Citrus Sinensis ID: 001235

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------112

MSSSRPAQSSSNTGKSRHSARVIAQTTIDAKLHADFETSGTSFDYSNSVRVSSTAGGDQQPRSDRVTTAYLHHIQKGKLIQPFGCLLALDEKTFKVIAYSENAPELLTMVNHAVPSVGDHPVLGIGSDIKTIFTAPSASALQKALGFGEVSLLNPILVHCKTSGKPFYAIVHRVTGSLIIDFEPVKPYEVPMTAAGALQSYKLAAKAITRLQSLPSGSMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDCRARHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWGLVVCHNTTPRFVPFPLRYACEFLAQVFAIHVNKELELEYQILEKNILRTQTLLCDMLMRDAPLGIVTQSPNIMDLVKCDGAALLYKNKIWRLGVTPNDFQLHDIVSWLSEYHMDSTGLSADSLYDAGYLGALALGDVVCGMAAVRISPKDMIFWFRSQTASEVRWGGAKHEPDEKDDGRKMHPRSSFKAFLEVVKTRSLPWKDYEMDAIHSLQLILRNAFKDVGTLDLDTKSIHSKLCDLKIEGMKELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQTALKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDDSDLDSIIDGYLDLEMVEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSEGDTSEEGISLLISRKLVKLMNGDVQYLREAGKSTFIVSVELAAAH

ccccccccccccccccccccEEEEEccccHHHHHHHHHcccccccccccccccccccccccccccHHHHHHcccccccccccccEEEEEEccccEEEEEcccHHHHHcccccccccccccccccccccHHHHccHHHHHHHHHHHccccccccccEEEEEEccccEEEEEEEEEccEEEEEEEEccccccccHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHcccEEEEEEEccccccEEEEEccccccccccccccccccccHHHHHHHHcccEEEEcccccccccccccccccccccccccccccccHHHHHHHHHccccEEEEEEEEEEccccccccccccccccEEEEEEccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccHHHHHccccEEEEEccEEEEccccccHHHHHHHHHHHHHHcccccEEEEcccccccccccccccccccEEEEEEcccccEEEEEccccccEEEcccccccccccccccccccccHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHcccccHHHHHHHHHHHHcccHHHHccccccccccccHHHHHHHHHHHHHcccccccEEEEEEccccccccccEEEEEEccccccccccEEEEEEEEEccccccccccccccccccEEEEEEccccccccccccccccccccccHHHHHHHccccHHHHHHHHHHHHHccccccEEccccHHHHHHHHHHHHccccccccccccEEEEEcccEEEEEEEccccccccccEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccEEEEEcHHHHHHHHHHHHHHHccccccEEEEEccccccccEEEccHHHHHHHHHHHHHHHHHcccccccEEEEEEEccccccccEEEEEEEEEEEEccccccccHHHHcccccccccccccHHHHHHHHHHHcccEEEEEEEccEEEEEEEEEccccc

cccccccccccccccccccEEEEEEEccccEEEEEEEcccccccccccEEcccccccccccccHHHHHHHHHHHHcccccccccEEEEEccccEEEEEEcccHHHHHccccccccccccccEEEEcccHHHHcccHHHHHHHHHHHHHHHcccccEEEEEccccccEEEEEEEEEEEEEEEccccccccccHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHccccEEEEEEEccccccEEEEEEcccccccccccccccccHHHHHHHHHHHccEEEEEEcccccEEEEEccccccccEEccccccccccHHHHHHHHHcHHHHHHEEEEEEcccccccccccccccEEEEEEEEcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccEEEEcccccHcHEccccEEEEEcccEEEEcccccHHHHHHHHHHHHHHcccccccccHHHHHcccccHHHHccHHcccEEEEEccccEEEEEccccHHHEccccccccccccccccccccccHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHcccccccccEEEcccccccccccHHHHHHHHHHHHHHHHHccccEEEEEccccEcccHHHHHHHccccHHHHHcHHHHHHHHHcHHHHHHHHHHHHHccccHccEEEEEEEcccccccccEEEEEEccccccccccEEEEEEEEEcccccHHHHHHEEEEccccEEEEccccccccccEccccccccHHHHHHHHHHccccHHHHHHHHcHHHHHcccccccccccHHHHHHHHHHHHHHcccccccccccccEcccccEEEEEEEEcccccccccEEEEEEEEEcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHcccHHHHHcccEEEccEEEEHHHHHHHHHHHHHHHHHHcccEEEccccHHHcccEccccHHHHHHHHHHHHHHHHHccccccEEEEEEEcccccccccEEEEEEEEEEEcccccccHHHHHHHHcccccccHHHHHHHHHHHHHHHHcccEEEEEEccccEEEEEEEEcccc

msssrpaqsssntgksrHSARVIAQTTIDAklhadfetsgtsfdysnsvrvsstaggdqqprsdrvTTAYLHHIQKGKLIQPFGCLLALDEKTFKVIAYSENAPELLTMVNhavpsvgdhpvlgigsdiktiftaPSASALQKALGFGEVSLLNPIlvhcktsgkpfYAIVHRVTGSliidfepvkpyevpmtaagALQSYKLAAKAITRlqslpsgsmeRLCDTMIQEVFELtgydrvmaykfheddhgeVVSEItksglepylglhypatdipQAARFLFMKNKVRMIVDCRARHVKVlqdeklpfdltlcgstlraphschLQYMENMNSIASLVMAVVVndeeeegdntlpqkrKRLWGlvvchnttprfvpfpLRYACEFLAQVFAIHVNKELELEYQILEKNILRTQTLLCDMlmrdaplgivtqspnimdlVKCDGAallyknkiwrlgvtpndfqLHDIVSWLSEYhmdstglsadslydagylGALALGDVVCGmaavrispkdMIFWFRSQTASevrwggakhepdekddgrkmhprssFKAFLEVVKtrslpwkdyeMDAIHSLQLILRNAFkdvgtldldtksIHSKLCDLKIEGMKELEAVTSEMVRLIETAtvpilavdvdglvngwnTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKthgskinddpiTLIVNACasrdlhdnvVGVCFvaqditpqktvmdKFTRIEGDYKaivqnpnplippifgsdefgwccewnpamvkltgWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNkamsgqdpekvpfgffarngkyAECLLCVNKkldregavTGVFCFLQLASHELQQALHVQRLSEQTALKRLKALAYTKRqirnplsgiiFSRKMMEGTELGAEQKRLLHTSAQCQRQLHkilddsdldsIIDGYLDLEMVEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISinfvpnggqlmvsssltkdqlgqSVHLAYLELRIThagggipeplldqmfgsegdtseEGISLLISRKLVKLMNGDVQYLREAGKSTFIVSVELAAAH

msssrpaqsssntgksrhsaRVIAQTTIDAKLHADfetsgtsfdysnsvrvsstaggdqqprsDRVTTAYLHHIQKGKLIQPFGCLLALDEKTFKVIAYSENAPELLTMVNHAVPSVGDHPVLGIGSDIKTIFTAPSASALQKALGFGEVSLLNPILVHCKTSGKPFYAIVHRVTGSLIIDFEPVKPYEVPMTAAGALQSYKLAAKAITRLqslpsgsmeRLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDCRARHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEegdntlpqkrkrlwgLVVCHNTTPRFVPFPLRYACEFLAQVFAIHVNKELELEYQILEKNILRTQTLLCDMLMRDAPLGIVTQSPNIMDLVKCDGAALLYKNKIWRLGVTPNDFQLHDIVSWLSEYHMDSTGLSADSLYDAGYLGALALGDVVCGMAAVRISPKDMIFWFRSQTasevrwggakhepdekddgrkmhprssfkaFLEVVKTRSLPWKDYEMDAIHSLQLILRNAFKDVGTLDLDTKSIHSKLCDLKIEGMKELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLtlvedssidTVKRMLYLALQGQEEQNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFvaqditpqktvMDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQTALKRLKAlaytkrqirnplsgiifsRKMMEGTELGAEQKRLLHTSAQCQRQLhkilddsdlDSIIDGYLDLEMVEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSEGDTSEEGISLLISRKLVKLMNGDVQYLreagkstfiVSVELAAAH

MSSSRPAQSSSNTGKSRHSARVIAQTTIDAKLHADFETSGTSFDYSNSVRVSSTAGGDQQPRSDRVTTAYLHHIQKGKLIQPFGCLLALDEKTFKVIAYSENAPELLTMVNHAVPSVGDHPVLGIGSDIKTIFTAPSASALQKALGFGEVSLLNPILVHCKTSGKPFYAIVHRVTGSLIIDFEPVKPYEVPMTAAGALQSYKLAAKAITRLQSLPSGSMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDCRARHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDeeeeGDNTLPQKRKRLWGLVVCHNTTPRFVPFPLRYACEFLAQVFAIHVNKELELEYQILEKNILRTQTLLCDMLMRDAPLGIVTQSPNIMDLVKCDGAALLYKNKIWRLGVTPNDFQLHDIVSWLSEYHMDSTGLSADSlydagylgalalgdVVCGMAAVRISPKDMIFWFRSQTASEVRWGGAKHEPDEKDDGRKMHPRSSFKAFLEVVKTRSLPWKDYEMDAIHSLQLILRNAFKDVGTLDLDTKSIHSKLCDLKIEGMKELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQTALKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKilddsdldsiidgyldlEMVEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSEGDTSEEGISLLISRKLVKLMNGDVQYLREAGKSTFIVSVELAAAH

