) [TaxId: 3885]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Polygalacturonase inhibiting protein PGIP
domain: Polygalacturonase inhibiting protein PGIP
species: Kidney bean (Phaseolus vulgaris) [TaxId: 3885]

Probab=99.07  E-value=1.3e-10  Score=117.02  Aligned_cols=136  Identities=14%  Similarity=0.217  Sum_probs=110.6

Q ss_pred             CceEEEEEEccCccc--cCChhhcCCCCCcEEEEcc-cCCCCcccCcccccccCCCCcEEEeccCCCCCcc--ccccccc
Q 042541          550 PEVKVVVLNIRTKKY--VLPDFLQKMDELKVLIVTN-YGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNH  624 (695)
Q Consensus       550 ~~l~~L~l~~~~~~~--~~p~~~~~l~~Lr~L~l~~-~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~  624 (695)
                      .+++.|.|+++...+  .+|..++++++|++|+|++ |.+. +.+  ++.+++|++|++|+|++|.+..++  .+..+.+
T Consensus        50 ~~v~~L~L~~~~l~g~~~lp~~l~~L~~L~~L~Ls~~N~l~-g~i--P~~i~~L~~L~~L~Ls~N~l~~~~~~~~~~~~~  126 (313)
T d1ogqa_          50 YRVNNLDLSGLNLPKPYPIPSSLANLPYLNFLYIGGINNLV-GPI--PPAIAKLTQLHYLYITHTNVSGAIPDFLSQIKT  126 (313)
T ss_dssp             CCEEEEEEECCCCSSCEECCGGGGGCTTCSEEEEEEETTEE-SCC--CGGGGGCTTCSEEEEEEECCEEECCGGGGGCTT
T ss_pred             EEEEEEECCCCCCCCCCCCChHHhcCccccccccccccccc-ccc--ccccccccccchhhhccccccccccccccchhh
Confidence            368889998885544  6899999999999999997 4442 223  234899999999999999998655  7889999


Q ss_pred             ccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCC-ceeecccccCCCCCC
Q 042541          625 LQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSM-EKLRITNCHRLSALP  692 (695)
Q Consensus       625 L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L-~~L~l~~~~~l~~lP  692 (695)
                      |++++++.|.+....|..+.    .+++|+++++++|...+.+|..++.+.+| +.+++++|...+..|
T Consensus       127 L~~l~l~~N~~~~~~p~~l~----~l~~L~~l~l~~n~l~~~ip~~~~~l~~l~~~l~~~~n~l~~~~~  191 (313)
T d1ogqa_         127 LVTLDFSYNALSGTLPPSIS----SLPNLVGITFDGNRISGAIPDSYGSFSKLFTSMTISRNRLTGKIP  191 (313)
T ss_dssp             CCEEECCSSEEESCCCGGGG----GCTTCCEEECCSSCCEEECCGGGGCCCTTCCEEECCSSEEEEECC
T ss_pred             hcccccccccccccCchhhc----cCcccceeecccccccccccccccccccccccccccccccccccc
Confidence            99999999987777666665    89999999999988777899999999886 788888876444444

>d1w8aa_ c.10.2.7 (A:) Slit {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Slit
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.04  E-value=1.3e-10  Score=107.86  Aligned_cols=106  Identities=10%  Similarity=0.133  Sum_probs=86.0

Q ss_pred             CceEEEEEEccCccccC-ChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--ccccccccc
Q 042541          550 PEVKVVVLNIRTKKYVL-PDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNHLQ  626 (695)
Q Consensus       550 ~~l~~L~l~~~~~~~~~-p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L~  626 (695)
                      ++++.|.|+.+.....+ +..|.++++|+.|++++|.+...   ....+..+++|++|+|++|.++.+|  .+.++++|+
T Consensus        29 ~~l~~L~Ls~N~i~~~~~~~~f~~l~~L~~L~L~~N~i~~~---~~~~~~~~~~L~~L~Ls~N~l~~l~~~~F~~l~~L~  105 (192)
T d1w8aa_          29 LHTTELLLNDNELGRISSDGLFGRLPHLVKLELKRNQLTGI---EPNAFEGASHIQELQLGENKIKEISNKMFLGLHQLK  105 (192)
T ss_dssp             TTCSEEECCSCCCCSBCCSCSGGGCTTCCEEECCSSCCCCB---CTTTTTTCTTCCEEECCSCCCCEECSSSSTTCTTCC
T ss_pred             CCCCEEEeCCCCCcccccccccCCCceEeeeeccccccccc---cccccccccccceeeeccccccccCHHHHhCCCccc
Confidence            57888888888765544 45788899999999998876422   1233678889999999999999887  788899999


Q ss_pred             EEeeccccCCcccccchhhhcccCCCccEEeccccc
Q 042541          627 KVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCN  662 (695)
Q Consensus       627 ~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~  662 (695)
                      +|+|++|.|+.+++..+.    .+++|++|+|+++.
T Consensus       106 ~L~L~~N~l~~i~~~~f~----~l~~L~~l~L~~N~  137 (192)
T d1w8aa_         106 TLNLYDNQISCVMPGSFE----HLNSLTSLNLASNP  137 (192)
T ss_dssp             EEECCSSCCCEECTTSST----TCTTCCEEECTTCC
T ss_pred             ccccCCccccccCHHHhc----CCcccccccccccc
Confidence            999999999999998876    88999999998864

>d2omxa2 c.10.2.1 (A:37-235) Internalin B {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin B
species: Listeria monocytogenes [TaxId: 1639]

Probab=98.99  E-value=1.5e-09  Score=101.07  Aligned_cols=139  Identities=17%  Similarity=0.229  Sum_probs=108.9

Q ss_pred             CccceEEeeecCCcccCCCCCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcE
Q 042541          526 PNNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKK  605 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~~~~~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~  605 (695)
                      ..+.++|.+.++.. ........+++|+.|.++.+... .++ .+.++++|+.|++.++....     .+.+..+++|++
T Consensus        61 l~nL~~L~Ls~N~l-~~~~~l~~l~~L~~L~l~~n~~~-~~~-~l~~l~~L~~L~l~~~~~~~-----~~~~~~l~~L~~  132 (199)
T d2omxa2          61 LNNLTQINFSNNQL-TDITPLKNLTKLVDILMNNNQIA-DIT-PLANLTNLTGLTLFNNQITD-----IDPLKNLTNLNR  132 (199)
T ss_dssp             CTTCCEEECCSSCC-CCCGGGTTCTTCCEEECCSSCCC-CCG-GGTTCTTCSEEECCSSCCCC-----CGGGTTCTTCSE
T ss_pred             CCCcCcCccccccc-cCcccccCCcccccccccccccc-ccc-cccccccccccccccccccc-----ccccchhhhhHH
Confidence            34677888876543 22223347899999999877432 333 48899999999999876532     233778999999


Q ss_pred             EEeccCCCCCcccccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCcee
Q 042541          606 IRLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKL  680 (695)
Q Consensus       606 L~L~~~~l~~lp~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L  680 (695)
                      |++++|.+..+|.+..+++|++|++.+|.++.+++ ..     .+++|++|++++| .+..+| .+++|++|+.|
T Consensus       133 L~l~~n~l~~~~~l~~~~~L~~L~l~~n~l~~l~~-l~-----~l~~L~~L~ls~N-~i~~i~-~l~~L~~L~~L  199 (199)
T d2omxa2         133 LELSSNTISDISALSGLTSLQQLNFSSNQVTDLKP-LA-----NLTTLERLDISSN-KVSDIS-VLAKLTNLESL  199 (199)
T ss_dssp             EECCSSCCCCCGGGTTCTTCSEEECCSSCCCCCGG-GT-----TCTTCCEEECCSS-CCCCCG-GGGGCTTCSEE
T ss_pred             hhhhhhhhcccccccccccccccccccccccCCcc-cc-----CCCCCCEEECCCC-CCCCCc-cccCCCCCCcC
Confidence            99999999887778899999999999999988754 33     8999999999997 578887 48999999886

>d1m9la_ c.10.3.1 (A:) Outer arm dynein light chain 1 {Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: Outer arm dynein light chain 1
family: Outer arm dynein light chain 1
domain: Outer arm dynein light chain 1
species: Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]

Probab=98.97  E-value=2.6e-11  Score=113.07  Aligned_cols=110  Identities=13%  Similarity=0.167  Sum_probs=63.9

Q ss_pred             cCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc-cccccccccEEeeccccCCcccccch
Q 042541          565 VLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL-ATVRMNHLQKVSLVMCNVGQVFRNST  643 (695)
Q Consensus       565 ~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp-~i~~l~~L~~L~l~~~~i~~~~~~~~  643 (695)
                      .+|.++..+++|++|+|++|.+.     .++.+..|++|++|+|++|.++.+| ....+++|++|++++|.++.+++ ..
T Consensus        39 ~l~~sl~~L~~L~~L~Ls~n~I~-----~i~~l~~l~~L~~L~Ls~N~i~~i~~~~~~~~~L~~L~l~~N~i~~l~~-~~  112 (198)
T d1m9la_          39 KMDATLSTLKACKHLALSTNNIE-----KISSLSGMENLRILSLGRNLIKKIENLDAVADTLEELWISYNQIASLSG-IE  112 (198)
T ss_dssp             CCHHHHHHTTTCCEEECSEEEES-----CCCCHHHHTTCCEEECCEEEECSCSSHHHHHHHCCEEECSEEECCCHHH-HH
T ss_pred             hhhhHHhcccccceeECcccCCC-----CcccccCCccccChhhccccccccccccccccccccccccccccccccc-cc
Confidence            34455666666666666665542     1223556666666666666666666 44445566666666666665422 22


Q ss_pred             hhhcccCCCccEEecccccccccCc--hhhcCCCCCceeeccccc
Q 042541          644 FRISDAFPNLLEMDIDYCNDLIELP--DGLCDIVSMEKLRITNCH  686 (695)
Q Consensus       644 ~~l~~~l~~L~~L~l~~c~~l~~lP--~~i~~L~~L~~L~l~~~~  686 (695)
                           .+++|++|++++| .+..+|  ..+..+++|+.|++++|+
T Consensus       113 -----~l~~L~~L~L~~N-~i~~~~~~~~l~~l~~L~~L~L~~N~  151 (198)
T d1m9la_         113 -----KLVNLRVLYMSNN-KITNWGEIDKLAALDKLEDLLLAGNP  151 (198)
T ss_dssp             -----HHHHSSEEEESEE-ECCCHHHHHHHTTTTTCSEEEECSSH
T ss_pred             -----ccccccccccccc-hhccccccccccCCCccceeecCCCc
Confidence                 5666666666664 345554  245666666666666654

>d1dcea3 c.10.2.2 (A:444-567) Rab geranylgeranyltransferase alpha-subunit, C-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Rab geranylgeranyltransferase alpha-subunit, C-terminal domain
domain: Rab geranylgeranyltransferase alpha-subunit, C-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=98.96  E-value=8e-10  Score=94.11  Aligned_cols=82  Identities=13%  Similarity=0.152  Sum_probs=72.8

Q ss_pred             cEEEeccCCCCCcccccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecc
Q 042541          604 KKIRLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRIT  683 (695)
Q Consensus       604 ~~L~L~~~~l~~lp~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~  683 (695)
                      |+|+|++|.++.+|.++++.+|++|++++|.++.+|+.+.     .+++|++|++++| .+..+| +++.+++|++|+++
T Consensus         1 R~L~Ls~n~l~~l~~l~~l~~L~~L~ls~N~l~~lp~~~~-----~l~~L~~L~l~~N-~i~~l~-~~~~l~~L~~L~l~   73 (124)
T d1dcea3           1 RVLHLAHKDLTVLCHLEQLLLVTHLDLSHNRLRALPPALA-----ALRCLEVLQASDN-ALENVD-GVANLPRLQELLLC   73 (124)
T ss_dssp             SEEECTTSCCSSCCCGGGGTTCCEEECCSSCCCCCCGGGG-----GCTTCCEEECCSS-CCCCCG-GGTTCSSCCEEECC
T ss_pred             CEEEcCCCCCCCCcccccCCCCCEEECCCCccCcchhhhh-----hhhcccccccccc-cccccC-ccccccccCeEECC
Confidence            6899999999988888899999999999999999887654     8999999999995 678887 49999999999999


Q ss_pred             cccCCCCCCC
Q 042541          684 NCHRLSALPE  693 (695)
Q Consensus       684 ~~~~l~~lP~  693 (695)
                      +|. +..+|.
T Consensus        74 ~N~-i~~~~~   82 (124)
T d1dcea3          74 NNR-LQQSAA   82 (124)
T ss_dssp             SSC-CCSSST
T ss_pred             CCc-cCCCCC
Confidence            965 777763

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=98.92  E-value=3.7e-08  Score=96.28  Aligned_cols=167  Identities=19%  Similarity=0.226  Sum_probs=110.9

Q ss_pred             CCCCCCCCcchHHHHHHHHHc------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHH
Q 042541          164 PPVISPGLDVPLKELKMELFK------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQ  237 (695)
Q Consensus       164 ~~~~~vGr~~~~~~l~~~L~~------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~  237 (695)
                      .|..++||+.++++|.++|..      ...+.+.|+|++|+|||++|+.+++  .+........+|+.............
T Consensus        14 ~p~~l~~Re~ei~~l~~~l~~~l~~~~~~~~~lll~GppGtGKT~l~~~l~~--~l~~~~~~~~~~~~~~~~~~~~~~~~   91 (276)
T d1fnna2          14 VPKRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWE--LYKDKTTARFVYINGFIYRNFTAIIG   91 (276)
T ss_dssp             CCSCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHH--HHTTSCCCEEEEEETTTCCSHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHhCCCCCCCceEEECCCCCCHHHHHHHHHH--HHhcccCCcEEEecchhhhhhhhhhh
Confidence            345679999999999998862      2357899999999999999999998  55555555567888888888999999


Q ss_pred             HHHHhcCCCCCCCCC-hHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChHHH---hhhcc-----CCCCCEEEEEcCCCC-
Q 042541          238 KVLHHKGYPVPEFQT-DEAAINDLERFFKQMRIEAILLVLDDVWPGSESLL---QKLGF-----QLPDYKILVTSRSEF-  307 (695)
Q Consensus       238 ~i~~~l~~~~~~~~~-~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~~~---~~l~~-----~~~gs~iivTtR~~~-  307 (695)
                      .+....+...+.... .......+...... .......++|+++.......   ..+..     ......+|.++.... 
T Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~  170 (276)
T d1fnna2          92 EIARSLNIPFPRRGLSRDEFLALLVEHLRE-RDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAV  170 (276)
T ss_dssp             HHHHHTTCCCCSSCCCHHHHHHHHHHHHHH-TTCCEEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESSTHH
T ss_pred             hhHHhhhhhhhhhccchhHHHHHHHHHHhh-cccccccchhHHHHhhhhhhhhHHHHHhccccccccceEEeecCCchhh
Confidence            999988765543322 22333333333322 35677788888876654311   11111     112234555554431 


Q ss_pred             ---C-------CCCCeEecCCCChHHHHHHHHHhcc
Q 042541          308 ---P-------QFGSVHYLKPLTYEAARTLFLHSAN  333 (695)
Q Consensus       308 ---~-------~~~~~~~l~~L~~~ea~~Lf~~~~~  333 (695)
                         .       .....+.+.+.+.++.++++.+++.
T Consensus       171 ~~~~~~~~~~r~~~~~i~~~~~~~~e~~~il~~r~~  206 (276)
T d1fnna2         171 LNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAK  206 (276)
T ss_dssp             HHTSCHHHHHHHTTCEEECCCCBHHHHHHHHHHHHH
T ss_pred             hhhcchhhhhhhcchhccccchhHHHHHHHHHHHHH
Confidence               0       1123688999999999999987653

>d1h6ua2 c.10.2.1 (A:36-262) Internalin H {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin H
species: Listeria monocytogenes [TaxId: 1639]

Probab=98.91  E-value=4.7e-09  Score=99.91  Aligned_cols=148  Identities=14%  Similarity=0.210  Sum_probs=81.5

Q ss_pred             CccceEEeeecCCcccCCCCCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcc---------------
Q 042541          526 PNNASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAE---------------  590 (695)
Q Consensus       526 ~~~~r~l~~~~~~~~~~~~~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~---------------  590 (695)
                      ....+++.+..+... .......+++++.+.++.+... .++ .+.++++|+++.+.++......               
T Consensus        62 l~~L~~L~ls~n~i~-~~~~l~~l~~l~~l~~~~n~~~-~i~-~l~~l~~L~~l~l~~~~~~~~~~~~~~~~~~~l~~~~  138 (227)
T d1h6ua2          62 LNNLIGLELKDNQIT-DLAPLKNLTKITELELSGNPLK-NVS-AIAGLQSIKTLDLTSTQITDVTPLAGLSNLQVLYLDL  138 (227)
T ss_dssp             CTTCCEEECCSSCCC-CCGGGTTCCSCCEEECCSCCCS-CCG-GGTTCTTCCEEECTTSCCCCCGGGTTCTTCCEEECCS
T ss_pred             CCCCcEeecCCceee-cccccccccccccccccccccc-ccc-cccccccccccccccccccccchhccccchhhhhchh
Confidence            456677777654322 2222346777887777665332 233 4677888888888776432110               


Q ss_pred             --cCcccccccCCCCcEEEeccCCCCCcccccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCc
Q 042541          591 --LNNFRVLSALSKLKKIRLEHVSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELP  668 (695)
Q Consensus       591 --~~~~~~l~~l~~L~~L~L~~~~l~~lp~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP  668 (695)
                        +.....+..+++|++|++.+|.+...+.++++++|++|++++|.++.+++ . .    .+++|++|++++| .+..+|
T Consensus       139 ~~~~~~~~~~~~~~L~~L~l~~n~~~~~~~l~~l~~L~~L~Ls~n~l~~l~~-l-~----~l~~L~~L~Ls~N-~lt~i~  211 (227)
T d1h6ua2         139 NQITNISPLAGLTNLQYLSIGNAQVSDLTPLANLSKLTTLKADDNKISDISP-L-A----SLPNLIEVHLKNN-QISDVS  211 (227)
T ss_dssp             SCCCCCGGGGGCTTCCEEECCSSCCCCCGGGTTCTTCCEEECCSSCCCCCGG-G-G----GCTTCCEEECTTS-CCCBCG
T ss_pred             hhhchhhhhccccccccccccccccccchhhcccccceecccCCCccCCChh-h-c----CCCCCCEEECcCC-cCCCCc
Confidence              01111234455566666666655544445556666666666666555433 2 2    5566666666665 355555


Q ss_pred             hhhcCCCCCceeeccc
Q 042541          669 DGLCDIVSMEKLRITN  684 (695)
Q Consensus       669 ~~i~~L~~L~~L~l~~  684 (695)
                      . ++++++|+.|++++
T Consensus       212 ~-l~~l~~L~~L~lsn  226 (227)
T d1h6ua2         212 P-LANTSNLFIVTLTN  226 (227)
T ss_dssp             G-GTTCTTCCEEEEEE
T ss_pred             c-cccCCCCCEEEeeC
Confidence            3 56666666666653

>d1h6ua2 c.10.2.1 (A:36-262) Internalin H {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin H
species: Listeria monocytogenes [TaxId: 1639]

Probab=98.90  E-value=6.9e-09  Score=98.74  Aligned_cols=148  Identities=13%  Similarity=0.139  Sum_probs=107.0

Q ss_pred             cceEEeeecCCcccCCCCCCCCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEE
Q 042541          528 NASLLSISTDETFSSNWPDMQGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIR  607 (695)
Q Consensus       528 ~~r~l~~~~~~~~~~~~~~~~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~  607 (695)
                      ..+.+.+.+...-. ...-..+++|+.|.++.+......  .+.++++|+++++.+|...     .++.+..+++|+++.
T Consensus        42 ~L~~L~l~~~~i~~-l~~l~~l~~L~~L~ls~n~i~~~~--~l~~l~~l~~l~~~~n~~~-----~i~~l~~l~~L~~l~  113 (227)
T d1h6ua2          42 GITTLSAFGTGVTT-IEGVQYLNNLIGLELKDNQITDLA--PLKNLTKITELELSGNPLK-----NVSAIAGLQSIKTLD  113 (227)
T ss_dssp             TCCEEECTTSCCCC-CTTGGGCTTCCEEECCSSCCCCCG--GGTTCCSCCEEECCSCCCS-----CCGGGTTCTTCCEEE
T ss_pred             CcCEEECCCCCCCc-chhHhcCCCCcEeecCCceeeccc--ccccccccccccccccccc-----ccccccccccccccc
Confidence            45666665544321 111236899999999888544332  3889999999999987652     233466777777777


Q ss_pred             eccCCCC----------------------CcccccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccc
Q 042541          608 LEHVSLP----------------------NSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLI  665 (695)
Q Consensus       608 L~~~~l~----------------------~lp~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~  665 (695)
                      ++++...                      ..+.+.++++|++|++++|.+...++ + .    .+++|+.|++++| .+.
T Consensus       114 l~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~L~~L~l~~n~~~~~~~-l-~----~l~~L~~L~Ls~n-~l~  186 (227)
T d1h6ua2         114 LTSTQITDVTPLAGLSNLQVLYLDLNQITNISPLAGLTNLQYLSIGNAQVSDLTP-L-A----NLSKLTTLKADDN-KIS  186 (227)
T ss_dssp             CTTSCCCCCGGGTTCTTCCEEECCSSCCCCCGGGGGCTTCCEEECCSSCCCCCGG-G-T----TCTTCCEEECCSS-CCC
T ss_pred             cccccccccchhccccchhhhhchhhhhchhhhhccccccccccccccccccchh-h-c----ccccceecccCCC-ccC
Confidence            7665432                      11245677889999999998876544 3 3    8999999999997 678


Q ss_pred             cCchhhcCCCCCceeecccccCCCCCC
Q 042541          666 ELPDGLCDIVSMEKLRITNCHRLSALP  692 (695)
Q Consensus       666 ~lP~~i~~L~~L~~L~l~~~~~l~~lP  692 (695)
                      .+|. ++++++|++|+|++|+ ++.+|
T Consensus       187 ~l~~-l~~l~~L~~L~Ls~N~-lt~i~  211 (227)
T d1h6ua2         187 DISP-LASLPNLIEVHLKNNQ-ISDVS  211 (227)
T ss_dssp             CCGG-GGGCTTCCEEECTTSC-CCBCG
T ss_pred             CChh-hcCCCCCCEEECcCCc-CCCCc
Confidence            8875 9999999999999985 87776

>d2omza2 c.10.2.1 (A:33-416) Internalin A {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin A
species: Listeria monocytogenes [TaxId: 1639]

Probab=98.84  E-value=9e-09  Score=106.20  Aligned_cols=128  Identities=15%  Similarity=0.182  Sum_probs=69.3

Q ss_pred             CCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCc-----------------ccCcccccccCCCCcEEEecc
Q 042541          548 QGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPA-----------------ELNNFRVLSALSKLKKIRLEH  610 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~-----------------~~~~~~~l~~l~~L~~L~L~~  610 (695)
                      .+++++.|.+..+.... ++ .+..+++|++|+++++.+...                 .+..++.+..+.++++|++++
T Consensus       239 ~l~~L~~L~l~~n~l~~-~~-~~~~~~~L~~L~l~~~~l~~~~~~~~~~~l~~l~~~~n~l~~~~~~~~~~~l~~L~ls~  316 (384)
T d2omza2         239 SLTNLTDLDLANNQISN-LA-PLSGLTKLTELKLGANQISNISPLAGLTALTNLELNENQLEDISPISNLKNLTYLTLYF  316 (384)
T ss_dssp             GCTTCSEEECCSSCCCC-CG-GGTTCTTCSEEECCSSCCCCCGGGTTCTTCSEEECCSSCCSCCGGGGGCTTCSEEECCS
T ss_pred             cccccchhccccCccCC-CC-cccccccCCEeeccCcccCCCCccccccccccccccccccccccccchhcccCeEECCC
Confidence            45566666665553322 22 255566666666666543210                 011122244555666666666


Q ss_pred             CCCCCcccccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeecccc
Q 042541          611 VSLPNSLATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNC  685 (695)
Q Consensus       611 ~~l~~lp~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~  685 (695)
                      |+++.++.+..+++|++|++++|+++.++ ...     .+++|++|++++| .+..+|+ +++|++|+.|+|++|
T Consensus       317 n~l~~l~~l~~l~~L~~L~L~~n~l~~l~-~l~-----~l~~L~~L~l~~N-~l~~l~~-l~~l~~L~~L~L~~N  383 (384)
T d2omza2         317 NNISDISPVSSLTKLQRLFFANNKVSDVS-SLA-----NLTNINWLSAGHN-QISDLTP-LANLTRITQLGLNDQ  383 (384)
T ss_dssp             SCCSCCGGGGGCTTCCEEECCSSCCCCCG-GGG-----GCTTCCEEECCSS-CCCBCGG-GTTCTTCSEEECCCE
T ss_pred             CCCCCCcccccCCCCCEEECCCCCCCCCh-hHc-----CCCCCCEEECCCC-cCCCChh-hccCCCCCEeeCCCC
Confidence            66665554556666666666666665543 222     5666666666654 3455553 666666666666654

>d2omza2 c.10.2.1 (A:33-416) Internalin A {Listeria monocytogenes [TaxId: 1639]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Internalin LRR domain
domain: Internalin A
species: Listeria monocytogenes [TaxId: 1639]

Probab=98.81  E-value=1.3e-08  Score=105.07  Aligned_cols=101  Identities=10%  Similarity=0.115  Sum_probs=76.5

Q ss_pred             CCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcccccccccccE
Q 042541          548 QGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSLATVRMNHLQK  627 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp~i~~l~~L~~  627 (695)
                      .++.++.+.+..+....  +..+..+.+++.|++++|.+..     ++.+..+++|++|++++|.++.+|.++++++|++
T Consensus       283 ~~~~l~~l~~~~n~l~~--~~~~~~~~~l~~L~ls~n~l~~-----l~~l~~l~~L~~L~L~~n~l~~l~~l~~l~~L~~  355 (384)
T d2omza2         283 GLTALTNLELNENQLED--ISPISNLKNLTYLTLYFNNISD-----ISPVSSLTKLQRLFFANNKVSDVSSLANLTNINW  355 (384)
T ss_dssp             TCTTCSEEECCSSCCSC--CGGGGGCTTCSEEECCSSCCSC-----CGGGGGCTTCCEEECCSSCCCCCGGGGGCTTCCE
T ss_pred             ccccccccccccccccc--ccccchhcccCeEECCCCCCCC-----CcccccCCCCCEEECCCCCCCCChhHcCCCCCCE
Confidence            34445555444432221  2346778888999998876632     2337889999999999999998888889999999


Q ss_pred             EeeccccCCcccccchhhhcccCCCccEEecccc
Q 042541          628 VSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYC  661 (695)
Q Consensus       628 L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c  661 (695)
                      |++++|++++++| . .    .|++|+.|+|++|
T Consensus       356 L~l~~N~l~~l~~-l-~----~l~~L~~L~L~~N  383 (384)
T d2omza2         356 LSAGHNQISDLTP-L-A----NLTRITQLGLNDQ  383 (384)
T ss_dssp             EECCSSCCCBCGG-G-T----TCTTCSEEECCCE
T ss_pred             EECCCCcCCCChh-h-c----cCCCCCEeeCCCC
Confidence            9999999998876 3 3    8999999999975

>d1xwdc1 c.10.2.7 (C:18-259) Follicle-stimulating hormone receptor {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Follicle-stimulating hormone receptor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.81  E-value=3.4e-08  Score=94.76  Aligned_cols=138  Identities=17%  Similarity=0.268  Sum_probs=63.5

Q ss_pred             CCCceEEEEEEcc-CccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc--cccccc-
Q 042541          548 QGPEVKVVVLNIR-TKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMN-  623 (695)
Q Consensus       548 ~~~~l~~L~l~~~-~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~-  623 (695)
                      .+++++.+.+..+ ......+..|.++++|++|++.++++..  .+....+..+..|..+...++.+..++  .+..+. 
T Consensus        76 ~l~~l~~l~~~~~n~l~~~~~~~~~~l~~L~~l~l~~~~l~~--~~~~~~~~~l~~l~~~~~~n~~l~~i~~~~~~~~~~  153 (242)
T d1xwdc1          76 NLPKLHEIRIEKANNLLYINPEAFQNLPNLQYLLISNTGIKH--LPDVHKIHSLQKVLLDIQDNINIHTIERNSFVGLSF  153 (242)
T ss_dssp             SCTTCCEEEEECCTTCCEECTTSEECCTTCCEEEEESCCCCS--CCCCTTTCBSSCEEEEEESCTTCCEECTTSSTTSBS
T ss_pred             cccccccccccccccccccccccccccccccccccchhhhcc--cccccccccccccccccccccccccccccccccccc
Confidence            3455555554443 3333344456667777777777665421  111111222333333333333333333  222222 


Q ss_pred             cccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCchh-hcCCCCCceeecccccCCCCCCC
Q 042541          624 HLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDG-LCDIVSMEKLRITNCHRLSALPE  693 (695)
Q Consensus       624 ~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~-i~~L~~L~~L~l~~~~~l~~lP~  693 (695)
                      .+++|++++|.++.+++..+     ..++++.+....++.+.++|.+ +.++++|++|++++|. +..+|.
T Consensus       154 ~l~~L~l~~n~l~~i~~~~~-----~~~~l~~~~~l~~n~l~~l~~~~f~~l~~L~~L~Ls~N~-l~~l~~  218 (242)
T d1xwdc1         154 ESVILWLNKNGIQEIHNCAF-----NGTQLDELNLSDNNNLEELPNDVFHGASGPVILDISRTR-IHSLPS  218 (242)
T ss_dssp             SCEEEECCSSCCCEECTTTT-----TTCCEEEEECTTCTTCCCCCTTTTTTSCCCSEEECTTSC-CCCCCS
T ss_pred             cceeeecccccccccccccc-----cchhhhccccccccccccccHHHhcCCCCCCEEECCCCc-CCccCH
Confidence            44455555555554444443     3444444443334455555543 4555666666665543 555554

>d2ifga3 c.10.2.7 (A:36-191) High affinity nerve growth factor receptor, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: High affinity nerve growth factor receptor, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.80  E-value=7e-09  Score=92.06  Aligned_cols=91  Identities=16%  Similarity=0.152  Sum_probs=66.4

Q ss_pred             ccCChhhcCCCCCcEEEEcccC-CCCcccCcccccccCCCCcEEEeccCCCCCcc--cccccccccEEeeccccCCcccc
Q 042541          564 YVLPDFLQKMDELKVLIVTNYG-FSPAELNNFRVLSALSKLKKIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFR  640 (695)
Q Consensus       564 ~~~p~~~~~l~~Lr~L~l~~~~-~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~  640 (695)
                      ...|..+..+++|+.|++.++. +.  .+ ....+..+++|+.|+|++|.++.++  .+..+++|++|+|++|+++.+++
T Consensus        21 ~~~p~~l~~l~~l~~L~l~~n~~l~--~i-~~~~f~~l~~L~~L~Ls~N~l~~i~~~~f~~l~~L~~L~Ls~N~l~~l~~   97 (156)
T d2ifga3          21 LDSLHHLPGAENLTELYIENQQHLQ--HL-ELRDLRGLGELRNLTIVKSGLRFVAPDAFHFTPRLSRLNLSFNALESLSW   97 (156)
T ss_dssp             CTTTTTSCSCSCCSEEECCSCSSCC--EE-CGGGSCSCCCCSEEECCSSCCCEECTTGGGSCSCCCEEECCSSCCSCCCS
T ss_pred             ccCcccccCccccCeeecCCCcccc--cc-CchhhccccccCcceeeccccCCcccccccccccccceeccCCCCcccCh
Confidence            4556677778888888887553 32  11 1223677888888888888888776  67888888888888888888888


Q ss_pred             cchhhhcccCCCccEEeccccc
Q 042541          641 NSTFRISDAFPNLLEMDIDYCN  662 (695)
Q Consensus       641 ~~~~~l~~~l~~L~~L~l~~c~  662 (695)
                      +.+     ...+|+.|+|++|.
T Consensus        98 ~~~-----~~~~l~~L~L~~Np  114 (156)
T d2ifga3          98 KTV-----QGLSLQELVLSGNP  114 (156)
T ss_dssp             TTT-----CSCCCCEEECCSSC
T ss_pred             hhh-----ccccccccccCCCc
Confidence            777     45578888888754

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.78  E-value=1.4e-08  Score=96.54  Aligned_cols=172  Identities=11%  Similarity=0.128  Sum_probs=109.3

Q ss_pred             CCCCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhcccccc-ccCCCcEEEEEeCCCCCHHHHHHHHHHh
Q 042541          164 PPVISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQ-GKFKDDIFYVTVSKNPNVKAIVQKVLHH  242 (695)
Q Consensus       164 ~~~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~-~~f~~~~~wv~~~~~~~~~~~~~~i~~~  242 (695)
                      .-+.+||.++.++.|..++..+..+.+.++|++|+||||+|+.+++.  +. ..+...++-.+.+...+...........
T Consensus        12 ~~~divg~~~~~~~L~~~i~~~~~~~lLl~Gp~G~GKttl~~~la~~--l~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~   89 (227)
T d1sxjc2          12 TLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALARE--IYGKNYSNMVLELNASDDRGIDVVRNQIKDF   89 (227)
T ss_dssp             SGGGCCSCHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHHHHHHH--HHTTSHHHHEEEECTTSCCSHHHHHTHHHHH
T ss_pred             CHHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCChhHHHHHHHHH--hhcCCCcceeEEecccccCCeeeeecchhhc
Confidence            34568999999999999999877766789999999999999999873  22 1111112222233332222221111111


Q ss_pred             cCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCC------CCCC
Q 042541          243 KGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFP------QFGS  312 (695)
Q Consensus       243 l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~------~~~~  312 (695)
                      ....                  ....++..++|+|++......    ++..+......+.++++|.....      ....
T Consensus        90 ~~~~------------------~~~~~~~kiiiiDe~d~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~i~~~i~sr~~  151 (227)
T d1sxjc2          90 ASTR------------------QIFSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSQCT  151 (227)
T ss_dssp             HHBC------------------CSSSCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSE
T ss_pred             cccc------------------cccCCCeEEEEEeccccchhhHHHHHHHHhhhcccceeeccccCcHHHhHHHHHHHHh
Confidence            0000                  111345568999999776543    34444445567788888776521      2234


Q ss_pred             eEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCch
Q 042541          313 VHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCP  358 (695)
Q Consensus       313 ~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~P  358 (695)
                      .+.+.+++.++-..++.+.+......   -..+....|++.++|-.
T Consensus       152 ~i~~~~~~~~~i~~~l~~I~~~e~i~---i~~~~l~~i~~~s~Gd~  194 (227)
T d1sxjc2         152 RFRFQPLPQEAIERRIANVLVHEKLK---LSPNAEKALIELSNGDM  194 (227)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHTTTCC---BCHHHHHHHHHHHTTCH
T ss_pred             hhcccccccccccccccccccccccc---CCHHHHHHHHHHcCCcH
Confidence            88999999999999998876543321   23567899999999864

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.78  E-value=1.8e-08  Score=95.57  Aligned_cols=175  Identities=14%  Similarity=0.158  Sum_probs=114.0

Q ss_pred             CCCCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhcccccccc-CCCcEEEEEeCCCCCHHHHHHHHHHh
Q 042541          164 PPVISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGK-FKDDIFYVTVSKNPNVKAIVQKVLHH  242 (695)
Q Consensus       164 ~~~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~-f~~~~~wv~~~~~~~~~~~~~~i~~~  242 (695)
                      .-+.+||-++.+++|..++.++..+.+.++|++|+||||+|+.+++.  +... +...++-++.+...+...+...+...
T Consensus        13 ~~~d~ig~~~~~~~L~~~~~~~~~~~~ll~Gp~G~GKTt~a~~la~~--l~~~~~~~~~~~~n~~~~~~~~~i~~~~~~~   90 (224)
T d1sxjb2          13 VLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHE--LLGRSYADGVLELNASDDRGIDVVRNQIKHF   90 (224)
T ss_dssp             SGGGCCSCTHHHHHHHHHHHSCCCCCEEEECSTTSSHHHHHHHHHHH--HHGGGHHHHEEEECTTSCCSHHHHHTHHHHH
T ss_pred             CHHHhcCCHHHHHHHHHHHHcCCCCeEEEECCCCCCchhhHHHHHHH--HhccccccccccccccccCCceehhhHHHHH
Confidence            34568999999999999999887777889999999999999988873  3221 12224455555555444433332221


