Citrus Sinensis ID: 037299

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------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-------700-------710-------720-------730-------740-------750-------760-------770-------780-------790-------800-------810-------820-------830-------840-------850-------860-------870-------880-------890-------900-------910-------920-------930-------940-------950-------960-------970-------980-------990------1000------1010------1020------1030------1040------1050------1060------1070------1080------1090------1100------1110-

MASNSQHQQQHRRSQSAAQSSGTSNIRAHHNATESMTVSKAIAQYTVDARLHAVFEQSGESGKSFDYSQSVRTMSHSVPEQQISAYLSKIQRGGHIQPFGCTIAVDEATFRVIAYSENAGEMLGLAPQSVPNLEKQEILTIGTDVRTLFTSSSSVLLEKAFGAREITLLNPIWIHSKNTGKPFYAILHRVDVGIVIDLEPARTEDPALSIAGAVQSQKLAVRAISQLQSLPGGDIKLLCDTVVESVRQLTGYDRVMVYRFHEDEHGEVVAESKRPDLEPYFGLHYPATDIPQASRFLFKQNRVRMIVDCHATPLCVIQDEGLMQPLCLVGSTLRAPHGCHAQYMANMGSIASLALAVIINGNDEEAVGGRSTTRLWAFGLQLNMELQLASQLSEKHVLRTQTLLCDMLLRDSPAGIVTQSPSIMDLVKCDGAALYYQGKYYPLGVTPTETQIKDIVEWLLTYHGDSTGLSTDSLADAGYPKAATLGDAVCGMAVAYITKRDFLFWFRSHTAKEIKWGGAKHHPEDKDDGQRMHPRSSFKAFLEVVKSRSLPWDNAEMDAIHSLQLILRDSFRDAEASNSKAVVNAQLVDLELQGVDELSSVAREMVRLIETATAPIFAVDVHGCVNGWNAKVAELTGLSVEEAMGKSLVHDLVYKEYEEIVDNLLHHALKGEEDKNVEIKLRTFGAENRKKAVFVVVNACSSKDYTNNIVGVCFVGQDVTDQKLVMDKFIHIQGDYKAIVHSPNPLIPPIFASDENTCCSEWNTAMEKLTGWSRGDIIGKMLVGEVFGSCCRLKGPDALTKFMIALHNAFGGQDTEKFPFPLFDRNGKYVQALLTANKRVNMEGQIVGAFCFLQIASPELQQALTVQRQQEKKCFARLKELAYICQEIKNPLSGVSFTNSLLEATDLTEDQKQLLETSAACEKQMLKIIKDVDLESIEDGSLEFEKAEFLLGSVINAVVSQVMMLLRERNLQLIRDIPEEIKTLAVYGDQARIQQVLADFLLNMVRYSPSAEGWVEIHVRPTLKQSSEGQTIVHNEFRMVCPGEGLPPELVQDMFHSSRWMTQEGLGLSMCRKILKLMNGEVQYIRESERCYFLIIFELPMPRRGSKSITD

ccccccccccccccccccccccccccccccccccccccccccEEEcccccccHHHHHcccccccEEEccccccccccccHHHHHccccccccccccccccEEEEEEccccEEEEEcccHHHHHcccccccccccHHHHHcccccHHHcccccHHHHHHHHHccccccccccEEEEEccccccEEEEEEEEccEEEEEEEEccccccccHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHccccEEEEEEEccccccEEEEEEcccccccccccccccccccHHHHHHHHHccEEEEEcccccccEEEccccccccccccccccccccHHHHHHHHHccccEEEEEEEEEccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHccccHHHHHcccEEEEEEccEEEEccccccHHHHHHHHHHHHHccccccEEEEcccccccccccccccccEEEEEEEEEccccEEEEEcccccEEEEcccccccccccccccccccccccHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHccccHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHcccccccEEEEEEEccccccccEEEEEEcccccccccccEEEEEEEEEccHHHHHHHHHHHHccccEEEEccccccccccccccccccccHHHcHHHHHHHccccccccccccccEEEcccccccccHHHHHHHHHHHHHcccccccccccEEEEccccEEEEEEEEcccccccccEEEEEEEEEcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHccHHHHccccccEEEEEcHHHHHHHHHHHHHHHHcccccEEEEEcccccccEEEEEcHHHHHHHHHHHHHHHHHcccccccEEEEEEEEcccccccccEEEEEEEEEEcccccccHHHHHHHcccccccccccHHHHHHHHHHHHcccEEEEEEEcccEEEEEEEEccccccccccccc

ccccccccccccccccccccccccccccccccccccccEEEEEEEcHccHHHEEEEcccccccccccccccccccccccHHHHHHHHHHHHHccccccccEEEEEccccEEEEEEcccHHHHHccccccccccccccEEEEcccHHHHcccHHHHHHHHHHHHHHHcccccEEEEEccccccEEEEEEEEEEEEEEEcccccccccHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHccccEEEEEEEccccccEEEEEEcccccccccccccccccHHHHHHHHHHHccEEEEEEcccccEEEEEccccccccEEccccccccccHHHHHHHHHcHHHHHHEEEEEccccccccccccccEEEEEEEEccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccEEEEcccccHcHEccccEEEEEcccEEEccccccHHHHHHHHHHHHHHcccccccccHHHHHcccccHHHHccHHcccEEEEEccccEEEEEccccHHHEccccccccccccccccccccccHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHcccccccEEEEccccHcccccHHHHHHHHHHHHHHHHHccccEEEEEccccEccHHHHHHHHccccHHHHHcHHHHHHHHHHcHHHHHHHHHHHHHcccHHccEEEEEEEcccccccccEEEEEEEcccccccccEEEEEEEEEcccccEEEHccEEEEcccEEEEEccccccccccEccccccccHHHHHHHHHHccccHHHHHHHHcHHHHcccccccccHHHHHHHHHHHHHHcccccccccccccEcccccEEEEEEEEcccccccccEEEEEEEEEcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHcccHHHHHcccEEEccEEEEHHHHHHHHHHHHHHHHHHcccEEEEcccHHHcccEccccHHHHHHHHHHHHHHHHHcccccccEEEEEEEcccccccccEEEEEEEEEEEcccccccHHHHHHHHcccccccHHHHHHHHHHHHHHHHcccEEEEEEcccEEEEEEEEEcccccccccccc

masnsqhqqqhrrsqsaaqssgtsnirahhnatesMTVSKAIAQYTVDARLHAVFeqsgesgksfdysqsvrtmshsvpeQQISAYLSKiqrgghiqpfgctiavdeATFRVIAYSEnagemlglapqsvpnlekqeiLTIGTDVRTLFTSSSSVLLEKAFGAreitllnpiwihskntgkpfyAILHRVDVGividlepartedpalsiaGAVQSQKLAVRAISQlqslpggdikLLCDTVVESVRQltgydrvmvyrfhedehgevvaeskrpdlepyfglhypatdipqasrflfkQNRVRMIVdchatplcviqdeglmqplclvgstlraphgchaQYMANMGSIASLALAVIIngndeeavggrsTTRLWAFGLQLNMELQLASQLSEKHVLRTQTLLCDMllrdspagivtqspsimdlvkcdgaalyyqgkyyplgvtpteTQIKDIVEWLLTYhgdstglstdsladagypkaatlgDAVCGMAVAYITKRDFLFWFRSHTAKeikwggakhhpedkddgqrmhprssFKAFLEVVKsrslpwdnaeMDAIHSLQLILRDSFrdaeasnsKAVVNAQLVDLELQGVDELSSVAREMVRLIETATAPIFAVDVHGCVNGWNAKVAELTGLSVEEAMGKSLVHDLVYKEYEEIVDNLLHHAlkgeedknvEIKLRtfgaenrkKAVFVVVNAcsskdytnnivgvcfvgqdvtdqklVMDKFIHIQGDYkaivhspnplippifasdentcCSEWNTAMEKltgwsrgdiiGKMLVGEVFgsccrlkgpdALTKFMIALHnafggqdtekfpfplfdrnGKYVQALLTANKRVNMEGQIVGAFCFLQIASPELQQALTVQRQQEKKCFARLKELAYICQEiknplsgvsftnslleatdlTEDQKQLLETSAACEKQMLKIIKDvdlesiedgslEFEKAEFLLGSVINAVVSQVMMLLRERNLQLIRDIPEEIKTLAVYGDQARIQQVLADFLLNMVRyspsaegwveihvrptlkqssegqtivhnefrmvcpgeglppelVQDMFHSSRWMTQEGLGLSMCRKILKLMNGEVQYIRESERCYFLIIFelpmprrgsksitd

masnsqhqqqhrrsqsaaqssgtSNIRAHHNATESMTVSKAIAQYTVDARLHAVFEQSGESGKSFDYSQSVRTMSHSVPEQQISAYLSKIQRGGHIQPFGCTIAVDEATFRVIAYSENAGEMLGLAPQSVPNLEKQEILTIGTDVRTLFTSSSSVLLEKAFGAREITLLNPIWIHSKNTGKPFYAILHRVDVGIVIDLEPARTEDPALSIAGAVQSQKLAVRAISQLqslpggdiKLLCDTVVESVRQLTGYDRVMVYRFHEDEHGEVVAESKRPDLEPYFGLHYPATDIPQASRFLFKQNRVRMIVDCHATPLCVIQDEGLMQPLCLVGSTLRAPHGCHAQYMANMGSIASLALAVIINGNDEEAVGGRSTTRLWAFGLQLNMELQLASQLSEKHVLRTQTLLCDMLLRDSPAgivtqspsiMDLVKCDGAALYYQGKYYPLGVTPTETQIKDIVEWLLTYHGDSTGLSTDSLADAGYPKAATLGDAVCGMAVAYITKRDFLFWFRSHTAKeikwggakhhpedkddgqrmhPRSSFKAFLEVVKSRSLPWDNAEMDAIHSLQLILRDSFRDAEASNSKAVVNAQLVDLELQGVDELSSVAREMVRLIETATAPIFAVDVHGCVNGWNAKVAELTGLSVEEAMGKSLVHDLVYKEYEEIVDNLLHhalkgeedknvEIKLRtfgaenrkkaVFVVVNAcsskdytnniVGVCFVGQDVTDQKLVMDKFIHIQGDYKAIVHSPNPLIPPIFASDENTCCSEWNTAMEKLTGWSRGDIIGKMLVGEVFGSCCRLKGPDALTKFMIALHNAFGGQDTEKFPFPLFDRNGKYVQALLTANKRVNMEGQIVGAFCFLQIASPELQQALTVQRQQEKKCFARLKELAYICQEIKNPLSGVSFTNSLLEATDLTEDQKQLLETSAACEKQMLKIIKDVDLESIEDGSLEFEKAEFLLGSVINAVVSQVMMLLRERNLQLIRDIPEEIKTLAVYGDQARIQQVLADFLLNMVRYSPSAEGWVEIHVRPtlkqssegqtIVHNEFRMVCPGEGLPPELVQDMFHSSRWMTQEGLGLSMCRKILKLMNGEVQYIRESERCYFLIIfelpmprrgsksitd

MASNsqhqqqhrrsqsaaqssGTSNIRAHHNATESMTVSKAIAQYTVDARLHAVFEQSGESGKSFDYSQSVRTMSHSVPEQQISAYLSKIQRGGHIQPFGCTIAVDEATFRVIAYSENAGEMLGLAPQSVPNLEKQEILTIGTDVRTLFTSSSSVLLEKAFGAREITLLNPIWIHSKNTGKPFYAILHRVDVGIVIDLEPARTEDPALSIAGAVQSQKLAVRAISQLQSLPGGDIKLLCDTVVESVRQLTGYDRVMVYRFHEDEHGEVVAESKRPDLEPYFGLHYPATDIPQASRFLFKQNRVRMIVDCHATPLCVIQDEGLMQPLCLVGSTLRAPHGCHAQYMANMGSIASLALAVIINGNDEEAVGGRSTTRLWAFGLQLNMELQLASQLSEKHVLRTQTLLCDMLLRDSPAGIVTQSPSIMDLVKCDGAALYYQGKYYPLGVTPTETQIKDIVEWLLTYHGDSTGLSTDSLADAGYPKAATLGDAVCGMAVAYITKRDFLFWFRSHTAKEIKWGGAKHHPEDKDDGQRMHPRSSFKAFLEVVKSRSLPWDNAEMDAIHSLQLILRDSFRDAEASNSKAVVNAQLVDLELQGVDELSSVAREMVRLIETATAPIFAVDVHGCVNGWNAKVAELTGLSVEEAMGKSLVHDLVYKEYEEIVDNLLHHALKGEEDKNVEIKLRTFGAENRKKAVFVVVNACSSKDYTNNIVGVCFVGQDVTDQKLVMDKFIHIQGDYKAIVHSPNPLIPPIFASDENTCCSEWNTAMEKLTGWSRGDIIGKMLVGEVFGSCCRLKGPDALTKFMIALHNAFGGQDTEKFPFPLFDRNGKYVQALLTANKRVNMEGQIVGAFCFLQIASPELQQALTVQRQQEKKCFARLKELAYICQEIKNPLSGVSFTNSLLEATDLTEDQKQLLETSAACEKQMLKIIKDVDLESIEDGSLEFEKAEFLLGSVINAVVSQVMMLLRERNLQLIRDIPEEIKTLAVYGDQARIQQVLADFLLNMVRYSPSAEGWVEIHVRPTLKQSSEGQTIVHNEFRMVCPGEGLPPELVQDMFHSSRWMTQEGLGLSMCRKILKLMNGEVQYIRESERCYFLIIFELPMPRRGSKSITD

***************************************KAIAQYTVDARLHAVF***************************ISAYLSKIQRGGHIQPFGCTIAVDEATFRVIAYSENAGEMLGLAPQSVPNLEKQEILTIGTDVRTLFTSSSSVLLEKAFGAREITLLNPIWIHSKNTGKPFYAILHRVDVGIVIDLEPARTEDPALSIAGAVQSQKLAVRAISQLQSLPGGDIKLLCDTVVESVRQLTGYDRVMVYRFHEDEHGEVVAES*RPDLEPYFGLHYPATDIPQASRFLFKQNRVRMIVDCHATPLCVIQDEGLMQPLCLVGSTLRAPHGCHAQYMANMGSIASLALAVIINGNDEEAVGGRSTTRLWAFGLQLNMELQLASQLSEKHVLRTQTLLCDMLLRDSPAGIVTQSPSIMDLVKCDGAALYYQGKYYPLGVTPTETQIKDIVEWLLTYHGDSTGLSTDSLADAGYPKAATLGDAVCGMAVAYITKRDFLFWFRSHTAKEIKWG*********************KAFLEVVKSRSLPWDNAEMDAIHSLQLILRDSFRDA****SKAVVNAQLVDLELQGVDELSSVAREMVRLIETATAPIFAVDVHGCVNGWNAKVAELTGLSVEEAMGKSLVHDLVYKEYEEIVDNLLHHALKGEEDKNVEIKLRTFGAENRKKAVFVVVNACSSKDYTNNIVGVCFVGQDVTDQKLVMDKFIHIQGDYKAIVHSPNPLIPPIFASDENTCCSEWNTAMEKLTGWSRGDIIGKMLVGEVFGSCCRLKGPDALTKFMIALHNAFGGQDTEKFPFPLFDRNGKYVQALLTANKRVNMEGQIVGAFCFLQIASPELQQALTVQRQQEKKCFARLKELAYICQEIKNPLSGVSFTNSLLEATDLTE**KQLLETSAACEKQMLKIIKDVDLESIEDGSLEFEKAEFLLGSVINAVVSQVMMLLRERNLQLIRDIPEEIKTLAVYGDQARIQQVLADFLLNMVRYSPSAEGWVEIHVRPTLKQ**EGQTIVHNEFRMVCPGEGLPPELVQDMFHSSRWMTQEGLGLSMCRKILKLMNGEVQYIRESERCYFLIIFEL************