***************************I*************************************VTTAYLHHIQKGKLIQPFGCLLALDEKTFKVIAYSENAPELLTMVNHAVPSVGDHPVLGIGSDIKTIFTAPSASALQKALGFGEVSLLNPILVHCKTSGKPFYAIVHRVTGSLIIDFEPVKPYEVPMTAAGALQSYKLAAKAITRLQSLPSGSMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDCRARHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVV****************RLWGLVVCHNTTPRFVPFPLRYACEFLAQVFAIHVNKELELEYQILEKNILRTQTLLCDMLMRDAPLGIVTQSPNIMDLVKCDGAALLYKNKIWRLGVTPNDFQLHDIVSWLSEYHMDSTGLSADSLYDAGYLGALALGDVVCGMAAVRISPKDMIFWFRSQTASEVRW*********************FKAFLEVVKTRSLPWKDYEMDAIHSLQLILRNAFKDVGTLDLDTKSIHSKLCDLKIEGMKELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQTALKRLKALAYTKRQIRNPLSGIIFSRKMMEGTEL****KRLLHTSAQCQRQLHKILDDSDLDSIIDGYLDLEMVEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMF*********GISLLISRKLVKLMNGDVQYLREAGKSTFIVSVEL****

*************************TTIDAKLHADFE**************************DRVTTAYLHHIQKGKLIQPFGCLLALDEKTFKVIAYSENAPELLTMVNHAVPSVGDHPVLGIGSDIKTIFTAPSASALQKALGFGEVSLLNPILVHCKTSGKPFYAIVHRVTGSLIIDFEPVKPYEVPMTAAGALQSYKLAAKAITRLQSLPSGSMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDCRARHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVN*****************WGLVVCHNTTPRFVPFPLRYACEFLAQVFAIHVNKELELEYQILEKNILRTQTLLCDMLMRDAPLGIVTQSPNIMDLVKCDGAALLYKNKIWRLGVTPNDFQLHDIVSWLSEYHMDSTGLSADSLYDAGYLGALALGDVVCGMAAVRISPKDMIFWFRSQTASEVRWGGA****************SSFKAFLEVVKTRSLPWKDYEMDAIHSLQLILRNAFKDVG*****************IEGMKELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQ***************RLKALAYTKRQIRNPLSGIIFSRKMME********************QLHKILDDSDLDSIIDGYLDLEMVEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSE****EEGISLLISRKLVKLMNGDVQYLREAGKSTFIVSVELAA**

********************RVIAQTTIDAKLHADFETSGTSFDYSNSV**************DRVTTAYLHHIQKGKLIQPFGCLLALDEKTFKVIAYSENAPELLTMVNHAVPSVGDHPVLGIGSDIKTIFTAPSASALQKALGFGEVSLLNPILVHCKTSGKPFYAIVHRVTGSLIIDFEPVKPYEVPMTAAGALQSYKLAAKAITRLQSLPSGSMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDCRARHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVND********LPQKRKRLWGLVVCHNTTPRFVPFPLRYACEFLAQVFAIHVNKELELEYQILEKNILRTQTLLCDMLMRDAPLGIVTQSPNIMDLVKCDGAALLYKNKIWRLGVTPNDFQLHDIVSWLSEYHMDSTGLSADSLYDAGYLGALALGDVVCGMAAVRISPKDMIFWFRSQTA**********************PRSSFKAFLEVVKTRSLPWKDYEMDAIHSLQLILRNAFKDVGTLDLDTKSIHSKLCDLKIEGMKELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQTALKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDDSDLDSIIDGYLDLEMVEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSEGDTSEEGISLLISRKLVKLMNGDVQYLREAGKSTFIVSVELAAAH

*****************HSARVIAQTTIDAKLHADFETSGTSFDYSN*VR**********PRSDRVTTAYLHHIQKGKLIQPFGCLLALDEKTFKVIAYSENAPELLTMVNHAVPSVGDHPVLGIGSDIKTIFTAPSASALQKALGFGEVSLLNPILVHCKTSGKPFYAIVHRVTGSLIIDFEPVKPYEVPMTAAGALQSYKLAAKAITRLQSLPSGSMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDCRARHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEE*********KRKRLWGLVVCHNTTPRFVPFPLRYACEFLAQVFAIHVNKELELEYQILEKNILRTQTLLCDMLMRDAPLGIVTQSPNIMDLVKCDGAALLYKNKIWRLGVTPNDFQLHDIVSWLSEYHMDSTGLSADSLYDAGYLGALALGDVVCGMAAVRISPKDMIFWFRSQTASEVRWGGAK***********MHPRSSFKAFLEVVKTRSLPWKDYEMDAIHSLQLILRNAFKDVGTLDLDTKSIHSKLCDLKIEGMKELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQTALKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDDSDLDSIIDGYLDLEMVEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSEGDTSEEGISLLISRKLVKLMNGDVQYLREAGKSTFIVSVELAA**

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MSSSRPAQSSSNTGKSRHSARVIAQTTIDAKLHADFETSGTSFDYSNSVRVSSTAGGDQQPRSDRVTTAYLHHIQKGKLIQPFGCLLALDEKTFKVIAYSENAPELLTMVNHAVPSVGDHPVLGIGSDIKTIFTAPSASALQKALGFGEVSLLNPILVHCKTSGKPFYAIVHRVTGSLIIDFEPVKPYEVPMTAAGALQSYKLAAKAITRLQSLPSGSMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDCRARHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWGLVVCHNTTPRFVPFPLRYACEFLAQVFAIHVxxxxxxxxxxxxxxxxxxxxxLCDMLMRDAPLGIVTQSPNIMDLVKCDGAALLYKNKIWRLGVTPNDFQLHDIVSWLSEYHMDSTGLSADSLYDAGYLGALALGDVVCGMAAVRISPKDMIFWFRSQTASEVRWGGAKHEPDEKDDGRKMHPRSSFKAFLEVVKTRSLPWKDYEMDAIHSLQLILRNAFKDVGTLDLDTKSIHSKLCDLKIEGMKELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQTALKRLKALAYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDDSDLDSIIDGYLDLEMVEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSEGDTSEEGISLLISRKLVKLMNGDVQYLREAGKSTFIVSVELAAAH

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		1117	2.2.26 [Sep-21-2011]
P14712		1122	Phytochrome A OS=Arabidop	yes	no	1.0	0.995	0.824	0.0
P93673		1124	Phytochrome type A OS=Lat	N/A	no	1.0	0.993	0.813	0.0
P33530		1124	Phytochrome A1 OS=Nicotia	N/A	no	0.987	0.981	0.819	0.0
P30733		1123	Phytochrome A OS=Solanum	N/A	no	0.984	0.979	0.816	0.0
P15001		1124	Phytochrome A OS=Pisum sa	N/A	no	1.0	0.993	0.815	0.0
P06592		1124	Phytochrome A OS=Cucurbit	N/A	no	0.982	0.975	0.821	0.0
O49934		1125	Phytochrome A OS=Populus	N/A	no	0.980	0.973	0.834	0.0
P42500		1131	Phytochrome A OS=Glycine	no	no	0.976	0.964	0.784	0.0
P55141		1129	Phytochrome A OS=Petrosel	N/A	no	0.988	0.977	0.742	0.0
Q10DU0		1128	Phytochrome A OS=Oryza sa	yes	no	0.992	0.983	0.653	0.0

>sp\|P14712\|PHYA_ARATH Phytochrome A OS=Arabidopsis thaliana GN=PHYA PE=1 SV=2	Back alignment and function desciption

 Score = 1944 bits (5037), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 924/1121 (82%), Positives = 1024/1121 (91%), Gaps = 4/1121 (0%)

Query: 1    MSSSRPAQSSSNTGKSRHSARVIAQTTIDAKLHADFETSGTSFDYSNSVRVSSTAGGDQQ 60
            MS SRP QSS  + +SRHSAR+IAQTT+DAKLHADFE SG+SFDYS SVRV+     +Q 
Sbjct: 1    MSGSRPTQSSEGSRRSRHSARIIAQTTVDAKLHADFEESGSSFDYSTSVRVTGPVVENQP 60

Query: 61   PRSDRVTTAYLHHIQKGKLIQPFGCLLALDEKTFKVIAYSENAPELLTMVNHAVPSVGDH 120
            PRSD+VTT YLHHIQKGKLIQPFGCLLALDEKTFKVIAYSENA ELLTM +HAVPSVG+H
Sbjct: 61   PRSDKVTTTYLHHIQKGKLIQPFGCLLALDEKTFKVIAYSENASELLTMASHAVPSVGEH 120

Query: 121  PVLGIGSDIKTIFTAPSASALQKALGFGEVSLLNPILVHCKTSGKPFYAIVHRVTGSLII 180
            PVLGIG+DI+++FTAPSASALQKALGFG+VSLLNPILVHC+TS KPFYAI+HRVTGS+II
Sbjct: 121  PVLGIGTDIRSLFTAPSASALQKALGFGDVSLLNPILVHCRTSAKPFYAIIHRVTGSIII 180

Query: 181  DFEPVKPYEVPMTAAGALQSYKLAAKAITRLQSLPSGSMERLCDTMIQEVFELTGYDRVM 240
            DFEPVKPYEVPMTAAGALQSYKLAAKAITRLQSLPSGSMERLCDTM+QEVFELTGYDRVM
Sbjct: 181  DFEPVKPYEVPMTAAGALQSYKLAAKAITRLQSLPSGSMERLCDTMVQEVFELTGYDRVM 240

Query: 241  AYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDCRARHVKV 300
            AYKFHEDDHGEVVSE+TK GLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDC A+H +V
Sbjct: 241  AYKFHEDDHGEVVSEVTKPGLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDCNAKHARV 300

Query: 301  LQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGD----NTLPQ 356
            LQDEKL FDLTLCGSTLRAPHSCHLQYM NM+SIASLVMAVVVN+E+ EGD     T PQ
Sbjct: 301  LQDEKLSFDLTLCGSTLRAPHSCHLQYMANMDSIASLVMAVVVNEEDGEGDAPDATTQPQ 360

Query: 357  KRKRLWGLVVCHNTTPRFVPFPLRYACEFLAQVFAIHVNKELELEYQILEKNILRTQTLL 416
            KRKRLWGLVVCHNTTPRFVPFPLRYACEFLAQVFAIHVNKE+EL+ Q++EKNILRTQTLL
Sbjct: 361  KRKRLWGLVVCHNTTPRFVPFPLRYACEFLAQVFAIHVNKEVELDNQMVEKNILRTQTLL 420