Q ss_pred             cCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCC------CCCC
Q 042541          243 KGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFP------QFGS  312 (695)
Q Consensus       243 l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~------~~~~  312 (695)
                      .....                 ....++.-++|+|++......    ++..+......+++++||.....      ....
T Consensus        91 ~~~~~-----------------~~~~~~~kviiiDe~d~~~~~~~~~ll~~~e~~~~~~~~i~~~~~~~~i~~~l~sr~~  153 (224)
T d1sxjb2          91 AQKKL-----------------HLPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSQCA  153 (224)
T ss_dssp             HHBCC-----------------CCCTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCGGGSCHHHHTTSE
T ss_pred             HHhhc-----------------cCCCcceEEEEEecccccchhHHHHHhhhccccccceeeeeccCchhhhhhHHHHHHH
Confidence            11100                 001345678999999777644    22333334456777777765521      2223


Q ss_pred             eEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhH
Q 042541          313 VHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLA  360 (695)
Q Consensus       313 ~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLa  360 (695)
                      .+++++++.++-...+.+.+......   -..+....|++.|+|-+..
T Consensus       154 ~i~~~~~~~~~i~~~l~~i~~~e~~~---i~~~~l~~I~~~s~Gd~R~  198 (224)
T d1sxjb2         154 ILRYSKLSDEDVLKRLLQIIKLEDVK---YTNDGLEAIIFTAEGDMRQ  198 (224)
T ss_dssp             EEECCCCCHHHHHHHHHHHHHHHTCC---BCHHHHHHHHHHHTTCHHH
T ss_pred             HhhhcccchhhhHHHHHHHHHhcccC---CCHHHHHHHHHHcCCcHHH
Confidence            78999999999999998776543321   2366789999999998754

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.76  E-value=4.9e-08  Score=93.27  Aligned_cols=188  Identities=15%  Similarity=0.106  Sum_probs=114.3

Q ss_pred             CCCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcC
Q 042541          165 PVISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKG  244 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~  244 (695)
                      -+.++|.+..++.|..++.....+.+.++|++|+||||+|+.+++...-..........++.+.......+...+-....
T Consensus        11 ~~diig~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   90 (237)
T d1sxjd2          11 LDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNFAR   90 (237)
T ss_dssp             TTTCCSCCTTHHHHHHHTTCTTCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHHTTHHHHHHH
T ss_pred             HHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCChHHHHHHHHHHHcCCcccccchhheeccccccchHHHHHHHHHhh
Confidence            34579999999999999987777778999999999999999998732111111222445566655555443333322211


Q ss_pred             CCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCCCC------CCeE
Q 042541          245 YPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFPQF------GSVH  314 (695)
Q Consensus       245 ~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~~~------~~~~  314 (695)
                      ...... ...       ..-....++.-++|+|++......    +...+......+++|+|+.......      ...+
T Consensus        91 ~~~~~~-~~~-------~~~~~~~~~~~viiiDe~d~l~~~~~~~l~~~~~~~~~~~~~i~~~~~~~~~~~~l~sr~~~i  162 (237)
T d1sxjd2          91 LTVSKP-SKH-------DLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASQCSKF  162 (237)
T ss_dssp             SCCCCC-CTT-------HHHHSCCCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHHSEEE
T ss_pred             hhhhhh-hHH-------HHhhccccCceEEEEecccccCHHHHHHHhhccccccccccccccccccccccccccchhhhh
Confidence            111000 000       000122344557999999776543    2222333444567777765542211      1378


Q ss_pred             ecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCch-hHHHH
Q 042541          315 YLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCP-LALKV  363 (695)
Q Consensus       315 ~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~P-Lai~~  363 (695)
                      ++.+++.++..+++.+.+.....   .-..+..+.|++.++|-+ .|+..
T Consensus       163 ~f~~~~~~~~~~~L~~i~~~e~i---~i~~~~l~~ia~~s~gd~R~ai~~  209 (237)
T d1sxjd2         163 RFKALDASNAIDRLRFISEQENV---KCDDGVLERILDISAGDLRRGITL  209 (237)
T ss_dssp             ECCCCCHHHHHHHHHHHHHTTTC---CCCHHHHHHHHHHTSSCHHHHHHH
T ss_pred             ccccccccccchhhhhhhhhhcC---cCCHHHHHHHHHHcCCCHHHHHHH
Confidence            99999999999999887754332   124678899999998854 34433

>d1m9la_ c.10.3.1 (A:) Outer arm dynein light chain 1 {Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: Outer arm dynein light chain 1
family: Outer arm dynein light chain 1
domain: Outer arm dynein light chain 1
species: Green algae (Chlamydomonas reinhardtii) [TaxId: 3055]

Probab=98.75  E-value=2e-10  Score=106.83  Aligned_cols=126  Identities=10%  Similarity=0.099  Sum_probs=95.3

Q ss_pred             CCCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcccccccccccE
Q 042541          548 QGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSLATVRMNHLQK  627 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp~i~~l~~L~~  627 (695)
                      .+++|+.|.++.+... .++ .+.++++|++|++++|.+.  .++.+  ...+++|++|++++|.++.++.+.++++|++
T Consensus        46 ~L~~L~~L~Ls~n~I~-~i~-~l~~l~~L~~L~Ls~N~i~--~i~~~--~~~~~~L~~L~l~~N~i~~l~~~~~l~~L~~  119 (198)
T d1m9la_          46 TLKACKHLALSTNNIE-KIS-SLSGMENLRILSLGRNLIK--KIENL--DAVADTLEELWISYNQIASLSGIEKLVNLRV  119 (198)
T ss_dssp             HTTTCCEEECSEEEES-CCC-CHHHHTTCCEEECCEEEEC--SCSSH--HHHHHHCCEEECSEEECCCHHHHHHHHHSSE
T ss_pred             cccccceeECcccCCC-Ccc-cccCCccccChhhcccccc--ccccc--ccccccccccccccccccccccccccccccc
Confidence            4778999999877433 444 5889999999999998763  23222  3445679999999999998887889999999


Q ss_pred             EeeccccCCcccc-cchhhhcccCCCccEEecccccccccCch----------hhcCCCCCceeecc
Q 042541          628 VSLVMCNVGQVFR-NSTFRISDAFPNLLEMDIDYCNDLIELPD----------GLCDIVSMEKLRIT  683 (695)
Q Consensus       628 L~l~~~~i~~~~~-~~~~~l~~~l~~L~~L~l~~c~~l~~lP~----------~i~~L~~L~~L~l~  683 (695)
                      |++++|.++.++. ..+.    .+++|+.|++++|+.....+.          -+.++++|+.||-.
T Consensus       120 L~L~~N~i~~~~~~~~l~----~l~~L~~L~L~~N~l~~~~~~~~~~~~~r~~vi~~lp~L~~LD~~  182 (198)
T d1m9la_         120 LYMSNNKITNWGEIDKLA----ALDKLEDLLLAGNPLYNDYKENNATSEYRIEVVKRLPNLKKLDGM  182 (198)
T ss_dssp             EEESEEECCCHHHHHHHT----TTTTCSEEEECSSHHHHHHCTTTTHHHHHHHHHHHCSSCCEESSG
T ss_pred             cccccchhcccccccccc----CCCccceeecCCCccccCcccccchhhHHHHHHHHCCCcCEeCCc
Confidence            9999999987654 2333    799999999999753322221          16678999999843

>d1xkua_ c.10.2.7 (A:) Decorin {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Decorin
species: Cow (Bos taurus) [TaxId: 9913]

Probab=98.70  E-value=4.2e-08  Score=97.68  Aligned_cols=141  Identities=16%  Similarity=0.280  Sum_probs=93.1

Q ss_pred             CCceEEEEEEccCccccCC-hhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCcc-c--------
Q 042541          549 GPEVKVVVLNIRTKKYVLP-DFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSL-A--------  618 (695)
Q Consensus       549 ~~~l~~L~l~~~~~~~~~p-~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp-~--------  618 (695)
                      .+.+++|.++.+.. ..+| ..|.++++|++|++++|.+....   ...+..+++|++|++++|+++.+| .        
T Consensus        30 ~~~l~~L~Ls~N~i-~~l~~~~f~~l~~L~~L~l~~n~~~~i~---~~~f~~l~~L~~L~l~~n~l~~l~~~~~~~l~~L  105 (305)
T d1xkua_          30 PPDTALLDLQNNKI-TEIKDGDFKNLKNLHTLILINNKISKIS---PGAFAPLVKLERLYLSKNQLKELPEKMPKTLQEL  105 (305)
T ss_dssp             CTTCCEEECCSSCC-CCBCTTTTTTCTTCCEEECCSSCCCCBC---TTTTTTCTTCCEEECCSSCCSBCCSSCCTTCCEE
T ss_pred             CCCCCEEECcCCcC-CCcChhHhhccccccccccccccccccc---hhhhhCCCccCEecccCCccCcCccchhhhhhhh
Confidence            36799999988754 4455 47999999999999998764211   123677888888888877655444 1        


Q ss_pred             ----------------------------------------ccccccccEEeeccccCCcccccchhhhc-----------
Q 042541          619 ----------------------------------------TVRMNHLQKVSLVMCNVGQVFRNSTFRIS-----------  647 (695)
Q Consensus       619 ----------------------------------------i~~l~~L~~L~l~~~~i~~~~~~~~~~l~-----------  647 (695)
                                                              +..+++|+++++++|.+..++...+..+.           
T Consensus       106 ~~~~n~l~~l~~~~~~~~~~~~~l~~~~n~~~~~~~~~~~~~~l~~L~~l~l~~n~l~~l~~~~~~~L~~L~l~~n~~~~  185 (305)
T d1xkua_         106 RVHENEITKVRKSVFNGLNQMIVVELGTNPLKSSGIENGAFQGMKKLSYIRIADTNITTIPQGLPPSLTELHLDGNKITK  185 (305)
T ss_dssp             ECCSSCCCBBCHHHHTTCTTCCEEECCSSCCCGGGBCTTGGGGCTTCCEEECCSSCCCSCCSSCCTTCSEEECTTSCCCE
T ss_pred             hccccchhhhhhhhhhccccccccccccccccccCCCccccccccccCccccccCCccccCcccCCccCEEECCCCcCCC
Confidence                                                    22345566666666665554432211110           


Q ss_pred             ------ccCCCccEEecccccccccC-chhhcCCCCCceeecccccCCCCCCCCC
Q 042541          648 ------DAFPNLLEMDIDYCNDLIEL-PDGLCDIVSMEKLRITNCHRLSALPEGI  695 (695)
Q Consensus       648 ------~~l~~L~~L~l~~c~~l~~l-P~~i~~L~~L~~L~l~~~~~l~~lP~~i  695 (695)
                            ..+++++.|++++|. +..+ |..+..+++|+.|+|++|. +..+|.++
T Consensus       186 ~~~~~~~~~~~l~~L~~s~n~-l~~~~~~~~~~l~~L~~L~L~~N~-L~~lp~~l  238 (305)
T d1xkua_         186 VDAASLKGLNNLAKLGLSFNS-ISAVDNGSLANTPHLRELHLNNNK-LVKVPGGL  238 (305)
T ss_dssp             ECTGGGTTCTTCCEEECCSSC-CCEECTTTGGGSTTCCEEECCSSC-CSSCCTTT
T ss_pred             CChhHhhcccccccccccccc-ccccccccccccccceeeeccccc-cccccccc
Confidence                  046677777777763 4454 4557888999999999974 88888754

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=98.68  E-value=4.4e-08  Score=93.23  Aligned_cols=172  Identities=15%  Similarity=0.138  Sum_probs=107.1

Q ss_pred             CCCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhcccccc-ccCCCcEEEEEeCCCCCHHHHHHHHHHhc
Q 042541          165 PVISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQ-GKFKDDIFYVTVSKNPNVKAIVQKVLHHK  243 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~-~~f~~~~~wv~~~~~~~~~~~~~~i~~~l  243 (695)
                      -+.++|.+..+++|..++..+..+.+.++|++|+||||+|+.+++  .+. ..+....+-++.+...+...+...+....
T Consensus        23 ~~diig~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtla~~iak--~l~~~~~~~~~~e~n~s~~~~~~~~~~~~~~~~  100 (231)
T d1iqpa2          23 LDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALAR--ELFGENWRHNFLELNASDERGINVIREKVKEFA  100 (231)
T ss_dssp             TTTCCSCHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHHHHHHH--HHHGGGHHHHEEEEETTCHHHHHTTHHHHHHHH
T ss_pred             HHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHH--HHHhcccCCCeeEEecCcccchhHHHHHHHHHH
Confidence            456899999999999999988888899999999999999999987  322 12222233344433211111111111100


Q ss_pred             CCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCCCCC------CCCe
Q 042541          244 GYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSEFPQ------FGSV  313 (695)
Q Consensus       244 ~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~~~~------~~~~  313 (695)
                      .                  .......+..++++||+......    ++..+........+|.||......      ....
T Consensus       101 ~------------------~~~~~~~~~~iilide~d~~~~~~~~~ll~~l~~~~~~~~~i~~~n~~~~i~~~l~sR~~~  162 (231)
T d1iqpa2         101 R------------------TKPIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAI  162 (231)
T ss_dssp             H------------------SCCGGGCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGGGSCHHHHHTEEE
T ss_pred             h------------------hhhccCCCceEEeehhhhhcchhHHHHHhhhcccCCcceEEEeccCChhhchHhHhCcccc
Confidence            0                  00111356789999999766543    223333333455666666544211      1237


Q ss_pred             EecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchh
Q 042541          314 HYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPL  359 (695)
Q Consensus       314 ~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PL  359 (695)
                      +.+.+.+.++....+.+.+....-.   -..+..+.|++.|+|-..
T Consensus       163 i~~~~~~~~~~~~~l~~~~~~e~i~---i~~~~l~~I~~~~~gdiR  205 (231)
T d1iqpa2         163 FRFRPLRDEDIAKRLRYIAENEGLE---LTEEGLQAILYIAEGDMR  205 (231)
T ss_dssp             EECCCCCHHHHHHHHHHHHHTTTCE---ECHHHHHHHHHHHTTCHH
T ss_pred             ccccccchhhHHHHHHHHHHHhCCC---CCHHHHHHHHHHcCCCHH
Confidence            8999999999999998877543321   135678999999998654

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=98.67  E-value=2.4e-07  Score=88.45  Aligned_cols=173  Identities=21%  Similarity=0.213  Sum_probs=110.3

Q ss_pred             CCCCCCcchHHHHHHHHHcCC-ceEEEEEcCCCCcHHHHHHHHhccccccccC--CC------------------cEEEE
Q 042541          166 VISPGLDVPLKELKMELFKDG-RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKF--KD------------------DIFYV  224 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~~-~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f--~~------------------~~~wv  224 (695)
                      +.++|.++.++.+..++..+. +..+.|+|+.|+||||+|+.+++.  +....  ..                  .++.+
T Consensus        12 ~dlig~~~~~~~L~~~i~~~~~~~~~Ll~Gp~G~GKtt~a~~~~~~--l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~   89 (239)
T d1njfa_          12 ADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKG--LNCETGITATPCGVCDNCREIEQGRFVDLIEI   89 (239)
T ss_dssp             GGSCSCHHHHHHHHHHHHTTCCCSEEEEECSTTSSHHHHHHHHHHH--HHCTTCSCSSCCSCSHHHHHHHHTCCTTEEEE
T ss_pred             HHccChHHHHHHHHHHHHcCCCCeeEEEECCCCCcHHHHHHHHHHH--hcCccccccCccccchHHHHHHcCCCCeEEEe
Confidence            467999999999999998766 456889999999999999988762  21111  00                  02233


Q ss_pred             EeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEE
Q 042541          225 TVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKIL  300 (695)
Q Consensus       225 ~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~ii  300 (695)
                      +.+....... .+.+++.+...                   ...++..++|+|+++.....    ++..+....+++.+|
T Consensus        90 ~~~~~~~i~~-ir~~~~~~~~~-------------------~~~~~~kviiIde~d~l~~~~q~~Llk~lE~~~~~~~~i  149 (239)
T d1njfa_          90 DAASRTKVED-TRDLLDNVQYA-------------------PARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFL  149 (239)
T ss_dssp             ETTCSSSHHH-HHHHHHSCCCS-------------------CSSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEE
T ss_pred             cchhcCCHHH-HHHHHHHHHhc-------------------cccCCCEEEEEECcccCCHHHHHHHHHHHhcCCCCeEEE
Confidence            3222222221 12222222111                   01356679999999877643    444454455678888


Q ss_pred             EEcCCCCC------CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchh-HHHH
Q 042541          301 VTSRSEFP------QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPL-ALKV  363 (695)
Q Consensus       301 vTtR~~~~------~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PL-ai~~  363 (695)
                      ++|.+...      .-...+.+.+++.++-.+.+.+.+.....   .-.++.+..|++.++|.+. |+..
T Consensus       150 l~tn~~~~i~~~i~SRc~~i~~~~~~~~~i~~~l~~i~~~e~~---~~~~~~l~~i~~~s~Gd~R~ain~  216 (239)
T d1njfa_         150 LATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHI---AHEPRALQLLARAAEGSLRDALSL  216 (239)
T ss_dssp             EEESCGGGSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTC---CBCHHHHHHHHHHTTTCHHHHHHH
T ss_pred             EEcCCccccChhHhhhhcccccccCcHHHhhhHHHHHHhhhcc---CCCHHHHHHHHHHcCCCHHHHHHH
Confidence            88876521      12238899999999999888877643332   1246778999999999885 4433

>d2astb2 c.10.1.3 (B:2136-2419) Cyclin A/CDK2-associated p19, Skp2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: Cyclin A/CDK2-associated p19, Skp2
domain: Cyclin A/CDK2-associated p19, Skp2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.62  E-value=7e-09  Score=102.31  Aligned_cols=37  Identities=16%  Similarity=0.070  Sum_probs=19.8

Q ss_pred             CCCceEEEEEEccCccccCChhhcCCCCCcEEEEccc
Q 042541          548 QGPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNY  584 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~  584 (695)
                      .|++|+.|.+.++......+..+.++++|++|++++|
T Consensus        69 ~c~~L~~L~L~~~~l~~~~~~~l~~~~~L~~L~Ls~c  105 (284)
T d2astb2          69 QCSKLQNLSLEGLRLSDPIVNTLAKNSNLVRLNLSGC  105 (284)
T ss_dssp             TBCCCSEEECTTCBCCHHHHHHHTTCTTCSEEECTTC
T ss_pred             hCCCcccccccccCCCcHHHHHHhcCCCCcCcccccc
Confidence            4555666655555433344445555556666666553

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=98.52  E-value=3.5e-07  Score=87.39  Aligned_cols=149  Identities=11%  Similarity=0.093  Sum_probs=91.6

Q ss_pred             CCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccc---cccccC-CCcEEEEEeCCCCCHHHHHHHHHHh
Q 042541          167 ISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDD---QVQGKF-KDDIFYVTVSKNPNVKAIVQKVLHH  242 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~---~~~~~f-~~~~~wv~~~~~~~~~~~~~~i~~~  242 (695)
                      .++||++++++++..|......-+.++|++|+|||+++..++...   ++.... ...+++++++.-             
T Consensus        19 ~~igRd~Ei~~l~~iL~r~~k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~~l-------------   85 (268)
T d1r6bx2          19 PLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSL-------------   85 (268)
T ss_dssp             CCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC---------------
T ss_pred             cccChHHHHHHHHHHHhcCccCCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeeechH-------------
Confidence            369999999999999986666677899999999999998887631   122222 233444444321             


Q ss_pred             cCCCCCCCCChHHHHHHHHHHHHhc-CCCcEEEEEeCCCCCC---------hHHHhhhccCC--CCCEEEEEcCCC----
Q 042541          243 KGYPVPEFQTDEAAINDLERFFKQM-RIEAILLVLDDVWPGS---------ESLLQKLGFQL--PDYKILVTSRSE----  306 (695)
Q Consensus       243 l~~~~~~~~~~~~~~~~l~~~~~~l-~~~~~LlVlDdv~~~~---------~~~~~~l~~~~--~gs~iivTtR~~----  306 (695)
                      +.+.    ....+..+++..+++.+ ..++.++++|++....         ......+.+..  ..-++|.||...    
T Consensus        86 iag~----~~~g~~e~r~~~i~~~~~~~~~iIlfiDeih~l~~~g~~~g~~~d~a~~Lkp~L~rg~i~vIgatT~eey~~  161 (268)
T d1r6bx2          86 LAGT----KYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSGKIRVIGSTTYQEFSN  161 (268)
T ss_dssp             -CCC----CCSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSSSCCCEEEEEECHHHHHC
T ss_pred             hccC----ccchhHHHHHHHHHHHhhccCCceEEecchHHHhcCCCCCCccccHHHHhhHHHhCCCCeEEEeCCHHHHHH
Confidence            0010    11222334455555443 4667999999975442         11233333332  346888877654    


Q ss_pred             C----CCCC---CeEecCCCChHHHHHHHHHhc
Q 042541          307 F----PQFG---SVHYLKPLTYEAARTLFLHSA  332 (695)
Q Consensus       307 ~----~~~~---~~~~l~~L~~~ea~~Lf~~~~  332 (695)
                      .    .+..   ..+.+++.+.+++..++....
T Consensus       162 ~~e~d~al~rrF~~I~V~Eps~e~t~~IL~~~~  194 (268)
T d1r6bx2         162 IFEKDRALARRFQKIDITEPSIEETVQIINGLK  194 (268)
T ss_dssp             CCCCTTSSGGGEEEEECCCCCHHHHHHHHHHHH
T ss_pred             HHhhcHHHHhhhcccccCCCCHHHHHHHHHHhh
Confidence            1    1111   178999999999999887543

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.47  E-value=3.4e-06  Score=82.33  Aligned_cols=189  Identities=17%  Similarity=0.139  Sum_probs=110.2

Q ss_pred             CCCCCCCCcchHHHHHHHHH----cC-C----ceEEEEEcCCCCcHHHHHHHHhcccc---ccccCCCcEEEEEeCCCCC
Q 042541          164 PPVISPGLDVPLKELKMELF----KD-G----RQFIVVSAPGGYGKTTLVQRLCKDDQ---VQGKFKDDIFYVTVSKNPN  231 (695)
Q Consensus       164 ~~~~~vGr~~~~~~l~~~L~----~~-~----~~vv~I~G~gGiGKTtLa~~~~~~~~---~~~~f~~~~~wv~~~~~~~  231 (695)
                      .|+.++||+.++++|.+++.    .+ .    ..++.|+|++|+|||++++.+++.-.   ..........+++......
T Consensus        14 ~P~~~~~Re~e~~~l~~~l~~~~~~~~~~~~~~~~l~l~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~   93 (287)
T d1w5sa2          14 IPPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPN   93 (287)
T ss_dssp             CCSSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCCS
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHcCCCCCCcceEEEeECCCCCCHHHHHHHHHHHHHhhcccccCCceeeeeccccccc
Confidence            45678999999999988774    11 1    23466789999999999999997411   1122223356788888888


Q ss_pred             HHHHHHHHHHhcCCCCCCCC-ChHHHHHHHHHHHHhcCCCcEEEEEeCCC------CCChHHH-------hhhccCC--C
Q 042541          232 VKAIVQKVLHHKGYPVPEFQ-TDEAAINDLERFFKQMRIEAILLVLDDVW------PGSESLL-------QKLGFQL--P  295 (695)
Q Consensus       232 ~~~~~~~i~~~l~~~~~~~~-~~~~~~~~l~~~~~~l~~~~~LlVlDdv~------~~~~~~~-------~~l~~~~--~  295 (695)
                      .......+...++....... ........+...... .+...++++|.+.      .......       ..+....  .
T Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~~iide~d~l~~~~~~~~~~~~~l~~l~~~l~~~~~~~  172 (287)
T d1w5sa2          94 LYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYV-ENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVN  172 (287)
T ss_dssp             HHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHH-HTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCTTSCC
T ss_pred             hhhHHHHHhhhcccccccccchHHHHHHHHHHHHHh-ccCccccceeEEEEeccccccchhHHHHHHHHHHhcchhhccc
Confidence            88888888888766543322 222223333333321 3567788888763      2221111       1111111  1


Q ss_pred             CCE-EEEEcCCC------------CCCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhc
Q 042541          296 DYK-ILVTSRSE------------FPQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRAC  354 (695)
Q Consensus       296 gs~-iivTtR~~------------~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c  354 (695)
                      ... |++++...            .......+.+++++.++..+++..++....... .-.++..+.|+++.
T Consensus       173 ~~~~i~i~~~~~~~~~~~~~~~~~~~r~~~~i~f~~y~~~el~~Il~~r~~~~~~~~-~~~~~al~~ia~~~  243 (287)
T d1w5sa2         173 RIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDT-VWEPRHLELISDVY  243 (287)
T ss_dssp             BEEEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHHBCTT-SCCHHHHHHHHHHH
T ss_pred             ceeEEeecccHHHHHHHHhhccchhcccceeeeccCCcHHHHHHHHhhhHHHhhccC-CCCHHHHHHHHHHH
Confidence            223 33443332            012234788999999999999997763211111 11356667777654

>d1xwdc1 c.10.2.7 (C:18-259) Follicle-stimulating hormone receptor {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: Follicle-stimulating hormone receptor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.46  E-value=9.4e-07  Score=84.29  Aligned_cols=160  Identities=12%  Similarity=0.113  Sum_probs=100.7

Q ss_pred             ccceEEeeecCCcccCCCC-CCCCCceEEEEEEccCccccCC-hhhcCCCCCcEEEEccc-CCCCcccCcccccccCCCC
Q 042541          527 NNASLLSISTDETFSSNWP-DMQGPEVKVVVLNIRTKKYVLP-DFLQKMDELKVLIVTNY-GFSPAELNNFRVLSALSKL  603 (695)
Q Consensus       527 ~~~r~l~~~~~~~~~~~~~-~~~~~~l~~L~l~~~~~~~~~p-~~~~~l~~Lr~L~l~~~-~~~~~~~~~~~~l~~l~~L  603 (695)
                      ..++.+.+.++....-... ..++++|+.|.++.+.....+| ..|..+++++.+.+..+ ....   .....+.++++|
T Consensus        29 ~~l~~L~Ls~n~i~~l~~~~f~~l~~L~~L~ls~n~~~~~i~~~~f~~l~~l~~l~~~~~n~l~~---~~~~~~~~l~~L  105 (242)
T d1xwdc1          29 RNAIELRFVLTKLRVIQKGAFSGFGDLEKIEISQNDVLEVIEADVFSNLPKLHEIRIEKANNLLY---INPEAFQNLPNL  105 (242)
T ss_dssp             SCCSEEEEESCCCCEECTTTTTTCTTCCEEEEESCTTCCEECSSSEESCTTCCEEEEECCTTCCE---ECTTSEECCTTC
T ss_pred             CCCCEEECcCCcCCccChhHhhccchhhhhhhccccccceeeccccccccccccccccccccccc---cccccccccccc
Confidence            4566666665443211111 1356777777777775544433 35677777777766543 2211   111225677788


Q ss_pred             cEEEeccCCCCCcc---cccccccccEEeeccccCCcccccchhhhcccCC-CccEEecccccccccCchhhcCCCCCce
Q 042541          604 KKIRLEHVSLPNSL---ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFP-NLLEMDIDYCNDLIELPDGLCDIVSMEK  679 (695)
Q Consensus       604 ~~L~L~~~~l~~lp---~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~-~L~~L~l~~c~~l~~lP~~i~~L~~L~~  679 (695)
                      ++|++.++.+...|   .+..+.+|..+...++.+..+++..+.    .++ .++.|++++ +.+..++....+..+++.
T Consensus       106 ~~l~l~~~~l~~~~~~~~~~~l~~l~~~~~~n~~l~~i~~~~~~----~~~~~l~~L~l~~-n~l~~i~~~~~~~~~l~~  180 (242)
T d1xwdc1         106 QYLLISNTGIKHLPDVHKIHSLQKVLLDIQDNINIHTIERNSFV----GLSFESVILWLNK-NGIQEIHNCAFNGTQLDE  180 (242)
T ss_dssp             CEEEEESCCCCSCCCCTTTCBSSCEEEEEESCTTCCEECTTSST----TSBSSCEEEECCS-SCCCEECTTTTTTCCEEE
T ss_pred             cccccchhhhcccccccccccccccccccccccccccccccccc----cccccceeeeccc-ccccccccccccchhhhc
Confidence            88888887776554   344556666666666677776665553    443 788899987 467888888888888888


Q ss_pred             eecccccCCCCCCCC
Q 042541          680 LRITNCHRLSALPEG  694 (695)
Q Consensus       680 L~l~~~~~l~~lP~~  694 (695)
                      +....++.++.+|.+
T Consensus       181 ~~~l~~n~l~~l~~~  195 (242)
T d1xwdc1         181 LNLSDNNNLEELPND  195 (242)
T ss_dssp             EECTTCTTCCCCCTT
T ss_pred             cccccccccccccHH
Confidence            876666779999875

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=98.45  E-value=1.5e-06  Score=80.55  Aligned_cols=164  Identities=17%  Similarity=0.143  Sum_probs=100.7

Q ss_pred             cchHHHHHHHHHcCC-ceEEEEEcCCCCcHHHHHHHHhcccc------------------ccccCCCcEEEEEeCCCC--
Q 042541          172 DVPLKELKMELFKDG-RQFIVVSAPGGYGKTTLVQRLCKDDQ------------------VQGKFKDDIFYVTVSKNP--  230 (695)
Q Consensus       172 ~~~~~~l~~~L~~~~-~~vv~I~G~gGiGKTtLa~~~~~~~~------------------~~~~f~~~~~wv~~~~~~--  230 (695)
                      +...+++...+..+. +..+.++|+.|+||||+|+.+++.--                  +...+...+.++......  
T Consensus         8 ~~~~~~l~~~~~~~~l~h~lLl~Gp~G~GKtt~a~~~a~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~   87 (207)
T d1a5ta2           8 RPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKGKNT   87 (207)
T ss_dssp             HHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECCCTTCSS
T ss_pred             HHHHHHHHHHHHcCCcCeEEEEECCCCCcHHHHHHHHHHhcccccccccccccccchhhhhhhccccccchhhhhhcccc
Confidence            455677888887666 45699999999999999998876210                  001111112222221110  


Q ss_pred             CHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCC
Q 042541          231 NVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSE  306 (695)
Q Consensus       231 ~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~  306 (695)
                      -..+..+++.+.+...                   ...+++-++|+||++.....    ++..+.....++.+|+||++.
T Consensus        88 i~~~~ir~l~~~~~~~-------------------~~~~~~kviIide~d~l~~~a~n~Llk~lEep~~~~~fIl~t~~~  148 (207)
T d1a5ta2          88 LGVDAVREVTEKLNEH-------------------ARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREP  148 (207)
T ss_dssp             BCHHHHHHHHHHTTSC-------------------CTTSSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCG
T ss_pred             cccchhhHHhhhhhhc-------------------cccCccceEEechhhhhhhhhhHHHHHHHHhhcccceeeeeecCh
Confidence            0011112222222111                   12467779999999877643    445555556678888888776


Q ss_pred             CC------CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHH
Q 042541          307 FP------QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALK  362 (695)
Q Consensus       307 ~~------~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~  362 (695)
                      ..      .-...+.+.+++.++....+.....        -..+.+..|++.++|.|-.+.
T Consensus       149 ~~ll~tI~SRc~~i~~~~~~~~~~~~~L~~~~~--------~~~~~~~~i~~~s~Gs~r~al  202 (207)
T d1a5ta2         149 ERLLATLRSRCRLHYLAPPPEQYAVTWLSREVT--------MSQDALLAALRLSAGSPGAAL  202 (207)
T ss_dssp             GGSCHHHHTTSEEEECCCCCHHHHHHHHHHHCC--------CCHHHHHHHHHHTTTCHHHHH
T ss_pred             hhhhhhhcceeEEEecCCCCHHHHHHHHHHcCC--------CCHHHHHHHHHHcCCCHHHHH
Confidence            21      1123889999999999998876531        135778899999999886543

>d2ifga3 c.10.2.7 (A:36-191) High affinity nerve growth factor receptor, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Ngr ectodomain-like
domain: High affinity nerve growth factor receptor, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.44  E-value=2.5e-07  Score=81.77  Aligned_cols=103  Identities=16%  Similarity=0.186  Sum_probs=85.1

Q ss_pred             CCcEEEEcccCCCCcccCcccccccCCCCcEEEeccC-CCCCcc--cccccccccEEeeccccCCcccccchhhhcccCC
Q 042541          575 ELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHV-SLPNSL--ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFP  651 (695)
Q Consensus       575 ~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~-~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~  651 (695)
                      ....++..+++..    ..+..+..+++|+.|++.++ .++.++  .+.++++|+.|+|++|.|+.+++..+.    .++
T Consensus         9 ~~~~l~c~~~~~~----~~p~~l~~l~~l~~L~l~~n~~l~~i~~~~f~~l~~L~~L~Ls~N~l~~i~~~~f~----~l~   80 (156)
T d2ifga3           9 GSSGLRCTRDGAL----DSLHHLPGAENLTELYIENQQHLQHLELRDLRGLGELRNLTIVKSGLRFVAPDAFH----FTP   80 (156)
T ss_dssp             SSSCEECCSSCCC----TTTTTSCSCSCCSEEECCSCSSCCEECGGGSCSCCCCSEEECCSSCCCEECTTGGG----SCS
T ss_pred             CCCeEEecCCCCc----cCcccccCccccCeeecCCCccccccCchhhccccccCcceeeccccCCccccccc----ccc
Confidence            3456777765552    12233677889999999876 489888  789999999999999999999998887    899


Q ss_pred             CccEEecccccccccCchhhcCCCCCceeeccccc
Q 042541          652 NLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCH  686 (695)
Q Consensus       652 ~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~  686 (695)
                      +|++|+|++| .+..+|.++....+|++|+|++|+
T Consensus        81 ~L~~L~Ls~N-~l~~l~~~~~~~~~l~~L~L~~Np  114 (156)
T d2ifga3          81 RLSRLNLSFN-ALESLSWKTVQGLSLQELVLSGNP  114 (156)
T ss_dssp             CCCEEECCSS-CCSCCCSTTTCSCCCCEEECCSSC
T ss_pred             cccceeccCC-CCcccChhhhccccccccccCCCc
Confidence            9999999995 688999987777789999999976

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.42  E-value=1.3e-07  Score=91.25  Aligned_cols=185  Identities=12%  Similarity=0.056  Sum_probs=98.7

Q ss_pred             CCCCCCCCcchHHHHHHHHHcC-CceEEEEEcCCCCcHHHHHHHHhccccc----cccCCCcEEEEEeCCC---------
Q 042541          164 PPVISPGLDVPLKELKMELFKD-GRQFIVVSAPGGYGKTTLVQRLCKDDQV----QGKFKDDIFYVTVSKN---------  229 (695)
Q Consensus       164 ~~~~~vGr~~~~~~l~~~L~~~-~~~vv~I~G~gGiGKTtLa~~~~~~~~~----~~~f~~~~~wv~~~~~---------  229 (695)
                      .-+.++|.++..+.|..++... ...-+.|+|++|+||||+|+.+++....    ....+. .-+...+..         
T Consensus         9 ~~~diig~~~~~~~L~~~~~~~~~~~~lll~Gp~G~GKTt~~~~la~~l~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~   87 (252)
T d1sxje2           9 SLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDV-RQFVTASNRKLELNVVSS   87 (252)
T ss_dssp             SGGGCCSCHHHHHHHHTTTTCTTCCCCEEEECSTTSSHHHHHHTHHHHHSCTTCCC-------------------CCEEC
T ss_pred             CHHHccCcHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHhhcCcccccccccc-ccccccccchhhhhhccC
Confidence            3456899988888887777644 3455779999999999999999873110    011111 001100000         