********************************************YTVDARLHAVF***************************ISAYLSKIQRGGHIQPFGCTIAVDEATFRVIAYSENAGEMLGLAPQSVPNLEKQEILTIGTDVRTLFTSSSSVLLEKAFGAREITLLNPIWIHSKNTGKPFYAILHRVDVGIVIDLEPARTEDPALSIAGAVQSQKLAVRAISQLQSLPGGDIKLLCDTVVESVRQLTGYDRVMVYRFHEDEHGEVVAESKRPDLEPYFGLHYPATDIPQASRFLFKQNRVRMIVDCHATPLCVIQDEGLMQPLCLVGSTLRAPHGCHAQYMANMGSIASLALAVIINGNDEEAVGGRSTTRLWAFGLQLNMELQLASQLSEKHVLRTQTLLCDMLLRDSPAGIVTQSPSIMDLVKCDGAALYYQGKYYPLGVTPTETQIKDIVEWLLTYHGDSTGLSTDSLADAGYPKAATLGDAVCGMAVAYITKRDFLFWFRSHTAKEIKWGGAK***************SSFKAFLEVVKSRSLPWDNAEMDAIHSLQLILRDSFRDAEASN******************ELSSVAREMVRLIETATAPIFAVDVHGCVNGWNAKVAELTGLSVEEAMGKSLVHDLVYKEYEEIVDNLLHHALKGEEDKNVEIKLRTFGAENRKKAVFVVVNACSSKDYTNNIVGVCFVGQDVTDQ*L*******IQGDYKAIVHSPNPLIPPIFASDENTCCSEWNTAMEKLTGWSRGDIIGKMLVGEVFGSCCRLKGPDALTKFMIALHNAFGGQDTEKFPFPLFDRNGKYVQALLTANKRVNMEGQIVGAFCFLQIASPELQQAL**********FARLKELAYICQEIKNPLSGVSFTNSLLEATDL***************KQMLKIIKDVDLESIEDGSLEFEKAEFLLGSVINAVVSQVMM*LRERNLQLIRDIPEEIKTLAVYGDQARIQQVLADFLLNMVRYSPSAEGWVEIHVRPTLKQSSEGQTIVHNEFRMVCPGEGLPPELVQDMFHSSRWMTQEGLGLSMCRKILKLMNGEVQYIRESERCYFLIIF**************

**************************RAHHNATESMTVSKAIAQYTVDARLHAVFEQSGESGKSFDYSQSVRTMSHSVPEQQISAYLSKIQRGGHIQPFGCTIAVDEATFRVIAYSENAGEMLGLAPQSVPNLEKQEILTIGTDVRTLFTSSSSVLLEKAFGAREITLLNPIWIHSKNTGKPFYAILHRVDVGIVIDLEPARTEDPALSIAGAVQSQKLAVRAISQLQSLPGGDIKLLCDTVVESVRQLTGYDRVMVYRFHEDEHGEVVAESKRPDLEPYFGLHYPATDIPQASRFLFKQNRVRMIVDCHATPLCVIQDEGLMQPLCLVGSTLRAPHGCHAQYMANMGSIASLALAVIINGNDEEAVGGRSTTRLWAFGLQLNMELQLASQLSEKHVLRTQTLLCDMLLRDSPAGIVTQSPSIMDLVKCDGAALYYQGKYYPLGVTPTETQIKDIVEWLLTYHGDSTGLSTDSLADAGYPKAATLGDAVCGMAVAYITKRDFLFWFRSHTAKEIKWG*****************RSSFKAFLEVVKSRSLPWDNAEMDAIHSLQLILRDSFRDAEASNSKAVVNAQLVDLELQGVDELSSVAREMVRLIETATAPIFAVDVHGCVNGWNAKVAELTGLSVEEAMGKSLVHDLVYKEYEEIVDNLLHHALKGEEDKNVEIKLRTFGAENRKKAVFVVVNACSSKDYTNNIVGVCFVGQDVTDQKLVMDKFIHIQGDYKAIVHSPNPLIPPIFASDENTCCSEWNTAMEKLTGWSRGDIIGKMLVGEVFGSCCRLKGPDALTKFMIALHNAFGGQDTEKFPFPLFDRNGKYVQALLTANKRVNMEGQIVGAFCFLQIASPELQQALTVQRQQEKKCFARLKELAYICQEIKNPLSGVSFTNSLLEATDLTEDQKQLLETSAACEKQMLKIIKDVDLESIEDGSLEFEKAEFLLGSVINAVVSQVMMLLRERNLQLIRDIPEEIKTLAVYGDQARIQQVLADFLLNMVRYSPSAEGWVEIHVRPTLKQSSEGQTIVHNEFRMVCPGEGLPPELVQDMFHSSRWMTQEGLGLSMCRKILKLMNGEVQYIRESERCYFLIIFELPMPRRGSKSITD

*************************************VSKAIAQYTVDARLHAVFEQS******************SVPEQQISAYLSKIQRGGHIQPFGCTIAVDEATFRVIAYSENAGEMLGLAPQSVPNLEKQEILTIGTDVRTLFTSSSSVLLEKAFGAREITLLNPIWIHSKNTGKPFYAILHRVDVGIVIDLEPARTEDPALSIAGAVQSQKLAVRAISQLQSLPGGDIKLLCDTVVESVRQLTGYDRVMVYRFHEDEHGEVVAESKRPDLEPYFGLHYPATDIPQASRFLFKQNRVRMIVDCHATPLCVIQDEGLMQPLCLVGSTLRAPHGCHAQYMANMGSIASLALAVIINGND******RSTTRLWAFGLQLNMELQLASQLSEKHVLRTQTLLCDMLLRDSPAGIVTQSPSIMDLVKCDGAALYYQGKYYPLGVTPTETQIKDIVEWLLTYHGDSTGLSTDSLADAGYPKAATLGDAVCGMAVAYITKRDFLFWFRSHTAKEIKWGGAK***********MHPRSSFKAFLEVVKSRSLPWDNAEMDAIHSLQLILRDSFRDAEASNSKAVVNAQLVDLELQGVDELSSVAREMVRLIETATAPIFAVDVHGCVNGWNAKVAELTGLSVEEAMGKSLVHDLVYKEYEEIVDNLLHHALKGEEDKNVEIKLRTFGAENRKKAVFVVVNACSSKDYTNNIVGVCFVGQDVTDQKLVMDKFIHIQGDYKAIVHSPNPLIPPIFASDENTCCSEWNTAMEKLTGWSRGDIIGKMLVGEVFGSCCRLKGPDALTKFMIALHNAFGGQDTEKFPFPLFDRNGKYVQALLTANKRVNMEGQIVGAFCFLQIASPELQQALTVQRQQEKKCFARLKELAYICQEIKNPLSGVSFTNSLLEATDLTEDQKQLLETSAACEKQMLKIIKDVDLESIEDGSLEFEKAEFLLGSVINAVVSQVMMLLRERNLQLIRDIPEEIKTLAVYGDQARIQQVLADFLLNMVRYSPSAEGWVEIHVRPTLKQSSEGQTIVHNEFRMVCPGEGLPPELVQDMFHSSRWMTQEGLGLSMCRKILKLMNGEVQYIRESERCYFLIIFELPMP*********

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

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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	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		1111	2.2.26 [Sep-21-2011]
P29130		1132	Phytochrome B OS=Nicotian	N/A	no	0.990	0.972	0.842	0.0
P34094		1130	Phytochrome B OS=Solanum	N/A	no	0.973	0.957	0.840	0.0
Q9ZS62		1131	Phytochrome B1 OS=Solanum	N/A	no	0.991	0.974	0.820	0.0
P14713		1172	Phytochrome B OS=Arabidop	yes	no	0.987	0.936	0.768	0.0
Q10MG9		1171	Phytochrome B OS=Oryza sa	yes	no	0.989	0.938	0.735	0.0
A2XFW2		1171	Phytochrome B OS=Oryza sa	N/A	no	0.989	0.938	0.735	0.0
P42499		1156	Phytochrome B OS=Glycine	no	no	0.959	0.922	0.756	0.0
P93527		1178	Phytochrome B OS=Sorghum	N/A	no	0.960	0.905	0.758	0.0
P42497		1164	Phytochrome D OS=Arabidop	no	no	0.988	0.943	0.736	0.0
Q41046		1131	Phytochrome OS=Pinus sylv	N/A	no	0.985	0.968	0.698	0.0

>sp\|P29130\|PHYB_TOBAC Phytochrome B OS=Nicotiana tabacum GN=PHYB PE=2 SV=2	Back alignment and function desciption

 Score = 1986 bits (5144), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 956/1135 (84%), Positives = 1030/1135 (90%), Gaps = 34/1135 (2%)

Query: 2    ASNSQHQQQHRRSQSAAQSSGTSNIRAHHNATESMTVSKAIAQYTVDARLHAVFEQSGES 61
             S ++H  Q  + Q  AQSSGTSN+    N  +S  +SKAIAQYT DARLHAVFEQSGES
Sbjct: 4    GSRTKHSHQSGQGQVQAQSSGTSNV----NYKDS--ISKAIAQYTADARLHAVFEQSGES 57

Query: 62   GKSFDYSQSVRTMSHSV-PEQQISAYLSKIQRGGHIQPFGCTIAVDEATFRVIAYSENAG 120
            GKSFDYSQS++T + SV PEQQI+AYL+KIQRGGHIQPFGC IAVDEA+FRVIAYSENA 
Sbjct: 58   GKSFDYSQSIKTTTQSVVPEQQITAYLTKIQRGGHIQPFGCMIAVDEASFRVIAYSENAC 117

Query: 121  EMLGLAPQSVPNLEKQEILTIGTDVRTLFTSSSSVLLEKAFGAREITLLNPIWIHSKNTG 180
            EML L PQSVP+LE+ EILT+GTDVRTLFT SSSVLLE+AFGAREITLLNPIWIHSKN+G
Sbjct: 118  EMLSLTPQSVPSLERPEILTVGTDVRTLFTPSSSVLLERAFGAREITLLNPIWIHSKNSG 177

Query: 181  KPFYAILHRVDVGIVIDLEPARTEDPALSIAGAVQSQKLAVRAISQLQSLPGGDIKLLCD 240
            KPFYAILHRVDVGIVIDLEPARTEDPALSIAGAVQSQKLAVRAIS LQSLPGGD+KLLCD
Sbjct: 178  KPFYAILHRVDVGIVIDLEPARTEDPALSIAGAVQSQKLAVRAISHLQSLPGGDVKLLCD 237

Query: 241  TVVESVRQLTGYDRVMVYRFHEDEHGEVVAESKRPDLEPYFGLHYPATDIPQASRFLFKQ 300
            TVVESVR+LTGYDRVMVY+FHEDEHGEVVAESK PDLEPY GLHYPATDIPQASRFLFKQ
Sbjct: 238  TVVESVRELTGYDRVMVYKFHEDEHGEVVAESKIPDLEPYIGLHYPATDIPQASRFLFKQ 297

Query: 301  NRVRMIVDCHATPLCVIQDEGLMQPLCLVGSTLRAPHGCHAQYMANMGSIASLALAVIIN 360
            NRVRMIVDCHATP+ V+QDE LMQPLCLVGSTLRAPHGCHAQYMANMGSIASL LAVIIN
Sbjct: 298  NRVRMIVDCHATPVRVVQDESLMQPLCLVGSTLRAPHGCHAQYMANMGSIASLTLAVIIN 357

Query: 361  GNDEEAVGGRSTTRLW--------------------------AFGLQLNMELQLASQLSE 394
            GNDEEAVGGRS+ RLW                          AFGLQLNMELQLASQLSE
Sbjct: 358  GNDEEAVGGRSSMRLWGLVVGHHTSARCIPFPLRYACEFLMQAFGLQLNMELQLASQLSE 417

Query: 395  KHVLRTQTLLCDMLLRDSPAGIVTQSPSIMDLVKCDGAALYYQGKYYPLGVTPTETQIKD 454
            KHVLRTQTLLCDMLLRDSP GIV QSPSIMDLVKCDGAALY QGKYYPLGVTPTE QIKD
Sbjct: 418  KHVLRTQTLLCDMLLRDSPTGIVIQSPSIMDLVKCDGAALYCQGKYYPLGVTPTEAQIKD 477

Query: 455  IVEWLLTYHGDSTGLSTDSLADAGYPKAATLGDAVCGMAVAYITKRDFLFWFRSHTAKEI 514
            IVEWLLTYHGDSTGLSTDSLADAGYP AA LGDAVCGMAVAYIT +DFLFWFRSHTAKEI
Sbjct: 478  IVEWLLTYHGDSTGLSTDSLADAGYPGAALLGDAVCGMAVAYITSKDFLFWFRSHTAKEI 537

Query: 515  KWGGAKHHPEDKDDGQRMHPRSSFKAFLEVVKSRSLPWDNAEMDAIHSLQLILRDSFRDA 574
            KWGGAKHHPEDKDDGQRMHPRSSFKAFLEVVKSRSLPW+NAEMDAIHSL LILRDSF+DA
Sbjct: 538  KWGGAKHHPEDKDDGQRMHPRSSFKAFLEVVKSRSLPWENAEMDAIHSL-LILRDSFKDA 596

Query: 575  EASNSKAVVNAQLVDLELQGVDELSSVAREMVRLIETATAPIFAVDVHGCVNGWNAKVAE 634
            EASNSKAVV+AQL ++ELQG+DELSSVAREMVRLIETATAPIFAVDV G +NGWNAKVAE
Sbjct: 597  EASNSKAVVHAQLGEMELQGIDELSSVAREMVRLIETATAPIFAVDVEGRINGWNAKVAE 656

Query: 635  LTGLSVEEAMGKSLVHDLVYKEYEEIVDNLLHHALKGEEDKNVEIKLRTFGAENRKKAVF 694
            LT LSVEEAMGKSLVHDLV+KE +E  + LL +AL+GEEDKNVEIKLRTFG E  KKAVF
Sbjct: 657  LTDLSVEEAMGKSLVHDLVHKESQETAEKLLFNALRGEEDKNVEIKLRTFGPEQLKKAVF 716

Query: 695  VVVNACSSKDYTNNIVGVCFVGQDVTDQKLVMDKFIHIQGDYKAIVHSPNPLIPPIFASD 754
            VVVNACSSKDYTNNIVGVCFVGQDVT QK+VMDKFIHIQGDYKAIVHSPNPLIPPIFASD
Sbjct: 717  VVVNACSSKDYTNNIVGVCFVGQDVTGQKVVMDKFIHIQGDYKAIVHSPNPLIPPIFASD 776

Query: 755  ENTCCSEWNTAMEKLTGWSRGDIIGKMLVGEVFGSCCRLKGPDALTKFMIALHNAFGGQD 814
            ENTCCSEWNTAMEKLTGWSRG+IIGKMLVGE+FGSCCRLKGPDA+TKFMI LHNA G QD
Sbjct: 777  ENTCCSEWNTAMEKLTGWSRGEIIGKMLVGEIFGSCCRLKGPDAMTKFMIVLHNAIGVQD 836