Query: 417  CDMLMRDAPLGIVTQSPNIMDLVKCDGAALLYKNKIWRLGVTPNDFQLHDIVSWLSEYHM 476
            CDMLMRDAPLGIV+QSPNIMDLVKCDGAALLYK+KIW+LG TP++F L +I SWL EYHM
Sbjct: 421  CDMLMRDAPLGIVSQSPNIMDLVKCDGAALLYKDKIWKLGTTPSEFHLQEIASWLCEYHM 480

Query: 477  DSTGLSADSLYDAGYLGALALGDVVCGMAAVRISPKDMIFWFRSQTASEVRWGGAKHEPD 536
            DSTGLS DSL+DAG+  AL+LGD VCGMAAVRIS KDMIFWFRS TA EVRWGGAKH+PD
Sbjct: 481  DSTGLSTDSLHDAGFPRALSLGDSVCGMAAVRISSKDMIFWFRSHTAGEVRWGGAKHDPD 540

Query: 537  EKDDGRKMHPRSSFKAFLEVVKTRSLPWKDYEMDAIHSLQLILRNAFKDVGTLDLDTKSI 596
            ++DD R+MHPRSSFKAFLEVVKTRSLPWKDYEMDAIHSLQLILRNAFKD  T D++TK I
Sbjct: 541  DRDDARRMHPRSSFKAFLEVVKTRSLPWKDYEMDAIHSLQLILRNAFKDSETTDVNTKVI 600

Query: 597  HSKLCDLKIEGMKELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKA 656
            +SKL DLKI+G++ELEAVTSEMVRLIETATVPILAVD DGLVNGWNTKIAELTGLSVD+A
Sbjct: 601  YSKLNDLKIDGIQELEAVTSEMVRLIETATVPILAVDSDGLVNGWNTKIAELTGLSVDEA 660

Query: 657  IGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKINDDPITLIVNACASRD 716
            IGKHFLTLVEDSS++ VKRML  AL+G EEQN+QFEIKTH S+ +  PI+L+VNACASRD
Sbjct: 661  IGKHFLTLVEDSSVEIVKRMLENALEGTEEQNVQFEIKTHLSRADAGPISLVVNACASRD 720

Query: 717  LHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNP 776
            LH+NVVGVCFVA D+T QKTVMDKFTRIEGDYKAI+QNPNPLIPPIFG+DEFGWC EWNP
Sbjct: 721  LHENVVGVCFVAHDLTGQKTVMDKFTRIEGDYKAIIQNPNPLIPPIFGTDEFGWCTEWNP 780

Query: 777  AMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFG 836
            AM KLTG KREEVIDK+LL EVFGT  +CCRLKNQEAFVNLGIVLN A++ QDPEKV F 
Sbjct: 781  AMSKLTGLKREEVIDKMLLGEVFGTQKSCCRLKNQEAFVNLGIVLNNAVTSQDPEKVSFA 840

Query: 837  FFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQTALKRLKAL 896
            FF R GKY ECLLCV+KKLDREG VTGVFCFLQLASHELQQALHVQRL+E+TA+KRLKAL
Sbjct: 841  FFTRGGKYVECLLCVSKKLDREGVVTGVFCFLQLASHELQQALHVQRLAERTAVKRLKAL 900

Query: 897  AYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKILDDSDLDSIIDGY 956
            AY KRQIRNPLSGI+F+RKM+EGTELG EQ+R+L TSA CQ+QL KILDDSDL+SII+G 
Sbjct: 901  AYIKRQIRNPLSGIMFTRKMIEGTELGPEQRRILQTSALCQKQLSKILDDSDLESIIEGC 960

Query: 957  LDLEMVEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFL 1016
            LDLEM EFTLNEVL AS SQVMMKSN K +RI NET E++MS+TLYGDSIRLQQVLADF+
Sbjct: 961  LDLEMKEFTLNEVLTASTSQVMMKSNGKSVRITNETGEEVMSDTLYGDSIRLQQVLADFM 1020

Query: 1017 SISINFVPNGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSEGDTS 1076
             +++NF P+GGQL VS+SL KDQLG+SVHLA LE+R+TH G GIPE LL+QMFG+E D S
Sbjct: 1021 LMAVNFTPSGGQLTVSASLRKDQLGRSVHLANLEIRLTHTGAGIPEFLLNQMFGTEEDVS 1080

Query: 1077 EEGISLLISRKLVKLMNGDVQYLREAGKSTFIVSVELAAAH 1117
            EEG+SL++SRKLVKLMNGDVQYLR+AGKS+FI++ ELAAA+
Sbjct: 1081 EEGLSLMVSRKLVKLMNGDVQYLRQAGKSSFIITAELAAAN 1121

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 morphogenetic 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. Involved in the flowering time regulation.
Arabidopsis thaliana (taxid: 3702)

>sp\|P93673\|PHYA_LATSA Phytochrome type A OS=Lathyrus sativus GN=PHYA PE=3 SV=1	Back alignment and function description

>sp\|P33530\|PHYA1_TOBAC Phytochrome A1 OS=Nicotiana tabacum GN=PHYA1 PE=3 SV=1	Back alignment and function description

>sp\|P30733\|PHYA_SOLTU Phytochrome A OS=Solanum tuberosum GN=PHYA PE=2 SV=2	Back alignment and function description

>sp\|P15001\|PHYA_PEA Phytochrome A OS=Pisum sativum GN=PHYA PE=3 SV=1	Back alignment and function description

>sp\|P06592\|PHYA_CUCPE Phytochrome A OS=Cucurbita pepo GN=PHYA PE=2 SV=1	Back alignment and function description

>sp\|O49934\|PHYA_POPTM Phytochrome A OS=Populus tremuloides GN=PHYA PE=2 SV=1	Back alignment and function description

>sp\|P42500\|PHYA_SOYBN Phytochrome A OS=Glycine max GN=PHYA PE=2 SV=1	Back alignment and function description

>sp\|P55141\|PHYA_PETCR Phytochrome A OS=Petroselinum crispum GN=PHYA PE=2 SV=1	Back alignment and function description

>sp\|Q10DU0\|PHYA_ORYSJ Phytochrome A OS=Oryza sativa subsp. japonica GN=PHYA 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		1117
224122788		1126	phytochrome [Populus trichocarpa] gi\|222	0.982	0.975	0.866	0.0
225450405		1124	PREDICTED: phytochrome A1 [Vitis vinifer	0.986	0.980	0.858	0.0
255543066		1124	phytochrome A, putative [Ricinus communi	0.982	0.975	0.850	0.0
183239022		1124	phytochrome A [Vitis riparia]	0.986	0.980	0.856	0.0
340007753		1109	phytochrome A [Populus tremula]	0.973	0.980	0.862	0.0
9049366		1122	phytochrome A [Armoracia rusticana]	1.0	0.995	0.818	0.0
9049368		1122	phytochrome A [Armoracia rusticana]	1.0	0.995	0.818	0.0
15217562		1122	phytochrome A [Arabidopsis thaliana] gi\|	1.0	0.995	0.824	0.0
2499555		1124	RecName: Full=Phytochrome type A gi\|1848	1.0	0.993	0.813	0.0
9049364		1122	phytochrome A [Armoracia rusticana]	1.0	0.995	0.822	0.0

>gi\|224122788\|ref\|XP_002318913.1\| phytochrome [Populus trichocarpa] gi\|222857289\|gb\|EEE94836.1\| phytochrome [Populus trichocarpa]	Back alignment and taxonomy information

 Score = 1991 bits (5159), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 954/1101 (86%), Positives = 1025/1101 (93%), Gaps = 3/1101 (0%)

Query: 20   ARVIAQTTIDAKLHADFETSGTSFDYSNSVRVSSTAGGDQQPRSDRVTTAYLHHIQKGKL 79
            AR+IAQTT+DAKLHADFE SG+SFDYS+SVRV+ + GGDQ PRSD+VTT YLHHIQKGKL
Sbjct: 20   ARIIAQTTVDAKLHADFEESGSSFDYSSSVRVTDSVGGDQPPRSDKVTTTYLHHIQKGKL 79

Query: 80   IQPFGCLLALDEKTFKVIAYSENAPELLTMVNHAVPSVGDHPVLGIGSDIKTIFTAPSAS 139
            IQPFGCLLALDEKTFKV+AYSENAPELLTMV+HAVPSVG+HPVLGIG+DI+TIFTAPSAS
Sbjct: 80   IQPFGCLLALDEKTFKVVAYSENAPELLTMVSHAVPSVGEHPVLGIGTDIRTIFTAPSAS 139

Query: 140  ALQKALGFGEVSLLNPILVHCKTSGKPFYAIVHRVTGSLIIDFEPVKPYEVPMTAAGALQ 199
            ALQKA+GFG+VSLLNPILVHCKTSGKPFYAIVHRVTGSLIIDFEPVKPYEVPMTAAGALQ
Sbjct: 140  ALQKAMGFGDVSLLNPILVHCKTSGKPFYAIVHRVTGSLIIDFEPVKPYEVPMTAAGALQ 199

Query: 200  SYKLAAKAITRLQSLPSGSMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITKS 259
            SYKLAAKAITRLQSLPSGSMERLCDTM+QEVFELTGYDR MAYKFH+DDHGEVVSE+TK 
Sbjct: 200  SYKLAAKAITRLQSLPSGSMERLCDTMVQEVFELTGYDRAMAYKFHDDDHGEVVSEVTKP 259

Query: 260  GLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDCRARHVKVLQDEKLPFDLTLCGSTLRA 319
            G+EPYLGLHYPATDIPQA+RFLFMKNKVRMIVDC A+HVKVLQDEKLPFDLTLCGSTLRA
Sbjct: 260  GMEPYLGLHYPATDIPQASRFLFMKNKVRMIVDCHAKHVKVLQDEKLPFDLTLCGSTLRA 319