Q ss_pred             ------------CCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhccC
Q 042541          230 ------------PNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGFQ  293 (695)
Q Consensus       230 ------------~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~  293 (695)
                                  ....................  ..       ........++.-++|+|+++.....    ++..+...
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~-------~~~~~~~~~~~~iiiide~d~l~~~~~~~l~~~~e~~  158 (252)
T d1sxje2          88 PYHLEITPSDMGNNDRIVIQELLKEVAQMEQV--DF-------QDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKY  158 (252)
T ss_dssp             SSEEEECCC----CCHHHHHHHHHHHTTTTC---------------------CCEEEEEECTTSSCHHHHHHHHHHHHHS
T ss_pred             CccceeeecccccCCcceeeehhhhhhhhhhh--hh-------hhcccccCCCceEEEeccccccccccchhhhcccccc
Confidence                        00011111111111100000  00       0000111344568999999876543    23334444


Q ss_pred             CCCCEEEEEcCCCCCCC------CCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhH
Q 042541          294 LPDYKILVTSRSEFPQF------GSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLA  360 (695)
Q Consensus       294 ~~gs~iivTtR~~~~~~------~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLa  360 (695)
                      ...+++|+||.+...-.      ...+++.+++.++..+++...+.....  ....++..+.|++.+.|-+..
T Consensus       159 ~~~~~~Il~tn~~~~i~~~l~sR~~~i~~~~~~~~~~~~~l~~i~~~e~~--~~~~~~~l~~i~~~s~Gd~R~  229 (252)
T d1sxje2         159 SKNIRLIMVCDSMSPIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNERI--QLETKDILKRIAQASNGNLRV  229 (252)
T ss_dssp             TTTEEEEEEESCSCSSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHHTC--EECCSHHHHHHHHHHTTCHHH
T ss_pred             cccccceeeeccccchhhhhhcchheeeecccchhhHHHHHHHHHHHcCC--CCCcHHHHHHHHHHcCCcHHH
Confidence            55678788776552211      137889999999999999776533221  122356778999999997653

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.39  E-value=1.2e-06  Score=84.12  Aligned_cols=180  Identities=12%  Similarity=0.075  Sum_probs=104.9

Q ss_pred             CCCCCCCCcchHHHHHHHHHc-----------------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEe
Q 042541          164 PPVISPGLDVPLKELKMELFK-----------------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTV  226 (695)
Q Consensus       164 ~~~~~vGr~~~~~~l~~~L~~-----------------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~  226 (695)
                      .-+.++|.+..+++|.++|..                 ...+.+.++|++|+||||+|+.+++.  .    ...+++++.
T Consensus        12 ~~~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~--~----~~~~~~~~~   85 (253)
T d1sxja2          12 NLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQE--L----GYDILEQNA   85 (253)
T ss_dssp             SGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHH--T----TCEEEEECT
T ss_pred             CHHHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHH--H----Hhhhhcccc
Confidence            345689999999999998852                 12468999999999999999999973  2    233567777


Q ss_pred             CCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH---HHhhhcc--CCCCCEEEE
Q 042541          227 SKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES---LLQKLGF--QLPDYKILV  301 (695)
Q Consensus       227 ~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~---~~~~l~~--~~~gs~iiv  301 (695)
                      +...+...+-.. ................     ........++..++++|++......   .+..+..  ......+++
T Consensus        86 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~vi~ide~~~~~~~~~~~~~~~~~~~~~~~~~ii~  159 (253)
T d1sxja2          86 SDVRSKTLLNAG-VKNALDNMSVVGYFKH-----NEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCRKTSTPLIL  159 (253)
T ss_dssp             TSCCCHHHHHHT-GGGGTTBCCSTTTTTC---------CCSSTTSEEEEECSGGGCCTTSTTHHHHHHHHHHHCSSCEEE
T ss_pred             ccchhhHHHHHH-HHHHhhcchhhhhhhh-----hhhcccccccceEEEeeeccccccchhhhhHHHhhhhccccccccc
Confidence            766655544332 2222111110000000     0001223567889999997543311   1111111  112234544


Q ss_pred             EcCCCC-------CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCch
Q 042541          302 TSRSEF-------PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCP  358 (695)
Q Consensus       302 TtR~~~-------~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~P  358 (695)
                      |+....       ......+.+.+.+.++-...+...+.......   ..+...+|++.++|-.
T Consensus       160 i~~~~~~~~~~~l~~~~~~i~f~~~~~~~i~~~l~~i~~~e~i~i---~~~~l~~i~~~s~GDi  220 (253)
T d1sxja2         160 ICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKL---DPNVIDRLIQTTRGDI  220 (253)
T ss_dssp             EESCTTSSTTGGGTTTSEEEECCCCCHHHHHHHHHHHHHHHTCCC---CTTHHHHHHHHTTTCH
T ss_pred             ccccccccccccccceeeeeeccccchhHHHHHHHHHHHHhCCCC---CHHHHHHHHHhCCCcH
Confidence            443321       12234899999999999988887654322211   2356789999999966

>d2astb2 c.10.1.3 (B:2136-2419) Cyclin A/CDK2-associated p19, Skp2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: Cyclin A/CDK2-associated p19, Skp2
domain: Cyclin A/CDK2-associated p19, Skp2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.33  E-value=1.7e-07  Score=92.05  Aligned_cols=132  Identities=14%  Similarity=0.128  Sum_probs=72.1

Q ss_pred             CCCceEEEEEEccCccc--cCChhhcCCCCCcEEEEcccCCC-CcccCccccccc-CCCCcEEEeccC--CCC--Ccc-c
Q 042541          548 QGPEVKVVVLNIRTKKY--VLPDFLQKMDELKVLIVTNYGFS-PAELNNFRVLSA-LSKLKKIRLEHV--SLP--NSL-A  618 (695)
Q Consensus       548 ~~~~l~~L~l~~~~~~~--~~p~~~~~l~~Lr~L~l~~~~~~-~~~~~~~~~l~~-l~~L~~L~L~~~--~l~--~lp-~  618 (695)
                      .+++|+.|.++++....  .+...+..+++|+.|++++|... ...+.  ..+.. .++|+.|+++++  .++  .+. -
T Consensus        93 ~~~~L~~L~Ls~c~~itd~~l~~l~~~~~~L~~L~ls~c~~~~~~~~~--~~~~~~~~~L~~L~l~~~~~~i~~~~l~~l  170 (284)
T d2astb2          93 KNSNLVRLNLSGCSGFSEFALQTLLSSCSRLDELNLSWCFDFTEKHVQ--VAVAHVSETITQLNLSGYRKNLQKSDLSTL  170 (284)
T ss_dssp             TCTTCSEEECTTCBSCCHHHHHHHHHHCTTCCEEECCCCTTCCHHHHH--HHHHHSCTTCCEEECCSCGGGSCHHHHHHH
T ss_pred             cCCCCcCccccccccccccccchhhHHHHhccccccccccccccccch--hhhcccccccchhhhccccccccccccccc
Confidence            45677777776653221  12233456677777777765321 11111  11222 356777777664  233  233 3


Q ss_pred             ccccccccEEeecccc-CCcccccchhhhcccCCCccEEeccccccccc-CchhhcCCCCCceeecccc
Q 042541          619 TVRMNHLQKVSLVMCN-VGQVFRNSTFRISDAFPNLLEMDIDYCNDLIE-LPDGLCDIVSMEKLRITNC  685 (695)
Q Consensus       619 i~~l~~L~~L~l~~~~-i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~-lP~~i~~L~~L~~L~l~~~  685 (695)
                      ..++++|++|++++|. ++......+.    .+++|++|++++|+.+.. -+..++++++|+.|++++|
T Consensus       171 ~~~~~~L~~L~L~~~~~itd~~~~~l~----~~~~L~~L~L~~C~~i~~~~l~~L~~~~~L~~L~l~~~  235 (284)
T d2astb2         171 VRRCPNLVHLDLSDSVMLKNDCFQEFF----QLNYLQHLSLSRCYDIIPETLLELGEIPTLKTLQVFGI  235 (284)
T ss_dssp             HHHCTTCSEEECTTCTTCCGGGGGGGG----GCTTCCEEECTTCTTCCGGGGGGGGGCTTCCEEECTTS
T ss_pred             ccccccccccccccccCCCchhhhhhc----ccCcCCEEECCCCCCCChHHHHHHhcCCCCCEEeeeCC
Confidence            3456777777777763 4432222222    677777777777765542 2234666777777777776

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=98.31  E-value=8.3e-06  Score=77.31  Aligned_cols=163  Identities=16%  Similarity=0.217  Sum_probs=99.2

Q ss_pred             CCCCCCcchHHHHHHHHH-----cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHH
Q 042541          166 VISPGLDVPLKELKMELF-----KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVL  240 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~-----~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~  240 (695)
                      +.+||-+..+++|..++.     ....+-+.++|++|+||||+|+.+++  .....    ...++.+......++.    
T Consensus         9 ~divGqe~~~~~l~~~i~~~~~~~~~~~~~L~~GPpGtGKT~lA~~la~--~~~~~----~~~~~~~~~~~~~~~~----   78 (238)
T d1in4a2           9 DEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIAS--ELQTN----IHVTSGPVLVKQGDMA----   78 (238)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHH--HHTCC----EEEEETTTCCSHHHHH----
T ss_pred             HHcCChHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHh--ccCCC----cccccCcccccHHHHH----
Confidence            567999999999988886     22345688999999999999999987  33222    3344444433333221    


Q ss_pred             HhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhc------------------cCCCCCE
Q 042541          241 HHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLG------------------FQLPDYK  298 (695)
Q Consensus       241 ~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~------------------~~~~gs~  298 (695)
                                           ..+.. .+++..+++|++......    +.....                  ...+...
T Consensus        79 ---------------------~~~~~-~~~~~~~~ide~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  136 (238)
T d1in4a2          79 ---------------------AILTS-LERGDVLFIDEIHRLNKAVEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPFT  136 (238)
T ss_dssp             ---------------------HHHHH-CCTTCEEEEETGGGCCHHHHHHHHHHHHTSCCCC---------------CCCE
T ss_pred             ---------------------HHHHh-hccCCchHHHHHHHhhhHHHhhcccceeeeeeeeeecCcccccccccCCCCeE
Confidence                                 11111 234456666766544321    111110                  1122445


Q ss_pred             EEEEcCCCC-------CCCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHH
Q 042541          299 ILVTSRSEF-------PQFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKV  363 (695)
Q Consensus       299 iivTtR~~~-------~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~  363 (695)
                      +|.+|....       ......+.+++.+.++...++...+.....   ...++....|++.++|-+..+..
T Consensus       137 ~I~at~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~~~~~~~~~---~~~~~~l~~i~~~s~gd~R~ai~  205 (238)
T d1in4a2         137 LVGATTRSGLLSSPLRSRFGIILELDFYTVKELKEIIKRAASLMDV---EIEDAAAEMIAKRSRGTPRIAIR  205 (238)
T ss_dssp             EEEEESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHTTC---CBCHHHHHHHHHTSTTCHHHHHH
T ss_pred             EEEecCCCccccccceeeeeEEEEecCCCHHHHHHHHHHhhhhccc---hhhHHHHHHHHHhCCCCHHHHHH
Confidence            665555542       123336789999999999999877654433   22466799999999998765543

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=98.31  E-value=1.2e-05  Score=76.32  Aligned_cols=165  Identities=18%  Similarity=0.200  Sum_probs=98.5

Q ss_pred             CCCCCCCcchHHHHHHHHHc-----CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHH
Q 042541          165 PVISPGLDVPLKELKMELFK-----DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKV  239 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~~-----~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i  239 (695)
                      -+.+||-+..++++..++..     ...+-+.++|++|+||||+|+.+++.  ..    ....+++.+........... 
T Consensus         8 ~ddivGq~~~~~~L~~~i~~~~~~~~~~~~~Ll~GPpG~GKTtla~~la~~--~~----~~~~~~~~~~~~~~~~~~~~-   80 (239)
T d1ixsb2           8 LDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHE--LG----VNLRVTSGPAIEKPGDLAAI-   80 (239)
T ss_dssp             GGGSCSCHHHHHHHHHHHHHHTTSSSCCCCEEEECCTTSCHHHHHHHHHHH--HT----CCEEEEETTTCCSHHHHHHH-
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHH--hC----CCeEeccCCccccchhhHHH-
Confidence            35679999988988888762     23566889999999999999999873  22    22445554443222221111 


Q ss_pred             HHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhc------------------cCCCCC
Q 042541          240 LHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLG------------------FQLPDY  297 (695)
Q Consensus       240 ~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~------------------~~~~gs  297 (695)
                                              +....+...++++|++......    ++..+.                  ...+..
T Consensus        81 ------------------------~~~~~~~~~i~~iDe~~~~~~~~~~~l~~~~e~~~~~~~~~~~~~~~~~~~~~~~~  136 (239)
T d1ixsb2          81 ------------------------LANSLEEGDILFIDEIHRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRF  136 (239)
T ss_dssp             ------------------------HHTTCCTTCEEEEETGGGCCHHHHHHHHHHHHHSEEEEECSCTTCCCEEEEECCCC
T ss_pred             ------------------------HHhhccCCCeeeeecccccchhHHHhhhhhhhhhhhhhhhccchhhhhcccCCCCE
Confidence                                    1111233446667877655422    111110                  011234


Q ss_pred             EEEEEcCCC-CC------CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchhHHHH
Q 042541          298 KILVTSRSE-FP------QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPLALKV  363 (695)
Q Consensus       298 ~iivTtR~~-~~------~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PLai~~  363 (695)
                      .++.+|-+. ..      .....+.+...+.++...++.+.+.....   ....+....|++.++|.+..+..
T Consensus       137 ~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~i---~~~~~~l~~ia~~s~gd~R~a~~  206 (239)
T d1ixsb2         137 TLIGATTRPGLITAPLLSRFGIVEHLEYYTPEELAQGVMRDARLLGV---RITEEAALEIGRRSRGTMRVAKR  206 (239)
T ss_dssp             EEEEEESCCSSCSCGGGGGCSEEEECCCCCHHHHHHHHHHHHGGGCC---CBCHHHHHHHHHHTTSSHHHHHH
T ss_pred             EEEeeccCcccccchhhcccceeeEeeccChhhhhHHHHHHHHHhCC---ccchHHHHHHHHHcCCCHHHHHH
Confidence            455444333 11      12337889999999999888876654332   22467899999999998765543

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.26  E-value=7.3e-06  Score=78.57  Aligned_cols=163  Identities=11%  Similarity=0.110  Sum_probs=97.3

Q ss_pred             CCCCCcchHHHHHHHHH----c---------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHH
Q 042541          167 ISPGLDVPLKELKMELF----K---------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVK  233 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~----~---------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~  233 (695)
                      .++|.+..+++|.+.+.    .         ...+-|.++|++|+|||++|+++++  ....    .++.++.+.     
T Consensus         5 dv~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~l~~ala~--~~~~----~~~~i~~~~-----   73 (258)
T d1e32a2           5 DVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVAN--ETGA----FFFLINGPE-----   73 (258)
T ss_dssp             GCCSCSHHHHHHHHHHHHHHHCHHHHHHCCCCCCCEEEEECCTTSSHHHHHHHHHH--HTTC----EEEEECHHH-----
T ss_pred             hhccHHHHHHHHHHHHHHHhcCHHHHHhCCCCCCceeEEecCCCCCchHHHHHHHH--HhCC----eEEEEEchh-----
Confidence            46899999888888643    1         1256789999999999999999987  2222    233333221     


Q ss_pred             HHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCCh-----------H----HHhhhcc--CCC
Q 042541          234 AIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGSE-----------S----LLQKLGF--QLP  295 (695)
Q Consensus       234 ~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~~-----------~----~~~~l~~--~~~  295 (695)
                               +...     ........++.++ ..-..++++|++||++....           .    ....+..  ..+
T Consensus        74 ---------l~~~-----~~g~~~~~l~~~f~~A~~~~p~il~iDeid~l~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~  139 (258)
T d1e32a2          74 ---------IMSK-----LAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRA  139 (258)
T ss_dssp             ---------HTTS-----CTTHHHHHHHHHHHHHHHTCSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCCCSS
T ss_pred             ---------hccc-----ccccHHHHHHHHHHHHHhcCCeEEEehhhhhhccCCCCCCCchHHHHHHHhccccccccccC
Confidence                     1100     0111223344444 33357889999999865421           0    1111111  222


Q ss_pred             CCEEEEEcCCC------CC---CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCch
Q 042541          296 DYKILVTSRSE------FP---QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCP  358 (695)
Q Consensus       296 gs~iivTtR~~------~~---~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~P  358 (695)
                      +.-||.||...      ..   .....+.++..+.++-.++|...........    ......|++.+.|+-
T Consensus       140 ~vlvi~tTn~~~~ld~al~r~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~----~~~~~~la~~t~G~s  207 (258)
T d1e32a2         140 HVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLAD----DVDLEQVANETHGHV  207 (258)
T ss_dssp             CEEEEEEESCGGGSCGGGTSTTSSCEEEECCCCCHHHHHHHHHHTTTTSCBCT----TCCHHHHHHHCTTCC
T ss_pred             CccEEEeCCCccccchhhhhcccccceeECCCCCHHHHHHHhhhhccCccccc----ccchhhhhhcccCCC
Confidence            34455577665      11   2445899999999999999987764322211    112578899998863

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=98.18  E-value=1.5e-06  Score=78.20  Aligned_cols=142  Identities=11%  Similarity=0.145  Sum_probs=84.0

Q ss_pred             CCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccc---cccccC-CCcEEEEEeCCCCCHHHHHHHHHHhc
Q 042541          168 SPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDD---QVQGKF-KDDIFYVTVSKNPNVKAIVQKVLHHK  243 (695)
Q Consensus       168 ~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~---~~~~~f-~~~~~wv~~~~~~~~~~~~~~i~~~l  243 (695)
                      +|||+++++++...|......-+.++|.+|+|||+++..++..-   ++.... +..++.++++.          ++.. 
T Consensus        24 ~igRd~Ei~~l~~iL~r~~k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~ld~~~----------LiAg-   92 (195)
T d1jbka_          24 VIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGA----------LVAG-   92 (195)
T ss_dssp             CCSCHHHHHHHHHHHTSSSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECHHH----------HHTT-
T ss_pred             CcCcHHHHHHHHHHHhccCCCCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEEeeHHH----------Hhcc-
Confidence            59999999999999996666678899999999999998888731   121222 33344443321          1111 


Q ss_pred             CCCCCCCCChHHHHHHHHHHHHhc--CCCcEEEEEeCCCCCCh-----------HHHhhhccCCCCCEEEEEcCCC----
Q 042541          244 GYPVPEFQTDEAAINDLERFFKQM--RIEAILLVLDDVWPGSE-----------SLLQKLGFQLPDYKILVTSRSE----  306 (695)
Q Consensus       244 ~~~~~~~~~~~~~~~~l~~~~~~l--~~~~~LlVlDdv~~~~~-----------~~~~~l~~~~~gs~iivTtR~~----  306 (695)
                            .....+..+++..+++.+  ...+.+|++||+.....           .++.+... ...-++|.||...    
T Consensus        93 ------~~~rG~~E~rl~~il~e~~~~~~~iILfIDeih~l~~~g~~~g~~d~~~~Lkp~L~-rg~l~~IgatT~eey~~  165 (195)
T d1jbka_          93 ------AKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALA-RGELHCVGATTLDEYRQ  165 (195)
T ss_dssp             ------TCSHHHHHHHHHHHHHHHHHSTTTEEEEEETGGGGTT------CCCCHHHHHHHHH-TTSCCEEEEECHHHHHH
T ss_pred             ------CCccHHHHHHHHHHHHHHhcCCCcEEEEcchHHHHhcCCCCCCcccHHHHHHHHHh-CCCceEEecCCHHHHHH
Confidence                  112334455666666444  35689999999843311           12222221 2345777766533    


Q ss_pred             CCCC-------CCeEecCCCChHHHHHH
Q 042541          307 FPQF-------GSVHYLKPLTYEAARTL  327 (695)
Q Consensus       307 ~~~~-------~~~~~l~~L~~~ea~~L  327 (695)
                      ....       -..+.+++.+.+++..+
T Consensus       166 ~~e~d~aL~rrF~~I~V~Ep~~e~t~~I  193 (195)
T d1jbka_         166 YIEKDAALERRFQKVFVAEPSVEDTIAI  193 (195)
T ss_dssp             HTTTCHHHHTTEEEEECCCCCHHHHHTT
T ss_pred             HHHcCHHHHhcCCEeecCCCCHHHHHHH
Confidence            0111       12667777777776543

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=98.14  E-value=9.9e-06  Score=77.16  Aligned_cols=164  Identities=12%  Similarity=0.111  Sum_probs=95.6

Q ss_pred             CCCCCCcchHHHHHHHH---Hc---------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHH
Q 042541          166 VISPGLDVPLKELKMEL---FK---------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVK  233 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L---~~---------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~  233 (695)
                      +.++|.+...++|.+.+   ..         ...+-+.++|++|+|||++|+.+++  ...    ..++.++.++-.+  
T Consensus        12 ~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g~~~~~~iLL~GppGtGKT~la~~iA~--~~~----~~~~~i~~~~l~~--   83 (256)
T d1lv7a_          12 ADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAG--EAK----VPFFTISGSDFVE--   83 (256)
T ss_dssp             GGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHH--HHT----CCEEEECSCSSTT--
T ss_pred             HHHhchHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEeeCCCCCCccHHHHHHHH--HcC----CCEEEEEhHHhhh--
Confidence            46799998877776543   21         1256788999999999999999997  332    2233444433211  


Q ss_pred             HHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCC------------Ch--H----HHhhhcc--
Q 042541          234 AIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPG------------SE--S----LLQKLGF--  292 (695)
Q Consensus       234 ~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~------------~~--~----~~~~l~~--  292 (695)
                                  ....  ..   ...++.++ ..-+..+++|++||++..            ..  .    ++..+..  
T Consensus        84 ------------~~~g--~~---~~~l~~~f~~A~~~~P~il~iDeiD~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~  146 (256)
T d1lv7a_          84 ------------MFVG--VG---ASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFE  146 (256)
T ss_dssp             ------------SCCC--CC---HHHHHHHHHHHHTTCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCC
T ss_pred             ------------cchh--HH---HHHHHHHHHHHHHcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCC
Confidence                        0000  11   12344444 333577899999998321            01  0    1222221  


Q ss_pred             CCCCCEEEEEcCCCC------C---CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCch
Q 042541          293 QLPDYKILVTSRSEF------P---QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCP  358 (695)
Q Consensus       293 ~~~gs~iivTtR~~~------~---~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~P  358 (695)
                      ...+.-||.||....      .   .....+.+++.+.++-.++|+..........    ......+++.+.|+.
T Consensus       147 ~~~~v~vIatTn~~~~ld~al~R~gRfd~~i~i~~P~~~~R~~il~~~l~~~~~~~----~~~~~~la~~t~G~s  217 (256)
T d1lv7a_         147 GNEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAP----DIDAAIIARGTPGFS  217 (256)
T ss_dssp             SSSCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCT----TCCHHHHHHTCTTCC
T ss_pred             CCCCEEEEEeCCCcccCCHhHcCCCCCCEEEECCCcCHHHHHHHHHHhccCCCcCc----ccCHHHHHHhCCCCC
Confidence            222334555776541      1   2345889999999999999987764332211    122567888888864

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=98.14  E-value=1.2e-05  Score=76.12  Aligned_cols=164  Identities=12%  Similarity=0.117  Sum_probs=95.1

Q ss_pred             CCCCCCcchHHHHHHHH---Hc---------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHH
Q 042541          166 VISPGLDVPLKELKMEL---FK---------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVK  233 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L---~~---------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~  233 (695)
                      +.++|.++.+++|.+.+   ..         ..++-|.++|++|+|||+||+.+++  ...    ..++.++.++     
T Consensus         9 ~di~G~~~~k~~l~~~i~~l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~--~~~----~~~~~i~~~~-----   77 (247)
T d1ixza_           9 KDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAG--EAR----VPFITASGSD-----   77 (247)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHH--HTT----CCEEEEEHHH-----
T ss_pred             HHHccHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHH--HcC----CCEEEEEhHH-----
Confidence            35789888777765543   21         1246689999999999999999997  332    2244554321     


Q ss_pred             HHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCC-----------ChH---HHhhh----ccCC
Q 042541          234 AIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPG-----------SES---LLQKL----GFQL  294 (695)
Q Consensus       234 ~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~-----------~~~---~~~~l----~~~~  294 (695)
                           +...         ...+....++.++ ..-...+++|++||++..           ...   .+..|    ....
T Consensus        78 -----l~~~---------~~g~~~~~l~~~f~~a~~~~p~Ii~iDeid~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~  143 (247)
T d1ixza_          78 -----FVEM---------FVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFE  143 (247)
T ss_dssp             -----HHHS---------CTTHHHHHHHHHHHHHTTSSSEEEEEETHHHHHC---------CHHHHHHHHHHHHHHHTCC
T ss_pred             -----hhhc---------cccHHHHHHHHHHHHHHHcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCC
Confidence                 1111         0112233455556 333567899999997421           000   12222    1111


Q ss_pred             C--CCEEEEEcCCC------CC---CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCch
Q 042541          295 P--DYKILVTSRSE------FP---QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCP  358 (695)
Q Consensus       295 ~--gs~iivTtR~~------~~---~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~P  358 (695)
                      .  +.-||.||...      ..   .....+.+++.+.++-.++|+..........    ......+++.|.|+.
T Consensus       144 ~~~~vivi~tTn~~~~ld~al~R~~Rf~~~i~~~~P~~~eR~~il~~~l~~~~~~~----~~~~~~la~~t~g~s  214 (247)
T d1ixza_         144 KDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAE----DVDLALLAKRTPGFV  214 (247)
T ss_dssp             TTCCEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBCT----TCCHHHHHHTCTTCC
T ss_pred             CCCCEEEEEeCCCccccCHhHcCCCCCcEEEEECCcCHHHHHHHHHHHhcccCCcc----ccCHHHHHHHCCCCC
Confidence            2  22333366543      11   2445889999999999999998775433211    112567888888863

>d1jl5a_ c.10.2.6 (A:) Leucine rich effector protein YopM {Yersinia pestis [TaxId: 632]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Leucine rich effector protein YopM
domain: Leucine rich effector protein YopM
species: Yersinia pestis [TaxId: 632]

Probab=98.13  E-value=3.8e-06  Score=84.51  Aligned_cols=99  Identities=19%  Similarity=0.211  Sum_probs=60.1

Q ss_pred             ceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccCCCCcEEEeccCCCCCccccccc-ccccEEe
Q 042541          551 EVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSALSKLKKIRLEHVSLPNSLATVRM-NHLQKVS  629 (695)
Q Consensus       551 ~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l~~L~~L~L~~~~l~~lp~i~~l-~~L~~L~  629 (695)
                      +++.|.|+.+.. ..+|+.   .++|++|++++|.+.  .++     ..+.+|+.|++.+|+++.++   .+ +.|++|+
T Consensus        39 ~l~~LdLs~~~L-~~lp~~---~~~L~~L~Ls~N~l~--~lp-----~~~~~L~~L~l~~n~l~~l~---~lp~~L~~L~  104 (353)
T d1jl5a_          39 QAHELELNNLGL-SSLPEL---PPHLESLVASCNSLT--ELP-----ELPQSLKSLLVDNNNLKALS---DLPPLLEYLG  104 (353)
T ss_dssp             TCSEEECTTSCC-SCCCSC---CTTCSEEECCSSCCS--SCC-----CCCTTCCEEECCSSCCSCCC---SCCTTCCEEE
T ss_pred             CCCEEEeCCCCC-CCCCCC---CCCCCEEECCCCCCc--ccc-----cchhhhhhhhhhhcccchhh---hhcccccccc
Confidence            455666655532 356643   356777777776552  222     12456777777777777665   22 3577778


Q ss_pred             eccccCCcccccchhhhcccCCCccEEecccccccccCchh
Q 042541          630 LVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDG  670 (695)
Q Consensus       630 l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~  670 (695)
                      +++|.+..+|+ ..     .+++|++|++++|. +...|..
T Consensus       105 L~~n~l~~lp~-~~-----~l~~L~~L~l~~~~-~~~~~~~  138 (353)
T d1jl5a_         105 VSNNQLEKLPE-LQ-----NSSFLKIIDVDNNS-LKKLPDL  138 (353)
T ss_dssp             CCSSCCSSCCC-CT-----TCTTCCEEECCSSC-CSCCCCC
T ss_pred             ccccccccccc-hh-----hhccceeecccccc-ccccccc
Confidence            87777776654 22     67777888777653 4455543

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=98.10  E-value=7.6e-06  Score=82.58  Aligned_cols=147  Identities=14%  Similarity=0.169  Sum_probs=83.7

Q ss_pred             CCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhcc---ccccc-cCCCcEEEEEeCCCCCHHHHHHHHHHhc
Q 042541          168 SPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKD---DQVQG-KFKDDIFYVTVSKNPNVKAIVQKVLHHK  243 (695)
Q Consensus       168 ~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~---~~~~~-~f~~~~~wv~~~~~~~~~~~~~~i~~~l  243 (695)
                      +|||+.+++++++.|......-+.++|.+|||||+++..++..   ..+.. -.+.++++++++.-.          ...
T Consensus        24 ~~gr~~ei~~~~~~L~r~~k~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~~l~----------ag~   93 (387)
T d1qvra2          24 VIGRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLL----------AGA   93 (387)
T ss_dssp             CCSCHHHHHHHHHHHHCSSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC-----------------
T ss_pred             CcCcHHHHHHHHHHHhcCCCCCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeHhhhh----------ccc
Confidence            5999999999999998555555678899999999988766652   12222 233446566554321          110


Q ss_pred             CCCCCCCCChHHHHHHHHHHHHhc--CCCcEEEEEeCCCCCCh-----------HHHhhhccCCCCCEEEEEcCCC----
Q 042541          244 GYPVPEFQTDEAAINDLERFFKQM--RIEAILLVLDDVWPGSE-----------SLLQKLGFQLPDYKILVTSRSE----  306 (695)
Q Consensus       244 ~~~~~~~~~~~~~~~~l~~~~~~l--~~~~~LlVlDdv~~~~~-----------~~~~~l~~~~~gs~iivTtR~~----  306 (695)
                      .       ...+...++..++..+  ...+++|++|++.....           .++.+.. ....-++|.||...    
T Consensus        94 ~-------~~g~~e~r~~~i~~~~~~~~~~~ilfide~h~l~~~g~~~g~~d~a~~Lkp~L-~rg~~~~I~~tT~~ey~~  165 (387)
T d1qvra2          94 K-------YRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKAEGAVDAGNMLKPAL-ARGELRLIGATTLDEYRE  165 (387)
T ss_dssp             -----------CHHHHHHHHHHHHHTTCSSEEEEECCC-------------------HHHH-HTTCCCEEEEECHHHHHH
T ss_pred             C-------cchhHHHHHHHHHHHhccCCCceEEEeccHHHHhcCCCCCCcccHHHHHHHHH-hCCCcceeeecCHHHHHH
Confidence            0       1112234455555333  24579999999865421           0111111 11235677666543    


Q ss_pred             ---CCCCC---CeEecCCCChHHHHHHHHHhc
Q 042541          307 ---FPQFG---SVHYLKPLTYEAARTLFLHSA  332 (695)
Q Consensus       307 ---~~~~~---~~~~l~~L~~~ea~~Lf~~~~  332 (695)
                         ..+..   ..+.+++.+.+++..++....
T Consensus       166 ~e~d~al~rrF~~v~v~ep~~~~~~~il~~~~  197 (387)
T d1qvra2         166 IEKDPALERRFQPVYVDEPTVEETISILRGLK  197 (387)
T ss_dssp             HTTCTTTCSCCCCEEECCCCHHHHHHHHHHHH
T ss_pred             hcccHHHHHhcccccCCCCcHHHHHHHHHHHH
Confidence               11221   288999999999999987544

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.01  E-value=1.2e-05  Score=77.38  Aligned_cols=164  Identities=12%  Similarity=0.126  Sum_probs=92.4

Q ss_pred             CCCCCcchHHHHHHHHH----c---------CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHH
Q 042541          167 ISPGLDVPLKELKMELF----K---------DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVK  233 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~----~---------~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~  233 (695)
                      .++|.++.+++|.+.+.    .         ...+-|.++|++|+|||+||+.+++  ...    ..++.++.+      
T Consensus         8 di~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~Gp~GtGKT~l~~ala~--~~~----~~~~~~~~~------   75 (265)
T d1r7ra3           8 DIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIAN--ECQ----ANFISIKGP------   75 (265)
T ss_dssp             SCSSSSCCCCHHHHHTHHHHHCHHHHHHCCCCCCCEEEEBCCTTSSHHHHHHHHHH--HTT----CEEEEECHH------
T ss_pred             HhcCHHHHHHHHHHHHHHHhhCHHHHHhCCCCCCCeEEEECCCCCcchhHHHHHHH--HhC----CcEEEEEHH------
Confidence            46888887777766542    1         1246788999999999999999987  332    222233211      


Q ss_pred             HHHHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCCCCCh--------------HHHhhhcc------
Q 042541          234 AIVQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVWPGSE--------------SLLQKLGF------  292 (695)
Q Consensus       234 ~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~~~~~--------------~~~~~l~~------  292 (695)
                      .+    ....         .......++.++ ..-...+++|++||++....              .....+..      
T Consensus        76 ~l----~~~~---------~~~~~~~l~~~f~~A~~~~p~il~ideid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~  142 (265)
T d1r7ra3          76 EL----LTMW---------FGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMS  142 (265)
T ss_dssp             HH----HTSC---------TTTHHHHHHHHHHHHHHTCSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCC---
T ss_pred             Hh----hhcc---------ccchHHHHHHHHHHHHhcCCcceeHHhhhhccccCCCcCCCCcHHHHHHHHHHHHHhhCcC
Confidence            11    1100         111223344444 33346789999999863321              01222221      


Q ss_pred             CCCCCEEEEEcCCCCC---------CCCCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcCCchh
Q 042541          293 QLPDYKILVTSRSEFP---------QFGSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACKGCPL  359 (695)
Q Consensus       293 ~~~gs~iivTtR~~~~---------~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~G~PL  359 (695)
                      ..++.-||.||.....         .....+++++.+.++-.++|+............    ...+|++.+.|..-
T Consensus       143 ~~~~v~vi~ttn~~~~ld~al~r~gRf~~~i~~~~p~~~~R~~il~~~l~~~~~~~~~----~l~~la~~t~g~s~  214 (265)
T d1r7ra3         143 TKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDV----DLEFLAKMTNGFSG  214 (265)
T ss_dssp             ---CCEEEECCBSCTTTSCGGGSSTTSEEEEECCCCCCHHHHHHHHHHTTCC----CC----CCHHHHHHHCSSCC
T ss_pred             CCCCEEEEEeCCCchhCCHHHhCCCCccEEEEecchHHHHHHHHHHHHhccCCchhhh----hHHHHHhcCCCCCH
Confidence            1223455667765521         123478999999999999998765432221111    24667788887653

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=97.97  E-value=4.2e-05  Score=70.59  Aligned_cols=165  Identities=19%  Similarity=0.226  Sum_probs=94.6