Query: 815  TEKFPFPLFDRNGKYVQALLTANKRVNMEGQIVGAFCFLQIASPELQQALTVQRQQEKKC 874
            T+KFPF  FDRNGKYVQALLTANKRVNMEGQI+GAFCF+QIASPELQQAL VQRQQEKKC
Sbjct: 837  TDKFPFSFFDRNGKYVQALLTANKRVNMEGQIIGAFCFIQIASPELQQALRVQRQQEKKC 896

Query: 875  FARLKELAYICQEIKNPLSGVSFTNSLLEATDLTEDQKQLLETSAACEKQMLKIIKDVDL 934
            ++++KELAY+CQEIK+PL+G+ FTNSLLEATDLTE+QKQ LETSAACE+QM KII+DVDL
Sbjct: 897  YSQMKELAYLCQEIKSPLNGIRFTNSLLEATDLTENQKQYLETSAACERQMSKIIRDVDL 956

Query: 935  ESIEDGSLEFEKAEFLLGSVINAVVSQVMMLLRERNLQLIRDIPEEIKTLAVYGDQARIQ 994
            E+IEDGSL  EK EF LGSVI+AVVSQVM+LLRER++QLIRDIPEEIKTL V+GDQ RIQ
Sbjct: 957  ENIEDGSLTLEKEEFFLGSVIDAVVSQVMLLLRERSVQLIRDIPEEIKTLTVHGDQVRIQ 1016

Query: 995  QVLADFLLNMVRYSPSAEGWVEIHVRPTLKQSSEGQTIVHNEFRMVCPGEGLPPELVQDM 1054
            QVLADFLLNMVRY+PS +GWVEI ++P +KQ S+  T+VH EFR+VCPGEGLPPELVQDM
Sbjct: 1017 QVLADFLLNMVRYAPSPDGWVEIQLQPNMKQISDEVTVVHIEFRIVCPGEGLPPELVQDM 1076

Query: 1055 FHSSRWMTQEGLGLSMCRKILKLMNGEVQYIRESERCYFLIIFELPMPRRGSKSI 1109
            FHSSRW+T+EGLGLSMCRKILKLMNG++QYIRESERCYFLII +LPM RRGSKS+
Sbjct: 1077 FHSSRWVTKEGLGLSMCRKILKLMNGDIQYIRESERCYFLIILDLPMTRRGSKSL 1131

Regulatory photoreceptor which exists in two forms that are reversibly interconvertible by light: the Pr form that absorbs maximally in the red region of the spectrum and the Pfr form that absorbs maximally in the far-red region. Photoconversion of Pr to Pfr induces an array of morphogenic responses, whereas reconversion of Pfr to Pr cancels the induction of those responses. Pfr controls the expression of a number of nuclear genes including those encoding the small subunit of ribulose-bisphosphate carboxylase, chlorophyll A/B binding protein, protochlorophyllide reductase, rRNA, etc. It also controls the expression of its own gene(s) in a negative feedback fashion.
Nicotiana tabacum (taxid: 4097)

>sp\|P34094\|PHYB_SOLTU Phytochrome B OS=Solanum tuberosum GN=PHYB PE=3 SV=2	Back alignment and function description

>sp\|Q9ZS62\|PHYB1_SOLLC Phytochrome B1 OS=Solanum lycopersicum GN=PHYB1 PE=2 SV=1	Back alignment and function description

>sp\|P14713\|PHYB_ARATH Phytochrome B OS=Arabidopsis thaliana GN=PHYB PE=1 SV=1	Back alignment and function description

>sp\|Q10MG9\|PHYB_ORYSJ Phytochrome B OS=Oryza sativa subsp. japonica GN=PHYB PE=2 SV=1	Back alignment and function description

>sp\|A2XFW2\|PHYB_ORYSI Phytochrome B OS=Oryza sativa subsp. indica GN=PHYB PE=3 SV=2	Back alignment and function description

>sp\|P42499\|PHYB_SOYBN Phytochrome B OS=Glycine max GN=PHYB PE=3 SV=1	Back alignment and function description

>sp\|P93527\|PHYB_SORBI Phytochrome B OS=Sorghum bicolor GN=PHYB PE=3 SV=2	Back alignment and function description

>sp\|P42497\|PHYD_ARATH Phytochrome D OS=Arabidopsis thaliana GN=PHYD PE=1 SV=2	Back alignment and function description

>sp\|Q41046\|PHY_PINSY Phytochrome OS=Pinus sylvestris PE=2 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		1111
189409278		1129	phytochrome B [Vitis riparia]	0.990	0.975	0.855	0.0
225431962		1129	PREDICTED: phytochrome B-like [Vitis vin	0.990	0.975	0.854	0.0
189409279		1129	phytochrome B [Vitis vinifera]	0.990	0.975	0.852	0.0
255556392		1141	phytochrome B, putative [Ricinus communi	0.980	0.954	0.853	0.0
224101559		1142	predicted protein [Populus trichocarpa]	0.979	0.952	0.855	0.0
10954091		1151	phytochrome B1 [Populus trichocarpa]	0.981	0.947	0.853	0.0
464387		1132	RecName: Full=Phytochrome B gi\|295346\|gb	0.990	0.972	0.842	0.0
2370331		1135	phytochrome B [Nicotiana plumbaginifolia	0.974	0.954	0.844	0.0
85679505		1130	phytochrome B [Solanum tuberosum]	0.991	0.975	0.830	0.0
33302622		1130	RecName: Full=Phytochrome B gi\|2326872\|e	0.973	0.957	0.840	0.0

>gi\|189409278\|gb\|ACC60970.1\| phytochrome B [Vitis riparia]	Back alignment and taxonomy information

 Score = 2020 bits (5233), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 972/1136 (85%), Positives = 1037/1136 (91%), Gaps = 35/1136 (3%)

Query: 1    MASNSQHQQQHRRSQSAAQSSGTSNIRAHHNATESMTVSKAIAQYTVDARLHAVFEQSGE 60
            M+S ++  Q H +    AQSSGTSN+R +H  T+SM  SKAIAQYT+DARLHAV+EQSGE
Sbjct: 1    MSSGNRGTQSHHQ----AQSSGTSNLRVYH--TDSM--SKAIAQYTMDARLHAVYEQSGE 52

Query: 61   SGKSFDYSQSVRTMSHSVPEQQISAYLSKIQRGGHIQPFGCTIAVDEATFRVIAYSENAG 120
            SGKSFDYSQSVRT + SVPEQQI+AYLSKIQRGGHIQPFGC +AVDEATFRVIA+SENA 
Sbjct: 53   SGKSFDYSQSVRTTTQSVPEQQITAYLSKIQRGGHIQPFGCMLAVDEATFRVIAFSENAR 112

Query: 121  EMLGLAPQSVPNLEKQEILTIGTDVRTLFTSSSSVLLEKAFGAREITLLNPIWIHSKNTG 180
            EMLGL PQSVP+LEK EIL +GTDVRTLFT SS+VLLEKAFGAREITLLNP+WIHSKN+G
Sbjct: 113  EMLGLTPQSVPSLEKPEILLVGTDVRTLFTPSSAVLLEKAFGAREITLLNPVWIHSKNSG 172

Query: 181  KPFYAILHRVDVGIVIDLEPARTEDPALSIAGAVQSQKLAVRAISQLQSLPGGDIKLLCD 240
            KPFYAILHR+DVGIVIDLEPARTEDPALSIAGAVQSQKLAVRAIS LQSLPGGDI LLC+
Sbjct: 173  KPFYAILHRIDVGIVIDLEPARTEDPALSIAGAVQSQKLAVRAISHLQSLPGGDINLLCE 232

Query: 241  TVVESVRQLTGYDRVMVYRFHEDEHGEVVAESKRPDLEPYFGLHYPATDIPQASRFLFKQ 300
            TVVE+VR+LTGYDRVMVY+FHEDEHGEVVAESKR DLEPY GLHYPATDIPQASRFLF+Q
Sbjct: 233  TVVENVRELTGYDRVMVYKFHEDEHGEVVAESKRSDLEPYIGLHYPATDIPQASRFLFRQ 292

Query: 301  NRVRMIVDCHATPLCVIQDEGLMQPLCLVGSTLRAPHGCHAQYMANMGSIASLALAVIIN 360
            NRVRMIVDCHATP+ VIQDEGLMQPLCLVGSTLRAPHGCHAQYMANMGSIASLA+AVIIN
Sbjct: 293  NRVRMIVDCHATPVLVIQDEGLMQPLCLVGSTLRAPHGCHAQYMANMGSIASLAMAVIIN 352

Query: 361  GNDEEAVGGRSTTRLW--------------------------AFGLQLNMELQLASQLSE 394
            G+DEEA+GGR+  RLW                          AFGLQLNMELQLASQLSE
Sbjct: 353  GSDEEAIGGRNLMRLWGLVVCHHTSARCIPFPLRYACEFLMQAFGLQLNMELQLASQLSE 412

Query: 395  KHVLRTQTLLCDMLLRDSPAGIVTQSPSIMDLVKCDGAALYYQGKYYPLGVTPTETQIKD 454
            KHVLRTQTLLCDMLLRDSP GIVTQSPSIMDLVKCDGAALYY GKYYP GVTPTE QIKD
Sbjct: 413  KHVLRTQTLLCDMLLRDSPTGIVTQSPSIMDLVKCDGAALYYLGKYYPTGVTPTEAQIKD 472

Query: 455  IVEWLLTYHGDSTGLSTDSLADAGYPKAATLGDAVCGMAVAYITKRDFLFWFRSHTAKEI 514
            I EWLL  H DSTGLSTDSLADAGYP AA+LGDAVCGMAVAYIT RDFLFWFRSHTAKEI
Sbjct: 473  IAEWLLANHADSTGLSTDSLADAGYPGAASLGDAVCGMAVAYITSRDFLFWFRSHTAKEI 532

Query: 515  KWGGAKHHPEDKDDGQRMHPRSSFKAFLEVVKSRSLPWDNAEMDAIHSLQLILRDSFRDA 574
            KWGGAKHHPEDKDDGQRMHPRSSFKAFLEVVKSRSLPW+NAEMDAIHSLQLILRDSF+DA
Sbjct: 533  KWGGAKHHPEDKDDGQRMHPRSSFKAFLEVVKSRSLPWENAEMDAIHSLQLILRDSFKDA 592

Query: 575  -EASNSKAVVNAQLVDLELQGVDELSSVAREMVRLIETATAPIFAVDVHGCVNGWNAKVA 633
             + SNSKAV++AQL +LELQG+DELSSVAREMVRLIETATAPIFAVDV GC+NGWNAKVA
Sbjct: 593  TDGSNSKAVMHAQLGELELQGMDELSSVAREMVRLIETATAPIFAVDVDGCINGWNAKVA 652

Query: 634  ELTGLSVEEAMGKSLVHDLVYKEYEEIVDNLLHHALKGEEDKNVEIKLRTFGAENRKKAV 693
            ELTGLSVEEAMGKSLVHDLVYKE EE VD LLHHAL+GEEDKNVEIKLRTF ++  KKAV
Sbjct: 653  ELTGLSVEEAMGKSLVHDLVYKESEETVDKLLHHALRGEEDKNVEIKLRTFDSQQHKKAV 712

Query: 694  FVVVNACSSKDYTNNIVGVCFVGQDVTDQKLVMDKFIHIQGDYKAIVHSPNPLIPPIFAS 753
            FVVVNACSS+DYTNNIVGVCFVGQDVT QK+VMDKFIHIQGDYKAIVHSPNPLIPPIFAS
Sbjct: 713  FVVVNACSSRDYTNNIVGVCFVGQDVTGQKVVMDKFIHIQGDYKAIVHSPNPLIPPIFAS 772

Query: 754  DENTCCSEWNTAMEKLTGWSRGDIIGKMLVGEVFGSCCRLKGPDALTKFMIALHNAFGGQ 813
            DENT CSEWNTAMEKLTGWSRGDIIGKMLVGE+FGS CRLKGPDALTKFMI LHNA GGQ
Sbjct: 773  DENTVCSEWNTAMEKLTGWSRGDIIGKMLVGEIFGSSCRLKGPDALTKFMIVLHNAIGGQ 832

Query: 814  DTEKFPFPLFDRNGKYVQALLTANKRVNMEGQIVGAFCFLQIASPELQQALTVQRQQEKK 873
            DT+KFPF  FD+NGKYVQALLTANKRVN+EGQI+GAFCFLQIASPELQQAL VQRQQEKK
Sbjct: 833  DTDKFPFSFFDQNGKYVQALLTANKRVNIEGQIIGAFCFLQIASPELQQALKVQRQQEKK 892

Query: 874  CFARLKELAYICQEIKNPLSGVSFTNSLLEATDLTEDQKQLLETSAACEKQMLKIIKDVD 933
            CFAR+KELAYICQEIKNPLSG+ FTNSLLEATDLTEDQKQ LETSAACEKQM KII+DVD
Sbjct: 893  CFARMKELAYICQEIKNPLSGIRFTNSLLEATDLTEDQKQFLETSAACEKQMSKIIRDVD 952

Query: 934  LESIEDGSLEFEKAEFLLGSVINAVVSQVMMLLRERNLQLIRDIPEEIKTLAVYGDQARI 993
            L+SIEDGSLE E+AEFLLGSVINAVVSQVM+LLRER+LQLIRDIPEE+KTLAVYGDQ RI
Sbjct: 953  LDSIEDGSLELERAEFLLGSVINAVVSQVMILLRERDLQLIRDIPEEVKTLAVYGDQVRI 1012

Query: 994  QQVLADFLLNMVRYSPSAEGWVEIHVRPTLKQSSEGQTIVHNEFRMVCPGEGLPPELVQD 1053
            QQVLADFLLNMVRY+PS +GW+EI VRP LKQ SE   ++H EFRMVCPGEGLPP L+QD
Sbjct: 1013 QQVLADFLLNMVRYAPSPDGWIEIQVRPRLKQISEEVKLMHIEFRMVCPGEGLPPNLIQD 1072

Query: 1054 MFHSSRWMTQEGLGLSMCRKILKLMNGEVQYIRESERCYFLIIFELPMPRRGSKSI 1109
            MFHSSRWMTQEGLGLSMCRKILKL+NGEVQYIRESERCYFLI  ELP+PRRGSKS+
Sbjct: 1073 MFHSSRWMTQEGLGLSMCRKILKLINGEVQYIRESERCYFLISIELPIPRRGSKSV 1128

Source: Vitis riparia

Species: Vitis riparia

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|225431962\|ref\|XP_002278263.1\| PREDICTED: phytochrome B-like [Vitis vinifera]	Back alignment and taxonomy information

>gi\|189409279\|gb\|ACC60966.1\| phytochrome B [Vitis vinifera]	Back alignment and taxonomy information

>gi\|255556392\|ref\|XP_002519230.1\| phytochrome B, putative [Ricinus communis] gi\|223541545\|gb\|EEF43094.1\| phytochrome B, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|224101559\|ref\|XP_002312330.1\| predicted protein [Populus trichocarpa] gi\|222852150\|gb\|EEE89697.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|10954091\|gb\|AAG25725.1\|AF309806_1 phytochrome B1 [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|464387\|sp\|P29130.2\|PHYB_TOBAC RecName: Full=Phytochrome B gi\|295346\|gb\|AAA34092.1\| type II phytochrome [Nicotiana tabacum]	Back alignment and taxonomy information