Query: 320  PHSCHLQYMENMNSIASLVMAVVVNDEEEEGD---NTLPQKRKRLWGLVVCHNTTPRFVP 376
            PHSCHLQYMENMNSIASLVMAVVVND +E+GD   +  PQKRKRLWGLVVCHNT+PRFVP
Sbjct: 320  PHSCHLQYMENMNSIASLVMAVVVNDGDEDGDTPDSVNPQKRKRLWGLVVCHNTSPRFVP 379

Query: 377  FPLRYACEFLAQVFAIHVNKELELEYQILEKNILRTQTLLCDMLMRDAPLGIVTQSPNIM 436
            FPLRYACEFLAQVFAIHVNKELELE QI+EKNILRTQTLLCDMLMRDAPLGIVTQSPNIM
Sbjct: 380  FPLRYACEFLAQVFAIHVNKELELENQIVEKNILRTQTLLCDMLMRDAPLGIVTQSPNIM 439

Query: 437  DLVKCDGAALLYKNKIWRLGVTPNDFQLHDIVSWLSEYHMDSTGLSADSLYDAGYLGALA 496
            DLVKCDGA L Y+NKIWRLG+TP+D QL DI  WLSEYHMDSTGLS DSLYDAGY GALA
Sbjct: 440  DLVKCDGAVLFYRNKIWRLGITPSDLQLQDIAFWLSEYHMDSTGLSTDSLYDAGYPGALA 499

Query: 497  LGDVVCGMAAVRISPKDMIFWFRSQTASEVRWGGAKHEPDEKDDGRKMHPRSSFKAFLEV 556
            LGDVVCGMAAVRI+ KDM+FWFRSQTA+E+RWGGAKHEP EKDDGR+MHPRSSFKAFLEV
Sbjct: 500  LGDVVCGMAAVRITSKDMLFWFRSQTAAEIRWGGAKHEPGEKDDGRRMHPRSSFKAFLEV 559

Query: 557  VKTRSLPWKDYEMDAIHSLQLILRNAFKDVGTLDLDTKSIHSKLCDLKIEGMKELEAVTS 616
            VKTRSLPWKDYEMDAIHSLQLILRNAFKD+ T+D+DTK+IH++L DLKIEGM+ELEAVTS
Sbjct: 560  VKTRSLPWKDYEMDAIHSLQLILRNAFKDIETMDVDTKTIHARLSDLKIEGMQELEAVTS 619

Query: 617  EMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRM 676
            EMVRLIETATVPILAVDVDGLVNGWNTKI+ELTGL VDKAIGKH LTLVEDSS+D VKRM
Sbjct: 620  EMVRLIETATVPILAVDVDGLVNGWNTKISELTGLLVDKAIGKHLLTLVEDSSVDIVKRM 679

Query: 677  LYLALQGQEEQNIQFEIKTHGSKINDDPITLIVNACASRDLHDNVVGVCFVAQDITPQKT 736
            L+LALQG+EEQNIQFEIKTHGSK    PI L+VNACASRDLH+NVVGVCFV QDIT QK 
Sbjct: 680  LFLALQGKEEQNIQFEIKTHGSKSECGPICLVVNACASRDLHENVVGVCFVGQDITGQKM 739

Query: 737  VMDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGWKREEVIDKLLLA 796
            VMDKFTRIEGDYKAIVQN NPLIPPIFG+DEFGWC EWNPAM  LTGWKREEV+DK+LL 
Sbjct: 740  VMDKFTRIEGDYKAIVQNRNPLIPPIFGTDEFGWCSEWNPAMTNLTGWKREEVLDKMLLG 799

Query: 797  EVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLD 856
            EVFG NMACCRLKNQEAFVNLG+VLN AM+GQ+ EKV FGFFAR GKY ECLLCV+KKLD
Sbjct: 800  EVFGLNMACCRLKNQEAFVNLGVVLNTAMTGQESEKVSFGFFARTGKYVECLLCVSKKLD 859

Query: 857  REGAVTGVFCFLQLASHELQQALHVQRLSEQTALKRLKALAYTKRQIRNPLSGIIFSRKM 916
            REGAVTGVFCFLQLAS ELQQALHVQRLSEQTALKRLKALAY KRQI NPLSGIIFS KM
Sbjct: 860  REGAVTGVFCFLQLASQELQQALHVQRLSEQTALKRLKALAYLKRQIWNPLSGIIFSGKM 919

Query: 917  MEGTELGAEQKRLLHTSAQCQRQLHKILDDSDLDSIIDGYLDLEMVEFTLNEVLVASISQ 976
            MEGTELGAEQK LLHTSAQCQ QL KILDDSDLDSII+GYLDLEMVEFTL EVLVA+ SQ
Sbjct: 920  MEGTELGAEQKELLHTSAQCQCQLSKILDDSDLDSIIEGYLDLEMVEFTLREVLVAATSQ 979

Query: 977  VMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISINFVPNGGQLMVSSSLT 1036
            VMMKSN KGIRI+N+ AE+ M+ETLYGDSIRLQQVLADFL +S+NF P+GG L VS+SLT
Sbjct: 980  VMMKSNEKGIRIINDAAEETMAETLYGDSIRLQQVLADFLQMSVNFTPSGGLLSVSASLT 1039

Query: 1037 KDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSEGDTSEEGISLLISRKLVKLMNGDV 1096
            KDQLGQSV+L +LELRI H G GIPE LLDQMFG + D S EGISL+ISRKLVKLMNGDV
Sbjct: 1040 KDQLGQSVYLVHLELRIRHPGAGIPEALLDQMFGEDTDASVEGISLVISRKLVKLMNGDV 1099

Query: 1097 QYLREAGKSTFIVSVELAAAH 1117
            +Y+REAGKS+FI+SVELA  H
Sbjct: 1100 RYMREAGKSSFIISVELAGGH 1120

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|225450405\|ref\|XP_002278610.1\| PREDICTED: phytochrome A1 [Vitis vinifera] gi\|147838424\|emb\|CAN76586.1\| hypothetical protein VITISV_020287 [Vitis vinifera] gi\|183239014\|gb\|ACC60965.1\| phytochrome A [Vitis vinifera] gi\|296089871\|emb\|CBI39690.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|255543066\|ref\|XP_002512596.1\| phytochrome A, putative [Ricinus communis] gi\|223548557\|gb\|EEF50048.1\| phytochrome A, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|183239022\|gb\|ACC60969.1\| phytochrome A [Vitis riparia]	Back alignment and taxonomy information

>gi\|340007753\|gb\|AEK26583.1\| phytochrome A [Populus tremula]	Back alignment and taxonomy information

>gi\|9049366\|dbj\|BAA99409.1\| phytochrome A [Armoracia rusticana]	Back alignment and taxonomy information

>gi\|9049368\|dbj\|BAA99410.1\| phytochrome A [Armoracia rusticana]	Back alignment and taxonomy information

>gi|15217562|ref|NP_172428.1| phytochrome A [Arabidopsis thaliana] gi|6093714|sp|P14712.2|PHYA_ARATH RecName: Full=Phytochrome A; AltName: Full=Protein ELONGATED HYPOCOTYL 8; AltName: Full=Protein FAR RED ELONGATED 1; AltName: Full=Protein FAR RED ELONGATED HYPOCOTYL 2 gi|404670|gb|AAA21351.1| phytochrome A [Arabidopsis thaliana] gi|3482934|gb|AAC33219.1| phytochrome A [Arabidopsis thaliana] gi|14517372|gb|AAK62577.1| At1g09570/F14J9_27 [Arabidopsis thaliana] gi|332190341|gb|AEE28462.1| phytochrome A [Arabidopsis thaliana]

Back alignment and taxonomy information

>gi\|2499555\|sp\|P93673.1\|PHYA_LATSA RecName: Full=Phytochrome type A gi\|1848273\|gb\|AAB47994.1\| phytochrome type A [Lathyrus sativus]	Back alignment and taxonomy information

>gi\|9049364\|dbj\|BAA99408.1\| phytochrome A [Armoracia rusticana]	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		1117
TAIR\|locus:2012300		1122	PHYA "phytochrome A" [Arabidop	1.0	0.995	0.801	0.0
UNIPROTKB\|P06593		1129	PHYA3 "Phytochrome A type 3" [	0.997	0.986	0.636	0.0
TAIR\|locus:2005515		1172	PHYB "AT2G18790" [Arabidopsis	0.985	0.939	0.502	1.6e-299
TAIR\|locus:2005535		1164	PHYD "phytochrome D" [Arabidop	0.987	0.947	0.505	3.9e-298
TAIR\|locus:2165199		1111	PHYC "phytochrome C" [Arabidop	0.984	0.990	0.505	4.9e-298
TAIR\|locus:2005536		1112	PHYE "phytochrome E" [Arabidop	0.958	0.963	0.464	9.7e-254
UNIPROTKB\|Q55168		748	cph1 "Phytochrome-like protein	0.519	0.775	0.283	1.9e-56
UNIPROTKB\|Q4K656		746	bphP "Bacteriophytochrome hist	0.397	0.595	0.259	7.1e-40
UNIPROTKB\|Q48G81		745	bphP "Bacteriophytochrome hist	0.403	0.605	0.255	6.9e-38
UNIPROTKB\|Q7CY45		736	Atu1990 "Bacteriophytochrome p	0.338	0.513	0.301	2.2e-35

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

 Score = 4690 (1656.0 bits), Expect = 0., P = 0.
 Identities = 899/1121 (80%), Positives = 993/1121 (88%)

Query:     1 MSSSRPAQSSSNTGKSRHSARVIAQTTIDAKLHADFETSGTSFDYSNSVRVSSTAGGDQQ 60
             MS SRP QSS  + +SRHSAR+IAQTT+DAKLHADFE SG+SFDYS SVRV+     +Q 
Sbjct:     1 MSGSRPTQSSEGSRRSRHSARIIAQTTVDAKLHADFEESGSSFDYSTSVRVTGPVVENQP 60