Q ss_pred             CCCCCCCcch--HHHHHHHHHcCC--ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHH
Q 042541          165 PVISPGLDVP--LKELKMELFKDG--RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVL  240 (695)
Q Consensus       165 ~~~~vGr~~~--~~~l~~~L~~~~--~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~  240 (695)
                      ..++||-..+  .+.+.++....+  ...+.|+|++|+|||.|++++++  ........ +++++..      ++...+.
T Consensus        10 dnF~vg~~N~~a~~~~~~~~~~~~~~~n~l~l~G~~G~GKTHLl~A~~~--~~~~~~~~-~~~~~~~------~~~~~~~   80 (213)
T d1l8qa2          10 ENFIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGN--EAKKRGYR-VIYSSAD------DFAQAMV   80 (213)
T ss_dssp             SSCCCCTTTHHHHHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHH--HHHHTTCC-EEEEEHH------HHHHHHH
T ss_pred             hhccCCCcHHHHHHHHHHHHhCcCCCCCcEEEECCCCCcHHHHHHHHHH--HhccCccc-eEEechH------HHHHHHH
Confidence            4566776443  233444444333  23488999999999999999998  44444333 6666544      3444444


Q ss_pred             HhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCC---hH---HHhhhcc-CCCCCEEEEEcCCCCCCC---
Q 042541          241 HHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGS---ES---LLQKLGF-QLPDYKILVTSRSEFPQF---  310 (695)
Q Consensus       241 ~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~---~~---~~~~l~~-~~~gs~iivTtR~~~~~~---  310 (695)
                      ..+...     .    .......+   + .--+|++||+....   .+   +..-+.. ...|.+||+||+......   
T Consensus        81 ~~~~~~-----~----~~~~~~~~---~-~~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~p~~l~~~  147 (213)
T d1l8qa2          81 EHLKKG-----T----INEFRNMY---K-SVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGV  147 (213)
T ss_dssp             HHHHHT-----C----HHHHHHHH---H-TCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTS
T ss_pred             HHHHcc-----c----hhhHHHHH---h-hccchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCcchhcccc
Confidence            443211     0    11112222   2 35689999996442   11   1111111 235789999999873221   


Q ss_pred             ----------CCeEecCCCChHHHHHHHHHhccCCCCCCCCCchHHHHHHHHhcC
Q 042541          311 ----------GSVHYLKPLTYEAARTLFLHSANLQDGNSYIPDENIVSKILRACK  355 (695)
Q Consensus       311 ----------~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~~~I~~~c~  355 (695)
                                +..+.++ .+.++-.+++.+.+....-.   -..+++.-|++++.
T Consensus       148 ~~dL~SRL~~g~~~~i~-p~d~~~~~iL~~~a~~rgl~---l~~~v~~yl~~~~~  198 (213)
T d1l8qa2         148 SDRLVSRFEGGILVEIE-LDNKTRFKIIKEKLKEFNLE---LRKEVIDYLLENTK  198 (213)
T ss_dssp             CHHHHHHHHTSEEEECC-CCHHHHHHHHHHHHHHTTCC---CCHHHHHHHHHHCS
T ss_pred             chHHHHHhhCceEEEEC-CCcHHHHHHHHHHHHHcCCC---CCHHHHHHHHHhcC
Confidence                      2377886 57777788888777433321   23567777777764

>d1jl5a_ c.10.2.6 (A:) Leucine rich effector protein YopM {Yersinia pestis [TaxId: 632]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: Leucine rich effector protein YopM
domain: Leucine rich effector protein YopM
species: Yersinia pestis [TaxId: 632]

Probab=97.88  E-value=3.3e-05  Score=77.36  Aligned_cols=116  Identities=16%  Similarity=0.163  Sum_probs=80.6

Q ss_pred             CCceEEEEEEccCccccCChhhcCCCCCcEEEEcccCCCCcccCcccccccC-CCCcEEEeccCCCCCcccccccccccE
Q 042541          549 GPEVKVVVLNIRTKKYVLPDFLQKMDELKVLIVTNYGFSPAELNNFRVLSAL-SKLKKIRLEHVSLPNSLATVRMNHLQK  627 (695)
Q Consensus       549 ~~~l~~L~l~~~~~~~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~~~l~~l-~~L~~L~L~~~~l~~lp~i~~l~~L~~  627 (695)
                      +++|+.|.++.+.. ..+|..   +.+|+.|++.+|...  .++      .+ ++|++|++++|.+..+|.++++++|++
T Consensus        57 ~~~L~~L~Ls~N~l-~~lp~~---~~~L~~L~l~~n~l~--~l~------~lp~~L~~L~L~~n~l~~lp~~~~l~~L~~  124 (353)
T d1jl5a_          57 PPHLESLVASCNSL-TELPEL---PQSLKSLLVDNNNLK--ALS------DLPPLLEYLGVSNNQLEKLPELQNSSFLKI  124 (353)
T ss_dssp             CTTCSEEECCSSCC-SSCCCC---CTTCCEEECCSSCCS--CCC------SCCTTCCEEECCSSCCSSCCCCTTCTTCCE
T ss_pred             CCCCCEEECCCCCC-cccccc---hhhhhhhhhhhcccc--hhh------hhccccccccccccccccccchhhhcccee
Confidence            46888998877644 366754   457899999987653  222      23 359999999999999996678999999


Q ss_pred             EeeccccCCcccccchhhhcccCCCccEEecccccccccCchhhcCCCCCceeeccccc
Q 042541          628 VSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELPDGLCDIVSMEKLRITNCH  686 (695)
Q Consensus       628 L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP~~i~~L~~L~~L~l~~~~  686 (695)
                      |++++|.+...+.        ....+..|.+.++..  .-+..++.++.++.|++.+|.
T Consensus       125 L~l~~~~~~~~~~--------~~~~l~~l~~~~~~~--~~~~~l~~l~~l~~L~l~~n~  173 (353)
T d1jl5a_         125 IDVDNNSLKKLPD--------LPPSLEFIAAGNNQL--EELPELQNLPFLTAIYADNNS  173 (353)
T ss_dssp             EECCSSCCSCCCC--------CCTTCCEEECCSSCC--SSCCCCTTCTTCCEEECCSSC
T ss_pred             ecccccccccccc--------ccccccchhhccccc--cccccccccccceeccccccc
Confidence            9999998876554        334455565555332  223346667777777776654

>d1koha1 c.10.2.3 (A:201-362) mRNA export factor tap {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: mRNA export factor tap
domain: mRNA export factor tap
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.64  E-value=6.9e-06  Score=72.66  Aligned_cols=79  Identities=11%  Similarity=-0.026  Sum_probs=43.0

Q ss_pred             cCCCCcEEEeccCCCCCc---c-cccccccccEEeeccccCCcccccchhhhcccCCCccEEecccccccccCc------
Q 042541          599 ALSKLKKIRLEHVSLPNS---L-ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDLIELP------  668 (695)
Q Consensus       599 ~l~~L~~L~L~~~~l~~l---p-~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l~~lP------  668 (695)
                      .+++|++|+|++|.++.+   + .+..+++|++|+|++|.|+.+++-...    ...+|+.|++++|+.....+      
T Consensus        63 ~~~~L~~L~Ls~N~i~~l~~~~~~~~~l~~L~~L~Ls~N~i~~l~~l~~l----~~~~L~~L~L~~Npl~~~~~~~~~y~  138 (162)
T d1koha1          63 NIPELLSLNLSNNRLYRLDDMSSIVQKAPNLKILNLSGNELKSERELDKI----KGLKLEELWLDGNSLSDTFRDQSTYI  138 (162)
T ss_dssp             HCTTCCCCCCCSSCCCCCSGGGTHHHHSTTCCCCCCTTSCCCCGGGHHHH----TTCCCSSCCCTTSTTSSSSSSHHHHH
T ss_pred             hCCCCCEeeCCCccccCCchhHHHHhhCCcccccccccCccccchhhhhh----hccccceeecCCCCcCcCcccchhHH
Confidence            455666666666666543   2 344566666666666666665542222    34456666666654322222      


Q ss_pred             -hhhcCCCCCceee
Q 042541          669 -DGLCDIVSMEKLR  681 (695)
Q Consensus       669 -~~i~~L~~L~~L~  681 (695)
                       .-+..+++|+.||
T Consensus       139 ~~i~~~~P~L~~LD  152 (162)
T d1koha1         139 SAIRERFPKLLRLD  152 (162)
T ss_dssp             HHHHTTSTTCCEET
T ss_pred             HHHHHHCCCCCEEC
Confidence             1144567777665

>d1z7xw1 c.10.1.1 (W:1-460) Ribonuclease inhibitor {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Ribonuclease inhibitor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.60  E-value=8.3e-06  Score=85.14  Aligned_cols=112  Identities=15%  Similarity=0.208  Sum_probs=58.4

Q ss_pred             ceEEEEEEccCccc-cCChhhcCCCCCcEEEEcccCCCCcccCcc-cccccCCCCcEEEeccCCCCC-----cc-ccc-c
Q 042541          551 EVKVVVLNIRTKKY-VLPDFLQKMDELKVLIVTNYGFSPAELNNF-RVLSALSKLKKIRLEHVSLPN-----SL-ATV-R  621 (695)
Q Consensus       551 ~l~~L~l~~~~~~~-~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~-~~l~~l~~L~~L~L~~~~l~~-----lp-~i~-~  621 (695)
                      +|+.|.++.+.... .+...+..+++|++|+|.+|++....+..+ ..+..+++|++|+|++|.++.     +. .+. .
T Consensus         3 ~l~~ld~~~~~i~~~~~~~l~~~l~~l~~L~L~~~~i~~~~~~~l~~~L~~~~~L~~LdLs~N~i~~~~~~~l~~~l~~~   82 (460)
T d1z7xw1           3 DIQSLDIQCEELSDARWAELLPLLQQCQVVRLDDCGLTEARCKDISSALRVNPALAELNLRSNELGDVGVHCVLQGLQTP   82 (460)
T ss_dssp             EEEEEEEESCCCCHHHHHHHHHHHTTCSEEEEESSCCCHHHHHHHHHHHHTCTTCCEEECTTCCCHHHHHHHHHHTTCST
T ss_pred             CCCEEEeeCCcCChHHHHHHHHhCCCCCEEEeCCCCCCHHHHHHHHHHHhcCCCCCEEECcCCcCChHHHHHHHHHHhcC
Confidence            56777776664332 223345556777777777776543222211 124566677777777776642     11 111 1


Q ss_pred             cccccEEeeccccCCcccccchhhhcccCCCccEEeccccc
Q 042541          622 MNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCN  662 (695)
Q Consensus       622 l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~  662 (695)
                      ..+|++|+|++|.++...-..+...-..+++|++|++++|.
T Consensus        83 ~~~L~~L~L~~n~it~~~~~~l~~~l~~~~~L~~L~L~~N~  123 (460)
T d1z7xw1          83 SCKIQKLSLQNCCLTGAGCGVLSSTLRTLPTLQELHLSDNL  123 (460)
T ss_dssp             TCCCCEEECTTSCCBGGGHHHHHHHTTSCTTCCEEECCSSB
T ss_pred             CCCCCEEECCCCCccccccccccchhhcccccccccccccc
Confidence            23577777777766542111110000056667777777653

>d2ca6a1 c.10.1.2 (A:2-345) Rna1p (RanGAP1), N-terminal domain {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: Rna1p (RanGAP1), N-terminal domain
domain: Rna1p (RanGAP1), N-terminal domain
species: Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]

Probab=97.56  E-value=8.7e-06  Score=81.88  Aligned_cols=137  Identities=13%  Similarity=0.174  Sum_probs=90.9

Q ss_pred             CCceEEEEEEccCcc----ccCChhhcCCCCCcEEEEcccCCCCcccCc--ccccccCCCCcEEEeccCCCC-----Ccc
Q 042541          549 GPEVKVVVLNIRTKK----YVLPDFLQKMDELKVLIVTNYGFSPAELNN--FRVLSALSKLKKIRLEHVSLP-----NSL  617 (695)
Q Consensus       549 ~~~l~~L~l~~~~~~----~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~--~~~l~~l~~L~~L~L~~~~l~-----~lp  617 (695)
                      .+.++.+.++.+...    ..+...+...+.|+.|++.+|.+.......  ...+..+++|+.|+|++|.+.     .+.
T Consensus       157 ~~~L~~l~l~~n~i~~~~~~~l~~~l~~~~~L~~L~L~~n~i~~~g~~~~l~~~l~~~~~L~~L~Ls~N~i~~~g~~~L~  236 (344)
T d2ca6a1         157 APPLRSIICGRNRLENGSMKEWAKTFQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQDNTFTHLGSSALA  236 (344)
T ss_dssp             CCCCCEEECCSSCCTGGGHHHHHHHHHHCTTCCEEECCSSCCCHHHHHHHHHTTGGGCTTCCEEECCSSCCHHHHHHHHH
T ss_pred             Ccccceeecccccccccccccccchhhhhhhhcccccccccccccccccchhhhhcchhhhccccccccccccccccccc
Confidence            345566666554221    234556777889999999998765322211  123677889999999999875     244


Q ss_pred             -cccccccccEEeeccccCCcccccchh-hhcc-cCCCccEEeccccccccc-----Cchhhc-CCCCCceeeccccc
Q 042541          618 -ATVRMNHLQKVSLVMCNVGQVFRNSTF-RISD-AFPNLLEMDIDYCNDLIE-----LPDGLC-DIVSMEKLRITNCH  686 (695)
Q Consensus       618 -~i~~l~~L~~L~l~~~~i~~~~~~~~~-~l~~-~l~~L~~L~l~~c~~l~~-----lP~~i~-~L~~L~~L~l~~~~  686 (695)
                       .+...++|++|+|++|.++......+. .+.. ..++|++|++++|. +..     +...+. ++++|++|+|++|.
T Consensus       237 ~~l~~~~~L~~L~Ls~n~i~~~g~~~l~~~l~~~~~~~L~~L~ls~N~-i~~~~~~~l~~~l~~~~~~L~~L~l~~N~  313 (344)
T d2ca6a1         237 IALKSWPNLRELGLNDCLLSARGAAAVVDAFSKLENIGLQTLRLQYNE-IELDAVRTLKTVIDEKMPDLLFLELNGNR  313 (344)
T ss_dssp             HHGGGCTTCCEEECTTCCCCHHHHHHHHHHHHTCSSCCCCEEECCSSC-CBHHHHHHHHHHHHHHCTTCCEEECTTSB
T ss_pred             ccccccccchhhhhhcCccCchhhHHHHHHhhhccCCCCCEEECCCCc-CChHHHHHHHHHHHccCCCCCEEECCCCc
Confidence             677889999999999988753221111 1110 24679999999974 432     445553 68899999999966

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=97.45  E-value=0.00023  Score=67.07  Aligned_cols=91  Identities=12%  Similarity=0.119  Sum_probs=56.5

Q ss_pred             CCCCCCcchHHHHHHHHH-------c---CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHH
Q 042541          166 VISPGLDVPLKELKMELF-------K---DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAI  235 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~-------~---~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~  235 (695)
                      ..+||....++.+.+-..       .   ...+-|.++|++|+|||++|+.+++  .....    ++.++.+..      
T Consensus         9 ~~~i~~~~~i~~i~~~~~~~~~~~~~~~~~p~~~vLL~GppGtGKT~la~alA~--~~~~~----~~~i~~~~~------   76 (246)
T d1d2na_           9 NGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAE--ESNFP----FIKICSPDK------   76 (246)
T ss_dssp             TCCCCCSHHHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHH--HHTCS----EEEEECGGG------
T ss_pred             cCCcCcCHHHHHHHHHHHHHHHHHhccCCCCCeEEEEECcCCCCHHHHHHHHhh--ccccc----ccccccccc------
Confidence            347998888777766543       1   1245688999999999999999997  33222    334443321      


Q ss_pred             HHHHHHhcCCCCCCCCChHHHHHHHHHHH-HhcCCCcEEEEEeCCC
Q 042541          236 VQKVLHHKGYPVPEFQTDEAAINDLERFF-KQMRIEAILLVLDDVW  280 (695)
Q Consensus       236 ~~~i~~~l~~~~~~~~~~~~~~~~l~~~~-~~l~~~~~LlVlDdv~  280 (695)
                             +.+     .........++.++ ...+..+++|++|+++
T Consensus        77 -------~~g-----~~~~~~~~~i~~if~~A~~~~p~il~iDEid  110 (246)
T d1d2na_          77 -------MIG-----FSETAKCQAMKKIFDDAYKSQLSCVVVDDIE  110 (246)
T ss_dssp             -------CTT-----CCHHHHHHHHHHHHHHHHTSSEEEEEECCHH
T ss_pred             -------ccc-----ccccchhhhhhhhhhhhhhcccceeehhhhh
Confidence                   100     01222234455555 4446778999999974

>d2ca6a1 c.10.1.2 (A:2-345) Rna1p (RanGAP1), N-terminal domain {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: Rna1p (RanGAP1), N-terminal domain
domain: Rna1p (RanGAP1), N-terminal domain
species: Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]

Probab=97.44  E-value=2e-05  Score=79.06  Aligned_cols=114  Identities=13%  Similarity=0.281  Sum_probs=69.7

Q ss_pred             cCCCCCcEEEEcccCCCCcccCcc-cccccCCCCcEEEeccCCCCC------cc-cccccccccEEeeccccCCccccc-
Q 042541          571 QKMDELKVLIVTNYGFSPAELNNF-RVLSALSKLKKIRLEHVSLPN------SL-ATVRMNHLQKVSLVMCNVGQVFRN-  641 (695)
Q Consensus       571 ~~l~~Lr~L~l~~~~~~~~~~~~~-~~l~~l~~L~~L~L~~~~l~~------lp-~i~~l~~L~~L~l~~~~i~~~~~~-  641 (695)
                      ...+.|+.|.+.+|.+.......+ ..+..+.+|+.|+|++|.+..      +. .+..+++|++|+|++|.++..-.. 
T Consensus       155 ~~~~~L~~l~l~~n~i~~~~~~~l~~~l~~~~~L~~L~L~~n~i~~~g~~~~l~~~l~~~~~L~~L~Ls~N~i~~~g~~~  234 (344)
T d2ca6a1         155 KNAPPLRSIICGRNRLENGSMKEWAKTFQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQDNTFTHLGSSA  234 (344)
T ss_dssp             HTCCCCCEEECCSSCCTGGGHHHHHHHHHHCTTCCEEECCSSCCCHHHHHHHHHTTGGGCTTCCEEECCSSCCHHHHHHH
T ss_pred             ccCcccceeecccccccccccccccchhhhhhhhcccccccccccccccccchhhhhcchhhhccccccccccccccccc
Confidence            345667777777665543322221 224567788888888888762      23 566788888999988876532111 


Q ss_pred             chhhhcccCCCccEEeccccccccc-----CchhhcC--CCCCceeeccccc
Q 042541          642 STFRISDAFPNLLEMDIDYCNDLIE-----LPDGLCD--IVSMEKLRITNCH  686 (695)
Q Consensus       642 ~~~~l~~~l~~L~~L~l~~c~~l~~-----lP~~i~~--L~~L~~L~l~~~~  686 (695)
                      ....++ .+++|++|++++|. +..     +-..+..  .++|++|++++|.
T Consensus       235 L~~~l~-~~~~L~~L~Ls~n~-i~~~g~~~l~~~l~~~~~~~L~~L~ls~N~  284 (344)
T d2ca6a1         235 LAIALK-SWPNLRELGLNDCL-LSARGAAAVVDAFSKLENIGLQTLRLQYNE  284 (344)
T ss_dssp             HHHHGG-GCTTCCEEECTTCC-CCHHHHHHHHHHHHTCSSCCCCEEECCSSC
T ss_pred             cccccc-ccccchhhhhhcCc-cCchhhHHHHHHhhhccCCCCCEEECCCCc
Confidence            111111 67888899998875 332     2223333  3578899998865

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=97.35  E-value=0.00057  Score=61.87  Aligned_cols=112  Identities=13%  Similarity=0.074  Sum_probs=70.0

Q ss_pred             hHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccc-cccCCCcEEEEEeCCC-CCHHHHHHHHHHhcCCCCCCCC
Q 042541          174 PLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQV-QGKFKDDIFYVTVSKN-PNVKAIVQKVLHHKGYPVPEFQ  251 (695)
Q Consensus       174 ~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~-~~~f~~~~~wv~~~~~-~~~~~~~~~i~~~l~~~~~~~~  251 (695)
                      +++-+..++..+...-+.++|++|+||||+|..+.+.... ....+. ++++.-... ..++++ +++.+.+....    
T Consensus         2 ~~~~l~~~i~~~~~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D-~~~i~~~~~~I~Id~I-R~i~~~~~~~~----   75 (198)
T d2gnoa2           2 QLETLKRIIEKSEGISILINGEDLSYPREVSLELPEYVEKFPPKASD-VLEIDPEGENIGIDDI-RTIKDFLNYSP----   75 (198)
T ss_dssp             HHHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTT-EEEECCSSSCBCHHHH-HHHHHHHTSCC----
T ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHhccccCCCC-EEEEeCCcCCCCHHHH-HHHHHHHhhCc----
Confidence            4566777777778899999999999999999988873211 111223 556543321 133333 23433333221    


Q ss_pred             ChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH----HHhhhccCCCCCEEEEEcCCC
Q 042541          252 TDEAAINDLERFFKQMRIEAILLVLDDVWPGSES----LLQKLGFQLPDYKILVTSRSE  306 (695)
Q Consensus       252 ~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~----~~~~l~~~~~gs~iivTtR~~  306 (695)
                                     ..+++-++|+|+++.....    ++..+-...+++.+|++|.+.
T Consensus        76 ---------------~~~~~KviIId~ad~l~~~aqNaLLK~LEEPp~~t~fiLit~~~  119 (198)
T d2gnoa2          76 ---------------ELYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRW  119 (198)
T ss_dssp             ---------------SSSSSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCG
T ss_pred             ---------------ccCCCEEEEEeCccccchhhhhHHHHHHhCCCCCceeeeccCCh
Confidence                           1366679999999877644    455555556678888777665

>d1koha1 c.10.2.3 (A:201-362) mRNA export factor tap {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: L domain-like
family: mRNA export factor tap
domain: mRNA export factor tap
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.28  E-value=2.4e-05  Score=69.06  Aligned_cols=90  Identities=21%  Similarity=0.309  Sum_probs=65.5

Q ss_pred             ChhhcCCCCCcEEEEcccCCCCcccCcc-cccccCCCCcEEEeccCCCCCcc--cccccccccEEeeccccCCcccccch
Q 042541          567 PDFLQKMDELKVLIVTNYGFSPAELNNF-RVLSALSKLKKIRLEHVSLPNSL--ATVRMNHLQKVSLVMCNVGQVFRNST  643 (695)
Q Consensus       567 p~~~~~l~~Lr~L~l~~~~~~~~~~~~~-~~l~~l~~L~~L~L~~~~l~~lp--~i~~l~~L~~L~l~~~~i~~~~~~~~  643 (695)
                      +..+..+++|++|+|++|.+..  +..+ ..+..+++|++|+|++|.++.++  ...+..+|+.|++++|++........
T Consensus        58 ~~~~~~~~~L~~L~Ls~N~i~~--l~~~~~~~~~l~~L~~L~Ls~N~i~~l~~l~~l~~~~L~~L~L~~Npl~~~~~~~~  135 (162)
T d1koha1          58 RIIEENIPELLSLNLSNNRLYR--LDDMSSIVQKAPNLKILNLSGNELKSERELDKIKGLKLEELWLDGNSLSDTFRDQS  135 (162)
T ss_dssp             HHHHHHCTTCCCCCCCSSCCCC--CSGGGTHHHHSTTCCCCCCTTSCCCCGGGHHHHTTCCCSSCCCTTSTTSSSSSSHH
T ss_pred             HHHHHhCCCCCEeeCCCccccC--CchhHHHHhhCCcccccccccCccccchhhhhhhccccceeecCCCCcCcCcccch
Confidence            3345678999999999998742  2222 23678999999999999999888  44455679999999999887654321


Q ss_pred             ---hhhcccCCCccEEec
Q 042541          644 ---FRISDAFPNLLEMDI  658 (695)
Q Consensus       644 ---~~l~~~l~~L~~L~l  658 (695)
                         ..+...+|+|+.||=
T Consensus       136 ~y~~~i~~~~P~L~~LDg  153 (162)
T d1koha1         136 TYISAIRERFPKLLRLDG  153 (162)
T ss_dssp             HHHHHHHTTSTTCCEETT
T ss_pred             hHHHHHHHHCCCCCEECc
Confidence               112227899999863

>d1z7xw1 c.10.1.1 (W:1-460) Ribonuclease inhibitor {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Ribonuclease inhibitor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.05  E-value=7.1e-05  Score=77.71  Aligned_cols=89  Identities=17%  Similarity=0.142  Sum_probs=47.8

Q ss_pred             CCceEEEEEEccCcc----ccCChhhcCCCCCcEEEEcccCCCCcccCcc-cccc-cCCCCcEEEeccCCCCC-----cc
Q 042541          549 GPEVKVVVLNIRTKK----YVLPDFLQKMDELKVLIVTNYGFSPAELNNF-RVLS-ALSKLKKIRLEHVSLPN-----SL  617 (695)
Q Consensus       549 ~~~l~~L~l~~~~~~----~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~-~~l~-~l~~L~~L~L~~~~l~~-----lp  617 (695)
                      ++++++|.|+.+...    ..++..+..+++|+.|+|++|.+.+..+..+ ..+. ...+|+.|+|++|.++.     ++
T Consensus        26 l~~l~~L~L~~~~i~~~~~~~l~~~L~~~~~L~~LdLs~N~i~~~~~~~l~~~l~~~~~~L~~L~L~~n~it~~~~~~l~  105 (460)
T d1z7xw1          26 LQQCQVVRLDDCGLTEARCKDISSALRVNPALAELNLRSNELGDVGVHCVLQGLQTPSCKIQKLSLQNCCLTGAGCGVLS  105 (460)
T ss_dssp             HTTCSEEEEESSCCCHHHHHHHHHHHHTCTTCCEEECTTCCCHHHHHHHHHHTTCSTTCCCCEEECTTSCCBGGGHHHHH
T ss_pred             CCCCCEEEeCCCCCCHHHHHHHHHHHhcCCCCCEEECcCCcCChHHHHHHHHHHhcCCCCCCEEECCCCCcccccccccc
Confidence            456666777666322    2344455666777777777665432211111 0011 12357777777776652     33


Q ss_pred             -cccccccccEEeeccccCCc
Q 042541          618 -ATVRMNHLQKVSLVMCNVGQ  637 (695)
Q Consensus       618 -~i~~l~~L~~L~l~~~~i~~  637 (695)
                       .+..+++|++|++++|.++.
T Consensus       106 ~~l~~~~~L~~L~L~~N~i~~  126 (460)
T d1z7xw1         106 STLRTLPTLQELHLSDNLLGD  126 (460)
T ss_dssp             HHTTSCTTCCEEECCSSBCHH
T ss_pred             chhhccccccccccccccchh
Confidence             45566677777777776553

>d1qvra3 c.37.1.20 (A:536-850) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=96.71  E-value=0.00072  Score=66.00  Aligned_cols=110  Identities=13%  Similarity=0.164  Sum_probs=58.1

Q ss_pred             CCCCCcchHHHHHHHHH-------cC-C-ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHH
Q 042541          167 ISPGLDVPLKELKMELF-------KD-G-RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQ  237 (695)
Q Consensus       167 ~~vGr~~~~~~l~~~L~-------~~-~-~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~  237 (695)
                      .++|-++.++.|...+.       ++ . ..++.++|+.|+|||.+|+.+++  .+-..-.. .+-++.+...+...+  
T Consensus        24 ~v~GQ~~ai~~v~~~i~~~~~~l~~~~kp~~~~lf~Gp~G~GKt~lak~la~--~l~~~~~~-~~~~~~~~~~~~~~~--   98 (315)
T d1qvra3          24 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAA--TLFDTEEA-MIRIDMTEYMEKHAV--   98 (315)
T ss_dssp             HSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHH--HHHSSGGG-EEEECTTTCCSSGGG--
T ss_pred             eEeCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCcchHHHHHHHHHH--HhcCCCcc-eEEEeccccccchhh--
Confidence            36888888888877664       11 1 34788999999999999999887  33211111 334444443322111  


Q ss_pred             HHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChHHH
Q 042541          238 KVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSESLL  287 (695)
Q Consensus       238 ~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~~~  287 (695)
                         ..+-+..+..... +....+.+.++  +....+++||++......+.
T Consensus        99 ---~~L~g~~~gyvG~-~~~~~l~~~~~--~~p~~Vvl~DEieK~~~~v~  142 (315)
T d1qvra3          99 ---SRLIGAPPGYVGY-EEGGQLTEAVR--RRPYSVILFDEIEKAHPDVF  142 (315)
T ss_dssp             ---GGC---------------CHHHHHH--HCSSEEEEESSGGGSCHHHH
T ss_pred             ---hhhcCCCCCCcCc-ccCChHHHHHH--hCCCcEEEEehHhhcCHHHH
Confidence               0111111110000 01112333332  24578999999988875533

>d1m8pa3 c.37.1.15 (A:391-573) ATP sulfurylase C-terminal domain {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=96.69  E-value=0.00051  Score=60.98  Aligned_cols=36  Identities=11%  Similarity=0.068  Sum_probs=26.8

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEE
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYV  224 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv  224 (695)
                      ..+|.|+|++|+||||+|+.++.  ++...|-..+.++
T Consensus         6 g~~I~l~G~~GsGKTTia~~La~--~L~~~~~~~~~~~   41 (183)
T d1m8pa3           6 GFTIFLTGYMNSGKDAIARALQV--TLNQQGGRSVSLL   41 (183)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHH--HHHHHCSSCEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH--HHhhcCCCchhhh
Confidence            47899999999999999999987  5544333224444

>d1r6bx3 c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=96.66  E-value=0.0014  Score=63.99  Aligned_cols=109  Identities=15%  Similarity=0.192  Sum_probs=62.1

Q ss_pred             CCCCCCcchHHHHHHHHH-------cC--CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHH
Q 042541          166 VISPGLDVPLKELKMELF-------KD--GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIV  236 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~-------~~--~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~  236 (695)
                      ..++|-++.++.+...+.       ++  ...++.++|+.|+|||.||+.++.  .+.   . ..+-++++...+...  
T Consensus        22 ~~viGQ~~a~~~v~~~v~~~~~~l~~~~~p~~~~lf~Gp~GvGKT~lak~la~--~l~---~-~~i~~d~s~~~~~~~--   93 (315)
T d1r6bx3          22 MLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSK--ALG---I-ELLRFDMSEYMERHT--   93 (315)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHH--HHT---C-EEEEEEGGGCSSSSC--
T ss_pred             CeecChHHHHHHHHHHHHHHHccCCCCCCCceEEEEECCCcchhHHHHHHHHh--hcc---C-CeeEeccccccchhh--
Confidence            457999999999887774       11  245888999999999999999987  221   2 244555553321110  


Q ss_pred             HHHHHhcCCCCCCCCChHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChHHHh
Q 042541          237 QKVLHHKGYPVPEFQTDEAAINDLERFFKQMRIEAILLVLDDVWPGSESLLQ  288 (695)
Q Consensus       237 ~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~~~~  288 (695)
                         ...+-+..+.. ........+...+.  +....+++||++......++.
T Consensus        94 ---~~~l~g~~~gy-~g~~~~~~l~~~~~--~~~~~vvl~DeieKa~~~V~~  139 (315)
T d1r6bx3          94 ---VSRLIGAPPGY-VGFDQGGLLTDAVI--KHPHAVLLLDEIEKAHPDVFN  139 (315)
T ss_dssp             ---CSSSCCCCSCS-HHHHHTTHHHHHHH--HCSSEEEEEETGGGSCHHHHH
T ss_pred             ---hhhhcccCCCc-cccccCChhhHHHH--hCccchhhhcccccccchHhh
Confidence               01122221111 01111111222222  356789999999888765433

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=96.61  E-value=0.002  Score=58.20  Aligned_cols=92  Identities=15%  Similarity=0.134  Sum_probs=50.9

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCH--HHHHHHHHHhcCCCCCCCCChHHHHHHHHH
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNV--KAIVQKVLHHKGYPVPEFQTDEAAINDLER  262 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~--~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~  262 (695)
                      ..+.||.++|+.|+||||.+..++.  +.+. ....+..++. +.+.+  .+-++...+.++.+.....+..+....+.+
T Consensus         7 ~~p~vi~lvGptGvGKTTTiAKLA~--~~~~-~g~kV~lit~-Dt~R~gA~eQL~~~a~~l~v~~~~~~~~~d~~~~l~~   82 (211)
T d2qy9a2           7 KAPFVILMVGVNGVGKTTTIGKLAR--QFEQ-QGKSVMLAAG-DTFRAAAVEQLQVWGQRNNIPVIAQHTGADSASVIFD   82 (211)
T ss_dssp             CTTEEEEEECCTTSCHHHHHHHHHH--HHHT-TTCCEEEECC-CTTCHHHHHHHHHHHHHTTCCEECCSTTCCHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH--HHHH-CCCcEEEEec-ccccccchhhhhhhhhhcCCcccccccCCCHHHHHHH
Confidence            3478999999999999988777766  3332 2333544444 44443  555667777777654332222233333333


Q ss_pred             HHHhc-CCCcEEEEEeCCC
Q 042541          263 FFKQM-RIEAILLVLDDVW  280 (695)
Q Consensus       263 ~~~~l-~~~~~LlVlDdv~  280 (695)
                      ..+.. ....=++++|=.-
T Consensus        83 ~~~~a~~~~~d~ilIDTaG  101 (211)
T d2qy9a2          83 AIQAAKARNIDVLIADTAG  101 (211)
T ss_dssp             HHHHHHHTTCSEEEECCCC
T ss_pred             HHHHHHHcCCCEEEeccCC
Confidence            33221 1223366667654

>d1pgva_ c.10.1.1 (A:) Tropomodulin C-terminal domain {nematode (Caenorhabditis elegans) [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Tropomodulin C-terminal domain
species: nematode (Caenorhabditis elegans) [TaxId: 6239]

Probab=96.59  E-value=0.0006  Score=59.96  Aligned_cols=88  Identities=9%  Similarity=0.070  Sum_probs=40.0

Q ss_pred             cccCCCCcEEEeccCCCC-----Ccc-cccccccccEEeeccccCCccccc-chhhhcccCCCccEEeccccc--cc---
Q 042541          597 LSALSKLKKIRLEHVSLP-----NSL-ATVRMNHLQKVSLVMCNVGQVFRN-STFRISDAFPNLLEMDIDYCN--DL---  664 (695)
Q Consensus       597 l~~l~~L~~L~L~~~~l~-----~lp-~i~~l~~L~~L~l~~~~i~~~~~~-~~~~l~~~l~~L~~L~l~~c~--~l---  664 (695)
                      +...++|+.|+|++|.+.     .+. .+...+.|+.|+|++|.++..--. +...+. .-++|+.|++++|.  .+   
T Consensus        40 L~~n~~L~~L~Ls~n~l~~~~~~~la~~L~~n~~L~~L~L~~n~i~~~g~~~l~~aL~-~n~sL~~L~l~~n~~~~~g~~  118 (167)
T d1pgva_          40 ACNSKHIEKFSLANTAISDSEARGLIELIETSPSLRVLNVESNFLTPELLARLLRSTL-VTQSIVEFKADNQRQSVLGNQ  118 (167)
T ss_dssp             HTTCSCCCEEECTTSCCBHHHHTTHHHHHHHCSSCCEEECCSSBCCHHHHHHHHHHTT-TTCCCSEEECCCCSSCCCCHH
T ss_pred             HhhCCccceeeccccccchhHHHHHhhhhhhcccccceeeehhhcchHHHHHHHHHHH-hCCcCCEEECCCCcCCCccHH
Confidence            344455666666665554     122 333445566666666655431110 111111 34456666665532  11   


Q ss_pred             --ccCchhhcCCCCCceeecccc
Q 042541          665 --IELPDGLCDIVSMEKLRITNC  685 (695)
Q Consensus       665 --~~lP~~i~~L~~L~~L~l~~~  685 (695)
                        ..+...+..-++|+.|+++.+
T Consensus       119 ~~~~l~~~L~~n~sL~~l~l~~~  141 (167)
T d1pgva_         119 VEMDMMMAIEENESLLRVGISFA  141 (167)
T ss_dssp             HHHHHHHHHHHCSSCCEEECCCC
T ss_pred             HHHHHHHHHHhCCCccEeeCcCC
Confidence              113333444566666666553