>gi\|2370331\|emb\|CAA74992.1\| phytochrome B [Nicotiana plumbaginifolia]	Back alignment and taxonomy information

>gi\|85679505\|gb\|ABC72086.1\| phytochrome B [Solanum tuberosum]	Back alignment and taxonomy information

>gi\|33302622\|sp\|P34094.2\|PHYB_SOLTU RecName: Full=Phytochrome B gi\|2326872\|emb\|CAA74908.1\| phytochrome B [Solanum tuberosum]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		1111
TAIR\|locus:2005536		1112	PHYE "phytochrome E" [Arabidop	0.936	0.936	0.578	0.0
TAIR\|locus:2005515		1172	PHYB "AT2G18790" [Arabidopsis	0.654	0.620	0.785	0.0
TAIR\|locus:2005535		1164	PHYD "phytochrome D" [Arabidop	0.652	0.622	0.753	0.0
TAIR\|locus:2012300		1122	PHYA "phytochrome A" [Arabidop	0.645	0.639	0.536	9.2e-308
TAIR\|locus:2165199		1111	PHYC "phytochrome C" [Arabidop	0.646	0.646	0.501	3e-300
UNIPROTKB\|P06593		1129	PHYA3 "Phytochrome A type 3" [	0.648	0.637	0.504	4.2e-281
UNIPROTKB\|Q55168		748	cph1 "Phytochrome-like protein	0.427	0.635	0.277	3.7e-42
UNIPROTKB\|Q48G81		745	bphP "Bacteriophytochrome hist	0.159	0.237	0.353	9.6e-39
UNIPROTKB\|Q4K656		746	bphP "Bacteriophytochrome hist	0.162	0.241	0.336	8.9e-37
UNIPROTKB\|G4MU11		1523	MGG_12377 "Phytochrome-1" [Mag	0.355	0.259	0.261	3.9e-29

TAIR\|locus:2005536 PHYE "phytochrome E" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 3177 (1123.4 bits), Expect = 0., P = 0.
 Identities = 625/1080 (57%), Positives = 802/1080 (74%)

Query:    43 AQYTVDARLHAVFEQSGESGKSFDYSQSVRTMSHSVPEQQISAYLSKIQRGGHIQPFGCT 102
             AQY+VDA L A F QS  +GKSF+YS+SV +  + VP++ I+AYLS IQRGG +QPFGC 
Sbjct:    23 AQYSVDAALFADFAQSIYTGKSFNYSKSVISPPNHVPDEHITAYLSNIQRGGLVQPFGCL 82

Query:   103 IAVDEATFRVIAYSENAGEMLGLA--PQSVPNLEKQEIL-TIGTDVRTLFTSSSSVLLEK 159
             IAV+E +FR++  S+N+ + LGL   P +  + E  ++   IG D RTLFT SS   L K
Sbjct:    83 IAVEEPSFRILGLSDNSSDFLGLLSLPSTSHSGEFDKVKGLIGIDARTLFTPSSGASLSK 142

Query:   160 AFGAREITLLNPIWIHSKNTGKPFYAILHRVDVGIVIDLEPARTEDPALSIAGAVQSQKL 219
             A    EI+LLNP+ +HS+ T KPFYAILHR+D GIV+DLEPA++ DPAL++AGAVQSQKL
Sbjct:   143 AASFTEISLLNPVLVHSRTTQKPFYAILHRIDAGIVMDLEPAKSGDPALTLAGAVQSQKL 202

Query:   220 AVRAISQLQSLPGGDIKLLCDTVVESVRQLTGYDRVMVYRFHEDEHGEVVAESKRPDLEP 279
             AVRAIS+LQSLPGGDI  LCDTVVE V++LTGYDRVMVY+FHED+HGEVV+E +R DLEP
Sbjct:   203 AVRAISRLQSLPGGDIGALCDTVVEDVQRLTGYDRVMVYQFHEDDHGEVVSEIRRSDLEP 262

Query:   280 YFGLHYPATDIPQASRFLFKQNRVRMIVDCHATPLCVIQDEGLMQPLCLVGSTLRAPHGC 339
             Y GLHYPATDIPQA+RFLFKQNRVRMI DC+ATP+ V+Q E L +PLCLV STLRAPHGC
Sbjct:   263 YLGLHYPATDIPQAARFLFKQNRVRMICDCNATPVKVVQSEELKRPLCLVNSTLRAPHGC 322

Query:   340 HAQYMANMGSIASLALAVIINGNDEE-----AVGGRSTTR-------------LWAFGLQ 381
             H QYMANMGS+ASLALA+++ G D        VG   + R             + AFGLQ
Sbjct:   323 HTQYMANMGSVASLALAIVVKGKDSSKLWGLVVGHHCSPRYVPFPLRYACEFLMQAFGLQ 382

Query:   382 LNMELQLASQLSEKHVLRTQTLLCDMLLRDSPAGIVTQSPSIMDLVKCDGAALYYQGKYY 441
             L MELQLASQL+EK  +RTQTLLCDMLLRD+ + IVTQSP IMDLVKCDGAALYY+GK +
Sbjct:   383 LQMELQLASQLAEKKAMRTQTLLCDMLLRDTVSAIVTQSPGIMDLVKCDGAALYYKGKCW 442

Query:   442 PLGVTPTETQIKDIVEWLLTYHGD-STGLSTDSLADAGYPKAATLGDAVCGMAVAYITKR 500
              +GVTP E+Q+KD+V WL+  HGD STGL+TDSL DAGYP A +LGDAVCG+A A  + +
Sbjct:   443 LVGVTPNESQVKDLVNWLVENHGDDSTGLTTDSLVDAGYPGAISLGDAVCGVAAAGFSSK 502

Query:   501 DFLFWFRSHTAKEIKWGGAKHHPEDKDDGQRMHPRSSFKAFLEVVKSRSLPWDNAEMDAI 560
             D+L WFRS+TA  IKWGGAKHHP+DKDD  RMHPRSSF AFLEV KSRSLPW+ +E+DAI
Sbjct:   503 DYLLWFRSNTASAIKWGGAKHHPKDKDDAGRMHPRSSFTAFLEVAKSRSLPWEISEIDAI 562

Query:   561 HSLQLILRDSFRDAEASNSKAVVNAQLVDLELQGVDELSSVAREMVRLIETATAPIFAVD 620
             HSL+LI+R+SF     ++S+ V++   V    +  +EL+S   EMVR+IETATAPIF VD
Sbjct:   563 HSLRLIMRESF-----TSSRPVLSGNGV---ARDANELTSFVCEMVRVIETATAPIFGVD 614

Query:   621 VHGCVNGWNAKVAELTGLSVEEAMGKSLVHDLVYKEYEEIVDNLLHHALKGEEDKNVEIK 680
               GC+NGWN K AE+TGL   EAMGKSL  ++V +E    +++LL  AL+GEE+K+V +K
Sbjct:   615 SSGCINGWNKKTAEMTGLLASEAMGKSLADEIVQEESRAALESLLCKALQGEEEKSVMLK 674

Query:   681 LRTFGAENR---KKAVFVVVNACSSKDYTNNIVGVCFVGQDVTDQKLVMDKFIHIQGDYK 737
             LR FG  N       V V+VN+C+S+DYT NI+GVCFVGQD+T +K + D+FI +QGDYK
Sbjct:   675 LRKFGQNNHPDYSSDVCVLVNSCTSRDYTENIIGVCFVGQDITSEKAITDRFIRLQGDYK 734

Query:   738 AIVHSPNPLIPPIFASDENTCCSEWNTAMEKLTGWSRGDIIGKMLVGEVFGSCCRLKGPD 797
              IV S NPLIPPIFASDEN CCSEWN AMEKLTGWS+ ++IGKML GEVFG  C++K  D
Sbjct:   735 TIVQSLNPLIPPIFASDENACCSEWNAAMEKLTGWSKHEVIGKMLPGEVFGVFCKVKCQD 794

Query:   798 ALTKFMIALHNAFGGQDT-EKFPFPLFDRNGKYVQALLTANKRVNMEGQIVGAFCFLQIA 856
             +LTKF+I+L+    G +  E      F++ GKY++A LTANK  N+EG+++  F FLQI 
Sbjct:   795 SLTKFLISLYQGIAGDNVPESSLVEFFNKEGKYIEASLTANKSTNIEGKVIRCFFFLQII 854

Query:   857 SPELQQALTVQRQQEKKCFARLKELAYICQEIKNPLSGVSFTNSLLEATDLTEDQKQLLE 916
             + E    L+    +E      L EL Y+ QEIKNPL+G+ F + LLE+++++  Q+Q LE
Sbjct:   855 NKE--SGLSCPELKESA--QSLNELTYVRQEIKNPLNGIRFAHKLLESSEISASQRQFLE 910

Query:   917 TSAACEKQMLKIIKDVDLESIEDGSLEFEKAEFLLGSVINAVVSQVMMLLRERNLQLIRD 976
             TS ACEKQ+  II+  DL+SIE+G L+ E  EF L ++++ ++SQVM++LRERN QL  +
Sbjct:   911 TSDACEKQITTIIESTDLKSIEEGKLQLETEEFRLENILDTIISQVMIILRERNSQLRVE 970

Query:   977 IPEEIKTLAVYGDQARIQQVLADFLLNMVRYSPSAEGWVEIHVRPTLKQSSEGQTIVHNE 1036
             + EEIKTL + GD+ ++Q +LAD L N+V ++P    WV I + P  + S +    +H +
Sbjct:   971 VAEEIKTLPLNGDRVKLQLILADLLRNIVNHAPFPNSWVGISISPGQELSRDNGRYIHLQ 1030

Query:  1037 FRMVCPGEGLPPELVQDMFHS-SRWMTQEGLGLSMCRKILKLMNGEVQYIRESERCYFLI 1095
             FRM+ PG+GLP E++ DMF +   W+T +GLGL + RK+L+ MNG V Y+RE ERC+F +
Sbjct:  1031 FRMIHPGKGLPSEMLSDMFETRDGWVTPDGLGLKLSRKLLEQMNGRVSYVREDERCFFQV 1090

GO:0000155 "phosphorelay sensor kinase activity" evidence=IEA

GO:0004673 "protein histidine kinase activity" evidence=IEA;ISS

GO:0004871 "signal transducer activity" evidence=IEA;ISS

GO:0005524 "ATP binding" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA;ISS

GO:0007165 "signal transduction" evidence=IEA

GO:0008020 "G-protein coupled photoreceptor activity" evidence=IEA;ISS

GO:0009584 "detection of visible light" evidence=IEA

GO:0009585 "red, far-red light phototransduction" evidence=IEA

GO:0009881 "photoreceptor activity" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0017006 "protein-tetrapyrrole linkage" evidence=IEA

GO:0018106 "peptidyl-histidine phosphorylation" evidence=IEA

GO:0018298 "protein-chromophore linkage" evidence=IEA

GO:0042803 "protein homodimerization activity" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0006346 "methylation-dependent chromatin silencing" evidence=RCA

GO:0010155 "regulation of proton transport" evidence=RCA

GO:0016246 "RNA interference" evidence=RCA

GO:0046777 "protein autophosphorylation" evidence=RCA

TAIR\|locus:2005515 PHYB "AT2G18790" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2005535 PHYD "phytochrome D" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2012300 PHYA "phytochrome A" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2165199 PHYC "phytochrome C" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

UNIPROTKB\|P06593 PHYA3 "Phytochrome A type 3" [Avena sativa (taxid:4498)]	Back alignment and assigned GO terms

UNIPROTKB\|Q55168 cph1 "Phytochrome-like protein cph1" [Synechocystis sp. PCC 6803 substr. Kazusa (taxid:1111708)]	Back alignment and assigned GO terms

UNIPROTKB\|Q48G81 bphP "Bacteriophytochrome histidine kinase" [Pseudomonas syringae pv. phaseolicola 1448A (taxid:264730)]	Back alignment and assigned GO terms

UNIPROTKB\|Q4K656 bphP "Bacteriophytochrome histidine kinase" [Pseudomonas protegens Pf-5 (taxid:220664)]	Back alignment and assigned GO terms

UNIPROTKB\|G4MU11 MGG_12377 "Phytochrome-1" [Magnaporthe oryzae 70-15 (taxid:242507)]	Back alignment and assigned GO terms

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)
P30733	PHYA_SOLTU	No assigned EC number	0.5293	0.9567	0.9465	N/A	no
P42499	PHYB_SOYBN	No assigned EC number	0.7560	0.9594	0.9221	no	no
P42497	PHYD_ARATH	No assigned EC number	0.7362	0.9882	0.9432	no	no
P42496	PHY_ADICA	No assigned EC number	0.5668	0.9522	0.9463	N/A	no
P36505	PHY1_PHYPA	No assigned EC number	0.6248	0.9630	0.9452	N/A	no
P55004	PHYE_IPONI	No assigned EC number	0.6030	0.9684	0.9650	N/A	no
Q40762	PHY_PICAB	No assigned EC number	0.5954	0.9522	0.9313	N/A	no
Q41046	PHY_PINSY	No assigned EC number	0.6981	0.9855	0.9681	N/A	no
A2XFW2	PHYB_ORYSI	No assigned EC number	0.7359	0.9891	0.9385	N/A	no
P33529	PHY_MOUSC	No assigned EC number	0.5701	0.9621	0.9510	N/A	no
A2XM23	PHYC_ORYSI	No assigned EC number	0.5254	0.9729	0.9507	N/A	no
P14713	PHYB_ARATH	No assigned EC number	0.7684	0.9873	0.9360	yes	no
P15001	PHYA_PEA	No assigned EC number	0.5177	0.9630	0.9519	N/A	no
P29130	PHYB_TOBAC	No assigned EC number	0.8422	0.9909	0.9726	N/A	no
P34094	PHYB_SOLTU	No assigned EC number	0.8403	0.9738	0.9575	N/A	no
P06592	PHYA_CUCPE	No assigned EC number	0.5313	0.9504	0.9395	N/A	no
P93528	PHYC_SORBI	No assigned EC number	0.5312	0.9558	0.9356	N/A	no
O49934	PHYA_POPTM	No assigned EC number	0.5121	0.9558	0.944	N/A	no
P55141	PHYA_PETCR	No assigned EC number	0.5098	0.9522	0.9371	N/A	no
P93527	PHYB_SORBI	No assigned EC number	0.7583	0.9603	0.9057	N/A	no
P33530	PHYA1_TOBAC	No assigned EC number	0.5209	0.9612	0.9501	N/A	no
Q01549	PHY1_SELMA	No assigned EC number	0.6379	0.9675	0.9479	N/A	no
Q10MG9	PHYB_ORYSJ	No assigned EC number	0.7359	0.9891	0.9385	yes	no
P93673	PHYA_LATSA	No assigned EC number	0.5236	0.9657	0.9546	N/A	no
Q9ZS62	PHYB1_SOLLC	No assigned EC number	0.8205	0.9918	0.9743	N/A	no
Q39557	PHY2_CERPU	No assigned EC number	0.6211	0.9684	0.9598	N/A	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	2.7.13	LOW CONFIDENCE prediction!
3rd Layer	2.7.13.3	LOW CONFIDENCE prediction!