Query:    61 PRSDRVTTAYLHHIQKGKLIQPFGCLLALDEKTFKVIAYSENAPELLTMVNHAVPSVGDH 120
             PRSD+VTT YLHHIQKGKLIQPFGCLLALDEKTFKVIAYSENA ELLTM +HAVPSVG+H
Sbjct:    61 PRSDKVTTTYLHHIQKGKLIQPFGCLLALDEKTFKVIAYSENASELLTMASHAVPSVGEH 120

Query:   121 PVLGIGSDIKTIFTAPSASALQKALGFGEVSLLNPILVHCKTSGKPFYAIVHRVTGSLII 180
             PVLGIG+DI+++FTAPSASALQKALGFG+VSLLNPILVHC+TS KPFYAI+HRVTGS+II
Sbjct:   121 PVLGIGTDIRSLFTAPSASALQKALGFGDVSLLNPILVHCRTSAKPFYAIIHRVTGSIII 180

Query:   181 DFEPVKPYEVPMTAAGALQSYKLAAKAITRLQSLPSGSMERLCDTMIQEVFELTGYDRVM 240
             DFEPVKPYEVPMTAAGALQSYKLAAKAITRLQSLPSGSMERLCDTM+QEVFELTGYDRVM
Sbjct:   181 DFEPVKPYEVPMTAAGALQSYKLAAKAITRLQSLPSGSMERLCDTMVQEVFELTGYDRVM 240

Query:   241 AYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDCRARHVKV 300
             AYKFHEDDHGEVVSE+TK GLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDC A+H +V
Sbjct:   241 AYKFHEDDHGEVVSEVTKPGLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDCNAKHARV 300

Query:   301 LQDEKLPFDLTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDXXXXGD----NTLPQ 356
             LQDEKL FDLTLCGSTLRAPHSCHLQYM NM+SIASLVMAVVVN+    GD     T PQ
Sbjct:   301 LQDEKLSFDLTLCGSTLRAPHSCHLQYMANMDSIASLVMAVVVNEEDGEGDAPDATTQPQ 360

Query:   357 KRKRLWGLVVCHNTTPRFVPFPLRYACEFLAQVFAIHVNKELELEYQILEKNILRTQTLL 416
             KRKRLWGLVVCHNTTPRFVPFPLRYACEFLAQVFAIHVNKE+EL+ Q++EKNILRTQTLL
Sbjct:   361 KRKRLWGLVVCHNTTPRFVPFPLRYACEFLAQVFAIHVNKEVELDNQMVEKNILRTQTLL 420

Query:   417 CDMLMRDAPLGIVTQSPNIMDLVKCDGAALLYKNKIWRLGVTPNDFQLHDIVSWLSEYHM 476
             CDMLMRDAPLGIV+QSPNIMDLVKCDGAALLYK+KIW+LG TP++F L +I SWL EYHM
Sbjct:   421 CDMLMRDAPLGIVSQSPNIMDLVKCDGAALLYKDKIWKLGTTPSEFHLQEIASWLCEYHM 480

Query:   477 DSTGLSADSXXXXXXXXXXXXXXVVCGMAAVRISPKDMIFWFRSQTASEVRWGGAKHEPD 536
             DSTGLS DS               VCGMAAVRIS KDMIFWFRS TA EVRWGGAKH+PD
Sbjct:   481 DSTGLSTDSLHDAGFPRALSLGDSVCGMAAVRISSKDMIFWFRSHTAGEVRWGGAKHDPD 540

Query:   537 EKDDGRKMHPRSSFKAFLEVVKTRSLPWKDYEMDAIHSLQLILRNAFKDVGTLDLDTKSI 596
             ++DD R+MHPRSSFKAFLEVVKTRSLPWKDYEMDAIHSLQLILRNAFKD  T D++TK I
Sbjct:   541 DRDDARRMHPRSSFKAFLEVVKTRSLPWKDYEMDAIHSLQLILRNAFKDSETTDVNTKVI 600

Query:   597 HSKLCDLKIEGMKELEAVTSEMVRLIETATVPILAVDVDGLVNGWNTKIAELTGLSVDKA 656
             +SKL DLKI+G++ELEAVTSEMVRLIETATVPILAVD DGLVNGWNTKIAELTGLSVD+A
Sbjct:   601 YSKLNDLKIDGIQELEAVTSEMVRLIETATVPILAVDSDGLVNGWNTKIAELTGLSVDEA 660

Query:   657 IGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKINDDPITLIVNACASRD 716
             IGKHFLTLVEDSS++ VKRML  AL+G EEQN+QFEIKTH S+ +  PI+L+VNACASRD
Sbjct:   661 IGKHFLTLVEDSSVEIVKRMLENALEGTEEQNVQFEIKTHLSRADAGPISLVVNACASRD 720

Query:   717 LHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNP 776
             LH+NVVGVCFVA D+T QKTVMDKFTRIEGDYKAI+QNPNPLIPPIFG+DEFGWC EWNP
Sbjct:   721 LHENVVGVCFVAHDLTGQKTVMDKFTRIEGDYKAIIQNPNPLIPPIFGTDEFGWCTEWNP 780

Query:   777 AMVKLTGWKREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFG 836
             AM KLTG KREEVIDK+LL EVFGT  +CCRLKNQEAFVNLGIVLN A++ QDPEKV F 
Sbjct:   781 AMSKLTGLKREEVIDKMLLGEVFGTQKSCCRLKNQEAFVNLGIVLNNAVTSQDPEKVSFA 840

Query:   837 FFARNGKYAECLLCVNKKLDREGAVTGVFCFLQLASHELQQALHVQRLSEQTALKRLKAL 896
             FF R GKY ECLLCV+KKLDREG VTGVFCFLQLASHELQQALHVQRL+E+TA+KRLKAL
Sbjct:   841 FFTRGGKYVECLLCVSKKLDREGVVTGVFCFLQLASHELQQALHVQRLAERTAVKRLKAL 900

Query:   897 AYTKRQIRNPLSGIIFSRKMMEGTELGAEQKRLLHTSAQCQRQLHKXXXXXXXXXXXXXX 956
             AY KRQIRNPLSGI+F+RKM+EGTELG EQ+R+L TSA CQ+QL K              
Sbjct:   901 AYIKRQIRNPLSGIMFTRKMIEGTELGPEQRRILQTSALCQKQLSKILDDSDLESIIEGC 960

Query:   957 XXXEMVEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFL 1016
                EM EFTLNEVL AS SQVMMKSN K +RI NET E++MS+TLYGDSIRLQQVLADF+
Sbjct:   961 LDLEMKEFTLNEVLTASTSQVMMKSNGKSVRITNETGEEVMSDTLYGDSIRLQQVLADFM 1020

Query:  1017 SISINFVPNGGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSEGDTS 1076
              +++NF P+GGQL VS+SL KDQLG+SVHLA LE+R+TH G GIPE LL+QMFG+E D S
Sbjct:  1021 LMAVNFTPSGGQLTVSASLRKDQLGRSVHLANLEIRLTHTGAGIPEFLLNQMFGTEEDVS 1080

Query:  1077 EEGISLLISRKLVKLMNGDVQYLREAGKSTFIVSVELAAAH 1117
             EEG+SL++SRKLVKLMNGDVQYLR+AGKS+FI++ ELAAA+
Sbjct:  1081 EEGLSLMVSRKLVKLMNGDVQYLRQAGKSSFIITAELAAAN 1121

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:0042802 "identical protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0009638 "phototropism" evidence=IMP

GO:0009630 "gravitropism" evidence=RCA;IMP

GO:0016604 "nuclear body" evidence=IDA

GO:0010161 "red light signaling pathway" evidence=IMP

GO:0046685 "response to arsenic-containing substance" evidence=RCA;IMP

GO:0009640 "photomorphogenesis" evidence=IMP

GO:0031516 "far-red light photoreceptor activity" evidence=IMP

GO:0017148 "negative regulation of translation" evidence=IMP

GO:0007623 "circadian rhythm" evidence=RCA

GO:0010017 "red or far-red light signaling pathway" evidence=RCA

GO:0009883 "red or far-red light photoreceptor activity" evidence=TAS

GO:0010201 "response to continuous far red light stimulus by the high-irradiance response system" evidence=IMP