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=96.53  E-value=0.0029  Score=57.11  Aligned_cols=59  Identities=15%  Similarity=0.208  Sum_probs=40.6

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCC-CCCHHHHHHHHHHhcCCC
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSK-NPNVKAIVQKVLHHKGYP  246 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~-~~~~~~~~~~i~~~l~~~  246 (695)
                      ++.++|.++|+.|+||||.+..++..  .+.+ ...+..+++.. .....+-++...+.++.+
T Consensus         4 ~~~~vi~lvGptGvGKTTTiaKLA~~--~~~~-g~kV~lit~Dt~R~gA~eQL~~~a~~l~i~   63 (207)
T d1okkd2           4 PKGRVVLVVGVNGVGKTTTIAKLGRY--YQNL-GKKVMFCAGDTFRAAGGTQLSEWGKRLSIP   63 (207)
T ss_dssp             CSSSEEEEECSTTSSHHHHHHHHHHH--HHTT-TCCEEEECCCCSSTTHHHHHHHHHHHHTCC
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH--HHHC-CCcEEEEEeccccccchhhHhhcccccCce
Confidence            45689999999999999887777663  3322 33477777764 335566667777776654

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=96.52  E-value=0.00054  Score=61.23  Aligned_cols=23  Identities=22%  Similarity=0.374  Sum_probs=21.5

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+.|+|.|+.|+||||||+.+++
T Consensus         7 ~K~I~i~G~~GsGKTTla~~La~   29 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLVNKLAA   29 (192)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            57899999999999999999887

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=96.52  E-value=0.00039  Score=60.70  Aligned_cols=22  Identities=32%  Similarity=0.525  Sum_probs=20.2

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +.|.|+|++|+||||+|+.++.
T Consensus         3 k~I~l~G~~GsGKSTvak~La~   24 (169)
T d1kaga_           3 RNIFLVGPMGAGKSTIGRQLAQ   24 (169)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHH
Confidence            5688999999999999999987

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.50  E-value=0.0032  Score=55.35  Aligned_cols=25  Identities=24%  Similarity=0.303  Sum_probs=22.2

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +.+.+|.++|++|+||||+|+.++.
T Consensus        12 ~~p~liil~G~pGsGKST~a~~l~~   36 (172)
T d1yj5a2          12 PNPEVVVAVGFPGAGKSTFIQEHLV   36 (172)
T ss_dssp             SSCCEEEEECCTTSSHHHHHHHHTG
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            4568999999999999999998865

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

Probab=96.46  E-value=0.00063  Score=59.73  Aligned_cols=23  Identities=35%  Similarity=0.481  Sum_probs=21.5

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+|++|+|..|+|||||+.++.+
T Consensus         2 ~Pvi~itG~~GSGKTTL~~~L~~   24 (170)
T d1np6a_           2 IPLLAFAAWSGTGKTTLLKKLIP   24 (170)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHH
Confidence            47999999999999999999987

>d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Polynucleotide kinase, kinase domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=96.43  E-value=0.00071  Score=58.25  Aligned_cols=22  Identities=23%  Similarity=0.344  Sum_probs=19.9

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ++|.|+|++|+||||+|+++..
T Consensus         3 klIii~G~pGsGKTTla~~L~~   24 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWAREFIA   24 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
Confidence            6889999999999999998765

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=96.40  E-value=0.0031  Score=57.17  Aligned_cols=58  Identities=17%  Similarity=0.094  Sum_probs=39.0

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC-CHHHHHHHHHHhcCCC
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKGYP  246 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~~~  246 (695)
                      .+.||.++|+.|+||||.+..++..  ...+- ..+..+++.... ...+-++...+.++.+
T Consensus        10 ~p~vi~lvGptGvGKTTTiAKLAa~--~~~~~-~kV~lit~Dt~R~gA~eQL~~~a~~l~i~   68 (213)
T d1vmaa2          10 PPFVIMVVGVNGTGKTTSCGKLAKM--FVDEG-KSVVLAAADTFRAAAIEQLKIWGERVGAT   68 (213)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHH--HHHTT-CCEEEEEECTTCHHHHHHHHHHHHHHTCE
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH--HHHCC-CceEEEeecccccchhHHHHHHhhhcCcc
Confidence            4679999999999999877666653  33222 237777776443 4455666777777654

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein rbstp0775
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.35  E-value=0.0014  Score=58.93  Aligned_cols=26  Identities=31%  Similarity=0.451  Sum_probs=22.7

Q ss_pred             cCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          184 KDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       184 ~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+.-+|+|.|++|+||||||+.+..
T Consensus        19 ~~~~~iIgI~G~~GSGKSTla~~L~~   44 (198)
T d1rz3a_          19 TAGRLVLGIDGLSRSGKTTLANQLSQ   44 (198)
T ss_dssp             CSSSEEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHH
Confidence            34567899999999999999999986

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein BH3686
species: Bacillus halodurans [TaxId: 86665]

Probab=96.35  E-value=0.00081  Score=59.18  Aligned_cols=22  Identities=32%  Similarity=0.718  Sum_probs=20.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ++|.|.|++|+||||+|+.+..
T Consensus         3 klI~i~G~~GsGKTTva~~L~~   24 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCKRLAA   24 (176)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            6899999999999999999876

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Thermus aquaticus [TaxId: 271]

Probab=96.27  E-value=0.004  Score=56.23  Aligned_cols=58  Identities=21%  Similarity=0.255  Sum_probs=37.2

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC-CHHHHHHHHHHhcCCC
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKGYP  246 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~~~  246 (695)
                      +.+|+.++|+.|+||||.+..++..  .+.+- ..+..+++.... ...+-++...+.++.+
T Consensus         9 ~~~vi~lvGp~GvGKTTTiaKLA~~--~~~~g-~kV~lit~Dt~R~gA~eQL~~~a~~l~v~   67 (207)
T d1ls1a2           9 DRNLWFLVGLQGSGKTTTAAKLALY--YKGKG-RRPLLVAADTQRPAAREQLRLLGEKVGVP   67 (207)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHH--HHHTT-CCEEEEECCSSCHHHHHHHHHHHHHHTCC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH--HHHCC-CcEEEEecccccchHHHHHHHHHHhcCCc
Confidence            3589999999999999887777663  33332 236666664332 3445566666666654

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=96.25  E-value=0.0039  Score=56.39  Aligned_cols=58  Identities=19%  Similarity=0.116  Sum_probs=33.2

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC-CHHHHHHHHHHhcCCC
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKGYP  246 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~~~  246 (695)
                      .+.||.++|+.|+||||.+..++..  .+.. ...+..+++.... ...+-++...+.++.+
T Consensus        11 ~p~vi~lvGptGvGKTTTiAKLA~~--~~~~-g~kV~lit~Dt~R~ga~eQL~~~a~~l~v~   69 (211)
T d1j8yf2          11 IPYVIMLVGVQGTGKATTAGKLAYF--YKKK-GFKVGLVGADVYRPAALEQLQQLGQQIGVP   69 (211)
T ss_dssp             SSEEEEEECSCCC----HHHHHHHH--HHHT-TCCEEEEECCCSSHHHHHHHHHHHHHHTCC
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH--HHHC-CCceEEEEeeccccchhHHHHHhccccCcc
Confidence            4789999999999999877666653  3222 2336677765433 3344455666666654

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.25  E-value=0.0073  Score=56.78  Aligned_cols=86  Identities=17%  Similarity=0.193  Sum_probs=56.8

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCC-----CCChHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPE-----FQTDEAAINDLE  261 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~-----~~~~~~~~~~l~  261 (695)
                      .+++-|+|+.|+||||+|..++....-.+   ..++|++....++.+.     ++++|.....     ....++..+.+.
T Consensus        60 g~i~e~~G~~~~GKT~l~l~~~~~~q~~g---~~~vyIDtE~~~~~e~-----a~~~GvD~d~il~~~~~~~E~~~~~~~  131 (269)
T d1mo6a1          60 GRVIEIYGPESSGKTTVALHAVANAQAAG---GVAAFIDAEHALDPDY-----AKKLGVDTDSLLVSQPDTGEQALEIAD  131 (269)
T ss_dssp             SSEEEEECSSSSSHHHHHHHHHHHHHHTT---CEEEEEESSCCCCHHH-----HHHHTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             ceeEEEecCCCcHHHHHHHHHHHHHhcCC---CEEEEEECCccCCHHH-----HHHhCCCHHHeEEecCCCHHHHHHHHH
Confidence            58999999999999999987776333222   2378999999988764     4555554322     123444444444


Q ss_pred             HHHHhcCCCcEEEEEeCCCCC
Q 042541          262 RFFKQMRIEAILLVLDDVWPG  282 (695)
Q Consensus       262 ~~~~~l~~~~~LlVlDdv~~~  282 (695)
                      .+.+  .++..|+|+|.+-..
T Consensus       132 ~l~~--~~~~~liIiDSi~al  150 (269)
T d1mo6a1         132 MLIR--SGALDIVVIDSVAAL  150 (269)
T ss_dssp             HHHH--TTCEEEEEEECSTTC
T ss_pred             HHHh--cCCCCEEEEeccccc
Confidence            4333  466789999998543

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.23  E-value=0.0011  Score=59.04  Aligned_cols=23  Identities=30%  Similarity=0.622  Sum_probs=20.9

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhcc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      +.|.|+|++|+|||||+++++..
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~   24 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEV   24 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHHHHHHH
Confidence            57999999999999999999873

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=96.15  E-value=0.007  Score=56.96  Aligned_cols=85  Identities=18%  Similarity=0.181  Sum_probs=56.7

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCC-----CCChHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPE-----FQTDEAAINDLE  261 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~-----~~~~~~~~~~l~  261 (695)
                      .+++-|+|++|+|||+||..++...  +.. ...++|++....++.+     +++.+|.....     ..+.++..+.+.
T Consensus        57 g~itei~G~~~sGKT~l~l~~~~~a--qk~-g~~v~yiDtE~~~~~~-----~a~~~Gvd~d~i~~~~~~~~E~~~~~~~  128 (268)
T d1xp8a1          57 GRITEIYGPESGGKTTLALAIVAQA--QKA-GGTCAFIDAEHALDPV-----YARALGVNTDELLVSQPDNGEQALEIME  128 (268)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHH--HHT-TCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             ceEEEEecCCccchHHHHHHHHHHH--HhC-CCEEEEEECCccCCHH-----HHHHhCCCchhEEEEcCCCHHHHHHHHH
Confidence            5799999999999999998887632  222 2348899999998874     56677765332     123444444444


Q ss_pred             HHHHhcCCCcEEEEEeCCCC
Q 042541          262 RFFKQMRIEAILLVLDDVWP  281 (695)
Q Consensus       262 ~~~~~l~~~~~LlVlDdv~~  281 (695)
                      .+++  .+..-|+|+|-+-.
T Consensus       129 ~l~~--~~~~~liIiDSi~a  146 (268)
T d1xp8a1         129 LLVR--SGAIDVVVVDSVAA  146 (268)
T ss_dssp             HHHT--TTCCSEEEEECTTT
T ss_pred             HHHh--cCCCcEEEEecccc
Confidence            3332  34566899999843

>d1io0a_ c.10.1.1 (A:) Tropomodulin C-terminal domain {Chicken (Gallus gallus) [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Tropomodulin C-terminal domain
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=96.15  E-value=0.0014  Score=57.51  Aligned_cols=116  Identities=14%  Similarity=0.079  Sum_probs=66.7

Q ss_pred             hcCCCCCcEEEEccc-CCCCcccCcc-cccccCCCCcEEEeccCCCCC-----cc-cccccccccEEeeccccCCcccc-
Q 042541          570 LQKMDELKVLIVTNY-GFSPAELNNF-RVLSALSKLKKIRLEHVSLPN-----SL-ATVRMNHLQKVSLVMCNVGQVFR-  640 (695)
Q Consensus       570 ~~~l~~Lr~L~l~~~-~~~~~~~~~~-~~l~~l~~L~~L~L~~~~l~~-----lp-~i~~l~~L~~L~l~~~~i~~~~~-  640 (695)
                      ..+.+.|+.|+++++ .+....+..+ ..+...++|+.|++++|.++.     +- .+...++|+.|++++|.+..-.- 
T Consensus        13 ~~~~~~L~~L~L~~~~~i~~~~~~~l~~al~~n~~L~~L~Ls~n~l~~~~~~~L~~~l~~~~~l~~l~l~~~~~~~~g~~   92 (166)
T d1io0a_          13 QNNDPDLEEVNLNNIMNIPVPTLKACAEALKTNTYVKKFSIVGTRSNDPVAFALAEMLKVNNTLKSLNVESNFISGSGIL   92 (166)
T ss_dssp             HTTCTTCCEEECTTCTTCCHHHHHHHHHHHTTCCSCCEEECTTSCCCHHHHHHHHHHHHHCSSCCEEECCSSCCCHHHHH
T ss_pred             HhcCCCCcEEEcCCCCCCCHHHHHHHHHHHhcCCccCeeeccCCcccHHHHHHHHHHHhhcccchhhhhccccccchhHH
Confidence            345677777877763 3433222221 224566778888888887752     22 44556778888888876653211 


Q ss_pred             cchhhhcccCCCccEEeccccc-ccc-----cCchhhcCCCCCceeeccccc
Q 042541          641 NSTFRISDAFPNLLEMDIDYCN-DLI-----ELPDGLCDIVSMEKLRITNCH  686 (695)
Q Consensus       641 ~~~~~l~~~l~~L~~L~l~~c~-~l~-----~lP~~i~~L~~L~~L~l~~~~  686 (695)
                      .+...+. ..++|+.++|+.|. .++     .+...+.+.++|++|+++.+.
T Consensus        93 ~l~~~l~-~~~~L~~l~L~l~~n~i~~~~~~~La~~L~~n~~L~~L~l~~~~  143 (166)
T d1io0a_          93 ALVEALQ-SNTSLIELRIDNQSQPLGNNVEMEIANMLEKNTTLLKFGYHFTQ  143 (166)
T ss_dssp             HHHHGGG-GCSSCCEEECCCCSSCCCHHHHHHHHHHHHHCSSCCEEECCCSS
T ss_pred             HHHHHHH-hCccccEEeeccCCCcCcHHHHHHHHHHHHhCCCcCEEeCcCCC
Confidence            1111112 56778776665442 222     244556677888888887643

>d1pgva_ c.10.1.1 (A:) Tropomodulin C-terminal domain {nematode (Caenorhabditis elegans) [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Tropomodulin C-terminal domain
species: nematode (Caenorhabditis elegans) [TaxId: 6239]

Probab=96.09  E-value=0.0014  Score=57.42  Aligned_cols=113  Identities=13%  Similarity=0.153  Sum_probs=75.0

Q ss_pred             CCceEEEEEEccC-cc----ccCChhhcCCCCCcEEEEcccCCCCcccCcc-cccccCCCCcEEEeccCCCCC-----cc
Q 042541          549 GPEVKVVVLNIRT-KK----YVLPDFLQKMDELKVLIVTNYGFSPAELNNF-RVLSALSKLKKIRLEHVSLPN-----SL  617 (695)
Q Consensus       549 ~~~l~~L~l~~~~-~~----~~~p~~~~~l~~Lr~L~l~~~~~~~~~~~~~-~~l~~l~~L~~L~L~~~~l~~-----lp  617 (695)
                      .+.|+.|.|+.+. ..    ..+-..+...++|+.|++++|.+.......+ ..+...+.|+.|+|++|.+..     +.
T Consensus        14 ~~~L~~L~L~~~~~i~~~~~~~l~~~L~~n~~L~~L~Ls~n~l~~~~~~~la~~L~~n~~L~~L~L~~n~i~~~g~~~l~   93 (167)
T d1pgva_          14 DTDLKEVNINNMKRVSKERIRSLIEAACNSKHIEKFSLANTAISDSEARGLIELIETSPSLRVLNVESNFLTPELLARLL   93 (167)
T ss_dssp             CSSCCEEECTTCCSSCHHHHHHHHHHHTTCSCCCEEECTTSCCBHHHHTTHHHHHHHCSSCCEEECCSSBCCHHHHHHHH
T ss_pred             CCCCcEEEeCCCCCCCHHHHHHHHHHHhhCCccceeeccccccchhHHHHHhhhhhhcccccceeeehhhcchHHHHHHH
Confidence            4667777776532 21    1244467788899999999987754333332 235667889999999999873     33


Q ss_pred             -cccccccccEEeeccccCCcccccchhhhc---ccCCCccEEecccc
Q 042541          618 -ATVRMNHLQKVSLVMCNVGQVFRNSTFRIS---DAFPNLLEMDIDYC  661 (695)
Q Consensus       618 -~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~---~~l~~L~~L~l~~c  661 (695)
                       .+..-+.|++|+|++|.+..+-......+.   ..-++|+.|+++++
T Consensus        94 ~aL~~n~sL~~L~l~~n~~~~~g~~~~~~l~~~L~~n~sL~~l~l~~~  141 (167)
T d1pgva_          94 RSTLVTQSIVEFKADNQRQSVLGNQVEMDMMMAIEENESLLRVGISFA  141 (167)
T ss_dssp             HHTTTTCCCSEEECCCCSSCCCCHHHHHHHHHHHHHCSSCCEEECCCC
T ss_pred             HHHHhCCcCCEEECCCCcCCCccHHHHHHHHHHHHhCCCccEeeCcCC
Confidence             566678899999999876554322111111   14678999999875

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.09  E-value=0.0012  Score=59.43  Aligned_cols=31  Identities=19%  Similarity=0.073  Sum_probs=25.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCC
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKD  219 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~  219 (695)
                      ..+|.++|++|+||||+|+.+..  +....+..
T Consensus        19 g~vI~L~G~pGSGKTTiAk~La~--~l~~~~~~   49 (195)
T d1x6va3          19 GCTVWLTGLSGAGKTTVSMALEE--YLVCHGIP   49 (195)
T ss_dssp             CEEEEEESSCHHHHHHHHHHHHH--HHHHTTCC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH--HHHhcCCC
Confidence            46899999999999999999987  55544444

>d1qf9a_ c.37.1.1 (A:) UMP/CMP kinase {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Dictyostelium discoideum [TaxId: 44689]

Probab=96.08  E-value=0.0015  Score=58.84  Aligned_cols=25  Identities=20%  Similarity=0.282  Sum_probs=22.7

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +.+.+|.|+|++|+||||+|+.+++
T Consensus         4 ~kp~iI~i~G~pGSGKsT~a~~La~   28 (194)
T d1qf9a_           4 SKPNVVFVLGGPGSGKGTQCANIVR   28 (194)
T ss_dssp             CCCEEEEEEESTTSSHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHH
Confidence            4578999999999999999999886

>d2jdid3 c.37.1.11 (D:82-357) Central domain of beta subunit of F1 ATP synthase {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of beta subunit of F1 ATP synthase
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=96.05  E-value=0.023  Score=53.14  Aligned_cols=102  Identities=13%  Similarity=0.147  Sum_probs=59.9

Q ss_pred             HHHHHHH-cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC-CHHHHHHHHHHhcCCC--------
Q 042541          177 ELKMELF-KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKGYP--------  246 (695)
Q Consensus       177 ~l~~~L~-~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~~~--------  246 (695)
                      +.++.+. -...+-++|.|..|+|||+|+..+.++. .+.+=+. ++++-+++.. ...++.+++.+.--..        
T Consensus        57 raID~l~pigkGQr~~If~~~g~GKt~l~~~i~~~~-~~~~~~v-~V~~~iGer~~ev~~~~~~~~~~~~~~~~~~~~~t  134 (276)
T d2jdid3          57 KVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNV-AKAHGGY-SVFAGVGERTREGNDLYHEMIESGVINLKDATSKV  134 (276)
T ss_dssp             HHHHHHSCEETTCEEEEEECTTSSHHHHHHHHHHHH-TTTCSSE-EEEEEESCCHHHHHHHHHHHHHHTSSCSSSSCCCE
T ss_pred             eeeeeeccccCCCEEEeeCCCCCCHHHHHHHHHHHH-HhhCCCe-EEEEEeccChHHHHHHHHHHHhcCccccccccceE
Confidence            4556555 2334669999999999999999988731 2223233 5688888764 4667777777641100        


Q ss_pred             -----CCCCCChHH-----HHHHHHHHHHhcCCCcEEEEEeCCC
Q 042541          247 -----VPEFQTDEA-----AINDLERFFKQMRIEAILLVLDDVW  280 (695)
Q Consensus       247 -----~~~~~~~~~-----~~~~l~~~~~~l~~~~~LlVlDdv~  280 (695)
                           ....+....     ..-.+.+.+..-+++++|+++||+.
T Consensus       135 vvv~~~s~~~~~~r~~~~~~a~~iAEyf~~~~G~~VLv~~Dslt  178 (276)
T d2jdid3         135 ALVYGQMNEPPGARARVALTGLTVAEYFRDQEGQDVLLFIDNIF  178 (276)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHHHHHHHHTTCSCEEEEEECTH
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHHHHHhcCCCeEEEEEcchh
Confidence                 001111111     1112333333335899999999983

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=96.05  E-value=0.0012  Score=57.89  Aligned_cols=22  Identities=36%  Similarity=0.490  Sum_probs=19.7

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..|.|.|++|+||||+|+.++.
T Consensus         5 ~~I~i~G~pGsGKTTia~~La~   26 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGKELAS   26 (173)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
Confidence            4578999999999999999986

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=96.05  E-value=0.0016  Score=57.02  Aligned_cols=25  Identities=16%  Similarity=0.368  Sum_probs=22.6

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+.+++.|.|++|+||||+|+.+..
T Consensus         4 ~~~~iivl~G~~GsGKsT~a~~La~   28 (171)
T d1knqa_           4 HDHHIYVLMGVSGSGKSAVASEVAH   28 (171)
T ss_dssp             TTSEEEEEECSTTSCHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHH
Confidence            3578999999999999999999986

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=96.04  E-value=0.0021  Score=62.57  Aligned_cols=44  Identities=25%  Similarity=0.313  Sum_probs=34.6

Q ss_pred             CCCCCCcchHHHHHHHHH--------------cCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          166 VISPGLDVPLKELKMELF--------------KDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~--------------~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..++|-++.++.+...+.              ....+-+.++||+|+|||.||+.+++
T Consensus        14 ~~ViGQd~A~~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GPpG~GKT~lAkalA~   71 (309)
T d1ofha_          14 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAK   71 (309)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHH
T ss_pred             CcccChHHHHHHHHHHHHHHHHHhccCCCCccCCCCceEEEECCCCCCHHHHHHHHhh
Confidence            356899988888876552              11346678999999999999999987

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=96.00  E-value=0.0024  Score=60.82  Aligned_cols=23  Identities=22%  Similarity=0.346  Sum_probs=21.5

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ++.|.++|++|+||||||+.+++
T Consensus        32 P~~ilL~GpPGtGKT~la~~la~   54 (273)
T d1gvnb_          32 PTAFLLGGQPGSGKTSLRSAIFE   54 (273)
T ss_dssp             CEEEEEECCTTSCTHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH
Confidence            67799999999999999999987

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=96.00  E-value=0.0014  Score=57.71  Aligned_cols=23  Identities=22%  Similarity=0.401  Sum_probs=21.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .++|.|.|++|+||||+|+.+.+
T Consensus         3 ~kiI~l~G~~GsGKsTva~~L~~   25 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRCLQS   25 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            47899999999999999999887

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

Probab=95.99  E-value=0.0026  Score=61.42  Aligned_cols=72  Identities=21%  Similarity=0.222  Sum_probs=43.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChHHHHHHHHHHHHh
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDEAAINDLERFFKQ  266 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~l~~~~~~  266 (695)
                      ..++.++|++|+|||.||+.++.  .+...+..  +-++.++-.+          .         -..+....++.+++.
T Consensus       123 ~g~~l~~G~pG~GKT~la~ala~--~~~~~~~~--~~~~~~~~~~----------~---------~~G~~e~~~~~~f~~  179 (321)
T d1w44a_         123 SGMVIVTGKGNSGKTPLVHALGE--ALGGKDKY--ATVRFGEPLS----------G---------YNTDFNVFVDDIARA  179 (321)
T ss_dssp             SEEEEEECSSSSCHHHHHHHHHH--HHHTTSCC--EEEEBSCSST----------T---------CBCCHHHHHHHHHHH
T ss_pred             CceEEEECCCCccHHHHHHHHHH--HhcCCCCe--EEEEhhHhhh----------c---------ccchHHHHHHHHHHH
Confidence            35667799999999999999998  55444432  2344444321          0         011123344555533


Q ss_pred             cCCCcEEEEEeCCCCC
Q 042541          267 MRIEAILLVLDDVWPG  282 (695)
Q Consensus       267 l~~~~~LlVlDdv~~~  282 (695)
                      .+ ++++|++|.++..
T Consensus       180 a~-~~~ilf~DEid~~  194 (321)
T d1w44a_         180 ML-QHRVIVIDSLKNV  194 (321)
T ss_dssp             HH-HCSEEEEECCTTT
T ss_pred             Hh-hccEEEeehhhhh
Confidence            33 3679999999654

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, ATPase-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Escherichia coli [TaxId: 562]

Probab=95.90  E-value=0.0098  Score=55.83  Aligned_cols=84  Identities=17%  Similarity=0.208  Sum_probs=54.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCC-----CCChHHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPE-----FQTDEAAINDLE  261 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~-----~~~~~~~~~~l~  261 (695)
                      .+++-|+|++|+||||||.+++...  +.. ...++|++....++..     .++.++.....     ....++..+.+.
T Consensus        54 g~itei~G~~gsGKTtl~l~~~~~~--q~~-g~~~vyidtE~~~~~~-----~a~~~Gvd~d~v~~~~~~~~E~~~~~i~  125 (263)
T d1u94a1          54 GRIVEIYGPESSGKTTLTLQVIAAA--QRE-GKTCAFIDAEHALDPI-----YARKLGVDIDNLLCSQPDTGEQALEICD  125 (263)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHH--HHT-TCCEEEEESSCCCCHH-----HHHHTTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             ceEEEEecCCCcHHHHHHHHHHHHH--HcC-CCEEEEEccccccCHH-----HHHHhCCCHHHEEEecCCCHHHHHHHHH
Confidence            4799999999999999998888743  222 2237899999988864     35566654322     123444444444


Q ss_pred             HHHHhcCCCcEEEEEeCCC
Q 042541          262 RFFKQMRIEAILLVLDDVW  280 (695)
Q Consensus       262 ~~~~~l~~~~~LlVlDdv~  280 (695)
                      .+.+.  ++.-|+|+|.+-
T Consensus       126 ~l~~~--~~~~liViDSi~  142 (263)
T d1u94a1         126 ALARS--GAVDVIVVDSVA  142 (263)
T ss_dssp             HHHHH--TCCSEEEEECGG
T ss_pred             HHHhc--CCCCEEEEECcc
Confidence            44432  445588899873

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.89  E-value=0.0015  Score=57.18  Aligned_cols=20  Identities=40%  Similarity=0.532  Sum_probs=17.6

Q ss_pred             EEEEcCCCCcHHHHHHHHhc
Q 042541          190 IVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~  209 (695)
                      |.++|++|+||||+++.+++
T Consensus         4 IvliG~~G~GKSTig~~La~   23 (165)
T d2iyva1           4 AVLVGLPGSGKSTIGRRLAK   23 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            44669999999999999987

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=95.85  E-value=0.0022  Score=56.44  Aligned_cols=23  Identities=26%  Similarity=0.507  Sum_probs=21.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .++|.|.|++|+||||+|+.+.+
T Consensus         4 g~iI~l~G~~GsGKSTia~~La~   26 (176)
T d1zp6a1           4 GNILLLSGHPGSGKSTIAEALAN   26 (176)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            57999999999999999998875

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=95.85  E-value=0.0018  Score=57.53  Aligned_cols=22  Identities=32%  Similarity=0.351  Sum_probs=20.9

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ++|+|.|+.|+||||+++.+..
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~   23 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMD   23 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
Confidence            7899999999999999999987

>d1ihua2 c.37.1.10 (A:308-586) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=95.81  E-value=0.0051  Score=58.71  Aligned_cols=53  Identities=21%  Similarity=0.342  Sum_probs=39.3

Q ss_pred             hHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCC
Q 042541          174 PLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKN  229 (695)
Q Consensus       174 ~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~  229 (695)
                      ++..+.+.+...+.++|.+.|-||+||||+|..++.  ..... ..+++-|+....
T Consensus         7 ~~~~~~~~~~~~~~~iii~sGKGGVGKTT~a~nLA~--~lA~~-G~rVllvD~Dp~   59 (279)
T d1ihua2           7 SLSALVDDIARNEHGLIMLMGKGGVGKTTMAAAIAV--RLADM-GFDVHLTTSDPA   59 (279)
T ss_dssp             CHHHHHHHHHTTSCEEEEEECSTTSSHHHHHHHHHH--HHHHT-TCCEEEEESCCC
T ss_pred             cHHHHHHHhhcCCCEEEEEECCCCCCHHHHHHHHHH--HHHHC-CCcEEEEeCCCC
Confidence            456777888888899999999999999999877765  23222 223777877654

>d1m7ga_ c.37.1.4 (A:) Adenosine-5'phosphosulfate kinase (APS kinase) {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=95.79  E-value=0.0033  Score=57.14  Aligned_cols=28  Identities=25%  Similarity=0.204  Sum_probs=24.5

Q ss_pred             HHcCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          182 LFKDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       182 L~~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .......+|.+.|++|+||||||+++..
T Consensus        19 ~~~~kg~vIwltGlsGsGKTTia~~L~~   46 (208)
T d1m7ga_          19 LRNQRGLTIWLTGLSASGKSTLAVELEH   46 (208)
T ss_dssp             HHTSSCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             HhCCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            3456678999999999999999999986

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.78  E-value=0.0024  Score=57.52  Aligned_cols=25  Identities=36%  Similarity=0.405  Sum_probs=22.6

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +..++|.|.|++|+||||+|+.+++
T Consensus         6 ~~~~iI~i~GppGSGKsT~a~~La~   30 (196)
T d1ukza_           6 DQVSVIFVLGGPGAGKGTQCEKLVK   30 (196)
T ss_dssp             TTCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHH
Confidence            3578999999999999999999976

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=95.72  E-value=0.0025  Score=55.88  Aligned_cols=24  Identities=21%  Similarity=0.371  Sum_probs=21.2

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..-.|.|.|++|+||||+|+.+++
T Consensus         4 k~~~I~i~G~~GsGKTT~~~~La~   27 (174)
T d1y63a_           4 KGINILITGTPGTGKTSMAEMIAA   27 (174)
T ss_dssp             SSCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHH
Confidence            345799999999999999999986

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=95.72  E-value=0.0019  Score=56.40  Aligned_cols=22  Identities=27%  Similarity=0.253  Sum_probs=20.7

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ++++|+|..|+|||||+.++..
T Consensus         2 kii~I~G~~gSGKTTli~~l~~   23 (165)
T d1xjca_           2 NVWQVVGYKHSGKTTLMEKWVA   23 (165)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHH
Confidence            6899999999999999999987

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=95.64  E-value=0.002  Score=55.99  Aligned_cols=20  Identities=45%  Similarity=0.502  Sum_probs=18.6

Q ss_pred             EEEEcCCCCcHHHHHHHHhc
Q 042541          190 IVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~  209 (695)
                      |.|+||+|+||||+++.++.
T Consensus         3 I~liG~~GsGKsTi~k~La~   22 (161)
T d1viaa_           3 IVFIGFMGSGKSTLARALAK   22 (161)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            67889999999999999987

>d1bifa1 c.37.1.7 (A:37-249) 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
domain: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=95.63  E-value=0.0028  Score=57.74  Aligned_cols=23  Identities=26%  Similarity=0.392  Sum_probs=20.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +.+|.++|.+|+||||+|+++++
T Consensus         2 p~li~l~GlpgsGKSTla~~L~~   24 (213)
T d1bifa1           2 PTLIVMVGLPARGKTYISKKLTR   24 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH
Confidence            35799999999999999999987

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=95.60  E-value=0.0074  Score=56.09  Aligned_cols=40  Identities=20%  Similarity=0.323  Sum_probs=31.6

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCC
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKN  229 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~  229 (695)
                      ..++.|+|.+|+|||++|.+++.  ....+... ++|+++...
T Consensus        26 gsl~li~G~pGsGKT~l~~qia~--~~~~~~~~-~~~is~e~~   65 (242)
T d1tf7a2          26 DSIILATGATGTGKTLLVSRFVE--NACANKER-AILFAYEES   65 (242)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHH--HHHTTTCC-EEEEESSSC
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHH--HHHHhccc-cceeeccCC
Confidence            57999999999999999999987  34444454 778887653

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Erwinia chrysanthemi [TaxId: 556]

Probab=95.50  E-value=0.0025  Score=55.91  Aligned_cols=22  Identities=27%  Similarity=0.400  Sum_probs=19.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +.|.++|++|+||||+|+.+++
T Consensus         3 ~~Iil~G~~GsGKSTia~~LA~   24 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGRELAR   24 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHHHHHH
Confidence            3467889999999999999987

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=95.49  E-value=0.0028  Score=55.85  Aligned_cols=20  Identities=40%  Similarity=0.767  Sum_probs=19.0

Q ss_pred             EEEEcCCCCcHHHHHHHHhc
Q 042541          190 IVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~  209 (695)
                      |+|+|++|+|||||++.+..
T Consensus         3 i~I~G~~G~GKSTLl~~i~~   22 (178)
T d1ye8a1           3 IIITGEPGVGKTTLVKKIVE   22 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcHHHHHHHHHHh
Confidence            78999999999999999987

>d1nksa_ c.37.1.1 (A:) Adenylate kinase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=95.42  E-value=0.0054  Score=54.52  Aligned_cols=26  Identities=19%  Similarity=0.374  Sum_probs=22.5

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhccccccc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKDDQVQG  215 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~~~~~~  215 (695)
                      ++|.|.|+.|+||||+++.+.+  +...
T Consensus         2 kiivi~G~~GsGKTT~~~~La~--~L~~   27 (194)
T d1nksa_           2 KIGIVTGIPGVGKSTVLAKVKE--ILDN   27 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHH--HHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHH--HHHH
Confidence            6899999999999999999987  4543

>d1teva_ c.37.1.1 (A:) UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.29  E-value=0.0043  Score=55.63  Aligned_cols=23  Identities=26%  Similarity=0.319  Sum_probs=21.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +.+|.|.|++|+||||.|+.+++
T Consensus         1 p~iI~i~GppGSGKsT~a~~La~   23 (194)
T d1teva_           1 PLVVFVLGGPGAGKGTQCARIVE   23 (194)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999986

>d1ckea_ c.37.1.1 (A:) CMP kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Escherichia coli [TaxId: 562]

Probab=95.18  E-value=0.0044  Score=56.85  Aligned_cols=23  Identities=30%  Similarity=0.586  Sum_probs=21.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+||+|.|++|+||||+|+.+.+
T Consensus         3 ~piI~I~GppGSGKgT~ak~La~   25 (225)
T d1ckea_           3 APVITIDGPSGAGKGTLCKAMAE   25 (225)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            46999999999999999999887

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Uridine-cytidine kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.10  E-value=0.0054  Score=55.91  Aligned_cols=23  Identities=22%  Similarity=0.329  Sum_probs=20.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +-+|+|.|..|+||||+|+.+.+
T Consensus         2 P~iIgI~G~~gSGKSTla~~L~~   24 (213)
T d1uj2a_           2 PFLIGVSGGTASGKSSVCAKIVQ   24 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999998876

>d1xpua3 c.37.1.11 (A:129-417) Transcription termination factor Rho, ATPase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Transcription termination factor Rho, ATPase domain
species: Escherichia coli [TaxId: 562]

Probab=94.87  E-value=0.012  Score=55.46  Aligned_cols=34  Identities=24%  Similarity=0.160  Sum_probs=27.6