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	Alignment Graph	Length	Definition	E-value
Query		1111
pfam00360		183	pfam00360, PHY, Phytochrome region	1e-90
COG4251		750	COG4251, COG4251, Bacteriophytochrome (light-regul	2e-84
pfam08446		107	pfam08446, PAS_2, PAS fold	2e-52
pfam00989		113	pfam00989, PAS, PAS fold	4e-21
pfam00989		113	pfam00989, PAS, PAS fold	4e-20
pfam02518		111	pfam02518, HATPase_c, Histidine kinase-, DNA gyras	1e-19
COG0642		336	COG0642, BaeS, Signal transduction histidine kinas	1e-18
cd00075		103	cd00075, HATPase_c, Histidine kinase-like ATPases;	2e-18
smart00387		111	smart00387, HATPase_c, Histidine kinase-like ATPas	8e-18
smart00065		149	smart00065, GAF, Domain present in phytochromes an	6e-16
TIGR02956		968	TIGR02956, TMAO_torS, TMAO reductase sytem sensor	4e-15
PRK15347		921	PRK15347, PRK15347, two component system sensor ki	1e-13
pfam00512		66	pfam00512, HisKA, His Kinase A (phospho-acceptor)	2e-13
smart00388		66	smart00388, HisKA, His Kinase A (phosphoacceptor)	6e-13
pfam01590		143	pfam01590, GAF, GAF domain	2e-12
COG2205		890	COG2205, KdpD, Osmosensitive K+ channel histidine	3e-12
PRK09303		380	PRK09303, PRK09303, adaptive-response sensory kina	5e-12
PRK11107		919	PRK11107, PRK11107, hybrid sensory histidine kinas	1e-10
PRK10841		924	PRK10841, PRK10841, hybrid sensory kinase in two-c	3e-10
PRK11360		607	PRK11360, PRK11360, sensory histidine kinase AtoS;	2e-09
pfam13426		101	pfam13426, PAS_9, PAS domain	1e-07
PRK11466		914	PRK11466, PRK11466, hybrid sensory histidine kinas	1e-07
cd00130		103	cd00130, PAS, PAS domain; PAS motifs appear in arc	2e-07
cd00082		65	cd00082, HisKA, Histidine Kinase A (dimerization/p	3e-07
COG5002		459	COG5002, VicK, Signal transduction histidine kinas	4e-07
PRK09959		1197	PRK09959, PRK09959, hybrid sensory histidine kinas	7e-07
TIGR01386		457	TIGR01386, cztS_silS_copS, heavy metal sensor kina	4e-06
cd00130		103	cd00130, PAS, PAS domain; PAS motifs appear in arc	5e-06
smart00091		67	smart00091, PAS, PAS domain	6e-06
COG4251		750	COG4251, COG4251, Bacteriophytochrome (light-regul	7e-06
TIGR00229		124	TIGR00229, sensory_box, PAS domain S-box	1e-05
COG2202		232	COG2202, AtoS, FOG: PAS/PAC domain [Signal transdu	1e-05
COG3852		363	COG3852, NtrB, Signal transduction histidine kinas	2e-05
PRK13560		807	PRK13560, PRK13560, hypothetical protein; Provisio	2e-05
pfam13426		101	pfam13426, PAS_9, PAS domain	3e-05
COG2202		232	COG2202, AtoS, FOG: PAS/PAC domain [Signal transdu	9e-05
COG4192		673	COG4192, COG4192, Signal transduction histidine ki	1e-04
COG4191		603	COG4191, COG4191, Signal transduction histidine ki	1e-04
smart00091		67	smart00091, PAS, PAS domain	4e-04
PRK11073		348	PRK11073, glnL, nitrogen regulation protein NR(II)	5e-04
PRK10618		894	PRK10618, PRK10618, phosphotransfer intermediate p	5e-04
PRK10549		466	PRK10549, PRK10549, signal transduction histidine-	0.001
pfam08448		110	pfam08448, PAS_4, PAS fold	0.002

>gnl\|CDD\|215877 pfam00360, PHY, Phytochrome region	Back alignment and domain information

 Score =  287 bits (737), Expect = 1e-90
 Identities = 101/185 (54%), Positives = 126/185 (68%), Gaps = 7/185 (3%)

Query: 397 VLRTQTLLCDMLLR--DSPAGIVTQSPSIMDLVKCDGAALYYQGKYYPLGVTPTETQIKD 454
           +LRTQTLLCDML R  D P G+VTQSP+++DLVK DGAALYY G+ + LG TPTE QI+D
Sbjct: 1   ILRTQTLLCDMLSREADLPEGLVTQSPNLLDLVKADGAALYYGGQIWTLGETPTEEQIRD 60

Query: 455 IVEWLLTYHGDSTGLSTDSLADAGYPKAATLGDAVCGMAVAYITKRDF--LFWFRSHTAK 512
           +  WL     DST  STDSL++A YP AA LGD   GM    I+ +D   L WFR  T +
Sbjct: 61  LAAWLNR-ESDSTVFSTDSLSEA-YPGAAALGDVASGMLAIPISSKDRDYLLWFRPETVR 118

Query: 513 EIKWGGAKHHPEDKDD-GQRMHPRSSFKAFLEVVKSRSLPWDNAEMDAIHSLQLILRDSF 571
            + WGG  H P + DD G+R+HPR SF+A+LEVV+ RSLPW + E+DA HSL+LIL +  
Sbjct: 119 TVTWGGNPHKPVEIDDGGRRLHPRKSFEAWLEVVRGRSLPWTDVELDAAHSLRLILLEVV 178

Query: 572 RDAEA 576
                
Sbjct: 179 LKRAD 183

Phytochromes are red/far-red photochromic biliprotein photoreceptors which regulate plant development. They are widely represented in both photosynthetic and non-photosynthetic bacteria and are known in a variety of fungi. Although sequence similarities are low, this domain is structurally related to pfam01590, which is generally located immediately N-terminal to this domain. Compared with pfam01590, this domain carries an additional tongue-like hairpin loop between the fifth beta-sheet and the sixth alpha-helix which functions to seal the chromophore pocket and stabilise the photoactivated far-red-absorbing state (Pfr). The tongue carries a conserved PRxSF motif, from which an arginine finger points into the chromophore pocket close to ring D forming a salt bridge with a conserved aspartate residue. Length = 183

>gnl\|CDD\|226702 COG4251, COG4251, Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]	Back alignment and domain information

>gnl\|CDD\|203947 pfam08446, PAS_2, PAS fold	Back alignment and domain information

>gnl\|CDD\|216228 pfam00989, PAS, PAS fold	Back alignment and domain information

>gnl\|CDD\|216228 pfam00989, PAS, PAS fold	Back alignment and domain information

>gnl\|CDD\|217081 pfam02518, HATPase_c, Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase	Back alignment and domain information

>gnl\|CDD\|223715 COG0642, BaeS, Signal transduction histidine kinase [Signal transduction mechanisms]	Back alignment and domain information

>gnl\|CDD\|238030 cd00075, HATPase_c, Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins	Back alignment and domain information

>gnl\|CDD\|214643 smart00387, HATPase_c, Histidine kinase-like ATPases	Back alignment and domain information

>gnl\|CDD\|214500 smart00065, GAF, Domain present in phytochromes and cGMP-specific phosphodiesterases	Back alignment and domain information

>gnl\|CDD\|234070 TIGR02956, TMAO_torS, TMAO reductase sytem sensor TorS	Back alignment and domain information

>gnl\|CDD\|237951 PRK15347, PRK15347, two component system sensor kinase SsrA; Provisional	Back alignment and domain information

>gnl\|CDD\|215963 pfam00512, HisKA, His Kinase A (phospho-acceptor) domain	Back alignment and domain information

>gnl\|CDD\|214644 smart00388, HisKA, His Kinase A (phosphoacceptor) domain	Back alignment and domain information

>gnl\|CDD\|216590 pfam01590, GAF, GAF domain	Back alignment and domain information

>gnl\|CDD\|225115 COG2205, KdpD, Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]	Back alignment and domain information

>gnl\|CDD\|236462 PRK09303, PRK09303, adaptive-response sensory kinase; Validated	Back alignment and domain information

>gnl\|CDD\|236848 PRK11107, PRK11107, hybrid sensory histidine kinase BarA; Provisional	Back alignment and domain information

>gnl\|CDD\|182772 PRK10841, PRK10841, hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional	Back alignment and domain information

>gnl\|CDD\|236901 PRK11360, PRK11360, sensory histidine kinase AtoS; Provisional	Back alignment and domain information

>gnl\|CDD\|222120 pfam13426, PAS_9, PAS domain	Back alignment and domain information

>gnl\|CDD\|236914 PRK11466, PRK11466, hybrid sensory histidine kinase TorS; Provisional	Back alignment and domain information

>gnl\|CDD\|238075 cd00130, PAS, PAS domain; PAS motifs appear in archaea, eubacteria and eukarya	Back alignment and domain information

>gnl\|CDD\|119399 cd00082, HisKA, Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-autophosphorylation by the catalytic domain of the histidine kinase	Back alignment and domain information

>gnl\|CDD\|227335 COG5002, VicK, Signal transduction histidine kinase [Signal transduction mechanisms]	Back alignment and domain information

>gnl\|CDD\|182169 PRK09959, PRK09959, hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional	Back alignment and domain information

>gnl\|CDD\|233391 TIGR01386, cztS_silS_copS, heavy metal sensor kinase	Back alignment and domain information

>gnl\|CDD\|238075 cd00130, PAS, PAS domain; PAS motifs appear in archaea, eubacteria and eukarya	Back alignment and domain information

>gnl\|CDD\|214512 smart00091, PAS, PAS domain	Back alignment and domain information

>gnl\|CDD\|226702 COG4251, COG4251, Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]	Back alignment and domain information

>gnl\|CDD\|232884 TIGR00229, sensory_box, PAS domain S-box	Back alignment and domain information

>gnl\|CDD\|225112 COG2202, AtoS, FOG: PAS/PAC domain [Signal transduction mechanisms]	Back alignment and domain information

>gnl\|CDD\|226370 COG3852, NtrB, Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]	Back alignment and domain information

>gnl\|CDD\|106506 PRK13560, PRK13560, hypothetical protein; Provisional	Back alignment and domain information

>gnl\|CDD\|222120 pfam13426, PAS_9, PAS domain	Back alignment and domain information

>gnl\|CDD\|225112 COG2202, AtoS, FOG: PAS/PAC domain [Signal transduction mechanisms]	Back alignment and domain information

>gnl\|CDD\|226655 COG4192, COG4192, Signal transduction histidine kinase regulating phosphoglycerate transport system [Signal transduction mechanisms]	Back alignment and domain information

>gnl\|CDD\|226654 COG4191, COG4191, Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]	Back alignment and domain information

>gnl\|CDD\|214512 smart00091, PAS, PAS domain	Back alignment and domain information

>gnl\|CDD\|182947 PRK11073, glnL, nitrogen regulation protein NR(II); Provisional	Back alignment and domain information

>gnl\|CDD\|236726 PRK10618, PRK10618, phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional	Back alignment and domain information

>gnl\|CDD\|182539 PRK10549, PRK10549, signal transduction histidine-protein kinase BaeS; Provisional	Back alignment and domain information