GO:0010203 "response to very low fluence red light stimulus" evidence=IMP

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

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

TAIR\|locus:2005536 PHYE "phytochrome E" [Arabidopsis thaliana (taxid:3702)]	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\|Q4K656 bphP "Bacteriophytochrome histidine kinase" [Pseudomonas protegens Pf-5 (taxid:220664)]	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\|Q7CY45 Atu1990 "Bacteriophytochrome protein" [Agrobacterium fabrum str. C58 (taxid:176299)]	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	0.8168	0.9847	0.9795	N/A	no
P93528	PHYC_SORBI	No assigned EC number	0.5661	0.9758	0.9603	N/A	no
P42496	PHY_ADICA	No assigned EC number	0.5560	0.9686	0.9677	N/A	no
P36505	PHY1_PHYPA	No assigned EC number	0.5858	0.9767	0.9637	N/A	no
P55141	PHYA_PETCR	No assigned EC number	0.7423	0.9883	0.9778	N/A	no
Q40762	PHY_PICAB	No assigned EC number	0.6019	0.9946	0.9779	N/A	no
Q41046	PHY_PINSY	No assigned EC number	0.5605	0.9713	0.9593	N/A	no
A2XFW2	PHYB_ORYSI	No assigned EC number	0.5309	0.9686	0.9239	N/A	no
P33529	PHY_MOUSC	No assigned EC number	0.5326	0.9731	0.9670	N/A	no
A2XM23	PHYC_ORYSI	No assigned EC number	0.5644	0.9937	0.9762	N/A	no
P14712	PHYA_ARATH	No assigned EC number	0.8242	1.0	0.9955	yes	no
P15001	PHYA_PEA	No assigned EC number	0.8151	1.0	0.9937	N/A	no
A2XLG5	PHYA_ORYSI	No assigned EC number	0.6537	0.9928	0.9831	N/A	no
P34094	PHYB_SOLTU	No assigned EC number	0.5385	0.9740	0.9628	N/A	no
P29130	PHYB_TOBAC	No assigned EC number	0.5323	0.9803	0.9673	N/A	no
P06592	PHYA_CUCPE	No assigned EC number	0.8216	0.9820	0.9759	N/A	no
P06593	PHYA3_AVESA	No assigned EC number	0.6582	0.9803	0.9698	N/A	no
Q10DU0	PHYA_ORYSJ	No assigned EC number	0.6537	0.9928	0.9831	yes	no
P06594	PHYA4_AVESA	No assigned EC number	0.6521	0.9785	0.9681	N/A	no
P42500	PHYA_SOYBN	No assigned EC number	0.7846	0.9767	0.9646	no	no
O49934	PHYA_POPTM	No assigned EC number	0.8340	0.9803	0.9733	N/A	no
P55004	PHYE_IPONI	No assigned EC number	0.5022	0.9641	0.9659	N/A	no
P93527	PHYB_SORBI	No assigned EC number	0.5265	0.9686	0.9185	N/A	no
P93526	PHYA_SORBI	No assigned EC number	0.6491	0.9803	0.9681	N/A	no
P33530	PHYA1_TOBAC	No assigned EC number	0.8191	0.9874	0.9813	N/A	no
Q01549	PHY1_SELMA	No assigned EC number	0.5952	0.9928	0.9779	N/A	no
P93673	PHYA_LATSA	No assigned EC number	0.8133	1.0	0.9937	N/A	no
P19862	PHYA1_MAIZE	No assigned EC number	0.6494	0.9785	0.9664	N/A	no
Q9ZS62	PHYB1_SOLLC	No assigned EC number	0.5307	0.9811	0.9690	N/A	no
Q39557	PHY2_CERPU	No assigned EC number	0.5903	0.9910	0.9875	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	2.7.13.3	LOW CONFIDENCE prediction!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	PHYA	SubName- Full=Phytochrome A; Flags- Fragment; (1126 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	estExt_fgenesh4_pm.C_LG_II0442	hypothetical protein (681 aa)	•	•	•	0.835
	eugene3.00050718	hypothetical protein (680 aa)	•	•	•	0.835
	fgenesh4_pm.C_LG_XVIII000281	hypothetical protein (613 aa)		•	•	0.819
	estExt_fgenesh4_pg.C_LG_V1131	hypothetical protein (1171 aa)		•	•	0.807
	estExt_fgenesh4_pg.C_LG_X0958	hypothetical protein (587 aa)		•	•	0.803
	rbcL	RecName- Full=Ribulose bisphosphate carboxylase large chain; Short=RuBisCO large subunit; EC=4. [...] (101 aa)			•	0.683
	grail3.0064002701	SubName- Full=Putative uncharacterized protein; (382 aa)			•	0.510
	GA20ox7	gibberellin 20-oxidase (EC-1.14.11.12) (372 aa)			•	0.510
	GA20ox5	gibberellin 20-oxidase (EC-1.14.11.12) (378 aa)			•	0.510
	GA20ox2-1	gibberellin 20-oxidase (EC-1.14.11.12) (366 aa)			•	0.510

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		1117
COG4251		750	COG4251, COG4251, Bacteriophytochrome (light-regul	1e-100
pfam00360		183	pfam00360, PHY, Phytochrome region	5e-91
pfam08446		107	pfam08446, PAS_2, PAS fold	1e-45
pfam01590		143	pfam01590, GAF, GAF domain	5e-20
pfam00989		113	pfam00989, PAS, PAS fold	4e-19
pfam02518		111	pfam02518, HATPase_c, Histidine kinase-, DNA gyras	2e-16
TIGR02956		968	TIGR02956, TMAO_torS, TMAO reductase sytem sensor	4e-16
pfam00989		113	pfam00989, PAS, PAS fold	7e-16
smart00387		111	smart00387, HATPase_c, Histidine kinase-like ATPas	3e-15
smart00065		149	smart00065, GAF, Domain present in phytochromes an	3e-13
cd00075		103	cd00075, HATPase_c, Histidine kinase-like ATPases;	3e-13
COG0642		336	COG0642, BaeS, Signal transduction histidine kinas	2e-12
PRK11107		919	PRK11107, PRK11107, hybrid sensory histidine kinas	1e-11
TIGR00229		124	TIGR00229, sensory_box, PAS domain S-box	1e-10
PRK11091		779	PRK11091, PRK11091, aerobic respiration control se	1e-10
PRK15347		921	PRK15347, PRK15347, two component system sensor ki	4e-10
PRK10841		924	PRK10841, PRK10841, hybrid sensory kinase in two-c	3e-09
pfam13426		101	pfam13426, PAS_9, PAS domain	5e-09
smart00388		66	smart00388, HisKA, His Kinase A (phosphoacceptor)	6e-09
cd00130		103	cd00130, PAS, PAS domain; PAS motifs appear in arc	6e-09
pfam00512		66	pfam00512, HisKA, His Kinase A (phospho-acceptor)	2e-08
PRK10364		457	PRK10364, PRK10364, sensor protein ZraS; Provision	3e-08
COG2202		232	COG2202, AtoS, FOG: PAS/PAC domain [Signal transdu	5e-07
smart00091		67	smart00091, PAS, PAS domain	3e-06
COG2205		890	COG2205, KdpD, Osmosensitive K+ channel histidine	2e-05
PRK11360		607	PRK11360, PRK11360, sensory histidine kinase AtoS;	2e-05
cd00130		103	cd00130, PAS, PAS domain; PAS motifs appear in arc	3e-05
PRK13560		807	PRK13560, PRK13560, hypothetical protein; Provisio	3e-05
pfam08448		110	pfam08448, PAS_4, PAS fold	3e-05
PRK11466		914	PRK11466, PRK11466, hybrid sensory histidine kinas	4e-05
PRK09959		1197	PRK09959, PRK09959, hybrid sensory histidine kinas	6e-05
COG2202		232	COG2202, AtoS, FOG: PAS/PAC domain [Signal transdu	8e-05
PRK11100		475	PRK11100, PRK11100, sensory histidine kinase CreC;	1e-04
smart00091		67	smart00091, PAS, PAS domain	3e-04
PRK11360		607	PRK11360, PRK11360, sensory histidine kinase AtoS;	3e-04
TIGR01386		457	TIGR01386, cztS_silS_copS, heavy metal sensor kina	7e-04
cd00082		65	cd00082, HisKA, Histidine Kinase A (dimerization/p	0.003

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

 Score =  333 bits (855), Expect = e-100
 Identities = 166/523 (31%), Positives = 249/523 (47%), Gaps = 64/523 (12%)

Query: 79  LIQPFGCLLALDEKTFKVIAYSENAPELLTMVNHAVPSVGDHPVLGIGSDIKTIFTAPSA 138
            IQP G LL LDE    V+  SEN   +L          G  P   +G  +  + T+   
Sbjct: 25  AIQPHGALLVLDEADLMVLQASENCANIL----------GREPEDLLGRTLGAVLTSEQV 74

Query: 139 SALQKALGFGEVSLLNPILVHCKTSGKPFYAIVHRVTGSLIIDFEPVKPYEVPMTAAGAL 198
             LQ AL  G ++ LNP  +  +  G  F    HR    LI++FEP    E     A  L
Sbjct: 75  PPLQSALTVGGLTTLNPTKMWTR-KGGSFDVSAHRSKELLILEFEPAGTGE----TASFL 129

Query: 199 QSYKLAAKAITRLQSLPSGSMERLCDTMIQEVFELTGYDRVMAYKFHEDDHGEVVSEITK 258
             Y LA  A+ RLQS  +  +  L     QEV  +TG+DRVM Y+F ED  GEV++E  +
Sbjct: 130 GFYHLAKLAMNRLQSAAN--LRDLLSRTTQEVRRMTGFDRVMLYRFDEDGSGEVIAEAKR 187

Query: 259 SGLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDCRARHVKVL------QDEKLPFDLTL 312
             LE YLGL YPA+DIPQ AR L+++N +R+I D     V VL       +E  P DL+ 
Sbjct: 188 EDLESYLGLRYPASDIPQQARALYIQNPLRLIPDVSYTPVPVLPAVNPETNE--PLDLS- 244

Query: 313 CGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWGLVVCHNTTP 372
             S LR+    HL+Y+ NM   AS+ +++VV+               +LWGL+ CH+ +P
Sbjct: 245 -YSVLRSVSPIHLEYLRNMGVGASMSISIVVDG--------------KLWGLIACHHQSP 289

Query: 373 RFVPFPLRYACEFLAQVFAIHVNKELELEYQILE-KNILRTQTLLCDMLMRDAPL---GI 428
           + +P+ +R ACEF  QV ++ +      + +  + +  L          M  A     G+
Sbjct: 290 KVIPYEVRKACEFFGQVLSMEI--SALEQSEDADYRVQLTEHHARLLRYMAHAADFVDGL 347

Query: 429 VTQSPNIMDLVKCDGAALLYKNKIWRLGVTPNDFQLHDIVSWLSE------YHMDSTGLS 482
           +    +++DL+  DGAAL +  +   +G TP    +  ++ WL+E      +  DS    
Sbjct: 348 IDHQDDLLDLMPADGAALCFGGRWHLVGETPPRPAVQRLLQWLAEREEGDVFATDSLS-- 405

Query: 483 ADSLYDAGYLGALALGDVVCGMAAVRIS--PKDMIFWFRSQTASEVRWGGAKHEPDE-KD 539
                   Y  A     V  G+ A+ IS    + + WFR +    V WGG   +P E   
Sbjct: 406 ------QVYPDAEDYASVASGLLAIPISRVKSNYLLWFRPEVVQTVNWGGDPEKPYEAGP 459