Q ss_pred             HHHHHHH-cCCceEEEEEcCCCCcHHHHHHHHhcc
Q 042541          177 ELKMELF-KDGRQFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       177 ~l~~~L~-~~~~~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      ++++.+. -...+-++|.|..|+|||+|+..+.+.
T Consensus        32 r~ID~l~PigrGQr~~I~g~~g~GKT~l~~~i~~~   66 (289)
T d1xpua3          32 RVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQS   66 (289)
T ss_dssp             HHHHHHSCCBTTCEEEEEECSSSSHHHHHHHHHHH
T ss_pred             eeeeecccccCCCeeeEeCCCCCCHHHHHHHHHHH
Confidence            5667766 334578999999999999999999874

>d1ihua1 c.37.1.10 (A:1-296) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=94.81  E-value=0.012  Score=56.57  Aligned_cols=48  Identities=17%  Similarity=0.336  Sum_probs=34.1

Q ss_pred             cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHH
Q 042541          184 KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKA  234 (695)
Q Consensus       184 ~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~  234 (695)
                      +..+++|.+.|-||+||||+|..++.  ....+ ..+++.|++....+...
T Consensus         5 ~~~p~~i~~sGKGGVGKTTvaa~lA~--~lA~~-G~rVLlvD~Dp~~~l~~   52 (296)
T d1ihua1           5 QNIPPYLFFTGKGGVGKTSISCATAI--RLAEQ-GKRVLLVSTDPASNVGQ   52 (296)
T ss_dssp             SSCCSEEEEECSTTSSHHHHHHHHHH--HHHHT-TCCEEEEECCTTCCHHH
T ss_pred             CCCCeEEEEECCCcChHHHHHHHHHH--HHHHC-CCCEEEEeCCCCCCHHH
Confidence            44578999999999999999988776  33322 22477888776555443

>d1lvga_ c.37.1.1 (A:) Guanylate kinase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.78  E-value=0.005  Score=55.04  Aligned_cols=21  Identities=43%  Similarity=0.763  Sum_probs=19.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .|+|+|++|+|||||++.+..
T Consensus         2 pIvl~GPsGsGK~tl~~~L~~   22 (190)
T d1lvga_           2 PVVLSGPSGAGKSTLLKKLFQ   22 (190)
T ss_dssp             CEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHH
Confidence            477999999999999999876

>d2qm8a1 c.37.1.10 (A:5-327) Metallochaperone MeaB {Methylobacterium extorquens [TaxId: 408]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Metallochaperone MeaB
species: Methylobacterium extorquens [TaxId: 408]

Probab=94.75  E-value=0.012  Score=56.99  Aligned_cols=55  Identities=16%  Similarity=0.173  Sum_probs=36.2

Q ss_pred             HHHHHHHHH--cCCceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC
Q 042541          175 LKELKMELF--KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP  230 (695)
Q Consensus       175 ~~~l~~~L~--~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~  230 (695)
                      ..++.+.+.  .+...+|+|.|++|+|||||.-++... .....+...|+-++.+..+
T Consensus        37 ~~~~~~~~~~~~~~~~~igitG~pGaGKSTli~~l~~~-~~~~g~~vaViavDpss~~   93 (323)
T d2qm8a1          37 VRDLIDAVLPQTGRAIRVGITGVPGVGKSTTIDALGSL-LTAAGHKVAVLAVDPSSTR   93 (323)
T ss_dssp             HHHHHHHHGGGCCCSEEEEEECCTTSCHHHHHHHHHHH-HHHTTCCEEEEEECGGGGS
T ss_pred             HHHHHHHhhhccCCceEEeeeCCCCCCHHHHHHHHHHH-HhhcCCceeeeecccccHH
Confidence            344444443  456789999999999999999988762 1233445445555555444

>d1gkya_ c.37.1.1 (A:) Guanylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.75  E-value=0.0054  Score=54.58  Aligned_cols=22  Identities=45%  Similarity=0.761  Sum_probs=19.8

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +.|.|+|++|+|||||++.+.+
T Consensus         2 rpIvl~GpsG~GK~tl~~~L~~   23 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLLKKLFA   23 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHH
Confidence            4578999999999999999877

>d1kgda_ c.37.1.1 (A:) Guanylate kinase-like domain of Cask {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase-like domain of Cask
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.66  E-value=0.0072  Score=53.27  Aligned_cols=29  Identities=17%  Similarity=0.371  Sum_probs=23.1

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhccccccccCC
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKDDQVQGKFK  218 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~  218 (695)
                      +.|.|+|++|+|||||++.+..  +....|.
T Consensus         4 k~ivl~Gpsg~GK~tl~~~L~~--~~~~~~~   32 (178)
T d1kgda_           4 KTLVLLGAHGVGRRHIKNTLIT--KHPDRFA   32 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH--HCTTTEE
T ss_pred             CcEEEECCCCCCHHHHHHHHHH--hCCcCee
Confidence            6799999999999999998886  3334443

>d3adka_ c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=94.64  E-value=0.0078  Score=53.88  Aligned_cols=24  Identities=25%  Similarity=0.390  Sum_probs=21.8

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..++|.|.|++|+||||+|+.+++
T Consensus         7 ~~~iI~l~G~pGSGKsT~a~~La~   30 (194)
T d3adka_           7 KSKIIFVVGGPGSGKGTQCEKIVQ   30 (194)
T ss_dssp             TSCEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            358999999999999999999876

>d1zaka1 c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Maize (Zea mays) [TaxId: 4577]

Probab=94.63  E-value=0.0068  Score=54.02  Aligned_cols=23  Identities=17%  Similarity=0.164  Sum_probs=20.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +-.|.|.|++|+||||+|+.+++
T Consensus         3 Pm~I~i~GppGsGKsT~a~~La~   25 (189)
T d1zaka1           3 PLKVMISGAPASGKGTQCELIKT   25 (189)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            44578999999999999998876

>d1znwa1 c.37.1.1 (A:20-201) Guanylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=94.54  E-value=0.0081  Score=53.15  Aligned_cols=22  Identities=36%  Similarity=0.626  Sum_probs=20.2

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ++|.|+|++|+|||||++.+..
T Consensus         3 ~iivl~GpsG~GK~tl~~~L~~   24 (182)
T d1znwa1           3 RVVVLSGPSAVGKSTVVRCLRE   24 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            6899999999999999998876

>d1cp2a_ c.37.1.10 (A:) Nitrogenase iron protein {Clostridium pasteurianum [TaxId: 1501]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Clostridium pasteurianum [TaxId: 1501]

Probab=94.49  E-value=0.017  Score=54.63  Aligned_cols=38  Identities=24%  Similarity=0.370  Sum_probs=29.2

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCC
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSK  228 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~  228 (695)
                      +.|+|+|-||+||||+|..++.  ..... ..+++-|++..
T Consensus         2 r~Iai~gKGGvGKTT~a~nLA~--~LA~~-G~rVllID~D~   39 (269)
T d1cp2a_           2 RQVAIYGKGGIGKSTTTQNLTS--GLHAM-GKTIMVVGCDP   39 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHH--HHHTT-TCCEEEEEECT
T ss_pred             CEEEEECCCcCCHHHHHHHHHH--HHHhC-CCcEEEEecCC
Confidence            6799999999999999988876  33332 33478888864

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=94.45  E-value=0.0081  Score=53.00  Aligned_cols=20  Identities=25%  Similarity=0.403  Sum_probs=18.6

Q ss_pred             EEEEcCCCCcHHHHHHHHhc
Q 042541          190 IVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~  209 (695)
                      |.|.|++|+||||+|+.++.
T Consensus         3 I~i~G~pGSGKsT~a~~La~   22 (182)
T d1zina1           3 LVLMGLPGAGKGTQAEKIVA   22 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            77999999999999999876

>d2p67a1 c.37.1.10 (A:1-327) LAO/AO transport system kinase ArgK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: LAO/AO transport system kinase ArgK
species: Escherichia coli [TaxId: 562]

Probab=94.45  E-value=0.017  Score=56.06  Aligned_cols=62  Identities=16%  Similarity=0.136  Sum_probs=32.5

Q ss_pred             HHHHHHHH--cCCceEEEEEcCCCCcHHHHHHHHhcccccccc-CCCcEEEEEeCCCCCHHHHHHHH
Q 042541          176 KELKMELF--KDGRQFIVVSAPGGYGKTTLVQRLCKDDQVQGK-FKDDIFYVTVSKNPNVKAIVQKV  239 (695)
Q Consensus       176 ~~l~~~L~--~~~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~-f~~~~~wv~~~~~~~~~~~~~~i  239 (695)
                      .++...+.  .++..+|+|+|++|+|||||...+...  .... ...+++-++.+..++--.++..-
T Consensus        41 ~~ll~~~~~~~~~~~~IgitG~pGaGKSTLi~~l~~~--~~~~g~~vavlavDpss~~~ggailgdr  105 (327)
T d2p67a1          41 TQLLDAIMPYCGNTLRLGVTGTPGAGKSTFLEAFGML--LIREGLKVAVIAVDPSSPVTGGSILGDK  105 (327)
T ss_dssp             HHHHHHHGGGCSCSEEEEEEECTTSCHHHHHHHHHHH--HHHTTCCEEEEEECCC------------
T ss_pred             HHHHHHhhhccCCceEEEeeCCCCCCHHHHHHHHHHH--HHhcCCceeeecCCCceeeeccccccch
Confidence            34444444  456899999999999999999888763  2222 23334444444444444454443

>d1q3ta_ c.37.1.1 (A:) CMP kinase {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=94.35  E-value=0.0092  Score=54.64  Aligned_cols=21  Identities=29%  Similarity=0.532  Sum_probs=19.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +|+|-|++|+||||+|+.++.
T Consensus         5 ~IaIdGp~GsGKgT~ak~La~   25 (223)
T d1q3ta_           5 QIAIDGPASSGKSTVAKIIAK   25 (223)
T ss_dssp             EEEEECSSCSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            688999999999999999887

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=94.32  E-value=0.011  Score=52.59  Aligned_cols=22  Identities=32%  Similarity=0.468  Sum_probs=18.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .++| |.|++|+||||+|+.++.
T Consensus         4 ~rii-l~G~pGSGKsT~a~~La~   25 (190)
T d1ak2a1           4 VRAV-LLGPPGAGKGTQAPKLAK   25 (190)
T ss_dssp             CEEE-EECCTTSSHHHHHHHHHH
T ss_pred             cEEE-EECCCCCCHHHHHHHHHH
Confidence            4555 789999999999999886

>d2cdna1 c.37.1.1 (A:1-181) Adenylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=94.23  E-value=0.0098  Score=52.47  Aligned_cols=20  Identities=30%  Similarity=0.536  Sum_probs=18.6

Q ss_pred             EEEEcCCCCcHHHHHHHHhc
Q 042541          190 IVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~  209 (695)
                      |.|.|++|+||||+|+.+++
T Consensus         3 I~i~G~pGsGKsT~a~~La~   22 (181)
T d2cdna1           3 VLLLGPPGAGKGTQAVKLAE   22 (181)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            78889999999999999987

>d1uf9a_ c.37.1.1 (A:) Dephospho-CoA kinase {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Thermus thermophilus [TaxId: 274]

Probab=94.14  E-value=0.011  Score=52.62  Aligned_cols=22  Identities=27%  Similarity=0.280  Sum_probs=19.5

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHh
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLC  208 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~  208 (695)
                      +-+|+|+|+.|+||||+|..+-
T Consensus         3 p~IIgitG~~gSGKstva~~l~   24 (191)
T d1uf9a_           3 PIIIGITGNIGSGKSTVAALLR   24 (191)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHH
Confidence            4689999999999999998764

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=94.13  E-value=0.011  Score=52.74  Aligned_cols=21  Identities=29%  Similarity=0.384  Sum_probs=18.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .|.|.|++|+||||+|+.++.
T Consensus         8 rIiliG~PGSGKtT~a~~La~   28 (189)
T d2ak3a1           8 RAAIMGAPGSGKGTVSSRITK   28 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHH
Confidence            466789999999999999886

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=94.12  E-value=0.0082  Score=58.94  Aligned_cols=43  Identities=23%  Similarity=0.192  Sum_probs=31.8

Q ss_pred             CCCCCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHh
Q 042541          166 VISPGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLC  208 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~  208 (695)
                      ..++|.+..+..|.-.+...+..-|.|+|.+|+||||||+.+.
T Consensus         7 ~~I~Gq~~~kral~laa~~~~~h~vLl~G~pG~GKT~lar~~~   49 (333)
T d1g8pa_           7 SAIVGQEDMKLALLLTAVDPGIGGVLVFGDRGTGKSTAVRALA   49 (333)
T ss_dssp             GGSCSCHHHHHHHHHHHHCGGGCCEEEECCGGGCTTHHHHHHH
T ss_pred             hhccCcHHHHHHHHHHHhccCCCeEEEECCCCccHHHHHHHHH
Confidence            3569998766655544433333568999999999999999875

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus globisporus [TaxId: 1459]

Probab=94.12  E-value=0.011  Score=52.34  Aligned_cols=21  Identities=33%  Similarity=0.398  Sum_probs=19.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .|.|.|++|+||||+|+.++.
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~   22 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQADRIVE   22 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            377999999999999999987

>d2vp4a1 c.37.1.1 (A:12-208) Deoxyribonucleoside kinase {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyribonucleoside kinase
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=93.96  E-value=0.013  Score=52.30  Aligned_cols=24  Identities=25%  Similarity=0.299  Sum_probs=21.2

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+-+|+|-|..|+||||+++.+.+
T Consensus         8 kp~~I~ieG~~GsGKTTl~~~L~~   31 (197)
T d2vp4a1           8 QPFTVLIEGNIGSGKTTYLNHFEK   31 (197)
T ss_dssp             CCEEEEEECSTTSCHHHHHHTTGG
T ss_pred             CceEEEEECCCCCCHHHHHHHHHH
Confidence            356899999999999999998875

>d4tmka_ c.37.1.1 (A:) Thymidylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Escherichia coli [TaxId: 562]

Probab=93.95  E-value=0.072  Score=47.85  Aligned_cols=51  Identities=18%  Similarity=0.354  Sum_probs=31.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhcccccccc-CCCcEEEEEeCCCCCHHHHHHHHHH
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKDDQVQGK-FKDDIFYVTVSKNPNVKAIVQKVLH  241 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~~~~~~~-f~~~~~wv~~~~~~~~~~~~~~i~~  241 (695)
                      +.|+|-|+.|+||||+++.+.+  .+... +.. +.+..-.......+.+++...
T Consensus         3 kfIviEG~dGsGKsT~~~~L~~--~L~~~g~~~-~~~~~ep~~~~~g~~i~~~~~   54 (210)
T d4tmka_           3 KYIVIEGLEGAGKTTARNVVVE--TLEQLGIRD-MVFTREPGGTQLAEKLRSLLL   54 (210)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHH--HHHHTTCCC-EEEEESSCSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHH--HHHhCCCCe-EEEecCCCCccchhhhHHHHh
Confidence            5789999999999999999887  44333 333 434333322333444444443

>d1io0a_ c.10.1.1 (A:) Tropomodulin C-terminal domain {Chicken (Gallus gallus) [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
superfamily: RNI-like
family: 28-residue LRR
domain: Tropomodulin C-terminal domain
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=93.86  E-value=0.016  Score=50.20  Aligned_cols=88  Identities=17%  Similarity=0.180  Sum_probs=60.4

Q ss_pred             ccCCCCcEEEecc-CCCC-----Ccc-cccccccccEEeeccccCCcccccchhhhcccCCCccEEeccccccc----cc
Q 042541          598 SALSKLKKIRLEH-VSLP-----NSL-ATVRMNHLQKVSLVMCNVGQVFRNSTFRISDAFPNLLEMDIDYCNDL----IE  666 (695)
Q Consensus       598 ~~l~~L~~L~L~~-~~l~-----~lp-~i~~l~~L~~L~l~~~~i~~~~~~~~~~l~~~l~~L~~L~l~~c~~l----~~  666 (695)
                      .+.++|++|+|++ +.++     .+- .+...++|+.|+|++|.++...-..........++|+.|++++|..-    ..
T Consensus        14 ~~~~~L~~L~L~~~~~i~~~~~~~l~~al~~n~~L~~L~Ls~n~l~~~~~~~L~~~l~~~~~l~~l~l~~~~~~~~g~~~   93 (166)
T d1io0a_          14 NNDPDLEEVNLNNIMNIPVPTLKACAEALKTNTYVKKFSIVGTRSNDPVAFALAEMLKVNNTLKSLNVESNFISGSGILA   93 (166)
T ss_dssp             TTCTTCCEEECTTCTTCCHHHHHHHHHHHTTCCSCCEEECTTSCCCHHHHHHHHHHHHHCSSCCEEECCSSCCCHHHHHH
T ss_pred             hcCCCCcEEEcCCCCCCCHHHHHHHHHHHhcCCccCeeeccCCcccHHHHHHHHHHHhhcccchhhhhccccccchhHHH
Confidence            4568899999998 4565     233 56678999999999998765322211111126789999999987532    22


Q ss_pred             CchhhcCCCCCceeecccc
Q 042541          667 LPDGLCDIVSMEKLRITNC  685 (695)
Q Consensus       667 lP~~i~~L~~L~~L~l~~~  685 (695)
                      +-..+...++|+.++|+.|
T Consensus        94 l~~~l~~~~~L~~l~L~l~  112 (166)
T d1io0a_          94 LVEALQSNTSLIELRIDNQ  112 (166)
T ss_dssp             HHHGGGGCSSCCEEECCCC
T ss_pred             HHHHHHhCccccEEeeccC
Confidence            4456778899998777643

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=93.83  E-value=0.025  Score=52.51  Aligned_cols=42  Identities=14%  Similarity=0.145  Sum_probs=34.7

Q ss_pred             CCCCcchHHHHHHHHH--cCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          168 SPGLDVPLKELKMELF--KDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       168 ~vGr~~~~~~l~~~L~--~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      |||....++++.+.+.  .....-|.|.|..|+|||++|+.+.+
T Consensus         2 ~v~~S~~~~~~~~~~~~~a~~~~pvlI~Ge~GtGK~~~A~~ih~   45 (247)
T d1ny5a2           2 YVFESPKMKEILEKIKKISCAECPVLITGESGVGKEVVARLIHK   45 (247)
T ss_dssp             CCCCSHHHHHHHHHHHHHTTCCSCEEEECSTTSSHHHHHHHHHH
T ss_pred             eEecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHH
Confidence            7999999999988887  22234478999999999999999975

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.82  E-value=0.042  Score=50.66  Aligned_cols=47  Identities=13%  Similarity=0.097  Sum_probs=32.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccC---CCcEEEEEeCCCCCHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKF---KDDIFYVTVSKNPNVK  233 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f---~~~~~wv~~~~~~~~~  233 (695)
                      .+++.|+|.+|+||||||.++.........+   ...++|++....+...
T Consensus        34 G~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~   83 (251)
T d1szpa2          34 GSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPV   83 (251)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESSSCCCGG
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEeecchHHHH
Confidence            5799999999999999998887643222111   2336788877766533

>d1akya1 c.37.1.1 (A:3-130,A:169-220) Adenylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.80  E-value=0.013  Score=51.53  Aligned_cols=20  Identities=35%  Similarity=0.491  Sum_probs=17.8

Q ss_pred             EEEEcCCCCcHHHHHHHHhc
Q 042541          190 IVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~  209 (695)
                      |.|.|++|+||||+|+.++.
T Consensus         5 Ivl~G~pGSGKtT~a~~La~   24 (180)
T d1akya1           5 MVLIGPPGAGKGTQAPNLQE   24 (180)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            45779999999999999986

>d2afhe1 c.37.1.10 (E:1-289) Nitrogenase iron protein {Azotobacter vinelandii [TaxId: 354]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Azotobacter vinelandii [TaxId: 354]

Probab=93.79  E-value=0.024  Score=54.12  Aligned_cols=39  Identities=21%  Similarity=0.315  Sum_probs=28.8

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCC
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKN  229 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~  229 (695)
                      +.|+|+|-||+||||+|..++.  ..... ..+++-|++...
T Consensus         3 r~IaisgKGGVGKTT~a~NLA~--~LA~~-G~rVLlID~DpQ   41 (289)
T d2afhe1           3 RQCAIYGKGGIGKSTTTQNLVA--ALAEM-GKKVMIVGCDPK   41 (289)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHH--HHHHT-TCCEEEEEECSS
T ss_pred             cEEEEECCCCCCHHHHHHHHHH--HHHHC-CCCEEEEecCCC
Confidence            5788999999999999988776  33322 334888888643

>d1sq5a_ c.37.1.6 (A:) Pantothenate kinase PanK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Pantothenate kinase PanK
species: Escherichia coli [TaxId: 562]

Probab=93.65  E-value=0.048  Score=52.04  Aligned_cols=43  Identities=14%  Similarity=0.069  Sum_probs=30.4

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCC-CcEEEEEeCCCCC
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFK-DDIFYVTVSKNPN  231 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~-~~~~wv~~~~~~~  231 (695)
                      +-+|+|.|..|+||||+|+.+..  .+...+. ..+.-++..+-+-
T Consensus        80 P~iIGIaG~sgSGKSTla~~L~~--lL~~~~~~~~v~~Is~D~F~~  123 (308)
T d1sq5a_          80 PYIISIAGSVAVGKSTTARVLQA--LLSRWPEHRRVELITTDGFLH  123 (308)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHH--HHTTSTTCCCEEEEEGGGGBC
T ss_pred             CEEEEEeCCCCCCCcHHHHHHHH--HHhhhcCCCceEEEeeeeeEC
Confidence            67999999999999999999876  4443332 2255566555443

>d1odfa_ c.37.1.6 (A:) Hypothetical protein Ygr205W {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein Ygr205W
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.63  E-value=0.11  Score=48.86  Aligned_cols=54  Identities=20%  Similarity=0.212  Sum_probs=33.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhcccccccc--CCCcEEEEEeCCCCCHHHHHHHHHHh
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGK--FKDDIFYVTVSKNPNVKAIVQKVLHH  242 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~--f~~~~~wv~~~~~~~~~~~~~~i~~~  242 (695)
                      +-+|+|.|..|+||||||..+..  .+...  ....+.-++..+-+-..+-...+.+.
T Consensus        27 P~iIGi~G~qGSGKSTl~~~l~~--~L~~~~~~~~~v~~iS~DdfY~t~~~r~~L~~~   82 (286)
T d1odfa_          27 PLFIFFSGPQGSGKSFTSIQIYN--HLMEKYGGEKSIGYASIDDFYLTHEDQLKLNEQ   82 (286)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH--HHHHHHGGGSCEEEEEGGGGBCCHHHHHHHHHH
T ss_pred             CEEEEeECCCCCCHHHHHHHHHH--HHHHHhCCCcceEeeccCCCCCCHHHHHHHhhh
Confidence            56899999999999999988876  33332  22335566666544333323344443

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=93.58  E-value=0.027  Score=55.56  Aligned_cols=44  Identities=25%  Similarity=0.371  Sum_probs=34.0

Q ss_pred             CCCCCCcchHHHHHHHHH------------------------------cCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          166 VISPGLDVPLKELKMELF------------------------------KDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       166 ~~~vGr~~~~~~l~~~L~------------------------------~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .++||-++.++.+..++.                              .-...-+..+|+.|+|||.||+.++.
T Consensus        17 ~~ViGQd~Akkava~Avrn~~rR~~~~~~~r~~~~~~~~~~~~~~~~~~~p~~niLfiGPTGvGKTElAk~LA~   90 (364)
T d1um8a_          17 NYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAK   90 (364)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHH
T ss_pred             CeecChHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccccccCCCcceeeeCCCCccHHHHHHHHHh
Confidence            568999998887765541                              11245688999999999999999875

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=93.58  E-value=0.077  Score=49.02  Aligned_cols=49  Identities=20%  Similarity=0.270  Sum_probs=34.5

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhcccccc---ccCCCcEEEEEeCCCCCHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQ---GKFKDDIFYVTVSKNPNVKAI  235 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~---~~f~~~~~wv~~~~~~~~~~~  235 (695)
                      .+++.|+|++|+||||+|.+++.+....   ......++|+......+...+
T Consensus        36 G~~~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (254)
T d1pzna2          36 QAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERI   87 (254)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHHH
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEeccchhHHHHH
Confidence            5799999999999999998887532211   122344778888777665444

>d1e4va1 c.37.1.1 (A:1-121,A:157-214) Adenylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Escherichia coli [TaxId: 562]

Probab=93.48  E-value=0.016  Score=50.97  Aligned_cols=20  Identities=25%  Similarity=0.215  Sum_probs=18.3

Q ss_pred             EEEEcCCCCcHHHHHHHHhc
Q 042541          190 IVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~  209 (695)
                      |.|.|++|+||||+|+.++.
T Consensus         3 I~i~G~pGSGKsT~~~~La~   22 (179)
T d1e4va1           3 IILLGAPVAGKGTQAQFIME   22 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            67899999999999999886

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.48  E-value=0.29  Score=44.78  Aligned_cols=48  Identities=19%  Similarity=0.200  Sum_probs=33.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccc---cccCCCcEEEEEeCCCCCHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQV---QGKFKDDIFYVTVSKNPNVKA  234 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~---~~~f~~~~~wv~~~~~~~~~~  234 (695)
                      .+++.|+|.+|+|||++|.+++.....   .......+.|+.....+....
T Consensus        37 G~~~~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (258)
T d1v5wa_          37 MAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDR   87 (258)
T ss_dssp             SEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHhhhhcccccceEEEechHHHHHHHH
Confidence            579999999999999999988753211   112223367888777766443

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=93.46  E-value=0.097  Score=51.25  Aligned_cols=64  Identities=19%  Similarity=0.180  Sum_probs=36.3

Q ss_pred             cchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhccc-cccccCCCcEEEEEeCCCCCHHHHHHHH
Q 042541          172 DVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKDD-QVQGKFKDDIFYVTVSKNPNVKAIVQKV  239 (695)
Q Consensus       172 ~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~~-~~~~~f~~~~~wv~~~~~~~~~~~~~~i  239 (695)
                      +.....+...+.   .++..|.|++|.||||++..+...- +....-.. .+.+..........+...+
T Consensus       151 ~~Q~~A~~~al~---~~~~vI~G~pGTGKTt~i~~~l~~l~~~~~~~~~-~I~l~ApTgkAA~~L~e~~  215 (359)
T d1w36d1         151 NWQKVAAAVALT---RRISVISGGPGTGKTTTVAKLLAALIQMADGERC-RIRLAAPTGKAAARLTESL  215 (359)
T ss_dssp             CHHHHHHHHHHT---BSEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCC-CEEEEBSSHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHc---CCeEEEEcCCCCCceehHHHHHHHHHHHHhccCC-eEEEecCcHHHHHHHHHHH
Confidence            345555555553   3789999999999999886554311 11111122 3466666554444444443

>d1s96a_ c.37.1.1 (A:) Guanylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Escherichia coli [TaxId: 562]

Probab=93.34  E-value=0.021  Score=51.42  Aligned_cols=22  Identities=50%  Similarity=0.795  Sum_probs=20.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+|.|+|++|+|||||.+.+..
T Consensus         3 ~livi~GPSG~GK~tl~~~L~~   24 (205)
T d1s96a_           3 TLYIVSAPSGAGKSSLIQALLK   24 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            6889999999999999998876

>d1l2ta_ c.37.1.12 (A:) MJ0796 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=93.17  E-value=0.021  Score=52.01  Aligned_cols=23  Identities=26%  Similarity=0.572  Sum_probs=20.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|+|||||.+.+..
T Consensus        31 Ge~~~iiG~sGsGKSTLl~~i~g   53 (230)
T d1l2ta_          31 GEFVSIMGPSGSGKSTMLNIIGC   53 (230)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCcchhhHhccC
Confidence            46899999999999999998875

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=93.17  E-value=0.036  Score=54.52  Aligned_cols=25  Identities=28%  Similarity=0.418  Sum_probs=22.7

Q ss_pred             CCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          185 DGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       185 ~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +..+.+.++|++|+|||++|+.+++
T Consensus       152 ~~~~~~~~~g~~~~gk~~~~~~~~~  176 (362)
T d1svma_         152 PKKRYWLFKGPIDSGKTTLAAALLE  176 (362)
T ss_dssp             TTCCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCcCeEEEECCCCCCHHHHHHHHHH
Confidence            4467999999999999999999988

>d1sgwa_ c.37.1.12 (A:) Putative ABC transporter PF0895 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter PF0895
species: Pyrococcus furiosus [TaxId: 2261]

Probab=93.13  E-value=0.018  Score=51.50  Aligned_cols=23  Identities=30%  Similarity=0.579  Sum_probs=21.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|+|||||.+.++.
T Consensus        27 Gei~~l~G~NGsGKSTLl~~i~g   49 (200)
T d1sgwa_          27 GNVVNFHGPNGIGKTTLLKTIST   49 (200)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCChHHHHHHHHhc
Confidence            46899999999999999999976

>d1yrba1 c.37.1.10 (A:1-244) ATP(GTP)-binding protein PAB0955 {Pyrococcus abyssi [TaxId: 29292]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: ATP(GTP)-binding protein PAB0955
species: Pyrococcus abyssi [TaxId: 29292]

Probab=93.09  E-value=0.021  Score=52.82  Aligned_cols=22  Identities=32%  Similarity=0.463  Sum_probs=20.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHhcc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      ||+|+|+.|+|||||..++.++
T Consensus         2 vi~v~G~~GsGKTTLl~~ll~~   23 (244)
T d1yrba1           2 IVVFVGTAGSGKTTLTGEFGRY   23 (244)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Confidence            7899999999999999998763

>d1g2912 c.37.1.12 (1:1-240) Maltose transport protein MalK, N-terminal domain {Archaeon Thermococcus litoralis [TaxId: 2265]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Archaeon Thermococcus litoralis [TaxId: 2265]

Probab=93.00  E-value=0.023  Score=52.10  Aligned_cols=23  Identities=30%  Similarity=0.651  Sum_probs=21.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|+|||||++.++.
T Consensus        29 Ge~~~liG~sGaGKSTll~~i~g   51 (240)
T d1g2912          29 GEFMILLGPSGCGKTTTLRMIAG   51 (240)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCChHHHHHHHHhc
Confidence            46899999999999999999875

>d3dhwc1 c.37.1.12 (C:1-240) Methionine import ATP-binding protein MetN {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Methionine import ATP-binding protein MetN
species: Escherichia coli [TaxId: 562]

Probab=92.95  E-value=0.023  Score=52.09  Aligned_cols=23  Identities=30%  Similarity=0.349  Sum_probs=21.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|+|||||++.++-
T Consensus        31 Ge~~~iiG~sGsGKSTLl~~i~G   53 (240)
T d3dhwc1          31 GQIYGVIGASGAGKSTLIRCVNL   53 (240)
T ss_dssp             SCEEEEEESTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHcC
Confidence            47899999999999999999976

>d2ocpa1 c.37.1.1 (A:37-277) Deoxyguanosine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyguanosine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.94  E-value=0.026  Score=52.21  Aligned_cols=24  Identities=29%  Similarity=0.401  Sum_probs=22.0

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +++.|+|-|+-|+||||+++.+.+
T Consensus         1 ~pk~IviEG~~GsGKST~~~~L~~   24 (241)
T d2ocpa1           1 GPRRLSIEGNIAVGKSTFVKLLTK   24 (241)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHH
Confidence            468999999999999999999886

>d2awna2 c.37.1.12 (A:4-235) Maltose transport protein MalK, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=92.94  E-value=0.025  Score=51.63  Aligned_cols=23  Identities=35%  Similarity=0.718  Sum_probs=21.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|+|||||.+.++-
T Consensus        26 Gei~~liGpsGsGKSTLl~~i~G   48 (232)
T d2awna2          26 GEFVVFVGPSGCGKSTLLRMIAG   48 (232)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCChHHHHHHHHhc
Confidence            47899999999999999999875

>d1hyqa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=92.94  E-value=0.035  Score=50.81  Aligned_cols=38  Identities=29%  Similarity=0.364  Sum_probs=28.8

Q ss_pred             eEEEEE-cCCCCcHHHHHHHHhccccccccCCCcEEEEEeCC
Q 042541          188 QFIVVS-APGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSK  228 (695)
Q Consensus       188 ~vv~I~-G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~  228 (695)
                      ++|+|+ |-||+||||+|..++.  ..... ..++.+|++..
T Consensus         2 kvIav~s~KGGvGKTtia~nlA~--~la~~-g~~VlliD~D~   40 (232)
T d1hyqa_           2 RTITVASGKGGTGKTTITANLGV--ALAQL-GHDVTIVDADI   40 (232)
T ss_dssp             EEEEEEESSSCSCHHHHHHHHHH--HHHHT-TCCEEEEECCC
T ss_pred             EEEEEECCCCCChHHHHHHHHHH--HHHhC-CCCEEEEeCCC
Confidence            688888 8999999999998887  34333 23488998863

>d1a7ja_ c.37.1.6 (A:) Phosphoribulokinase {Rhodobacter sphaeroides [TaxId: 1063]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Phosphoribulokinase
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=92.85  E-value=0.014  Score=55.01  Aligned_cols=24  Identities=21%  Similarity=0.362  Sum_probs=18.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +.+||+|.|.+|+||||+++.+.+
T Consensus         3 k~pIIgIaG~SGSGKTTva~~l~~   26 (288)
T d1a7ja_           3 KHPIISVTGSSGAGTSTVKHTFDQ   26 (288)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHH
Confidence            467999999999999999998876

>d1r8sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF1 [TaxId: 9606]

Probab=92.85  E-value=0.022  Score=48.50  Aligned_cols=21  Identities=29%  Similarity=0.360  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |.|+|.+|+|||||...+..+
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~   23 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLG   23 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            679999999999999998765

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=92.81  E-value=0.028  Score=52.24  Aligned_cols=24  Identities=17%  Similarity=0.379  Sum_probs=21.2

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+++|+|+.|+|||||++.+..
T Consensus        40 ~Ge~iaivG~sGsGKSTLl~ll~g   63 (253)
T d3b60a1          40 AGKTVALVGRSGSGKSTIASLITR   63 (253)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCChHHHHHHHHhc
Confidence            347899999999999999999864

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=92.81  E-value=0.33  Score=45.30  Aligned_cols=93  Identities=11%  Similarity=0.126  Sum_probs=52.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCC-hH---HHHHHHHH
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQT-DE---AAINDLER  262 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~-~~---~~~~~l~~  262 (695)
                      ..++.|.|.+|+|||+++..++.+.-....+  .+++++..  .+...+...++.....-...... ..   .....+.+
T Consensus        35 G~l~vi~G~~G~GKT~~~~~la~~~a~~~g~--~v~~~s~E--~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~  110 (277)
T d1cr2a_          35 GEVIMVTSGSGMGKSTFVRQQALQWGTAMGK--KVGLAMLE--ESVEETAEDLIGLHNRVRLRQSDSLKREIIENGKFDQ  110 (277)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHHHHHTSCC--CEEEEESS--SCHHHHHHHHHHHHTTCCGGGCHHHHHHHHHTSHHHH
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHhhhhhccc--ceeEeeec--cchhhHHhHHHHHhhcCCchhhcccccchhhhHHHHH
Confidence            3688999999999999998887632222233  36676655  45667777776654432111101 00   11123444


Q ss_pred             HHHhcCCCcEEEEEeCCCCCC
Q 042541          263 FFKQMRIEAILLVLDDVWPGS  283 (695)
Q Consensus       263 ~~~~l~~~~~LlVlDdv~~~~  283 (695)
                      ..+.+.+...+.+.|......
T Consensus       111 ~~~~~~~~~~~~~~~~~~~~~  131 (277)
T d1cr2a_         111 WFDELFGNDTFHLYDSFAEAE  131 (277)
T ss_dssp             HHHHHHSSSCEEEECCC-CCC
T ss_pred             HHHHhhccceeeeeccccchh
Confidence            445555666777777654443

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=92.78  E-value=0.026  Score=51.98  Aligned_cols=23  Identities=26%  Similarity=0.414  Sum_probs=20.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...|+|+|..|+|||||++.+..
T Consensus        29 Ge~vaIvG~sGsGKSTLl~ll~g   51 (241)
T d2pmka1          29 GEVIGIVGRSGSGKSTLTKLIQR   51 (241)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHh
Confidence            47899999999999999999875