>gnl\|CDD\|219845 pfam08448, PAS_4, PAS fold	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		1111
COG4251		750	Bacteriophytochrome (light-regulated signal transd	100.0
TIGR02938		494	nifL_nitrog nitrogen fixation negative regulator N	100.0
PRK13560		807	hypothetical protein; Provisional	100.0
PRK11091		779	aerobic respiration control sensor protein ArcB; P	100.0
COG5002		459	VicK Signal transduction histidine kinase [Signal	100.0
COG3852		363	NtrB Signal transduction histidine kinase, nitroge	100.0
PRK11006		430	phoR phosphate regulon sensor protein; Provisional	100.0
PRK10618		894	phosphotransfer intermediate protein in two-compon	100.0
PRK13557		540	histidine kinase; Provisional	100.0
PRK10841		924	hybrid sensory kinase in two-component regulatory	100.0
PRK11073		348	glnL nitrogen regulation protein NR(II); Provision	100.0
PRK11360		607	sensory histidine kinase AtoS; Provisional	100.0
PF00360		182	PHY: Phytochrome region; InterPro: IPR013515 Phyto	100.0
TIGR02966		333	phoR_proteo phosphate regulon sensor kinase PhoR.	100.0
PRK09959		1197	hybrid sensory histidine kinase in two-component r	100.0
COG2205		890	KdpD Osmosensitive K+ channel histidine kinase [Si	100.0
COG5000		712	NtrY Signal transduction histidine kinase involved	99.98
PRK13559		361	hypothetical protein; Provisional	99.98
PRK09303		380	adaptive-response sensory kinase; Validated	99.97
PRK11086		542	sensory histidine kinase DcuS; Provisional	99.97
COG4191		603	Signal transduction histidine kinase regulating C4	99.97
PRK15053		545	dpiB sensor histidine kinase DpiB; Provisional	99.97
TIGR02956		968	TMAO_torS TMAO reductase sytem sensor TorS. This p	99.96
PRK15347		921	two component system sensor kinase SsrA; Provision	99.96
PRK11107		919	hybrid sensory histidine kinase BarA; Provisional	99.96
PRK11466		914	hybrid sensory histidine kinase TorS; Provisional	99.96
COG3290		537	CitA Signal transduction histidine kinase regulati	99.95
PRK10490		895	sensor protein KdpD; Provisional	99.95
PRK13837		828	two-component VirA-like sensor kinase; Provisional	99.95
PRK10364		457	sensor protein ZraS; Provisional	99.94
PRK10604		433	sensor protein RstB; Provisional	99.94
PRK10815		485	sensor protein PhoQ; Provisional	99.93
PRK10549		466	signal transduction histidine-protein kinase BaeS;	99.92
PRK10755		356	sensor protein BasS/PmrB; Provisional	99.92
TIGR03785		703	marine_sort_HK proteobacterial dedicated sortase s	99.92
PRK09835		482	sensor kinase CusS; Provisional	99.91
TIGR01386		457	cztS_silS_copS heavy metal sensor kinase. Members	99.9
PF08446		110	PAS_2: PAS fold; InterPro: IPR013654 The PAS fold	99.9
PRK11100		475	sensory histidine kinase CreC; Provisional	99.9
PRK09776		1092	putative diguanylate cyclase; Provisional	99.9
PRK10337		449	sensor protein QseC; Provisional	99.9
TIGR02916		679	PEP_his_kin putative PEP-CTERM system histidine ki	99.9
PRK09776		1092	putative diguanylate cyclase; Provisional	99.9
COG4192		673	Signal transduction histidine kinase regulating ph	99.89
PRK09470		461	cpxA two-component sensor protein; Provisional	99.89
PRK09467		435	envZ osmolarity sensor protein; Provisional	99.89
COG0642		336	BaeS Signal transduction histidine kinase [Signal	99.88
TIGR02040		442	PpsR-CrtJ transcriptional regulator PpsR. This mod	99.86
PRK13560		807	hypothetical protein; Provisional	99.84
PRK11644		495	sensory histidine kinase UhpB; Provisional	99.83
PRK11359		799	cyclic-di-GMP phosphodiesterase; Provisional	99.79
TIGR02040		442	PpsR-CrtJ transcriptional regulator PpsR. This mod	99.75
PRK10935		565	nitrate/nitrite sensor protein NarQ; Provisional	99.7
PF02518		111	HATPase_c: Histidine kinase-, DNA gyrase B-, and H	99.69
PRK10600		569	nitrate/nitrite sensor protein NarX; Provisional	99.68
COG3920		221	Signal transduction histidine kinase [Signal trans	99.63
PRK10547		670	chemotaxis protein CheA; Provisional	99.56
COG4585		365	Signal transduction histidine kinase [Signal trans	99.51
PF08448		110	PAS_4: PAS fold; InterPro: IPR013656 The PAS fold	99.46
PF13426		104	PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_	99.45
COG3850		574	NarQ Signal transduction histidine kinase, nitrate	99.44
COG3851		497	UhpB Signal transduction histidine kinase, glucose	99.43
PF00989		113	PAS: PAS fold; InterPro: IPR013767 PAS domains are	99.42
COG4564		459	Signal transduction histidine kinase [Signal trans	99.39
PRK11091		779	aerobic respiration control sensor protein ArcB; P	99.38
smart00387		111	HATPase_c Histidine kinase-like ATPases. Histidine	99.31
PF13426		104	PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_	99.28
PRK04184		535	DNA topoisomerase VI subunit B; Validated	99.24
COG0643		716	CheA Chemotaxis protein histidine kinase and relat	99.21
PF00989		113	PAS: PAS fold; InterPro: IPR013767 PAS domains are	99.18
PRK13559		361	hypothetical protein; Provisional	99.12
PF08448		110	PAS_4: PAS fold; InterPro: IPR013656 The PAS fold	99.11
cd00075		103	HATPase_c Histidine kinase-like ATPases; This fami	99.11
PRK14868		795	DNA topoisomerase VI subunit B; Provisional	99.1
KOG0519		786	consensus Sensory transduction histidine kinase [S	99.08
PRK10060		663	RNase II stability modulator; Provisional	99.08
TIGR01052		488	top6b DNA topoisomerase VI, B subunit. This model	99.07
PRK13557		540	histidine kinase; Provisional	99.06
PRK13558		665	bacterio-opsin activator; Provisional	99.04
PRK10060		663	RNase II stability modulator; Provisional	99.04
TIGR00229		124	sensory_box PAS domain S-box. The PAS domain was p	99.01
TIGR01925		137	spIIAB anti-sigma F factor. This model describes t	98.98
PRK11359		799	cyclic-di-GMP phosphodiesterase; Provisional	98.98
PRK04069		161	serine-protein kinase RsbW; Provisional	98.92
PRK03660		146	anti-sigma F factor; Provisional	98.92
COG3275		557	LytS Putative regulator of cell autolysis [Signal	98.91
PRK14867		659	DNA topoisomerase VI subunit B; Provisional	98.89
COG3829		560	RocR Transcriptional regulator containing PAS, AAA	98.87
COG2972		456	Predicted signal transduction protein with a C-ter	98.83
PF13596		106	PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.	98.8
PF00512		68	HisKA: His Kinase A (phospho-acceptor) domain; Int	98.77
TIGR01924		159	rsbW_low_gc serine-protein kinase RsbW. This model	98.74
PF08447		91	PAS_3: PAS fold; InterPro: IPR013655 The PAS fold	98.71
PRK11360		607	sensory histidine kinase AtoS; Provisional	98.68
PF14501		100	HATPase_c_5: GHKL domain	98.65
PRK13558		665	bacterio-opsin activator; Provisional	98.65
PF08447		91	PAS_3: PAS fold; InterPro: IPR013655 The PAS fold	98.62
TIGR00229		124	sensory_box PAS domain S-box. The PAS domain was p	98.6
TIGR02938		494	nifL_nitrog nitrogen fixation negative regulator N	98.59
cd00130		103	PAS PAS domain; PAS motifs appear in archaea, euba	98.55
TIGR02966		333	phoR_proteo phosphate regulon sensor kinase PhoR.	98.51
PF01590		154	GAF: GAF domain; InterPro: IPR003018 This domain i	98.47
PF12860		115	PAS_7: PAS fold	98.44
PRK11073		348	glnL nitrogen regulation protein NR(II); Provision	98.41
PRK11388		638	DNA-binding transcriptional regulator DhaR; Provis	98.4
KOG3558		768	consensus Hypoxia-inducible factor 1/Neuronal PAS	98.37
PF13581		125	HATPase_c_2: Histidine kinase-like ATPase domain	98.36
PRK11006		430	phoR phosphate regulon sensor protein; Provisional	98.27
COG3829		560	RocR Transcriptional regulator containing PAS, AAA	98.22
COG2202		232	AtoS FOG: PAS/PAC domain [Signal transduction mech	98.21
cd00130		103	PAS PAS domain; PAS motifs appear in archaea, euba	98.18
KOG0787		414	consensus Dehydrogenase kinase [Signal transductio	98.17
PRK10820		520	DNA-binding transcriptional regulator TyrR; Provis	98.16
PRK11086		542	sensory histidine kinase DcuS; Provisional	98.15
PF13596		106	PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.	98.11
PF14598		111	PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W	97.98
PF12860		115	PAS_7: PAS fold	97.93
COG1389		538	DNA topoisomerase VI, subunit B [DNA replication,	97.91
smart00065		149	GAF Domain present in phytochromes and cGMP-specif	97.9
COG5000		712	NtrY Signal transduction histidine kinase involved	97.89
COG2172		146	RsbW Anti-sigma regulatory factor (Ser/Thr protein	97.86
COG2202		232	AtoS FOG: PAS/PAC domain [Signal transduction mech	97.72
smart00388		66	HisKA His Kinase A (phosphoacceptor) domain. Dimer	97.66
COG3290		537	CitA Signal transduction histidine kinase regulati	97.62
PF14598		111	PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W	97.61
PRK15053		545	dpiB sensor histidine kinase DpiB; Provisional	97.56
TIGR00585		312	mutl DNA mismatch repair protein MutL. All protein	97.54
PF13188		64	PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.	97.46
COG5002		459	VicK Signal transduction histidine kinase [Signal	97.25
PRK10820		520	DNA-binding transcriptional regulator TyrR; Provis	97.21
PRK09959		1197	hybrid sensory histidine kinase in two-component r	97.2
PRK11388		638	DNA-binding transcriptional regulator DhaR; Provis	97.17
KOG3559		598	consensus Transcriptional regulator SIM1 [Transcri	97.12
cd00082		65	HisKA Histidine Kinase A (dimerization/phosphoacce	97.1
PF13589		137	HATPase_c_3: Histidine kinase-, DNA gyrase B-, and	97.01
KOG0501		971	consensus K+-channel KCNQ [Inorganic ion transport	96.95
KOG0501		971	consensus K+-channel KCNQ [Inorganic ion transport	96.83
KOG3560		712	consensus Aryl-hydrocarbon receptor [Transcription	96.82
smart00091		67	PAS PAS domain. PAS motifs appear in archaea, euba	96.8
COG2203		175	FhlA FOG: GAF domain [Signal transduction mechanis	96.53
COG2461		409	Uncharacterized conserved protein [Function unknow	96.48
PRK00095		617	mutL DNA mismatch repair protein; Reviewed	96.43
PF13188		64	PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.	96.4
PF08670		148	MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEK	96.29
TIGR01817		534	nifA Nif-specific regulatory protein. This model r	96.27
PRK05559		631	DNA topoisomerase IV subunit B; Reviewed	95.91
TIGR02373		124	photo_yellow photoactive yellow protein. Members o	95.91
PF13492		129	GAF_3: GAF domain; PDB: 3EEA_A 4DMZ_A 4DN0_A 1VHM_	95.86
KOG1229		775	consensus 3'5'-cyclic nucleotide phosphodiesterase	95.75
PF10090		182	DUF2328: Uncharacterized protein conserved in bact	95.63
KOG3558		768	consensus Hypoxia-inducible factor 1/Neuronal PAS	95.57
PRK05022		509	anaerobic nitric oxide reductase transcription reg	95.46
COG3604		550	FhlA Transcriptional regulator containing GAF, AAA	95.4
TIGR01055		625	parE_Gneg DNA topoisomerase IV, B subunit, proteob	95.37
TIGR01059		654	gyrB DNA gyrase, B subunit. This model describes t	95.25
COG5385		214	Uncharacterized protein conserved in bacteria [Fun	95.16
PF13185		148	GAF_2: GAF domain; PDB: 2QYB_A 3KSG_B 3KSF_C 3KSI_	95.15
TIGR02373		124	photo_yellow photoactive yellow protein. Members o	94.98
PRK05644		638	gyrB DNA gyrase subunit B; Validated	94.88
PRK10841		924	hybrid sensory kinase in two-component regulatory	94.82
COG3283		511	TyrR Transcriptional regulator of aromatic amino a	94.78
PF07568		76	HisKA_2: Histidine kinase; InterPro: IPR011495 Two	94.73
COG3852		363	NtrB Signal transduction histidine kinase, nitroge	94.39
PRK15429		686	formate hydrogenlyase transcriptional activator Fh	94.18
KOG1229		775	consensus 3'5'-cyclic nucleotide phosphodiesterase	93.89
PRK05218		613	heat shock protein 90; Provisional	93.69
smart00433		594	TOP2c TopoisomeraseII. Eukaryotic DNA topoisomeras	93.53
PRK14939		756	gyrB DNA gyrase subunit B; Provisional	93.44
COG0323		638	MutL DNA mismatch repair enzyme (predicted ATPase)	93.25
PRK10618		894	phosphotransfer intermediate protein in two-compon	93.08
KOG3753		1114	consensus Circadian clock protein period [Signal t	92.52
COG2461		409	Uncharacterized conserved protein [Function unknow	92.12
PF08670		148	MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEK	91.92
COG3284		606	AcoR Transcriptional activator of acetoin/glycerol	91.61
KOG0519		786	consensus Sensory transduction histidine kinase [S	90.84
PTZ00272		701	heat shock protein 83 kDa (Hsp83); Provisional	90.61
smart00091		67	PAS PAS domain. PAS motifs appear in archaea, euba	90.45
TIGR01058		637	parE_Gpos DNA topoisomerase IV, B subunit, Gram-po	90.16
smart00086		43	PAC Motif C-terminal to PAS motifs (likely to cont	89.85
COG0326		623	HtpG Molecular chaperone, HSP90 family [Posttransl	89.35
PRK11061		748	fused phosphoenolpyruvate-protein phosphotransfera	89.29
PRK14083		601	HSP90 family protein; Provisional	88.48
PTZ00108		1388	DNA topoisomerase 2-like protein; Provisional	88.16
smart00086		43	PAC Motif C-terminal to PAS motifs (likely to cont	87.94
PLN03237		1465	DNA topoisomerase 2; Provisional	86.36
KOG3559		598	consensus Transcriptional regulator SIM1 [Transcri	85.74
PTZ00109		903	DNA gyrase subunit b; Provisional	85.3
COG5381		184	Uncharacterized protein conserved in bacteria [Fun	84.68
PHA02569		602	39 DNA topoisomerase II large subunit; Provisional	84.47
KOG3560		712	consensus Aryl-hydrocarbon receptor [Transcription	84.24
COG0187		635	GyrB Type IIA topoisomerase (DNA gyrase/topo II, t	82.94
KOG3561		803	consensus Aryl-hydrocarbon receptor nuclear transl	82.88
PTZ00130		814	heat shock protein 90; Provisional	82.87
COG3283		511	TyrR Transcriptional regulator of aromatic amino a	81.65
PF07310		137	PAS_5: PAS domain; InterPro: IPR009922 This family	80.01

>COG4251 Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]	Back alignment and domain information

Probab=100.00  E-value=4.3e-144  Score=1210.47  Aligned_cols=697  Identities=28%  Similarity=0.478  Sum_probs=588.6

Q ss_pred             hhccCCCCCCccceEEEEeCCCceEEeeccchhhhhCCCCCCCCcchhhhhhhcCCchhhhcCchhHHHHHHHhcccccc
Q 037299           88 SKIQRGGHIQPFGCTIAVDEATFRVIAYSENAGEMLGLAPQSVPNLEKQEILTIGTDVRTLFTSSSSVLLEKAFGAREIT  167 (1111)
Q Consensus        88 ~~i~~~g~iQp~G~ll~~~~~~~~i~~~S~N~~~~lg~~~~~~~~~~~~~~~~lg~~~~~~~~~~~~~~~~~~~~~~~~~  167 (1111)
                      ++||+||+||||||||++|+.++.|+|+|+||..+||+.|+.          ++|+++.++|+.+++..++.++......
T Consensus        18 ePIHipG~IQPHG~Llvl~~~~~~Vlq~S~N~~~~LG~~~e~----------l~~~tl~~vl~~~qv~~l~~~l~~~~~~   87 (750)
T COG4251          18 EPIHIPGAIQPHGALLVLDEADLMVLQASENCANILGREPED----------LLGRTLGAVLTSEQVPPLQSALTVGGLT   87 (750)
T ss_pred             CCccCCCccCCceeEEEeecCCchhhhhhhhHHHHhCCChhh----------hhcCCHHHhcchhhccHHHHhccccCcc
Confidence            579999999999999999999999999999999999998864          6999999999999999999999998888


Q ss_pred             cCCcEEEEecCCCceEEEEEEEeCCEEEEEeeeCCCCCCcchhhhhhHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHH
Q 037299          168 LLNPIWIHSKNTGKPFYAILHRVDVGIVIDLEPARTEDPALSIAGAVQSQKLAVRAISQLQSLPGGDIKLLCDTVVESVR  247 (1111)
Q Consensus       168 ~~~~~~~~~~~~~~~f~~~~h~~~~~~i~e~E~~~~~~~~~~~~~~~~~~~~~~~~i~~l~~~~~~~~~~l~~~~~~~vr  247 (1111)
                      ..||-.+..+. +..||+++||+++.+|+||||....+. .+   .+.+|.++..++.+||+.+  ++.++|+.+++|||
T Consensus        88 ~~np~~~w~~~-~~~fDv~~HR~~~llIlEfEp~~t~e~-~~---~l~f~h~~k~a~~~lq~a~--~l~~l~~~~tqeVr  160 (750)
T COG4251          88 TLNPTKMWTRK-GGSFDVSAHRSKELLILEFEPAGTGET-AS---FLGFYHLAKLAMNRLQSAA--NLRDLLSRTTQEVR  160 (750)
T ss_pred             cCCchhhhhhc-CCceeEEEEecCcEEEEEEecCccccc-cc---ccchHHHHHHHHHHHhcCc--cHHHHHHHHHHHHH
Confidence            88885543333 337999999999999999999754332 22   3357888888999999955  99999999999999


Q ss_pred             HhhCCCeEEEEeecCCCCcEEEEEecCCCCCCccCCCCCCCCchHHHHHHHHhCCeeEeeccCCCcceeec--CCCCCCc
Q 037299          248 QLTGYDRVMVYRFHEDEHGEVVAESKRPDLEPYFGLHYPATDIPQASRFLFKQNRVRMIVDCHATPLCVIQ--DEGLMQP  325 (1111)
Q Consensus       248 ~~~g~DRVmiY~F~~d~~G~VvaE~~~~~~~~~lg~~~pa~dip~~ar~ly~~n~~r~i~d~~~~~~~~~~--~~~~~~~  325 (1111)
                      ++|||||||+|||++||||+||||+++++|+||||+||||||||+|||+||.+|++|+|||+.|+||||+|  +|.+++|
T Consensus       161 ~~tGfDRVMlYrF~~d~~G~VIAEak~e~LesyLGl~yPaSDIP~qAR~LY~~N~lRlIpD~~~~~vpv~PavNp~t~~p  240 (750)
T COG4251         161 RMTGFDRVMLYRFDEDGSGEVIAEAKREDLESYLGLRYPASDIPQQARALYIQNPLRLIPDVSYTPVPVLPAVNPETNEP  240 (750)
T ss_pred             HhcCCceEEEEeecCCCCccEEeccccccchhhhcccCCcccCCHHHHHHHhcCceeecccccCcccccccccCcccCCc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999  7999999