Query: 540 DGRKMHPRSSFKAFLEVVKTRSLPWKDYEMDAIHSLQLILRNA 582
            G ++ PR SF+ + E V+ +S PW + E++A   L+  +   
Sbjct: 460 MGIRLTPRKSFELWKETVRLQSQPWSEVEIEAALELRKAIVGI 502

Length = 750

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

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

>gnl\|CDD\|216590 pfam01590, GAF, GAF domain	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\|234070 TIGR02956, TMAO_torS, TMAO reductase sytem sensor TorS	Back alignment and domain information

>gnl\|CDD\|216228 pfam00989, PAS, PAS fold	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\|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\|223715 COG0642, BaeS, Signal transduction histidine kinase [Signal transduction mechanisms]	Back alignment and domain information

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

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

>gnl\|CDD\|236842 PRK11091, PRK11091, aerobic respiration control sensor protein ArcB; Provisional	Back alignment and domain information

>gnl\|CDD\|237951 PRK15347, PRK15347, two component system sensor kinase SsrA; 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\|222120 pfam13426, PAS_9, PAS domain	Back alignment and domain information

>gnl\|CDD\|214644 smart00388, HisKA, His Kinase A (phosphoacceptor) domain	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\|215963 pfam00512, HisKA, His Kinase A (phospho-acceptor) domain	Back alignment and domain information

>gnl\|CDD\|236674 PRK10364, PRK10364, sensor protein ZraS; Provisional	Back alignment and domain information

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

>gnl\|CDD\|214512 smart00091, PAS, PAS 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\|236901 PRK11360, PRK11360, sensory histidine kinase AtoS; 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\|106506 PRK13560, PRK13560, hypothetical protein; Provisional	Back alignment and domain information

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

>gnl\|CDD\|236914 PRK11466, PRK11466, hybrid sensory histidine kinase TorS; Provisional	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\|225112 COG2202, AtoS, FOG: PAS/PAC domain [Signal transduction mechanisms]	Back alignment and domain information

>gnl\|CDD\|236846 PRK11100, PRK11100, sensory histidine kinase CreC; Provisional	Back alignment and domain information

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

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

>gnl\|CDD\|233391 TIGR01386, cztS_silS_copS, heavy metal sensor kinase	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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		1117
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
PRK11006		430	phoR phosphate regulon sensor protein; Provisional	100.0
COG3852		363	NtrB Signal transduction histidine kinase, nitroge	100.0
PRK13557		540	histidine kinase; Provisional	100.0
PRK10618		894	phosphotransfer intermediate protein in two-compon	100.0
PRK11073		348	glnL nitrogen regulation protein NR(II); Provision	100.0
PRK11360		607	sensory histidine kinase AtoS; Provisional	100.0
TIGR02966		333	phoR_proteo phosphate regulon sensor kinase PhoR.	100.0
PRK10841		924	hybrid sensory kinase in two-component regulatory	100.0
PF00360		182	PHY: Phytochrome region; InterPro: IPR013515 Phyto	100.0
PRK09959		1197	hybrid sensory histidine kinase in two-component r	100.0
PRK13559		361	hypothetical protein; Provisional	100.0
COG2205		890	KdpD Osmosensitive K+ channel histidine kinase [Si	100.0
PRK11086		542	sensory histidine kinase DcuS; Provisional	99.98
PRK09303		380	adaptive-response sensory kinase; Validated	99.97
COG5000		712	NtrY Signal transduction histidine kinase involved	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
PRK11466		914	hybrid sensory histidine kinase TorS; Provisional	99.95
PRK10490		895	sensor protein KdpD; Provisional	99.95
PRK11107		919	hybrid sensory histidine kinase BarA; Provisional	99.95
PRK13837		828	two-component VirA-like sensor kinase; Provisional	99.95
COG3290		537	CitA Signal transduction histidine kinase regulati	99.95
PRK10364		457	sensor protein ZraS; Provisional	99.94
PRK10604		433	sensor protein RstB; Provisional	99.94
PRK10815		485	sensor protein PhoQ; Provisional	99.94
PRK10549		466	signal transduction histidine-protein kinase BaeS;	99.93
PRK10755		356	sensor protein BasS/PmrB; Provisional	99.92
TIGR03785		703	marine_sort_HK proteobacterial dedicated sortase s	99.92
PRK09776		1092	putative diguanylate cyclase; Provisional	99.91
PRK09835		482	sensor kinase CusS; Provisional	99.91
PRK09776		1092	putative diguanylate cyclase; Provisional	99.91
TIGR02916		679	PEP_his_kin putative PEP-CTERM system histidine ki	99.91
TIGR01386		457	cztS_silS_copS heavy metal sensor kinase. Members	99.91
PRK11100		475	sensory histidine kinase CreC; Provisional	99.9
PRK10337		449	sensor protein QseC; Provisional	99.9
PF08446		110	PAS_2: PAS fold; InterPro: IPR013654 The PAS fold	99.9
PRK09470		461	cpxA two-component sensor protein; Provisional	99.9
PRK09467		435	envZ osmolarity sensor protein; Provisional	99.89
COG0642		336	BaeS Signal transduction histidine kinase [Signal	99.89
COG4192		673	Signal transduction histidine kinase regulating ph	99.87
TIGR02040		442	PpsR-CrtJ transcriptional regulator PpsR. This mod	99.87
PRK13560		807	hypothetical protein; Provisional	99.86
PRK11644		495	sensory histidine kinase UhpB; Provisional	99.83
PRK11359		799	cyclic-di-GMP phosphodiesterase; Provisional	99.81
TIGR02040		442	PpsR-CrtJ transcriptional regulator PpsR. This mod	99.79
PF02518		111	HATPase_c: Histidine kinase-, DNA gyrase B-, and H	99.73
PRK10935		565	nitrate/nitrite sensor protein NarQ; Provisional	99.69
PRK10600		569	nitrate/nitrite sensor protein NarX; Provisional	99.67
COG3920		221	Signal transduction histidine kinase [Signal trans	99.62
PRK10547		670	chemotaxis protein CheA; Provisional	99.6
PF08448		110	PAS_4: PAS fold; InterPro: IPR013656 The PAS fold	99.48
PF13426		104	PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_	99.45
PF00989		113	PAS: PAS fold; InterPro: IPR013767 PAS domains are	99.44
COG3851		497	UhpB Signal transduction histidine kinase, glucose	99.42
COG4585		365	Signal transduction histidine kinase [Signal trans	99.4
COG0643		716	CheA Chemotaxis protein histidine kinase and relat	99.39
COG4564		459	Signal transduction histidine kinase [Signal trans	99.38
smart00387		111	HATPase_c Histidine kinase-like ATPases. Histidine	99.33
PRK11091		779	aerobic respiration control sensor protein ArcB; P	99.33
PF01590		154	GAF: GAF domain; InterPro: IPR003018 This domain i	99.32
PF13426		104	PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_	99.31
COG3850		574	NarQ Signal transduction histidine kinase, nitrate	99.29
PF00989		113	PAS: PAS fold; InterPro: IPR013767 PAS domains are	99.26
PRK04184		535	DNA topoisomerase VI subunit B; Validated	99.25
PF08448		110	PAS_4: PAS fold; InterPro: IPR013656 The PAS fold	99.19
PRK13559		361	hypothetical protein; Provisional	99.15
PRK10060		663	RNase II stability modulator; Provisional	99.12
COG3275		557	LytS Putative regulator of cell autolysis [Signal	99.11
PRK14868		795	DNA topoisomerase VI subunit B; Provisional	99.1
cd00075		103	HATPase_c Histidine kinase-like ATPases; This fami	99.1
KOG0519		786	consensus Sensory transduction histidine kinase [S	99.08
PRK13558		665	bacterio-opsin activator; Provisional	99.07
PRK13557		540	histidine kinase; Provisional	99.07
TIGR01925		137	spIIAB anti-sigma F factor. This model describes t	99.05
PRK10060		663	RNase II stability modulator; Provisional	99.04
TIGR00229		124	sensory_box PAS domain S-box. The PAS domain was p	99.03
TIGR01052		488	top6b DNA topoisomerase VI, B subunit. This model	99.02
COG3829		560	RocR Transcriptional regulator containing PAS, AAA	99.0
PRK03660		146	anti-sigma F factor; Provisional	98.98
PRK14867		659	DNA topoisomerase VI subunit B; Provisional	98.97
smart00065		149	GAF Domain present in phytochromes and cGMP-specif	98.97
PRK11359		799	cyclic-di-GMP phosphodiesterase; Provisional	98.91
PF13596		106	PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.	98.86
COG2972		456	Predicted signal transduction protein with a C-ter	98.83
PRK04069		161	serine-protein kinase RsbW; Provisional	98.82
PRK13558		665	bacterio-opsin activator; Provisional	98.81
TIGR02938		494	nifL_nitrog nitrogen fixation negative regulator N	98.8
PF08447		91	PAS_3: PAS fold; InterPro: IPR013655 The PAS fold	98.78
TIGR00229		124	sensory_box PAS domain S-box. The PAS domain was p	98.78
PF08447		91	PAS_3: PAS fold; InterPro: IPR013655 The PAS fold	98.75
PF00512		68	HisKA: His Kinase A (phospho-acceptor) domain; Int	98.7
PRK11360		607	sensory histidine kinase AtoS; Provisional	98.69
PF14501		100	HATPase_c_5: GHKL domain	98.68
TIGR01924		159	rsbW_low_gc serine-protein kinase RsbW. This model	98.66
COG5002		459	VicK Signal transduction histidine kinase [Signal	98.6
KOG3558		768	consensus Hypoxia-inducible factor 1/Neuronal PAS	98.59
cd00130		103	PAS PAS domain; PAS motifs appear in archaea, euba	98.59
TIGR02966		333	phoR_proteo phosphate regulon sensor kinase PhoR.	98.52
COG2203		175	FhlA FOG: GAF domain [Signal transduction mechanis	98.52
PRK11388		638	DNA-binding transcriptional regulator DhaR; Provis	98.48
PF12860		115	PAS_7: PAS fold	98.45
PF13492		129	GAF_3: GAF domain; PDB: 3EEA_A 4DMZ_A 4DN0_A 1VHM_	98.39
COG2202		232	AtoS FOG: PAS/PAC domain [Signal transduction mech	98.39
PRK11073		348	glnL nitrogen regulation protein NR(II); Provision	98.33
PF13581		125	HATPase_c_2: Histidine kinase-like ATPase domain	98.31
KOG0787		414	consensus Dehydrogenase kinase [Signal transductio	98.27
cd00130		103	PAS PAS domain; PAS motifs appear in archaea, euba	98.26
PRK11006		430	phoR phosphate regulon sensor protein; Provisional	98.22
PF13185		148	GAF_2: GAF domain; PDB: 2QYB_A 3KSG_B 3KSF_C 3KSI_	98.15
PF13596		106	PAS_10: PAS domain; PDB: 3CAX_A 2QKP_D.	98.13
PRK11086		542	sensory histidine kinase DcuS; Provisional	98.08
PRK10820		520	DNA-binding transcriptional regulator TyrR; Provis	98.05
PF14598		111	PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W	98.01
TIGR01817		534	nifA Nif-specific regulatory protein. This model r	98.0
COG1389		538	DNA topoisomerase VI, subunit B [DNA replication,	97.99
COG3829		560	RocR Transcriptional regulator containing PAS, AAA	97.98
COG3604		550	FhlA Transcriptional regulator containing GAF, AAA	97.84
COG2172		146	RsbW Anti-sigma regulatory factor (Ser/Thr protein	97.84
PF14598		111	PAS_11: PAS domain; PDB: 1P97_A 3F1O_A 2A24_A 3H7W	97.78
PRK05022		509	anaerobic nitric oxide reductase transcription reg	97.76
COG2202		232	AtoS FOG: PAS/PAC domain [Signal transduction mech	97.75
PF12860		115	PAS_7: PAS fold	97.74
PRK15429		686	formate hydrogenlyase transcriptional activator Fh	97.7
COG3290		537	CitA Signal transduction histidine kinase regulati	97.64
PRK15053		545	dpiB sensor histidine kinase DpiB; Provisional	97.57
PRK10820		520	DNA-binding transcriptional regulator TyrR; Provis	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.	97.51
PRK11061		748	fused phosphoenolpyruvate-protein phosphotransfera	97.51
smart00388		66	HisKA His Kinase A (phosphoacceptor) domain. Dimer	97.48
COG5000		712	NtrY Signal transduction histidine kinase involved	97.45
KOG3559		598	consensus Transcriptional regulator SIM1 [Transcri	97.35
KOG0501		971	consensus K+-channel KCNQ [Inorganic ion transport	97.27
PRK09959		1197	hybrid sensory histidine kinase in two-component r	97.13
KOG3560		712	consensus Aryl-hydrocarbon receptor [Transcription	97.02
PRK11388		638	DNA-binding transcriptional regulator DhaR; Provis	97.01
KOG0501		971	consensus K+-channel KCNQ [Inorganic ion transport	97.01
PRK15429		686	formate hydrogenlyase transcriptional activator Fh	97.01
PF13589		137	HATPase_c_3: Histidine kinase-, DNA gyrase B-, and	96.87
smart00091		67	PAS PAS domain. PAS motifs appear in archaea, euba	96.83
cd00082		65	HisKA Histidine Kinase A (dimerization/phosphoacce	96.78
PF13188		64	PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.	96.66
COG2461		409	Uncharacterized conserved protein [Function unknow	96.53
PF08670		148	MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEK	96.23
PRK00095		617	mutL DNA mismatch repair protein; Reviewed	96.23
COG5385		214	Uncharacterized protein conserved in bacteria [Fun	96.16
PF07568		76	HisKA_2: Histidine kinase; InterPro: IPR011495 Two	95.53
KOG1229		775	consensus 3'5'-cyclic nucleotide phosphodiesterase	95.36
PRK05559		631	DNA topoisomerase IV subunit B; Reviewed	95.3
KOG3558		768	consensus Hypoxia-inducible factor 1/Neuronal PAS	95.3
TIGR02373		124	photo_yellow photoactive yellow protein. Members o	95.05
TIGR02916		679	PEP_his_kin putative PEP-CTERM system histidine ki	94.97
COG3852		363	NtrB Signal transduction histidine kinase, nitroge	94.6
PF10090		182	DUF2328: Uncharacterized protein conserved in bact	94.41
PRK10841		924	hybrid sensory kinase in two-component regulatory	94.28
COG3283		511	TyrR Transcriptional regulator of aromatic amino a	94.18
TIGR01059		654	gyrB DNA gyrase, B subunit. This model describes t	94.03
PF08670		148	MEKHLA: MEKHLA domain; InterPro: IPR013978 The MEK	93.89
PRK05644		638	gyrB DNA gyrase subunit B; Validated	93.8
TIGR01055		625	parE_Gneg DNA topoisomerase IV, B subunit, proteob	93.75
KOG1229		775	consensus 3'5'-cyclic nucleotide phosphodiesterase	93.67
TIGR02373		124	photo_yellow photoactive yellow protein. Members o	93.64
smart00091		67	PAS PAS domain. PAS motifs appear in archaea, euba	93.53
KOG3753		1114	consensus Circadian clock protein period [Signal t	93.53
COG2461		409	Uncharacterized conserved protein [Function unknow	93.05
COG0323		638	MutL DNA mismatch repair enzyme (predicted ATPase)	92.63
COG3284		606	AcoR Transcriptional activator of acetoin/glycerol	91.96
KOG0519		786	consensus Sensory transduction histidine kinase [S	91.57
smart00086		43	PAC Motif C-terminal to PAS motifs (likely to cont	91.5
smart00433		594	TOP2c TopoisomeraseII. Eukaryotic DNA topoisomeras	91.28
PRK14939		756	gyrB DNA gyrase subunit B; Provisional	91.22
PRK10618		894	phosphotransfer intermediate protein in two-compon	91.09
PRK05218		613	heat shock protein 90; Provisional	91.04
smart00086		43	PAC Motif C-terminal to PAS motifs (likely to cont	89.81
PRK14083		601	HSP90 family protein; Provisional	89.11
TIGR02851		180	spore_V_T stage V sporulation protein T. Members o	88.07
PF07310		137	PAS_5: PAS domain; InterPro: IPR009922 This family	87.48
PTZ00272		701	heat shock protein 83 kDa (Hsp83); Provisional	85.7
COG0326		623	HtpG Molecular chaperone, HSP90 family [Posttransl	84.75
KOG3561		803	consensus Aryl-hydrocarbon receptor nuclear transl	83.3
TIGR01058		637	parE_Gpos DNA topoisomerase IV, B subunit, Gram-po	81.42
COG5381		184	Uncharacterized protein conserved in bacteria [Fun	81.25
KOG3560		712	consensus Aryl-hydrocarbon receptor [Transcription	80.44