>d1b0ua_ c.37.1.12 (A:) ATP-binding subunit of the histidine permease {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ATP-binding subunit of the histidine permease
species: Salmonella typhimurium [TaxId: 90371]

Probab=92.72  E-value=0.027  Score=52.46  Aligned_cols=23  Identities=22%  Similarity=0.362  Sum_probs=21.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|+|||||++.+.-
T Consensus        28 GEi~~iiG~sGsGKSTLl~~i~G   50 (258)
T d1b0ua_          28 GDVISIIGSSGSGKSTFLRCINF   50 (258)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHHc
Confidence            47999999999999999999975

>d1mv5a_ c.37.1.12 (A:) Multidrug resistance ABC transporter LmrA, C-terminal domain {Lactococcus lactis [TaxId: 1358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter LmrA, C-terminal domain
species: Lactococcus lactis [TaxId: 1358]

Probab=92.71  E-value=0.033  Score=51.37  Aligned_cols=24  Identities=29%  Similarity=0.483  Sum_probs=21.2

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ....++|+|+.|+|||||++.+..
T Consensus        27 ~Ge~vaivG~sGsGKSTLl~ll~g   50 (242)
T d1mv5a_          27 PNSIIAFAGPSGGGKSTIFSLLER   50 (242)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHH
Confidence            357999999999999999999864

>d1fx0a3 c.37.1.11 (A:97-372) Central domain of alpha subunit of F1 ATP synthase {Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]

Probab=92.68  E-value=0.072  Score=49.79  Aligned_cols=89  Identities=18%  Similarity=0.235  Sum_probs=50.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC-CHHHHHHHHHHhcCC-------CCCCCCC-----h
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKGY-------PVPEFQT-----D  253 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~~-------~~~~~~~-----~  253 (695)
                      .+-++|+|..|+|||+|+......  ...+-.. ++++-+.+.. ...++..++.+.=..       ...+.+.     .
T Consensus        67 GQr~~Ifg~~g~GKt~l~~~~~~~--~~~~~~v-~V~~~iGer~~Ev~e~~~~~~~~~~~~~tvvv~~tsd~p~~~r~~a  143 (276)
T d1fx0a3          67 GQRELIIGDRQTGKTAVATDTILN--QQGQNVI-CVYVAIGQKASSVAQVVTNFQERGAMEYTIVVAETADSPATLQYLA  143 (276)
T ss_dssp             TCBCBEEESSSSSHHHHHHHHHHT--CCTTTCE-EEEEEESCCHHHHHHHHHHTGGGTGGGSEEEEEECTTSCGGGTTHH
T ss_pred             CceEeeccCCCCChHHHHHHHHhh--hcccCce-eeeeeecchhHHHHHHHHhhccCCcceeeeecccccCccHHHHHHH
Confidence            356899999999999999875542  2222233 5677777654 334444444432100       0011111     1


Q ss_pred             HHHHHHHHHHHHhcCCCcEEEEEeCC
Q 042541          254 EAAINDLERFFKQMRIEAILLVLDDV  279 (695)
Q Consensus       254 ~~~~~~l~~~~~~l~~~~~LlVlDdv  279 (695)
                      ....-.+.+.+.. +++++|+++||+
T Consensus       144 ~~~a~tiAEyfrd-~G~~Vlll~Dsl  168 (276)
T d1fx0a3         144 PYTGAALAEYFMY-RERHTLIIYDDL  168 (276)
T ss_dssp             HHHHHHHHHHHHH-TTCEEEEEEECH
T ss_pred             HHHHHHHHHHHHH-cCCceeEEeecc
Confidence            1223344555533 589999999997

>d2jdia3 c.37.1.11 (A:95-379) Central domain of alpha subunit of F1 ATP synthase {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Cow (Bos taurus) [TaxId: 9913]

Probab=92.67  E-value=0.14  Score=47.87  Aligned_cols=102  Identities=15%  Similarity=0.177  Sum_probs=56.2

Q ss_pred             HHHHHHH-cCCceEEEEEcCCCCcHHHHHHHHhcccc-----ccccCCCcEEEEEeCCCC-CHHHHHHHHHHhcCCC---
Q 042541          177 ELKMELF-KDGRQFIVVSAPGGYGKTTLVQRLCKDDQ-----VQGKFKDDIFYVTVSKNP-NVKAIVQKVLHHKGYP---  246 (695)
Q Consensus       177 ~l~~~L~-~~~~~vv~I~G~gGiGKTtLa~~~~~~~~-----~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~~l~~~---  246 (695)
                      +.++.|. -...+-++|.|.+|+|||+|+..+.....     ....-...++++-+++.. ...++...+...-...   
T Consensus        57 raID~l~pig~GQr~~If~~~g~GKt~ll~~~~~~~~~~~~~~~~~~~~~~v~~~IGer~~E~~e~~~~~~~~~~~~~tv  136 (285)
T d2jdia3          57 KAVDSLVPIGRGQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTI  136 (285)
T ss_dssp             HHHHHHSCCBTTCBCEEEESTTSSHHHHHHHHHHHTHHHHTSSCTTTCCEEEEEEESCCHHHHHHHHHHHHHTTCGGGEE
T ss_pred             eEEecccCccCCCEEEeecCCCCChHHHHHHHHHhHHhhccccccccceEEEEeeeCccHHHHHHHHHHhcccccccceE
Confidence            4455555 23346789999999999999887765311     111122224566666654 3455666655442110   


Q ss_pred             ----CCCCCChH-----HHHHHHHHHHHhcCCCcEEEEEeCC
Q 042541          247 ----VPEFQTDE-----AAINDLERFFKQMRIEAILLVLDDV  279 (695)
Q Consensus       247 ----~~~~~~~~-----~~~~~l~~~~~~l~~~~~LlVlDdv  279 (695)
                          ........     ...-.+.+.+.. +++++|+++||+
T Consensus       137 vv~~ts~~~~~~r~~~~~~a~tiAEyfrd-~G~~VLll~Dsl  177 (285)
T d2jdia3         137 VVSATASDAAPLQYLAPYSGCSMGEYFRD-NGKHALIIYDDL  177 (285)
T ss_dssp             EEEECTTSCHHHHHHHHHHHHHHHHHHHH-TTCEEEEEEETH
T ss_pred             EEEECCCCCHHHHHHHHHHHHHHHHHHHH-cCCcEEEEEcCh
Confidence                11111111     112234455533 699999999997

>d1v43a3 c.37.1.12 (A:7-245) Hypothetical protein PH0022, N-terminal domain {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Hypothetical protein PH0022, N-terminal domain
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=92.62  E-value=0.032  Score=51.03  Aligned_cols=23  Identities=35%  Similarity=0.660  Sum_probs=21.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|+|||||.+.+..
T Consensus        32 Ge~~~liGpsGaGKSTLl~~i~G   54 (239)
T d1v43a3          32 GEFLVLLGPSGCGKTTTLRMIAG   54 (239)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCChHHHHHHHHHc
Confidence            46899999999999999999875

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.56  E-value=0.032  Score=51.75  Aligned_cols=24  Identities=25%  Similarity=0.396  Sum_probs=21.5

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+++|+|+.|+|||||++.+..
T Consensus        39 ~Ge~vaivG~sGsGKSTLl~li~g   62 (251)
T d1jj7a_          39 PGEVTALVGPNGSGKSTVAALLQN   62 (251)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhc
Confidence            357999999999999999999875

>d1nn5a_ c.37.1.1 (A:) Thymidylate kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.44  E-value=0.044  Score=49.38  Aligned_cols=51  Identities=14%  Similarity=0.215  Sum_probs=31.5

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCC-CHHHHHHHHHH
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNP-NVKAIVQKVLH  241 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~-~~~~~~~~i~~  241 (695)
                      ..|+|.|+.|+||||+++.+.+  .+..+--. +.++.-.... ...++++.++.
T Consensus         4 ~lI~ieG~dGsGKsT~~~~L~~--~L~~~g~~-v~~~~~p~~~~~~~~~i~~~l~   55 (209)
T d1nn5a_           4 ALIVLEGVDRAGKSTQSRKLVE--ALCAAGHR-AELLRFPERSTEIGKLLSSYLQ   55 (209)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHH--HHHHTTCC-EEEEESSCTTSHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHH--HHHHCCCc-EEEEeCCCCCcccchhhhhhhh
Confidence            6789999999999999999987  45443222 4444433222 23344444443

>d2onka1 c.37.1.12 (A:1-240) Molybdate/tungstate import ATP-binding protein WtpC (ModC) {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Molybdate/tungstate import ATP-binding protein WtpC (ModC)
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=92.40  E-value=0.032  Score=51.00  Aligned_cols=22  Identities=23%  Similarity=0.549  Sum_probs=20.1

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+++|+|+.|+|||||.+.++.
T Consensus        25 e~~~liGpnGaGKSTll~~i~G   46 (240)
T d2onka1          25 DYCVLLGPTGAGKSVFLELIAG   46 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHT
T ss_pred             EEEEEECCCCChHHHHHHHHHc
Confidence            4788999999999999999986

>d1nlfa_ c.37.1.11 (A:) Hexameric replicative helicase repA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric replicative helicase repA
species: Escherichia coli [TaxId: 562]

Probab=92.39  E-value=0.2  Score=46.81  Aligned_cols=22  Identities=32%  Similarity=0.531  Sum_probs=19.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+..|+|.+|+||||||..++-
T Consensus        30 ~~~~i~G~~G~GKS~l~l~la~   51 (274)
T d1nlfa_          30 TVGALVSPGGAGKSMLALQLAA   51 (274)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHH
Confidence            5788999999999999977764

>d1upta_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARL1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL1 [TaxId: 9606]

Probab=92.38  E-value=0.029  Score=48.15  Aligned_cols=22  Identities=36%  Similarity=0.436  Sum_probs=19.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHhcc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      -|+|+|.+|+|||||...+.++
T Consensus         7 kI~ivG~~~vGKSSLi~~~~~~   28 (169)
T d1upta_           7 RILILGLDGAGKTTILYRLQVG   28 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3789999999999999998775

>d1p5zb_ c.37.1.1 (B:) Deoxycytidine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxycytidine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.23  E-value=0.025  Score=52.22  Aligned_cols=23  Identities=26%  Similarity=0.229  Sum_probs=20.9

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .+.|+|-|+-|+||||+|+.+.+
T Consensus         2 ~k~I~ieG~dGsGKST~~~~L~~   24 (241)
T d1p5zb_           2 IKKISIEGNIAAGKSTFVNILKQ   24 (241)
T ss_dssp             CEEEEEECSTTSSHHHHHTTTGG
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            47899999999999999998876

>d3d31a2 c.37.1.12 (A:1-229) Sulfate/molybdate ABC transporter, ATP-binding protein {Methanosarcina acetivorans [TaxId: 2214]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Sulfate/molybdate ABC transporter, ATP-binding protein
species: Methanosarcina acetivorans [TaxId: 2214]

Probab=92.14  E-value=0.028  Score=51.12  Aligned_cols=24  Identities=25%  Similarity=0.549  Sum_probs=21.5

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ...+++|+|+.|+|||||.+.+..
T Consensus        25 ~Ge~~~liGpsGaGKSTll~~l~G   48 (229)
T d3d31a2          25 SGEYFVILGPTGAGKTLFLELIAG   48 (229)
T ss_dssp             TTCEEEEECCCTHHHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhc
Confidence            346899999999999999999976

>d1r0wa_ c.37.1.12 (A:) Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.06  E-value=0.038  Score=52.17  Aligned_cols=23  Identities=22%  Similarity=0.449  Sum_probs=21.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|+|||||++.+..
T Consensus        62 Ge~vaivG~nGsGKSTLl~~i~G   84 (281)
T d1r0wa_          62 GEMLAITGSTGSGKTSLLMLILG   84 (281)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCChHHHHHHHHhC
Confidence            57899999999999999999875

>d2a5ja1 c.37.1.8 (A:9-181) Rab2b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab2b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.96  E-value=0.035  Score=48.25  Aligned_cols=21  Identities=19%  Similarity=0.428  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |.|+|.+|+|||||+..+.++
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (173)
T d2a5ja1           6 YIIIGDTGVGKSCLLLQFTDK   26 (173)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            679999999999999998764

>d1vhta_ c.37.1.1 (A:) Dephospho-CoA kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Escherichia coli [TaxId: 562]

Probab=91.96  E-value=0.038  Score=49.77  Aligned_cols=20  Identities=20%  Similarity=0.416  Sum_probs=18.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHh
Q 042541          189 FIVVSAPGGYGKTTLVQRLC  208 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~  208 (695)
                      +|+|+|+.|+||||.|+.+-
T Consensus         5 iIgitG~igSGKStv~~~l~   24 (208)
T d1vhta_           5 IVALTGGIGSGKSTVANAFA   24 (208)
T ss_dssp             EEEEECCTTSCHHHHHHHHH
T ss_pred             EEEEECCCcCCHHHHHHHHH
Confidence            89999999999999998663

>d1svia_ c.37.1.8 (A:) Probable GTPase EngB {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Bacillus subtilis [TaxId: 1423]

Probab=91.94  E-value=0.04  Score=48.96  Aligned_cols=24  Identities=21%  Similarity=0.400  Sum_probs=21.2

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +.+.|+|+|.+|+|||||...+.+
T Consensus        22 ~~~~I~lvG~~n~GKSTLin~L~g   45 (195)
T d1svia_          22 GLPEIALAGRSNVGKSSFINSLIN   45 (195)
T ss_dssp             CCCEEEEEEBTTSSHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCCHHHHHHHhcC
Confidence            356799999999999999999975

>d1z06a1 c.37.1.8 (A:32-196) Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-33b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.93  E-value=0.037  Score=47.61  Aligned_cols=21  Identities=38%  Similarity=0.638  Sum_probs=19.1

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |.++|.+|+|||||+..+.++
T Consensus         5 v~liG~~~vGKTsLl~~~~~~   25 (165)
T d1z06a1           5 IIVIGDSNVGKTCLTYRFCAG   25 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998764

>d1htwa_ c.37.1.18 (A:) Hypothetical protein HI0065 {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: YjeE-like
domain: Hypothetical protein HI0065
species: Haemophilus influenzae [TaxId: 727]

Probab=91.91  E-value=0.072  Score=45.05  Aligned_cols=25  Identities=24%  Similarity=0.331  Sum_probs=22.0

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhcc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      ..-+|.+.|.=|+||||+++.+++.
T Consensus        32 ~g~ii~L~G~LGaGKTtfvr~~~~~   56 (158)
T d1htwa_          32 KAIMVYLNGDLGAGKTTLTRGMLQG   56 (158)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEecCCCccHHHHHHHHHhh
Confidence            3468999999999999999999874

>d1wb9a2 c.37.1.12 (A:567-800) DNA repair protein MutS, the C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=91.74  E-value=0.41  Score=43.38  Aligned_cols=103  Identities=14%  Similarity=0.214  Sum_probs=56.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccc-------------cccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCC
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQV-------------QGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQT  252 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~-------------~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~  252 (695)
                      +.+++.|+|+.+.||||+.+.+.-..-.             -.-|+  .++..+....++..-.              ..
T Consensus        40 ~~~~~iiTGpN~~GKSt~lk~i~l~~~laq~G~~VpA~~a~~~~~d--~I~~~~~~~d~~~~~~--------------S~  103 (234)
T d1wb9a2          40 QRRMLIITGPNMGGKSTYMRQTALIALMAYIGSYVPAQKVEIGPID--RIFTRVGAADDLASGR--------------ST  103 (234)
T ss_dssp             SSCEEEEECCTTSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCC--EEEEEEC-------------------------
T ss_pred             CceEEEEeccCchhhHHHHHHHHHHHHHHHcCCeEecCceecccch--hheeEEccCcccccch--------------hH
Confidence            4588999999999999999987542110             11233  2244444332221111              12


Q ss_pred             hHHHHHHHHHHHHhcCCCcEEEEEeCCCCCChH---------HHhhhccCCCCCEEEEEcCCC
Q 042541          253 DEAAINDLERFFKQMRIEAILLVLDDVWPGSES---------LLQKLGFQLPDYKILVTSRSE  306 (695)
Q Consensus       253 ~~~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~---------~~~~l~~~~~gs~iivTtR~~  306 (695)
                      -...+.++..+++.. +++.|+++|.+-.....         .+..+. ...++.+|+||-..
T Consensus       104 F~~E~~~~~~il~~~-~~~sLvliDE~~~gT~~~eg~~l~~a~l~~l~-~~~~~~~i~tTH~~  164 (234)
T d1wb9a2         104 FMVEMTETANILHNA-TEYSLVLMDEIGRGTSTYDGLSLAWACAENLA-NKIKALTLFATHYF  164 (234)
T ss_dssp             CHHHHHHHHHHHHHC-CTTEEEEEESCCCCSSSSHHHHHHHHHHHHHH-HTTCCEEEEECSCG
T ss_pred             HHHHHHHHHHHHHhc-ccccEEeecccccCCChhhhhHHHHHhhhhhh-ccccceEEEecchH
Confidence            233345566666443 56889999999654321         222231 23467899998754

>d1jjva_ c.37.1.1 (A:) Dephospho-CoA kinase {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Haemophilus influenzae [TaxId: 727]

Probab=91.74  E-value=0.041  Score=49.41  Aligned_cols=21  Identities=24%  Similarity=0.306  Sum_probs=18.7

Q ss_pred             eEEEEEcCCCCcHHHHHHHHh
Q 042541          188 QFIVVSAPGGYGKTTLVQRLC  208 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~  208 (695)
                      -+|+|+|..|+||||+|+.+-
T Consensus         3 ~iIgITG~igSGKStv~~~l~   23 (205)
T d1jjva_           3 YIVGLTGGIGSGKTTIANLFT   23 (205)
T ss_dssp             EEEEEECSTTSCHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHH
Confidence            479999999999999998763

>d2erxa1 c.37.1.8 (A:6-176) di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: di-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.60  E-value=0.043  Score=47.46  Aligned_cols=21  Identities=43%  Similarity=0.719  Sum_probs=18.7

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |.|+|.+|+|||||...+.++
T Consensus         5 i~viG~~~vGKTsLi~r~~~~   25 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVKG   25 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            679999999999999988764

>d1z0fa1 c.37.1.8 (A:8-173) Rab14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.60  E-value=0.041  Score=47.40  Aligned_cols=21  Identities=19%  Similarity=0.445  Sum_probs=18.8

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |+|+|.+|+|||+|+..+.++
T Consensus         7 ivlvG~~~vGKTsli~~~~~~   27 (166)
T d1z0fa1           7 YIIIGDMGVGKSCLLHQFTEK   27 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999988764

>d1z2aa1 c.37.1.8 (A:8-171) Rab23 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab23
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.57  E-value=0.041  Score=47.28  Aligned_cols=21  Identities=43%  Similarity=0.869  Sum_probs=18.7

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |.++|.+|+|||||+..+.+.
T Consensus         5 v~liG~~~vGKSsLi~rl~~~   25 (164)
T d1z2aa1           5 MVVVGNGAVGKSSMIQRYCKG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            679999999999999988763

>d1f6ba_ c.37.1.8 (A:) SAR1 {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=91.44  E-value=0.061  Score=46.85  Aligned_cols=25  Identities=32%  Similarity=0.290  Sum_probs=20.8

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhcc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      +..-|+|+|.+|+|||||...+...
T Consensus        12 k~~kI~lvG~~~vGKTsLl~~l~~~   36 (186)
T d1f6ba_          12 KTGKLVFLGLDNAGKTTLLHMLKDD   36 (186)
T ss_dssp             CCEEEEEEEETTSSHHHHHHHHSCC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3455789999999999999988664

>d1g3qa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=91.37  E-value=0.091  Score=47.93  Aligned_cols=37  Identities=24%  Similarity=0.387  Sum_probs=27.9

Q ss_pred             eEEEEE-cCCCCcHHHHHHHHhccccccccCCCcEEEEEeC
Q 042541          188 QFIVVS-APGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVS  227 (695)
Q Consensus       188 ~vv~I~-G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~  227 (695)
                      ++|+|+ +-||+||||+|..++.  .....-. .++.++..
T Consensus         3 ~vIav~~~kGGvGKTtia~nLA~--~la~~g~-~VlliD~D   40 (237)
T d1g3qa_           3 RIISIVSGKGGTGKTTVTANLSV--ALGDRGR-KVLAVDGD   40 (237)
T ss_dssp             EEEEEECSSTTSSHHHHHHHHHH--HHHHTTC-CEEEEECC
T ss_pred             eEEEEECCCCCCcHHHHHHHHHH--HHHhCCC-CEEEEeCC
Confidence            789999 6899999999999886  3333322 37788875

>d1yzqa1 c.37.1.8 (A:14-177) Rab6 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.33  E-value=0.044  Score=47.02  Aligned_cols=21  Identities=33%  Similarity=0.506  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |+|+|.+|+|||+|+..+.++
T Consensus         3 v~vvG~~~vGKTsLi~r~~~~   23 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMYD   23 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            788999999999999998764

>d1z0ja1 c.37.1.8 (A:2-168) Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-22a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.33  E-value=0.047  Score=47.09  Aligned_cols=21  Identities=24%  Similarity=0.542  Sum_probs=18.8

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |+|+|.+|+|||||...+.++
T Consensus         7 i~lvG~~~vGKTsli~rl~~~   27 (167)
T d1z0ja1           7 VCLLGDTGVGKSSIMWRFVED   27 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999998764

>d1gsia_ c.37.1.1 (A:) Thymidylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=91.33  E-value=0.047  Score=48.96  Aligned_cols=25  Identities=32%  Similarity=0.553  Sum_probs=21.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHhccccccc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCKDDQVQG  215 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~~~~~~~  215 (695)
                      .|+|-|.-|+||||+++.+.+  ++..
T Consensus         2 lI~ieG~dGsGKST~~~~L~~--~l~~   26 (208)
T d1gsia_           2 LIAIEGVDGAGKRTLVEKLSG--AFRA   26 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH--HHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH--HHHH
Confidence            589999999999999999886  4443

>d1ksha_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL2 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL2 [TaxId: 10090]

Probab=91.32  E-value=0.047  Score=46.87  Aligned_cols=21  Identities=19%  Similarity=0.414  Sum_probs=18.8

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |.|+|.+|+|||||...+.+.
T Consensus         5 i~ivG~~~~GKTsLi~~l~~~   25 (165)
T d1ksha_           5 LLMLGLDNAGKTTILKKFNGE   25 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHTTC
T ss_pred             EEEECCCCCCHHHHHHHHcCC
Confidence            779999999999999998763

>d1ji0a_ c.37.1.12 (A:) Branched chain aminoacid ABC transporter {Thermotoga maritima, TM1139 [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Branched chain aminoacid ABC transporter
species: Thermotoga maritima, TM1139 [TaxId: 2336]

Probab=91.31  E-value=0.049  Score=50.07  Aligned_cols=23  Identities=26%  Similarity=0.414  Sum_probs=21.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|.|||||.+.+.-
T Consensus        32 Gei~~liGpnGaGKSTl~~~i~G   54 (240)
T d1ji0a_          32 GQIVTLIGANGAGKTTTLSAIAG   54 (240)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhC
Confidence            46999999999999999999986

>d1z08a1 c.37.1.8 (A:17-183) Rab21 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab21
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.24  E-value=0.048  Score=46.97  Aligned_cols=22  Identities=41%  Similarity=0.691  Sum_probs=19.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHhcc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      -|.|+|.+|+|||+|+..+.++
T Consensus         5 KivlvG~~~vGKTsLi~r~~~~   26 (167)
T d1z08a1           5 KVVLLGEGCVGKTSLVLRYCEN   26 (167)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3789999999999999988764

>d1tmka_ c.37.1.1 (A:) Thymidylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.23  E-value=0.052  Score=49.08  Aligned_cols=24  Identities=29%  Similarity=0.338  Sum_probs=21.6

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +.+.|+|-|+-|+||||+++.+.+
T Consensus         2 kGk~I~iEG~DGsGKST~~~~L~~   25 (214)
T d1tmka_           2 RGKLILIEGLDRTGKTTQCNILYK   25 (214)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHHH
T ss_pred             CeEEEEEECCCCCcHHHHHHHHHH
Confidence            357899999999999999999886

>d1kaoa_ c.37.1.8 (A:) Rap2a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap2a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.23  E-value=0.048  Score=46.97  Aligned_cols=22  Identities=32%  Similarity=0.540  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHhcc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      -|.|+|.+|+|||+|+..+.++
T Consensus         5 Ki~lvG~~~vGKTsLi~r~~~~   26 (167)
T d1kaoa_           5 KVVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3789999999999999998764

>d3raba_ c.37.1.8 (A:) Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=91.21  E-value=0.047  Score=47.16  Aligned_cols=21  Identities=29%  Similarity=0.506  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |.++|.+|+|||||+..+.++
T Consensus         8 i~vvG~~~vGKTsLi~~l~~~   28 (169)
T d3raba_           8 ILIIGNSSVGKTSFLFRYADD   28 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHcC
Confidence            789999999999999988764

>d1zj6a1 c.37.1.8 (A:2-178) ADP-ribosylation factor {Human (Homo sapiens), ARL5A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL5A [TaxId: 9606]

Probab=91.20  E-value=0.082  Score=45.75  Aligned_cols=33  Identities=12%  Similarity=0.200  Sum_probs=23.8

Q ss_pred             HHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhcc
Q 042541          177 ELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       177 ~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      ++..++...+ --|.|+|.+|+|||||...+..+
T Consensus         6 ~~~~~~~~k~-~kI~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1           6 RIWRLFNHQE-HKVIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             HHHHHHTTSC-EEEEEEESTTSSHHHHHHHHHTT
T ss_pred             HHHHHhCCCe-EEEEEECCCCCCHHHHHHHHhcC
Confidence            4444443334 45779999999999999988764

>d1vpla_ c.37.1.12 (A:) Putative ABC transporter TM0544 {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter TM0544
species: Thermotoga maritima [TaxId: 2336]

Probab=91.17  E-value=0.058  Score=49.42  Aligned_cols=23  Identities=26%  Similarity=0.432  Sum_probs=21.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|.|||||.+.+..
T Consensus        28 Gei~glvG~nGaGKSTLl~~l~G   50 (238)
T d1vpla_          28 GEIFGLIGPNGAGKTTTLRIIST   50 (238)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            47999999999999999999876

>d2atva1 c.37.1.8 (A:5-172) Ras-like estrogen-regulated growth inhibitor, RERG {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-like estrogen-regulated growth inhibitor, RERG
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.15  E-value=0.05  Score=46.98  Aligned_cols=21  Identities=29%  Similarity=0.515  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |.++|.+|+|||+|...+.++
T Consensus         5 i~lvG~~~vGKTsli~r~~~~   25 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLTK   25 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            678999999999999998874

>d1oxxk2 c.37.1.12 (K:1-242) Glucose transport protein GlcV, N-terminal domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Glucose transport protein GlcV, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=91.13  E-value=0.033  Score=51.01  Aligned_cols=23  Identities=26%  Similarity=0.419  Sum_probs=21.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|+|||||++.+..
T Consensus        31 Ge~~~iiG~sGsGKSTll~~i~g   53 (242)
T d1oxxk2          31 GERFGILGPSGAGKTTFMRIIAG   53 (242)
T ss_dssp             TCEEEEECSCHHHHHHHHHHHHT
T ss_pred             CCEEEEECCCCCcHHHHHHHHHc
Confidence            47899999999999999999875

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.04  E-value=0.17  Score=45.29  Aligned_cols=24  Identities=17%  Similarity=0.104  Sum_probs=21.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhcc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      ..++.|.|++|+|||+||.+++.+
T Consensus        23 G~v~~i~G~~GsGKT~l~l~la~~   46 (242)
T d1n0wa_          23 GSITEMFGEFRTGKTQICHTLAVT   46 (242)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHHH
Confidence            579999999999999999888754

>d1g6ha_ c.37.1.12 (A:) MJ1267 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ1267
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=91.04  E-value=0.053  Score=50.33  Aligned_cols=23  Identities=26%  Similarity=0.530  Sum_probs=21.1

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|.|||||++.+.-
T Consensus        30 Gei~~liG~nGaGKSTLl~~i~G   52 (254)
T d1g6ha_          30 GDVTLIIGPNGSGKSTLINVITG   52 (254)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHHC
Confidence            46899999999999999999986

>d1ky3a_ c.37.1.8 (A:) Rab-related protein ypt7p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein ypt7p
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=90.96  E-value=0.053  Score=47.08  Aligned_cols=21  Identities=33%  Similarity=0.694  Sum_probs=18.8

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |+|+|.+|+|||||+..+.++
T Consensus         5 i~~vG~~~vGKSsLi~~~~~~   25 (175)
T d1ky3a_           5 VIILGDSGVGKTSLMHRYVND   25 (175)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHcC
Confidence            789999999999999988753

>d2gjsa1 c.37.1.8 (A:91-258) Rad {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rad
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.93  E-value=0.055  Score=46.70  Aligned_cols=21  Identities=19%  Similarity=0.325  Sum_probs=18.6

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |+|+|.+|+|||+|+..+.+.
T Consensus         4 i~lvG~~~vGKTsLi~~~~~~   24 (168)
T d2gjsa1           4 VLLLGAPGVGKSALARIFGGV   24 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCcCHHHHHHHHhCC
Confidence            789999999999999988663

>d2ew1a1 c.37.1.8 (A:4-174) Rab30 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab30
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.93  E-value=0.05  Score=47.08  Aligned_cols=22  Identities=41%  Similarity=0.579  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHhcc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      -|.|+|.+|+|||||+..+.++
T Consensus         7 Ki~lvG~~~vGKTsLi~~l~~~   28 (171)
T d2ew1a1           7 KIVLIGNAGVGKTCLVRRFTQG   28 (171)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3789999999999999988764

>d2f7sa1 c.37.1.8 (A:5-190) Rab27b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab27b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.91  E-value=0.054  Score=47.60  Aligned_cols=21  Identities=29%  Similarity=0.510  Sum_probs=18.7

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |.|+|.+|+|||||+..+.+.
T Consensus         8 i~ivG~~~vGKTsLi~~l~~~   28 (186)
T d2f7sa1           8 LLALGDSGVGKTTFLYRYTDN   28 (186)
T ss_dssp             EEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            779999999999999988763

>d1r2qa_ c.37.1.8 (A:) Rab5a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab5a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.79  E-value=0.055  Score=46.76  Aligned_cols=21  Identities=33%  Similarity=0.545  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |.|+|.+|+|||||+..+.++
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~   29 (170)
T d1r2qa_           9 LVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999988764

>d1mkya1 c.37.1.8 (A:2-172) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=90.74  E-value=0.063  Score=46.40  Aligned_cols=21  Identities=29%  Similarity=0.487  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .|+|+|.+|+|||||+..+..
T Consensus         2 ~V~liG~~n~GKSsLi~~L~~   22 (171)
T d1mkya1           2 TVLIVGRPNVGKSTLFNKLVK   22 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            589999999999999999875

>d2fn4a1 c.37.1.8 (A:24-196) r-Ras {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.72  E-value=0.055  Score=46.94  Aligned_cols=22  Identities=32%  Similarity=0.526  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHhcc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      -|.|+|.+|+|||+|+..+.++
T Consensus         8 Kv~lvG~~~vGKTsLi~r~~~~   29 (173)
T d2fn4a1           8 KLVVVGGGGVGKSALTIQFIQS   29 (173)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999988764

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=90.66  E-value=0.095  Score=52.83  Aligned_cols=45  Identities=24%  Similarity=0.344  Sum_probs=34.7

Q ss_pred             CCCCCCCcchHHHHHHHHH--------cC------CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          165 PVISPGLDVPLKELKMELF--------KD------GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       165 ~~~~vGr~~~~~~l~~~L~--------~~------~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +.++||-++.++.+.-.+.        .+      ..+-|.++||.|+|||.||+.++.
T Consensus        13 d~yVvGQ~~AKk~lsvav~nhyrR~~~~~~~~~ei~ksNILliGPTGvGKTlLAr~LAk   71 (443)
T d1g41a_          13 DQHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAK   71 (443)
T ss_dssp             HTTCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHH
T ss_pred             cCcccCcHHHHHHHHHHHHHHHHHhhcccccccccccccEEEECCCCCCHHHHHHHHHH
Confidence            3467998888877766553        11      145699999999999999999987

>d2erya1 c.37.1.8 (A:10-180) r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.63  E-value=0.057  Score=46.69  Aligned_cols=22  Identities=32%  Similarity=0.528  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHhcc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      -|.|+|.+|+|||+|...+..+
T Consensus         7 Ki~lvG~~~vGKTsLi~r~~~~   28 (171)
T d2erya1           7 RLVVVGGGGVGKSALTIQFIQS   28 (171)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3789999999999999988764

>d1c1ya_ c.37.1.8 (A:) Rap1A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap1A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.63  E-value=0.059  Score=46.40  Aligned_cols=21  Identities=33%  Similarity=0.635  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |.|+|.+|+|||+|+..+.++
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (167)
T d1c1ya_           6 LVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            789999999999999998764

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=90.62  E-value=0.046  Score=50.68  Aligned_cols=24  Identities=21%  Similarity=0.315  Sum_probs=20.9

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ....++|+|..|+|||||++.+..
T Consensus        43 ~Ge~vaivG~sGsGKSTLl~ll~g   66 (255)
T d2hyda1          43 KGETVAFVGMSGGGKSTLINLIPR   66 (255)
T ss_dssp             TTCEEEEECSTTSSHHHHHTTTTT
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHh
Confidence            347899999999999999998754

>d1u0la2 c.37.1.8 (A:69-293) Probable GTPase EngC (YjeQ), C-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=90.59  E-value=0.11  Score=46.65  Aligned_cols=33  Identities=24%  Similarity=0.370  Sum_probs=26.5

Q ss_pred             HHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhcc
Q 042541          175 LKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       175 ~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      ++.|.++|.   .+..+++|.+|+|||||..++..+
T Consensus        86 ~~~L~~~l~---~kt~~~~G~SGVGKSTLiN~L~~~  118 (225)
T d1u0la2          86 IEELKEYLK---GKISTMAGLSGVGKSSLLNAINPG  118 (225)
T ss_dssp             HHHHHHHHS---SSEEEEECSTTSSHHHHHHHHSTT
T ss_pred             HhhHHHHhc---CCeEEEECCCCCCHHHHHHhhcch
Confidence            567777663   267789999999999999988753

>d1nija1 c.37.1.10 (A:2-223) Hypothetical protein YjiA, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Hypothetical protein YjiA, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=90.55  E-value=0.056  Score=49.11  Aligned_cols=24  Identities=25%  Similarity=0.306  Sum_probs=21.7

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+|..|.|.-|.|||||.+++..
T Consensus         2 ~iPv~iitGFLGaGKTTll~~lL~   25 (222)
T d1nija1           2 PIAVTLLTGFLGAGKTTLLRHILN   25 (222)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHH
T ss_pred             CCCEEEEeeCCCCCHHHHHHHHHh
Confidence            468999999999999999998876

>d1fzqa_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL3 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL3 [TaxId: 10090]

Probab=90.48  E-value=0.058  Score=46.81  Aligned_cols=23  Identities=30%  Similarity=0.410  Sum_probs=19.9

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhcc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      --|.|+|.+|+|||||...+...
T Consensus        17 ~kI~vvG~~~vGKSsLi~~l~~~   39 (176)
T d1fzqa_          17 VRILLLGLDNAGKTTLLKQLASE   39 (176)
T ss_dssp             EEEEEEESTTSSHHHHHHHHCCS
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            34789999999999999998764

>d1g16a_ c.37.1.8 (A:) Rab-related protein Sec4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein Sec4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=90.43  E-value=0.059  Score=46.29  Aligned_cols=21  Identities=33%  Similarity=0.623  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |.++|.+|+|||||+..+.++
T Consensus         5 i~vvG~~~vGKTSli~~l~~~   25 (166)
T d1g16a_           5 ILLIGDSGVGKSCLLVRFVED   25 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999988764