Q ss_pred             ccccCccccCCChhHHHHHHhcCcceEEEEEEEEcCCCccccC-CCCCccch---------HhhHhhcHHHHHHHH--HH
Q 037299          326 LCLVGSTLRAPHGCHAQYMANMGSIASLALAVIINGNDEEAVG-GRSTTRLW---------AFGLQLNMELQLASQ--LS  393 (1111)
Q Consensus       326 ldls~~~lRsvsp~h~~yl~nmgv~asl~~~i~~~~~~~~~~~-~~~~~~LW---------~~~~~~~~~~~~~~~--~~  393 (1111)
                      +|||+|.||||||||+|||+||||+||||||||+||++||+.. +....|+-         .||..++++++...+  ..
T Consensus       241 ~DLs~svLRSvSp~H~eYLrNMGV~ASmSISivv~g~LWGLIACHH~sPk~ip~~vR~acef~gq~~s~~i~~~e~~~~~  320 (750)
T COG4251         241 LDLSYSVLRSVSPIHLEYLRNMGVGASMSISIVVDGKLWGLIACHHQSPKVIPYEVRKACEFFGQVLSMEISALEQSEDA  320 (750)
T ss_pred             ccchHHHHhccChHHHHHHHhcCcceeeEEEEEECCeeEEeeeeccCCCccCCHHHHHHHHHHHHHHHHHHHHHhhhhhH
Confidence            9999999999999999999999999999999999988887762 22334443         445444444432211  11


Q ss_pred             HHHHH---HHHHHHHHHhccCC-CCccccCCcchhhhccCCEEEEEECCeEEEecCCCCHHHHHHHHHHHHhccCCCeeE
Q 037299          394 EKHVL---RTQTLLCDMLLRDS-PAGIVTQSPSIMDLVKCDGAALYYQGKYYPLGVTPTETQIKDIVEWLLTYHGDSTGL  469 (1111)
Q Consensus       394 ~~~~~---~~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~a~g~a~~~~~~~~~~g~~p~~~~i~~l~~~l~~~~~~~~~~  469 (1111)
                      +-+..   ....++..|...++ ..+++...++|++|++|||++||++|++.++|.||+..+|..|+.||.+.... .+|
T Consensus       321 d~r~~l~~~~arl~~~ma~~~~~~d~L~~~~~dll~L~~adGaal~fg~~~~~vG~tP~~~~v~~Ll~wl~~~~~~-~vf  399 (750)
T COG4251         321 DYRVQLTEHHARLLRYMAHAADFVDGLIDHQDDLLDLMPADGAALCFGGRWHLVGETPPRPAVQRLLQWLAEREEG-DVF  399 (750)
T ss_pred             HHHHHHHHHHHHHHHHHhhhcchhhhhcCCchhhHhhccCCceEEEECCEEEEecCCCChHHHHHHHHHHhcCCcc-cEE
Confidence            11111   12334555655444 68888999999999999999999999999999999999999999999887544 799


Q ss_pred             eecccccCCCCCccccccceeeEEEEEeCC--CcEEEEeecCCCcEEEecCCCCCCCC-CCCCCCccccchhHHHHHHHh
Q 037299          470 STDSLADAGYPKAATLGDAVCGMAVAYITK--RDFLFWFRSHTAKEIKWGGAKHHPED-KDDGQRMHPRSSFKAFLEVVK  546 (1111)
Q Consensus       470 ~t~~l~~~~~p~~~~~~~~~~G~l~~~~~~--~~~~~wfr~e~~~~v~Wag~p~~~~~-~~~g~~l~pr~SF~~w~e~v~  546 (1111)
                      +||+|++. ||+++.+++.+||||||+|+.  ++||+|||||.+++|+|||||+|+.. .++|.|++||+||+.|+|+|+
T Consensus       400 ~TdsL~q~-yPda~~~~~vAsGlLAI~is~~~s~~llWFRpEvv~tV~WGG~P~k~~e~~~~~~rL~PRkSFe~WkE~vR  478 (750)
T COG4251         400 ATDSLSQV-YPDAEDYASVASGLLAIPISRVKSNYLLWFRPEVVQTVNWGGDPEKPYEAGPMGIRLTPRKSFELWKETVR  478 (750)
T ss_pred             eecccccc-CcchhhhccccceeEEEEeeccccceEEEEchHHheeeccCCCCCCccccCCCCcccCCcccHHHHHHHHh
Confidence            99999995 999999999999999999997  89999999999999999999999976 455789999999999999999


Q ss_pred             ccccCCchhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhcCCcEEEEcCCccEE
Q 037299          547 SRSLPWDNAEMDAIHSLQLILRDSFRDAEASNSKAVVNAQLVDLELQGVDELSSVAREMVRLIETATAPIFAVDVHGCVN  626 (1111)
Q Consensus       547 g~s~pW~~~El~aa~~Lrl~L~~~l~~~~~~~e~~~~~~~l~~~l~~~~~eL~~~~~~l~~lie~~~~~I~~~D~dG~I~  626 (1111)
                      ++|.||+..|+++|.+||..+.+...+-.                    +|+...                         
T Consensus       479 l~s~PWs~~ei~~A~~LR~aiv~ivl~~a--------------------eela~l-------------------------  513 (750)
T COG4251         479 LQSQPWSEVEIEAALELRKAIVGIVLRHA--------------------EELAQL-------------------------  513 (750)
T ss_pred             ccCCCCCHHHHHHHHHHHHHHHHHHHHHH--------------------HHHHHH-------------------------
Confidence            99999999999999999554433321110                    000000                         


Q ss_pred             eecHHHHHHcCCChhhhcCCcccccccchhhHHHHHHHHHHHHcCCCccceEEEEEEeccccCCcEEEEEEEeEeeccCC
Q 037299          627 GWNAKVAELTGLSVEEAMGKSLVHDLVYKEYEEIVDNLLHHALKGEEDKNVEIKLRTFGAENRKKAVFVVVNACSSKDYT  706 (1111)
Q Consensus       627 ~~N~a~~~l~G~~~eeliG~~~~~~l~~~~~~~~~~~~l~~~l~~~~~~~~e~~l~~~~~~~dG~~~~v~v~~~pi~d~~  706 (1111)
                                                                                                      
T Consensus       514 --------------------------------------------------------------------------------  513 (750)
T COG4251         514 --------------------------------------------------------------------------------  513 (750)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             CCEEEEEEEEEechhHHHHHHHHHhHHHHHHHHHhCCCCCCCCccccCCCCccccchhhhHHHhCCCccccccccccccc
Q 037299          707 NNIVGVCFVGQDVTDQKLVMDKFIHIQGDYKAIVHSPNPLIPPIFASDENTCCSEWNTAMEKLTGWSRGDIIGKMLVGEV  786 (1111)
Q Consensus       707 G~v~gvv~v~~DITerK~ae~~L~~se~~l~~i~~~~~~l~~~I~v~D~~g~ii~~N~a~~~l~G~~~eeliGk~l~~~v  786 (1111)
                                                                                                      
T Consensus       514 --------------------------------------------------------------------------------  513 (750)
T COG4251         514 --------------------------------------------------------------------------------  513 (750)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             cccccccCChhhHHHHHHHHHhhhCCCCcceeeeeeecCCCCEEEEEEEEeeeecCCCCEEEEEeeeecccHHHHHHHHH
Q 037299          787 FGSCCRLKGPDALTKFMIALHNAFGGQDTEKFPFPLFDRNGKYVQALLTANKRVNMEGQIVGAFCFLQIASPELQQALTV  866 (1111)
Q Consensus       787 ~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~v~~~~DITer~~~e~el  866 (1111)
                                                                                                      
T Consensus       514 --------------------------------------------------------------------------------  513 (750)
T COG4251         514 --------------------------------------------------------------------------------  513 (750)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhcC---CCCHHHHHHHHHHHHHHHHHHHHHhhc-cccccccCCc
Q 037299          867 QRQQEKKCFARLKELAYICQEIKNPLSGVSFTNSLLEAT---DLTEDQKQLLETSAACEKQMLKIIKDV-DLESIEDGSL  942 (1111)
Q Consensus       867 ~~~~e~~~~~r~~~La~isHEIrnPLt~I~~~~~LL~~~---~l~e~~~~~l~~i~~~~~~l~~lI~dL-dlsri~~g~~  942 (1111)
                      ++..++.+....+|...++|++++||+.|.+++++|...   .++++.++++..+.+....|..||+++ .++++  |..
T Consensus       514 ~r~lersn~el~~f~yv~sHdlqePl~~I~~~a~lL~~~~~~~~d~~~~~~i~~~~~~~~~~~~lidd~l~~s~l--~~~  591 (750)
T COG4251         514 RRELERSNAELRAFAYVASHDLQEPLRQISNYAQLLSERYSDALDEEAKEFITFISRLTSLMQQLIDDLLTYSKL--GLT  591 (750)
T ss_pred             HHHHhhhhHHHHHHHHHhhhhhhHHHHHHHHHHHhhhhccccccChHHHHHHHHHHHHHHHHHHHHHHHhhhhhh--ccc
Confidence            001111111122333446999999999999999999754   578899999999999999999999997 99998  555


Q ss_pred             ceeeEeecHHHHHHHHHHHHHHHhhccCcEEEeecCCcccceEEEecHHHHHHHHHHHHHHHhhcCCCCCceEEEEEEEc
Q 037299          943 EFEKAEFLLGSVINAVVSQVMMLLRERNLQLIRDIPEEIKTLAVYGDQARIQQVLADFLLNMVRYSPSAEGWVEIHVRPT 1022 (1111)
Q Consensus       943 ~l~~~~~~L~~vi~~v~~~~~~~~~~~~i~l~~~~~~~~~~~~v~~D~~~L~qVl~nLl~NAik~t~~~~g~I~I~v~~~ 1022 (1111)
                      .....+.|+.++++.++..+.....+.++++.+..   +|  .+.+|+.++.||+.||+.||+||..+...+|+|++...
T Consensus       592 ~~~l~~td~~~vv~~vl~~l~~ri~dtgaei~i~~---lp--~v~~d~~~l~qv~~NLi~Naik~~~~e~~~i~I~~~r~  666 (750)
T COG4251         592 EAPLQPTDVQKVVDKVLLELSQRIADTGAEIRIAP---LP--VVAADATQLGQVFQNLIANAIKFGGPENPDIEISAERQ  666 (750)
T ss_pred             cCCCCCcchHHHHHHHHHhcccccccccceEEecc---cc--eeecCHHHHHHHHHHHHhhheecCCCCCCceEEeeecc
Confidence            56666889999999999999999999999988775   44  69999999999999999999999887458899997766


Q ss_pred             cccCCCCceeEEEEEEEeeCCCCCChhhhhhccCCC------CCCCCccchHHHHHHHHHHcCCEEEEEecCC-ceEEEE
Q 037299         1023 LKQSSEGQTIVHNEFRMVCPGEGLPPELVQDMFHSS------RWMTQEGLGLSMCRKILKLMNGEVQYIRESE-RCYFLI 1095 (1111)
Q Consensus      1023 ~~~~~~~~~~~~v~i~V~DnG~GIp~e~~~~iFepf------~~~~G~GLGL~i~r~iVe~~gG~I~v~s~~g-gstF~~ 1095 (1111)
                      ++         .+.+.|.|||+||++...+++|..|      ..+.|+|+||+|||+|++.|+|+||++|.+| |+||.|
T Consensus       667 ed---------~~t~sV~dng~Gi~~a~~~riF~iFqRl~s~~~y~gtG~GL~I~kkI~e~H~G~i~vEs~~gEgsTF~f  737 (750)
T COG4251         667 ED---------EWTFSVRDNGIGIDPAYFERIFVIFQRLHSRDEYLGTGLGLAICKKIAERHQGRIWVESTPGEGSTFYF  737 (750)
T ss_pred             CC---------ceEEEecCCCCCcCHHHHHHHHHHHHhcCchhhhcCCCccHHHHHHHHHHhCceEEEeecCCCceeEEE
Confidence            66         7899999999999999999999988      2567999999999999999999999999987 687777


Q ss_pred             EEEeeCCCCCC
Q 037299         1096 IFELPMPRRGS 1106 (1111)
Q Consensus      1096 ~L~LP~~~~~~ 1106 (1111)
                      +  +|..++.+
T Consensus       738 ~--lp~~~~e~  746 (750)
T COG4251         738 T--LPVGGEEP  746 (750)
T ss_pred             E--eecCCcCc
Confidence            5  47766554

>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL	Back alignment and domain information

>PRK13560 hypothetical protein; Provisional	Back alignment and domain information

>PRK11091 aerobic respiration control sensor protein ArcB; Provisional	Back alignment and domain information

>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]	Back alignment and domain information

>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]	Back alignment and domain information

>PRK11006 phoR phosphate regulon sensor protein; Provisional	Back alignment and domain information

>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional	Back alignment and domain information

>PRK13557 histidine kinase; Provisional	Back alignment and domain information

>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional	Back alignment and domain information

>PRK11073 glnL nitrogen regulation protein NR(II); Provisional	Back alignment and domain information

>PRK11360 sensory histidine kinase AtoS; Provisional	Back alignment and domain information

>PF00360 PHY: Phytochrome region; InterPro: IPR013515 Phytochrome belongs to a family of plant photoreceptors that mediate physiological and developmental responses to changes in red and far-red light conditions []	Back alignment and domain information

>TIGR02966 phoR_proteo phosphate regulon sensor kinase PhoR	Back alignment and domain information

>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional	Back alignment and domain information

>COG2205 KdpD Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]	Back alignment and domain information

>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]	Back alignment and domain information

>PRK13559 hypothetical protein; Provisional	Back alignment and domain information

>PRK09303 adaptive-response sensory kinase; Validated	Back alignment and domain information

>PRK11086 sensory histidine kinase DcuS; Provisional	Back alignment and domain information

>COG4191 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]	Back alignment and domain information

>PRK15053 dpiB sensor histidine kinase DpiB; Provisional	Back alignment and domain information

>TIGR02956 TMAO_torS TMAO reductase sytem sensor TorS	Back alignment and domain information

>PRK15347 two component system sensor kinase SsrA; Provisional	Back alignment and domain information

>PRK11107 hybrid sensory histidine kinase BarA; Provisional	Back alignment and domain information

>PRK11466 hybrid sensory histidine kinase TorS; Provisional	Back alignment and domain information

>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]	Back alignment and domain information

>PRK10490 sensor protein KdpD; Provisional	Back alignment and domain information

>PRK13837 two-component VirA-like sensor kinase; Provisional	Back alignment and domain information

>PRK10364 sensor protein ZraS; Provisional	Back alignment and domain information

>PRK10604 sensor protein RstB; Provisional	Back alignment and domain information

>PRK10815 sensor protein PhoQ; Provisional	Back alignment and domain information

>PRK10549 signal transduction histidine-protein kinase BaeS; Provisional	Back alignment and domain information

>PRK10755 sensor protein BasS/PmrB; Provisional	Back alignment and domain information

>TIGR03785 marine_sort_HK proteobacterial dedicated sortase system histidine kinase	Back alignment and domain information

>PRK09835 sensor kinase CusS; Provisional	Back alignment and domain information

>TIGR01386 cztS_silS_copS heavy metal sensor kinase	Back alignment and domain information

>PF08446 PAS_2: PAS fold; InterPro: IPR013654 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []	Back alignment and domain information