>d1xtqa1 c.37.1.8 (A:3-169) GTP-binding protein RheB {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein RheB
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.34  E-value=0.062  Score=46.23  Aligned_cols=23  Identities=17%  Similarity=0.273  Sum_probs=19.8

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhcc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      .-|+|+|..|+|||||...+.++
T Consensus         5 ~Kv~liG~~~vGKTsLl~~~~~~   27 (167)
T d1xtqa1           5 RKIAILGYRSVGKSSLTIQFVEG   27 (167)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCcCHHHHHHHHHhC
Confidence            45789999999999999988764

>d1ctqa_ c.37.1.8 (A:) cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: cH-p21 Ras protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.27  E-value=0.063  Score=46.13  Aligned_cols=21  Identities=38%  Similarity=0.692  Sum_probs=19.0

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |.|+|.+|+|||||+..+.++
T Consensus         6 i~viG~~~vGKTsli~~l~~~   26 (166)
T d1ctqa_           6 LVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            789999999999999998764

>d1e0sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF6 [TaxId: 9606]

Probab=90.27  E-value=0.1  Score=45.05  Aligned_cols=31  Identities=23%  Similarity=0.295  Sum_probs=22.8

Q ss_pred             HHHHcCCceEEEEEcCCCCcHHHHHHHHhcc
Q 042541          180 MELFKDGRQFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       180 ~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      +.+.+...--|.|+|.+|+|||||...+.++
T Consensus         5 ~~~~~~k~~kIvlvG~~~vGKTSli~rl~~~   35 (173)
T d1e0sa_           5 SKIFGNKEMRILMLGLDAAGKTTILYKLKLG   35 (173)
T ss_dssp             HHHHTTCCEEEEEEEETTSSHHHHHHHTTCC
T ss_pred             hhhhCCCeEEEEEECCCCCCHHHHHHHHhcC
Confidence            3344333334679999999999999998764

>d1egaa1 c.37.1.8 (A:4-182) GTPase Era, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=90.26  E-value=0.073  Score=46.22  Aligned_cols=24  Identities=29%  Similarity=0.454  Sum_probs=21.2

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhcc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      ...|+|+|.+|+|||||..++.+.
T Consensus         5 ~~~I~iiG~~nvGKSSLin~L~~~   28 (179)
T d1egaa1           5 CGFIAIVGRPNVGKSTLLNKLLGQ   28 (179)
T ss_dssp             EEEEEEECSSSSSHHHHHHHHHTC
T ss_pred             ccEEEEECCCCCCHHHHHHHHhCC
Confidence            467899999999999999999853

>d2f9la1 c.37.1.8 (A:8-182) Rab11b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab11b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.25  E-value=0.065  Score=46.53  Aligned_cols=21  Identities=29%  Similarity=0.653  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |.|+|..|+|||||+..+.++
T Consensus         7 i~vvG~~~vGKTsLi~~~~~~   27 (175)
T d2f9la1           7 VVLIGDSGVGKSNLLSRFTRN   27 (175)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999988764

>d1kmqa_ c.37.1.8 (A:) RhoA {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoA
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.21  E-value=0.064  Score=46.68  Aligned_cols=22  Identities=36%  Similarity=0.457  Sum_probs=19.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHhcc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      -|.|+|.+|+|||+|+..+.++
T Consensus         4 KivvvG~~~vGKTsLi~~~~~~   25 (177)
T d1kmqa_           4 KLVIVGDGACGKTCLLIVNSKD   25 (177)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4678999999999999888764

>d1wf3a1 c.37.1.8 (A:3-180) GTPase Era, N-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=90.17  E-value=0.078  Score=46.11  Aligned_cols=24  Identities=25%  Similarity=0.387  Sum_probs=21.3

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhcc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      .+.|+|+|.+|+|||||...+...
T Consensus         5 ~~~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           5 SGFVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            467999999999999999998864

>d1nrjb_ c.37.1.8 (B:) Signal recognition particle receptor beta-subunit {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=90.08  E-value=0.07  Score=47.67  Aligned_cols=23  Identities=35%  Similarity=0.574  Sum_probs=20.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhcc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      +.|+|+|.+|+|||||...+.+.
T Consensus         4 p~V~lvG~~n~GKTSLln~l~~~   26 (209)
T d1nrjb_           4 PSIIIAGPQNSGKTSLLTLLTTD   26 (209)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            57899999999999999998763

>d1ek0a_ c.37.1.8 (A:) Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ypt51
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=90.06  E-value=0.069  Score=46.04  Aligned_cols=21  Identities=24%  Similarity=0.512  Sum_probs=18.7

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |+|+|..|+|||+|+..+.++
T Consensus         6 i~vvG~~~vGKTsLi~~~~~~   26 (170)
T d1ek0a_           6 LVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999988764

>d2bmea1 c.37.1.8 (A:6-179) Rab4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.06  E-value=0.067  Score=46.36  Aligned_cols=21  Identities=24%  Similarity=0.495  Sum_probs=18.7

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |.++|.+|+|||||+..+..+
T Consensus         8 I~lvG~~~vGKTsll~~~~~~   28 (174)
T d2bmea1           8 FLVIGNAGTGKSCLLHQFIEK   28 (174)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999987653

>d2g6ba1 c.37.1.8 (A:58-227) Rab26 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab26
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.96  E-value=0.088  Score=45.37  Aligned_cols=22  Identities=27%  Similarity=0.433  Sum_probs=19.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHhcc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      -|+|+|.+|+|||+|+..+.+.
T Consensus         8 Ki~vvG~~~vGKTsli~~~~~~   29 (170)
T d2g6ba1           8 KVMLVGDSGVGKTCLLVRFKDG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3889999999999999988664

>d1svsa1 c.37.1.8 (A:32-60,A:182-347) Transducin (alpha subunit) {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=89.93  E-value=0.07  Score=46.97  Aligned_cols=21  Identities=24%  Similarity=0.415  Sum_probs=18.3

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |.++|.+|+|||+|...+..+
T Consensus         5 ivllG~~~vGKTsl~~r~~~~   25 (195)
T d1svsa1           5 LLLLGAGESGKSTIVKQMKII   25 (195)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhhC
Confidence            789999999999999887553

>d1mh1a_ c.37.1.8 (A:) Rac {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rac
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.84  E-value=0.073  Score=46.57  Aligned_cols=22  Identities=32%  Similarity=0.373  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHhcc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      -|.|+|.+|+|||+|...+.++
T Consensus         7 KivviG~~~vGKTsli~~~~~~   28 (183)
T d1mh1a_           7 KCVVVGDGAVGKTCLLISYTTN   28 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4889999999999999988763

>d2qtvb1 c.37.1.8 (B:24-189) SAR1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.80  E-value=0.074  Score=45.11  Aligned_cols=22  Identities=32%  Similarity=0.344  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHhcc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      -|+|+|.+|+|||||+..+.+.
T Consensus         2 KI~liG~~nvGKSSLln~l~~~   23 (166)
T d2qtvb1           2 KLLFLGLDNAGKTTLLHMLKND   23 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4789999999999999988763

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=89.79  E-value=0.084  Score=48.12  Aligned_cols=40  Identities=20%  Similarity=0.246  Sum_probs=27.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCC
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSK  228 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~  228 (695)
                      ..++.|+|.+|+|||+||.+++........ . .++|++...
T Consensus        26 G~~~~I~G~~G~GKT~la~~~~~~~~~~~~-~-~~~~~s~e~   65 (242)
T d1tf7a1          26 GRSTLVSGTSGTGKTLFSIQFLYNGIIEFD-E-PGVFVTFEE   65 (242)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHHHC-C-CEEEEESSS
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHhcC-C-CcccccccC
Confidence            589999999999999999776542112221 1 266776654

>d1l7vc_ c.37.1.12 (C:) ABC transporter involved in vitamin B12 uptake, BtuD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ABC transporter involved in vitamin B12 uptake, BtuD
species: Escherichia coli [TaxId: 562]

Probab=89.76  E-value=0.058  Score=49.30  Aligned_cols=23  Identities=30%  Similarity=0.616  Sum_probs=21.0

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..+++|+|+.|.|||||.+.+..
T Consensus        25 Gei~~iiG~nGaGKSTLl~~l~G   47 (231)
T d1l7vc_          25 GEILHLVGPNGAGKSTLLARMAG   47 (231)
T ss_dssp             TCEEECBCCTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhC
Confidence            47899999999999999998875

>d2atxa1 c.37.1.8 (A:9-193) RhoQ {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoQ
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.72  E-value=0.074  Score=46.65  Aligned_cols=21  Identities=38%  Similarity=0.523  Sum_probs=19.0

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |.|+|.+|+|||+|...+.++
T Consensus        12 i~lvG~~~vGKTsLi~r~~~~   32 (185)
T d2atxa1          12 CVVVGDGAVGKTCLLMSYAND   32 (185)
T ss_dssp             EEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhhC
Confidence            789999999999999988764

>d1deka_ c.37.1.1 (A:) Deoxynucleoside monophosphate kinase {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxynucleoside monophosphate kinase
species: Bacteriophage T4 [TaxId: 10665]

Probab=89.66  E-value=0.085  Score=48.49  Aligned_cols=22  Identities=23%  Similarity=0.261  Sum_probs=20.1

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ++|+|+|..|+||||+|+.+.+
T Consensus         2 ~iIgiTG~igSGKsTva~~l~e   23 (241)
T d1deka_           2 KLIFLSGVKRSGKDTTADFIMS   23 (241)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
Confidence            5899999999999999998865

>d2g3ya1 c.37.1.8 (A:73-244) GTP-binding protein GEM {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein GEM
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.60  E-value=0.082  Score=45.73  Aligned_cols=21  Identities=29%  Similarity=0.404  Sum_probs=18.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      -|.++|.+|+|||+|+..+..
T Consensus         5 Kv~lvG~~~vGKTsLi~~~~~   25 (172)
T d2g3ya1           5 RVVLIGEQGVGKSTLANIFAG   25 (172)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            378999999999999988764

>d1i2ma_ c.37.1.8 (A:) Ran {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ran
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.56  E-value=0.061  Score=46.51  Aligned_cols=21  Identities=43%  Similarity=0.656  Sum_probs=17.5

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |.|+|.+|+|||+|+..+.++
T Consensus         6 i~vvG~~~vGKTsli~~~~~~   26 (170)
T d1i2ma_           6 LVLVGDGGTGKTTFVKRHLTG   26 (170)
T ss_dssp             EEEEECTTSSHHHHHHTTC--
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            778999999999999987663

>d1zcba2 c.37.1.8 (A:47-75,A:202-372) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=89.52  E-value=0.079  Score=46.94  Aligned_cols=19  Identities=26%  Similarity=0.532  Sum_probs=17.2

Q ss_pred             EEEEEcCCCCcHHHHHHHH
Q 042541          189 FIVVSAPGGYGKTTLVQRL  207 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~  207 (695)
                      -|.|+|.+|+|||||+..+
T Consensus         4 KivllG~~~vGKTsll~r~   22 (200)
T d1zcba2           4 KILLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEEEECSTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            3779999999999999887

>d1udxa2 c.37.1.8 (A:157-336) Obg GTP-binding protein middle domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Thermus thermophilus [TaxId: 274]

Probab=89.41  E-value=0.064  Score=46.78  Aligned_cols=20  Identities=15%  Similarity=0.292  Sum_probs=18.6

Q ss_pred             EEEEcCCCCcHHHHHHHHhc
Q 042541          190 IVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~  209 (695)
                      |+|+|.+|+|||||...+..
T Consensus         4 VaivG~~nvGKSTLin~L~~   23 (180)
T d1udxa2           4 VGLVGYPNAGKSSLLAAMTR   23 (180)
T ss_dssp             EEEECCGGGCHHHHHHHHCS
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            89999999999999999875

>d2bcgy1 c.37.1.8 (Y:3-196) GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Ytp1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.39  E-value=0.079  Score=46.90  Aligned_cols=21  Identities=29%  Similarity=0.589  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |+|+|.+|+|||||+..+.++
T Consensus         9 ivvvG~~~vGKTsli~~l~~~   29 (194)
T d2bcgy1           9 LLLIGNSGVGKSCLLLRFSDD   29 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHhhC
Confidence            789999999999999988764

>d1vg8a_ c.37.1.8 (A:) Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab7
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=89.31  E-value=0.085  Score=46.16  Aligned_cols=21  Identities=24%  Similarity=0.569  Sum_probs=18.8

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |+|+|.+|+|||||+..+.+.
T Consensus         5 v~vvG~~~vGKSSLi~~l~~~   25 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVNK   25 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            779999999999999988763

>d1u8za_ c.37.1.8 (A:) Ras-related protein RalA {Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein RalA
species: Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]

Probab=89.30  E-value=0.087  Score=45.36  Aligned_cols=22  Identities=27%  Similarity=0.546  Sum_probs=19.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHhcc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      -|.|+|.+|+|||||+..+.++
T Consensus         6 KivlvG~~~vGKTsli~~~~~~   27 (168)
T d1u8za_           6 KVIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999988764

>d1x1ra1 c.37.1.8 (A:10-178) Ras-related protein M-Ras (XRas) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein M-Ras (XRas)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=89.25  E-value=0.089  Score=45.33  Aligned_cols=21  Identities=33%  Similarity=0.623  Sum_probs=18.7

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |.++|..|+|||||+..+.++
T Consensus         7 i~lvG~~~vGKTsll~~~~~~   27 (169)
T d1x1ra1           7 LVVVGDGGVGKSALTIQFFQK   27 (169)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            668899999999999998874

>d1lnza2 c.37.1.8 (A:158-342) Obg GTP-binding protein middle domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Bacillus subtilis [TaxId: 1423]

Probab=89.16  E-value=0.075  Score=46.55  Aligned_cols=21  Identities=19%  Similarity=0.165  Sum_probs=19.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHhc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      -|+|+|.+|+|||||...+..
T Consensus         3 ~VaiiG~~nvGKSSLin~L~~   23 (185)
T d1lnza2           3 DVGLVGFPSVGKSTLLSVVSS   23 (185)
T ss_dssp             CEEEESSTTSSHHHHHHHSEE
T ss_pred             eEEEECCCCCCHHHHHHHHhC
Confidence            489999999999999999865

>d2fh5b1 c.37.1.8 (B:63-269) Signal recognition particle receptor beta-subunit {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=89.15  E-value=0.092  Score=46.93  Aligned_cols=23  Identities=26%  Similarity=0.271  Sum_probs=20.2

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhcc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      +-|+|+|.+|+|||||..++...
T Consensus         1 k~V~ivG~~~~GKTsLl~~l~~~   23 (207)
T d2fh5b1           1 RAVLFVGLCDSGKTLLFVRLLTG   23 (207)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHHcC
Confidence            35899999999999999998764

>d1zd9a1 c.37.1.8 (A:18-181) ADP-ribosylation factor {Human (Homo sapiens), ARL8A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL8A [TaxId: 9606]

Probab=88.94  E-value=0.095  Score=44.82  Aligned_cols=21  Identities=24%  Similarity=0.276  Sum_probs=18.3

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |+|+|.+|+|||||...+...
T Consensus         5 i~i~G~~~~GKTsLl~~l~~~   25 (164)
T d1zd9a1           5 LTLVGLQYSGKTTFVNVIASG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            678899999999999988664

>d1m7ba_ c.37.1.8 (A:) RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoE (RND3)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=88.94  E-value=0.09  Score=45.83  Aligned_cols=21  Identities=43%  Similarity=0.585  Sum_probs=18.8

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |.++|..|+|||+|+..+.+.
T Consensus         5 ivliG~~~vGKTsli~r~~~~   25 (179)
T d1m7ba_           5 IVVVGDSQCGKTALLHVFAKD   25 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            679999999999999988774

>d1wmsa_ c.37.1.8 (A:) Rab9a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab9a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.91  E-value=0.095  Score=45.33  Aligned_cols=21  Identities=29%  Similarity=0.697  Sum_probs=18.7

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |.|+|.+|+|||||+..+.++
T Consensus         9 I~vvG~~~vGKSSli~~~~~~   29 (174)
T d1wmsa_           9 VILLGDGGVGKSSLMNRYVTN   29 (174)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            789999999999999887663

>d2cxxa1 c.37.1.8 (A:2-185) GTP-binding protein engB {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein engB
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=88.77  E-value=0.089  Score=45.87  Aligned_cols=22  Identities=32%  Similarity=0.489  Sum_probs=19.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHhcc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      -|+|+|.+|+|||||...+.+.
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~~   23 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTGK   23 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4899999999999999998763

>d1x3sa1 c.37.1.8 (A:2-178) Rab18 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab18
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.72  E-value=0.098  Score=45.41  Aligned_cols=21  Identities=33%  Similarity=0.657  Sum_probs=18.8

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |.|+|.+|+|||||...+.++
T Consensus        10 i~vvG~~~vGKTsli~~l~~~   30 (177)
T d1x3sa1          10 ILIIGESGVGKSSLLLRFTDD   30 (177)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999988654

>d2bmja1 c.37.1.8 (A:66-240) Centaurin gamma 1, G domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Centaurin gamma 1, G domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.40  E-value=0.11  Score=45.03  Aligned_cols=22  Identities=23%  Similarity=0.327  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHhcc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      -|+++|.+|+|||||+..+.+.
T Consensus         7 ki~vlG~~~vGKTsLi~~~~~~   28 (175)
T d2bmja1           7 RLGVLGDARSGKSSLIHRFLTG   28 (175)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4789999999999999988764

>d2ngra_ c.37.1.8 (A:) CDC42 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: CDC42
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.38  E-value=0.1  Score=45.94  Aligned_cols=21  Identities=33%  Similarity=0.442  Sum_probs=18.5

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |+++|.+|+|||+|+..+.++
T Consensus         6 vvllG~~~vGKTSli~r~~~~   26 (191)
T d2ngra_           6 CVVVGDGAVGKTCLLISYTTN   26 (191)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999888764

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=88.34  E-value=0.12  Score=47.53  Aligned_cols=24  Identities=21%  Similarity=0.390  Sum_probs=21.4

Q ss_pred             ceEEEEEcCCCCcHHHHHHHHhcc
Q 042541          187 RQFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       187 ~~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      ..++.|.|.+|+|||++|..++.+
T Consensus        34 G~l~~i~G~~G~GKT~~~l~~a~~   57 (258)
T d2i1qa2          34 QSVTEFAGVFGSGKTQIMHQSCVN   57 (258)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHH
Confidence            589999999999999999888753

>d2bcjq2 c.37.1.8 (Q:38-66,Q:184-354) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=88.24  E-value=0.1  Score=46.06  Aligned_cols=21  Identities=19%  Similarity=0.404  Sum_probs=18.6

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |.|+|.+|+|||+|...+..+
T Consensus         5 iv~lG~~~vGKTsll~r~~~~   25 (200)
T d2bcjq2           5 LLLLGTGESGKSTFIKQMRII   25 (200)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            789999999999999988653

>d2gj8a1 c.37.1.8 (A:216-376) Probable tRNA modification GTPase TrmE (MnmE), G domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable tRNA modification GTPase TrmE (MnmE), G domain
species: Escherichia coli [TaxId: 562]

Probab=88.16  E-value=0.11  Score=43.99  Aligned_cols=20  Identities=25%  Similarity=0.484  Sum_probs=18.2

Q ss_pred             EEEEcCCCCcHHHHHHHHhc
Q 042541          190 IVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~  209 (695)
                      |+|+|.+|+|||||..++..
T Consensus         4 I~lvG~~nvGKSsLin~l~~   23 (161)
T d2gj8a1           4 VVIAGRPNAGKSSLLNALAG   23 (161)
T ss_dssp             EEEEESTTSSHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            67999999999999998864

>d1moza_ c.37.1.8 (A:) ADP-ribosylation factor {Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]

Probab=88.00  E-value=0.09  Score=45.88  Aligned_cols=23  Identities=35%  Similarity=0.388  Sum_probs=19.5

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhcc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      --|.++|.+|+|||||...+.+.
T Consensus        18 ~KI~lvG~~~vGKTsLi~~l~~~   40 (182)
T d1moza_          18 LRILILGLDGAGKTTILYRLQIG   40 (182)
T ss_dssp             EEEEEEEETTSSHHHHHHHTCCS
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            44679999999999999988654

>d1puia_ c.37.1.8 (A:) Probable GTPase EngB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Escherichia coli [TaxId: 562]

Probab=87.80  E-value=0.1  Score=45.39  Aligned_cols=24  Identities=13%  Similarity=0.181  Sum_probs=20.9

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +..-|+|+|.+++|||||..++..
T Consensus        15 ~~~~I~lvG~~NvGKSSL~n~L~~   38 (188)
T d1puia_          15 TGIEVAFAGRSNAGKSSALNTLTN   38 (188)
T ss_dssp             CSEEEEEEECTTSSHHHHHTTTCC
T ss_pred             cCCEEEEECCCCCCHHHHHHHHhC
Confidence            356799999999999999988865

>d1byia_ c.37.1.10 (A:) Dethiobiotin synthetase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Dethiobiotin synthetase
species: Escherichia coli [TaxId: 562]

Probab=87.59  E-value=0.14  Score=46.08  Aligned_cols=22  Identities=23%  Similarity=0.191  Sum_probs=19.7

Q ss_pred             eEEEEEcCC-CCcHHHHHHHHhc
Q 042541          188 QFIVVSAPG-GYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~g-GiGKTtLa~~~~~  209 (695)
                      +.+.|.|-| |+||||++..++.
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~   24 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQ   24 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHH
T ss_pred             ceEEEEECCCCccHHHHHHHHHH
Confidence            568899998 9999999988876

>d1kkma_ c.91.1.2 (A:) HPr kinase HprK C-terminal domain {Lactobacillus casei [TaxId: 1582]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Lactobacillus casei [TaxId: 1582]

Probab=87.52  E-value=0.14  Score=44.17  Aligned_cols=22  Identities=18%  Similarity=0.345  Sum_probs=19.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +-|.|.|.+|+||||+|..+..
T Consensus        15 ~gvl~~G~sG~GKStlal~l~~   36 (176)
T d1kkma_          15 LGVLITGDSGVGKSETALELVQ   36 (176)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEEEeCCCCCHHHHHHHHHH
Confidence            5688999999999999988765

>d1knxa2 c.91.1.2 (A:133-309) HPr kinase HprK C-terminal domain {Mycoplasma pneumoniae [TaxId: 2104]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Mycoplasma pneumoniae [TaxId: 2104]

Probab=87.14  E-value=0.15  Score=44.01  Aligned_cols=22  Identities=18%  Similarity=0.289  Sum_probs=19.2

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .-|.|.|.+|+||||+|..+..
T Consensus        16 ~gvli~G~sG~GKS~lal~l~~   37 (177)
T d1knxa2          16 VGVLLTGRSGIGKSECALDLIN   37 (177)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHT
T ss_pred             EEEEEEcCCCCCHHHHHHHHHH
Confidence            5688999999999999988764

>d1azta2 c.37.1.8 (A:35-65,A:202-391) Transducin (alpha subunit) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=87.12  E-value=0.14  Score=46.34  Aligned_cols=22  Identities=23%  Similarity=0.433  Sum_probs=19.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .-|.++|.+|+|||||.+.+..
T Consensus         7 ~KilllG~~~vGKTsll~~~~~   28 (221)
T d1azta2           7 HRLLLLGAGESGKSTIVKQMRI   28 (221)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            4578999999999999988754

>d1mkya2 c.37.1.8 (A:173-358) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=87.08  E-value=0.15  Score=44.54  Aligned_cols=22  Identities=18%  Similarity=0.303  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHhcc
Q 042541          189 FIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       189 vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      -|+|+|..|+|||||..++...
T Consensus        10 kV~iiG~~~~GKSTLin~l~~~   31 (186)
T d1mkya2          10 KVAIVGRPNVGKSTLFNAILNK   31 (186)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
Confidence            4789999999999999888753

>d2fu5c1 c.37.1.8 (C:3-175) Rab8a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab8a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.95  E-value=0.098  Score=45.22  Aligned_cols=21  Identities=29%  Similarity=0.569  Sum_probs=8.3

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |.|+|.+|+|||||+..+.++
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~   29 (173)
T d2fu5c1           9 LLLIGDSGVGKTCVLFRFSED   29 (173)
T ss_dssp             EEEECCCCC------------
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            778999999999999877653

>d1ko7a2 c.91.1.2 (A:130-298) HPr kinase HprK C-terminal domain {Staphylococcus xylosus [TaxId: 1288]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Staphylococcus xylosus [TaxId: 1288]

Probab=86.32  E-value=0.17  Score=43.35  Aligned_cols=22  Identities=23%  Similarity=0.362  Sum_probs=19.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .-|.|.|.+|+||||+|..+..
T Consensus        16 ~gvli~G~sg~GKS~la~~l~~   37 (169)
T d1ko7a2          16 VGVLITGDSGIGKSETALELIK   37 (169)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEEEeCCCCCHHHHHHHHHH
Confidence            5688999999999999988765

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=86.01  E-value=1.1  Score=36.34  Aligned_cols=51  Identities=18%  Similarity=0.053  Sum_probs=31.3

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhccccccccCCCcEEEEEeCCCCCHHHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCKDDQVQGKFKDDIFYVTVSKNPNVKAIVQKVLHHK  243 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~~~~~~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l  243 (695)
                      +.++..|+++.|.|||+++-.++..      ... .+.+.+....-..+..+.+.+.+
T Consensus         7 ~~~~~ll~apTGsGKT~~~~~~~~~------~~~-~vli~~P~~~l~~q~~~~~~~~~   57 (136)
T d1a1va1           7 SFQVAHLHAPTGSGKSTKVPAAYAA------QGY-KVLVLNPSVAATLGFGAYMSKAH   57 (136)
T ss_dssp             SCEEEEEECCTTSCTTTHHHHHHHT------TTC-CEEEEESCHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHH------cCC-cEEEEcChHHHHHHHHHHHHHHh
Confidence            4578899999999999988665541      223 33555554433444444444443

>d1ewqa2 c.37.1.12 (A:542-765) DNA repair protein MutS, the C-terminal domain {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Thermus aquaticus [TaxId: 271]

Probab=85.96  E-value=1.1  Score=40.09  Aligned_cols=100  Identities=17%  Similarity=0.261  Sum_probs=55.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhccccc-------------cccCCCcEEEEEeCCCCCHHHHHHHHHHhcCCCCCCCCChH
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKDDQV-------------QGKFKDDIFYVTVSKNPNVKAIVQKVLHHKGYPVPEFQTDE  254 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~~~~-------------~~~f~~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~  254 (695)
                      +++.|+|+...||||+.+.+.--.-.             -.-|+.  ++..+....++..              ....-.
T Consensus        36 ~~~iiTGpN~~GKSt~lk~i~l~~ilAq~G~~vpA~~~~i~~~d~--I~~~~~~~d~~~~--------------~~StF~   99 (224)
T d1ewqa2          36 ELVLITGPNMAGKSTFLRQTALIALLAQVGSFVPAEEAHLPLFDG--IYTRIGASDDLAG--------------GKSTFM   99 (224)
T ss_dssp             CEEEEESCSSSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCSE--EEEECCC--------------------CCSHHH
T ss_pred             cEEEEECCCccccchhhhhhHHHHHHHhccceeecCceEEeecce--EEEEECCCccccC--------------CccHHH
Confidence            57899999999999999987532100             112332  2444433222111              111223


Q ss_pred             HHHHHHHHHHHhcCCCcEEEEEeCCCCCChH---------HHhhhccCCCCCEEEEEcCCC
Q 042541          255 AAINDLERFFKQMRIEAILLVLDDVWPGSES---------LLQKLGFQLPDYKILVTSRSE  306 (695)
Q Consensus       255 ~~~~~l~~~~~~l~~~~~LlVlDdv~~~~~~---------~~~~l~~~~~gs~iivTtR~~  306 (695)
                      ..+.++..+++. .+++.|+++|.+-.....         +++.+..  .++.+++||-..
T Consensus       100 ~el~~~~~il~~-~~~~sLvliDE~~~gT~~~eg~ala~aile~L~~--~~~~~i~tTH~~  157 (224)
T d1ewqa2         100 VEMEEVALILKE-ATENSLVLLDEVGRGTSSLDGVAIATAVAEALHE--RRAYTLFATHYF  157 (224)
T ss_dssp             HHHHHHHHHHHH-CCTTEEEEEESTTTTSCHHHHHHHHHHHHHHHHH--HTCEEEEECCCH
T ss_pred             HhHHHHHHHhcc-CCCCcEEeecccccCcchhhhcchHHHHHHHHhh--cCcceEEeeech
Confidence            344556666643 367899999999665421         3333422  367888888753

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=84.72  E-value=0.32  Score=46.59  Aligned_cols=22  Identities=27%  Similarity=0.499  Sum_probs=19.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +-|.|.|..|+||||+.++++.
T Consensus       167 ~nili~G~tgSGKTT~l~al~~  188 (323)
T d1g6oa_         167 KNVIVCGGTGSGKTTYIKSIME  188 (323)
T ss_dssp             CCEEEEESTTSSHHHHHHHHGG
T ss_pred             CCEEEEeeccccchHHHHHHhh
Confidence            3478999999999999999887

>d1tuea_ c.37.1.20 (A:) Replication protein E1 helicase domain {Human papillomavirus type 18 [TaxId: 333761]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication protein E1 helicase domain
species: Human papillomavirus type 18 [TaxId: 333761]

Probab=83.86  E-value=0.41  Score=41.78  Aligned_cols=35  Identities=23%  Similarity=0.271  Sum_probs=27.5

Q ss_pred             HHHHHHHHH-cCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          175 LKELKMELF-KDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       175 ~~~l~~~L~-~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +..+..+|. .++...+.|+|+++.|||++|..+.+
T Consensus        40 l~~l~~~l~~~PKkn~i~~~GP~~TGKS~f~~sl~~   75 (205)
T d1tuea_          40 LGALKSFLKGTPKKNCLVFCGPANTGKSYFGMSFIH   75 (205)
T ss_dssp             HHHHHHHHHTCTTCSEEEEESCGGGCHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCceEEEEECCCCccHHHHHHHHHH
Confidence            455555555 34568999999999999999988776

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=83.58  E-value=0.55  Score=46.44  Aligned_cols=41  Identities=24%  Similarity=0.292  Sum_probs=31.8

Q ss_pred             CCCcchHHHHHHHHHcCCceEEEEEcCCCCcHHHHHHHHhc
Q 042541          169 PGLDVPLKELKMELFKDGRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       169 vGr~~~~~~l~~~L~~~~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      .|.....-+....+.....++|.|.|+.|.||||....+.+
T Consensus       140 LG~~~~~~~~l~~l~~~~~GliLvtGpTGSGKSTTl~~~l~  180 (401)
T d1p9ra_         140 LGMTAHNHDNFRRLIKRPHGIILVTGPTGSGKSTTLYAGLQ  180 (401)
T ss_dssp             SCCCHHHHHHHHHHHTSSSEEEEEECSTTSCHHHHHHHHHH
T ss_pred             hcccHHHHHHHHHHHhhhhceEEEEcCCCCCccHHHHHHhh
Confidence            56665544444555666679999999999999999988877

>d1xzpa2 c.37.1.8 (A:212-371) TrmE GTPase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: TrmE GTPase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=83.00  E-value=0.099  Score=44.36  Aligned_cols=21  Identities=33%  Similarity=0.581  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHhcc
Q 042541          190 IVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       190 v~I~G~gGiGKTtLa~~~~~~  210 (695)
                      |+++|.+|+|||||+..+...
T Consensus         3 I~liG~~n~GKSSLin~l~g~   23 (160)
T d1xzpa2           3 MVIVGKPNVGKSTLLNRLLNE   23 (160)
T ss_dssp             EEEECCHHHHTCHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            789999999999999998753

>d1p6xa_ c.37.1.1 (A:) Thymidine kinase {Equine herpesvirus type 4 [TaxId: 10331]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Equine herpesvirus type 4 [TaxId: 10331]

Probab=82.55  E-value=0.32  Score=46.67  Aligned_cols=22  Identities=23%  Similarity=0.202  Sum_probs=20.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      -.|.|-|.-|+||||+++.+.+
T Consensus         7 ~rI~iEG~iGsGKSTl~~~L~~   28 (333)
T d1p6xa_           7 VRIYLDGVYGIGKSTTGRVMAS   28 (333)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHS
T ss_pred             EEEEEECCccCCHHHHHHHHHH
Confidence            4688999999999999999988

>d1h65a_ c.37.1.8 (A:) Chloroplast protein translocon GTPase Toc34 {Garden pea (Pisum sativum) [TaxId: 3888]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Chloroplast protein translocon GTPase Toc34
species: Garden pea (Pisum sativum) [TaxId: 3888]

Probab=81.84  E-value=0.59  Score=43.04  Aligned_cols=37  Identities=30%  Similarity=0.398  Sum_probs=26.7

Q ss_pred             hHHHHHHHHHcC--CceEEEEEcCCCCcHHHHHHHHhcc
Q 042541          174 PLKELKMELFKD--GRQFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       174 ~~~~l~~~L~~~--~~~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      .+.++...+.+.  ..--|+|+|..|+|||||...++..
T Consensus        17 ~l~e~~~~l~~~~~~~l~I~LvG~tg~GKSSliN~ilg~   55 (257)
T d1h65a_          17 KLLELLGNLKQEDVNSLTILVMGKGGVGKSSTVNSIIGE   55 (257)
T ss_dssp             HHHHHHHHHHHTTCCEEEEEEEESTTSSHHHHHHHHHTS
T ss_pred             HHHHHHHHHhhcCCCCcEEEEECCCCCcHHHHHHHHhCC
Confidence            344555555532  3456889999999999999999864

>d1t9ha2 c.37.1.8 (A:68-298) Probable GTPase EngC (YjeQ), C-terminal domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Bacillus subtilis [TaxId: 1423]

Probab=81.60  E-value=0.17  Score=45.59  Aligned_cols=23  Identities=22%  Similarity=0.482  Sum_probs=19.1

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhcc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCKD  210 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~~  210 (695)
                      +...++|.+|+|||||...+..+
T Consensus        98 ~~~vl~G~SGVGKSSLiN~L~~~  120 (231)
T d1t9ha2          98 KTTVFAGQSGVGKSSLLNAISPE  120 (231)
T ss_dssp             SEEEEEESHHHHHHHHHHHHCC-
T ss_pred             ceEEEECCCCccHHHHHHhhccH
Confidence            45678899999999999988753

>d2bv3a2 c.37.1.8 (A:7-282) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=80.65  E-value=0.36  Score=44.84  Aligned_cols=24  Identities=29%  Similarity=0.195  Sum_probs=21.0

Q ss_pred             CceEEEEEcCCCCcHHHHHHHHhc
Q 042541          186 GRQFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       186 ~~~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      +.|-|+|+|-+|.|||||+-++..
T Consensus         5 ~iRni~i~gh~~~GKTtL~e~ll~   28 (276)
T d2bv3a2           5 RLRNIGIAAHIDAGKTTTTERILY   28 (276)
T ss_dssp             GEEEEEEEECTTSCHHHHHHHHHH
T ss_pred             hceEEEEEeCCCCCHHHHHHHHHH
Confidence            357899999999999999988765

>d1e2ka_ c.37.1.1 (A:) Thymidine kinase {Herpes simplex virus type 1, different strains [TaxId: 10298]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Herpes simplex virus type 1, different strains [TaxId: 10298]

Probab=80.42  E-value=0.36  Score=46.09  Aligned_cols=22  Identities=36%  Similarity=0.478  Sum_probs=19.7

Q ss_pred             eEEEEEcCCCCcHHHHHHHHhc
Q 042541          188 QFIVVSAPGGYGKTTLVQRLCK  209 (695)
Q Consensus       188 ~vv~I~G~gGiGKTtLa~~~~~  209 (695)
                      ..|.|-|.-|+||||+++.+.+
T Consensus         5 lrI~IEG~iGsGKTTl~~~La~   26 (329)
T d1e2ka_           5 LRVYIDGPHGMGKTTTTQLLVA   26 (329)
T ss_dssp             EEEEECSCTTSSHHHHHHHHTC
T ss_pred             eEEEEECCcCCCHHHHHHHHHH
Confidence            4588999999999999999876