>PRK11100 sensory histidine kinase CreC; Provisional	Back alignment and domain information

>PRK09776 putative diguanylate cyclase; Provisional	Back alignment and domain information

>PRK10337 sensor protein QseC; Provisional	Back alignment and domain information

>TIGR02916 PEP_his_kin putative PEP-CTERM system histidine kinase	Back alignment and domain information

>PRK09776 putative diguanylate cyclase; Provisional	Back alignment and domain information

>COG4192 Signal transduction histidine kinase regulating phosphoglycerate transport system [Signal transduction mechanisms]	Back alignment and domain information

>PRK09470 cpxA two-component sensor protein; Provisional	Back alignment and domain information

>PRK09467 envZ osmolarity sensor protein; Provisional	Back alignment and domain information

>COG0642 BaeS Signal transduction histidine kinase [Signal transduction mechanisms]	Back alignment and domain information

>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR	Back alignment and domain information

>PRK13560 hypothetical protein; Provisional	Back alignment and domain information

>PRK11644 sensory histidine kinase UhpB; Provisional	Back alignment and domain information

>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional	Back alignment and domain information

>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR	Back alignment and domain information

>PRK10935 nitrate/nitrite sensor protein NarQ; Provisional	Back alignment and domain information

>PF02518 HATPase_c: Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; InterPro: IPR003594 This domain is found in several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases [], heat shock protein HSP90 [, , ], phytochrome-like ATPases and DNA mismatch repair proteins	Back alignment and domain information

>PRK10600 nitrate/nitrite sensor protein NarX; Provisional	Back alignment and domain information

>COG3920 Signal transduction histidine kinase [Signal transduction mechanisms]	Back alignment and domain information

>PRK10547 chemotaxis protein CheA; Provisional	Back alignment and domain information

>COG4585 Signal transduction histidine kinase [Signal transduction mechanisms]	Back alignment and domain information

>PF08448 PAS_4: PAS fold; InterPro: IPR013656 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []	Back alignment and domain information

>PF13426 PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_B 3P7N_B 1LL8_A 3MJQ_A 3BWL_A 4EET_B 4EEP_A	Back alignment and domain information

>COG3850 NarQ Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]	Back alignment and domain information

>COG3851 UhpB Signal transduction histidine kinase, glucose-6-phosphate specific [Signal transduction mechanisms]	Back alignment and domain information

>PF00989 PAS: PAS fold; InterPro: IPR013767 PAS domains are involved in many signalling proteins where they are used as a signal sensor domain []	Back alignment and domain information

>COG4564 Signal transduction histidine kinase [Signal transduction mechanisms]	Back alignment and domain information

>PRK11091 aerobic respiration control sensor protein ArcB; Provisional	Back alignment and domain information

>smart00387 HATPase_c Histidine kinase-like ATPases	Back alignment and domain information

>PF13426 PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_B 3P7N_B 1LL8_A 3MJQ_A 3BWL_A 4EET_B 4EEP_A	Back alignment and domain information

>PRK04184 DNA topoisomerase VI subunit B; Validated	Back alignment and domain information

>COG0643 CheA Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]	Back alignment and domain information

>PF00989 PAS: PAS fold; InterPro: IPR013767 PAS domains are involved in many signalling proteins where they are used as a signal sensor domain []	Back alignment and domain information

>PRK13559 hypothetical protein; Provisional	Back alignment and domain information

>PF08448 PAS_4: PAS fold; InterPro: IPR013656 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []	Back alignment and domain information

>cd00075 HATPase_c Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins	Back alignment and domain information

>PRK14868 DNA topoisomerase VI subunit B; Provisional	Back alignment and domain information

>KOG0519 consensus Sensory transduction histidine kinase [Signal transduction mechanisms]	Back alignment and domain information

>PRK10060 RNase II stability modulator; Provisional	Back alignment and domain information

>TIGR01052 top6b DNA topoisomerase VI, B subunit	Back alignment and domain information

>PRK13557 histidine kinase; Provisional	Back alignment and domain information

>PRK13558 bacterio-opsin activator; Provisional	Back alignment and domain information

>PRK10060 RNase II stability modulator; Provisional	Back alignment and domain information

>TIGR00229 sensory_box PAS domain S-box	Back alignment and domain information

>TIGR01925 spIIAB anti-sigma F factor	Back alignment and domain information

>PRK11359 cyclic-di-GMP phosphodiesterase; Provisional	Back alignment and domain information

>PRK04069 serine-protein kinase RsbW; Provisional	Back alignment and domain information

>PRK03660 anti-sigma F factor; Provisional	Back alignment and domain information

>COG3275 LytS Putative regulator of cell autolysis [Signal transduction mechanisms]	Back alignment and domain information

>PRK14867 DNA topoisomerase VI subunit B; Provisional	Back alignment and domain information

>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]	Back alignment and domain information

>COG2972 Predicted signal transduction protein with a C-terminal ATPase domain [Signal transduction mechanisms]	Back alignment and domain information

>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D	Back alignment and domain information

>PF00512 HisKA: His Kinase A (phospho-acceptor) domain; InterPro: IPR003661 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []	Back alignment and domain information

>TIGR01924 rsbW_low_gc serine-protein kinase RsbW	Back alignment and domain information

>PF08447 PAS_3: PAS fold; InterPro: IPR013655 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []	Back alignment and domain information

>PRK11360 sensory histidine kinase AtoS; Provisional	Back alignment and domain information

>PF14501 HATPase_c_5: GHKL domain	Back alignment and domain information

>PRK13558 bacterio-opsin activator; Provisional	Back alignment and domain information

>PF08447 PAS_3: PAS fold; InterPro: IPR013655 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []	Back alignment and domain information

>TIGR00229 sensory_box PAS domain S-box	Back alignment and domain information

>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL	Back alignment and domain information

>cd00130 PAS PAS domain; PAS motifs appear in archaea, eubacteria and eukarya	Back alignment and domain information

>TIGR02966 phoR_proteo phosphate regulon sensor kinase PhoR	Back alignment and domain information

>PF01590 GAF: GAF domain; InterPro: IPR003018 This domain is present in phytochromes and cGMP-specific phosphodiesterases	Back alignment and domain information

>PF12860 PAS_7: PAS fold	Back alignment and domain information

>PRK11073 glnL nitrogen regulation protein NR(II); Provisional	Back alignment and domain information

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional	Back alignment and domain information

>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]	Back alignment and domain information

>PF13581 HATPase_c_2: Histidine kinase-like ATPase domain	Back alignment and domain information

>PRK11006 phoR phosphate regulon sensor protein; Provisional	Back alignment and domain information

>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]	Back alignment and domain information

>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]	Back alignment and domain information

>cd00130 PAS PAS domain; PAS motifs appear in archaea, eubacteria and eukarya	Back alignment and domain information

>KOG0787 consensus Dehydrogenase kinase [Signal transduction mechanisms]	Back alignment and domain information

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional	Back alignment and domain information

>PRK11086 sensory histidine kinase DcuS; Provisional	Back alignment and domain information

>PF13596 PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D	Back alignment and domain information

>PF14598 PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W_A 3F1P_A 3H82_A 3F1N_A 4F3L_B 4DJ3_A 2KDK_A	Back alignment and domain information

>PF12860 PAS_7: PAS fold	Back alignment and domain information

>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]	Back alignment and domain information

>smart00065 GAF Domain present in phytochromes and cGMP-specific phosphodiesterases	Back alignment and domain information

>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]	Back alignment and domain information

>COG2172 RsbW Anti-sigma regulatory factor (Ser/Thr protein kinase) [Signal transduction mechanisms]	Back alignment and domain information

>COG2202 AtoS FOG: PAS/PAC domain [Signal transduction mechanisms]	Back alignment and domain information

>smart00388 HisKA His Kinase A (phosphoacceptor) domain	Back alignment and domain information

>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]	Back alignment and domain information

>PF14598 PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W_A 3F1P_A 3H82_A 3F1N_A 4F3L_B 4DJ3_A 2KDK_A	Back alignment and domain information

>PRK15053 dpiB sensor histidine kinase DpiB; Provisional	Back alignment and domain information

>TIGR00585 mutl DNA mismatch repair protein MutL	Back alignment and domain information

>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A	Back alignment and domain information

>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]	Back alignment and domain information

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional	Back alignment and domain information

>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional	Back alignment and domain information

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional	Back alignment and domain information

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]	Back alignment and domain information

>cd00082 HisKA Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-autophosphorylation by the catalytic domain of the histidine kinase	Back alignment and domain information

>PF13589 HATPase_c_3: Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; PDB: 3IED_A 2XCM_B 2JKI_B 3OPD_A 2O1V_B 2GQP_A 2O1W_C 1YT2_A 1TC6_A 2H8M_B	Back alignment and domain information

>KOG0501 consensus K+-channel KCNQ [Inorganic ion transport and metabolism]	Back alignment and domain information

>KOG0501 consensus K+-channel KCNQ [Inorganic ion transport and metabolism]	Back alignment and domain information

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]	Back alignment and domain information

>smart00091 PAS PAS domain	Back alignment and domain information

>COG2203 FhlA FOG: GAF domain [Signal transduction mechanisms]	Back alignment and domain information

>COG2461 Uncharacterized conserved protein [Function unknown]	Back alignment and domain information

>PRK00095 mutL DNA mismatch repair protein; Reviewed	Back alignment and domain information

>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A	Back alignment and domain information

>PF08670 MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEKHLA domain shares similarity with the PAS domain and is found in the 3' end of plant HD-ZIP III homeobox genes, and bacterial proteins	Back alignment and domain information

>TIGR01817 nifA Nif-specific regulatory protein	Back alignment and domain information

>PRK05559 DNA topoisomerase IV subunit B; Reviewed	Back alignment and domain information

>TIGR02373 photo_yellow photoactive yellow protein	Back alignment and domain information

>PF13492 GAF_3: GAF domain; PDB: 3EEA_A 4DMZ_A 4DN0_A 1VHM_A	Back alignment and domain information

>KOG1229 consensus 3'5'-cyclic nucleotide phosphodiesterases [Signal transduction mechanisms]	Back alignment and domain information

>PF10090 DUF2328: Uncharacterized protein conserved in bacteria (DUF2328); InterPro: IPR018762 Members of this family of hypothetical bacterial proteins have no known function	Back alignment and domain information

>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]	Back alignment and domain information

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional	Back alignment and domain information

>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]	Back alignment and domain information

>TIGR01055 parE_Gneg DNA topoisomerase IV, B subunit, proteobacterial	Back alignment and domain information

>TIGR01059 gyrB DNA gyrase, B subunit	Back alignment and domain information

>COG5385 Uncharacterized protein conserved in bacteria [Function unknown]	Back alignment and domain information

>PF13185 GAF_2: GAF domain; PDB: 2QYB_A 3KSG_B 3KSF_C 3KSI_A 3KSH_A 3MMH_A 3RFB_B 1F5M_A 3KO6_B 3HCY_A	Back alignment and domain information

>TIGR02373 photo_yellow photoactive yellow protein	Back alignment and domain information

>PRK05644 gyrB DNA gyrase subunit B; Validated	Back alignment and domain information

>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional	Back alignment and domain information

>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]	Back alignment and domain information

>PF07568 HisKA_2: Histidine kinase; InterPro: IPR011495 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []	Back alignment and domain information

>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]	Back alignment and domain information

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional	Back alignment and domain information

>KOG1229 consensus 3'5'-cyclic nucleotide phosphodiesterases [Signal transduction mechanisms]	Back alignment and domain information

>PRK05218 heat shock protein 90; Provisional	Back alignment and domain information

>smart00433 TOP2c TopoisomeraseII	Back alignment and domain information

>PRK14939 gyrB DNA gyrase subunit B; Provisional	Back alignment and domain information

>COG0323 MutL DNA mismatch repair enzyme (predicted ATPase) [DNA replication, recombination, and repair]	Back alignment and domain information

>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional	Back alignment and domain information

>KOG3753 consensus Circadian clock protein period [Signal transduction mechanisms]	Back alignment and domain information

>COG2461 Uncharacterized conserved protein [Function unknown]	Back alignment and domain information

>PF08670 MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEKHLA domain shares similarity with the PAS domain and is found in the 3' end of plant HD-ZIP III homeobox genes, and bacterial proteins	Back alignment and domain information

>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]	Back alignment and domain information

>KOG0519 consensus Sensory transduction histidine kinase [Signal transduction mechanisms]	Back alignment and domain information

>PTZ00272 heat shock protein 83 kDa (Hsp83); Provisional	Back alignment and domain information

>smart00091 PAS PAS domain	Back alignment and domain information

>TIGR01058 parE_Gpos DNA topoisomerase IV, B subunit, Gram-positive	Back alignment and domain information

>smart00086 PAC Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain)	Back alignment and domain information

>COG0326 HtpG Molecular chaperone, HSP90 family [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PRK11061 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional	Back alignment and domain information

>PRK14083 HSP90 family protein; Provisional	Back alignment and domain information

>PTZ00108 DNA topoisomerase 2-like protein; Provisional	Back alignment and domain information

>smart00086 PAC Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain)	Back alignment and domain information

>PLN03237 DNA topoisomerase 2; Provisional	Back alignment and domain information

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]	Back alignment and domain information

>PTZ00109 DNA gyrase subunit b; Provisional	Back alignment and domain information

>COG5381 Uncharacterized protein conserved in bacteria [Function unknown]	Back alignment and domain information

>PHA02569 39 DNA topoisomerase II large subunit; Provisional	Back alignment and domain information

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]	Back alignment and domain information

>COG0187 GyrB Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), B subunit [DNA replication, recombination, and repair]	Back alignment and domain information

>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]	Back alignment and domain information

>PTZ00130 heat shock protein 90; Provisional	Back alignment and domain information

>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]	Back alignment and domain information

>PF07310 PAS_5: PAS domain; InterPro: IPR009922 This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		1111
2vea_A		520	The Complete Sensory Module Of The Cyanobacterial P		1e-55
3zq5_A		520	Structure Of The Y263f Mutant Of The Cyanobacterial		3e-55
4gw9_A		655	Structure Of A Bacteriophytochrome And Light-Stimul		2e-42
3g6o_A		505	Crystal Structure Of P. Aeruginosa Bacteriophytochr		6e-39
3c2w_A		505	Crystal Structure Of The Photosensory Core Domain O		3e-38
3ibr_A		505	Crystal Structure Of P. Aeruginosa Bacteriophytochr		2e-35
2ool_A		337	Crystal Structure Of The Chromophore-Binding Domain		7e-27
4e04_A		327	Rpbphp2 Chromophore-binding Domain Crystallized By		1e-24
2o9b_A		342	Crystal Structure Of Bacteriophytochrome Chromophor		4e-21
3s7q_A		343	Crystal Structure Of A Monomeric Infrared Fluoresce		1e-20
3s7n_A		343	Crystal Structure Of The Alternate His 207 Conforma		3e-20
1ztu_A		341	Structure Of The Chromophore Binding Domain Of Bact		2e-19
2lb5_A		208	Refined Structural Basis For The Photoconversion Of		8e-15
2k2n_A		172	Solution Structure Of A Cyanobacterial Phytochrome		1e-14
3a0r_A		349	Crystal Structure Of Histidine Kinase Thka (Tm1359)		4e-06

>pdb|2VEA|A Chain A, The Complete Sensory Module Of The Cyanobacterial Phytochrome Cph1 In The Pr-State Length = 520