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

Probab=100.00  E-value=3.2e-152  Score=1279.02  Aligned_cols=708  Identities=28%  Similarity=0.484  Sum_probs=617.6

Q ss_pred             hhccCCCCCCCceeEEEEecCCceEEEEccChhhhhcCCcCCCCCCCCCCccCCCCchhhhcChhHHHHHHHHhccCCcc
Q 001235           72 HHIQKGKLIQPFGCLLALDEKTFKVIAYSENAPELLTMVNHAVPSVGDHPVLGIGSDIKTIFTAPSASALQKALGFGEVS  151 (1117)
Q Consensus        72 ~~i~~~g~iQp~G~ll~~~~~~~~i~~~S~N~~~~l~~~~~~~~~~~~~~~~~lg~~~~~~~~~~~~~~l~~~~~~~~~~  151 (1117)
                      +|||+||+||||||||++|+.++.|+|+|+|+..+||+.|+.          ++|+++.++|+......++.++..+...
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            689999999999999999999999999999999999998854          7999999999999999999999998888


Q ss_pred             ccCcEEEEecCCCCeEEEEEEeeCCeEEEEeeecCCCCCcchhhhhhHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHH
Q 001235          152 LLNPILVHCKTSGKPFYAIVHRVTGSLIIDFEPVKPYEVPMTAAGALQSYKLAAKAITRLQSLPSGSMERLCDTMIQEVF  231 (1117)
Q Consensus       152 ~~~~~~~~~~~~~~~f~~~~hr~~~~~~~e~Ep~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vr  231 (1117)
                      ..||-.+..+..+ .|++++||+++.+|+||||....+. .   ..+.+|+++..++.+||+.+  ++.++|+.+++|||
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 TLNPTKMWTRKGG-SFDVSAHRSKELLILEFEPAGTGET-A---SFLGFYHLAKLAMNRLQSAA--NLRDLLSRTTQEVR  160 (750)
T ss_pred             cCCchhhhhhcCC-ceeEEEEecCcEEEEEEecCccccc-c---cccchHHHHHHHHHHHhcCc--cHHHHHHHHHHHHH
Confidence            8888555434433 7999999999999999999754442 2   23447888889999999955  99999999999999


Q ss_pred             hhhCCCEEEEEeecCCCCceEEEEeccCCCCCccCCcCCCCCchHHHHHHHHhCCeEEEeccCCccccccc--CCCCCCc
Q 001235          232 ELTGYDRVMAYKFHEDDHGEVVSEITKSGLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDCRARHVKVLQ--DEKLPFD  309 (1117)
Q Consensus       232 ~~~~~dRv~iy~f~~d~~g~vvaE~~~~~~~~~lg~~~p~~dip~~~r~l~~~~~~r~i~d~~~~~v~~~~--~~~~~~~  309 (1117)
                      ++|||||||+|||++||+|+||||+++++++||||+||||||||+|||+||.+|++|+|+|+.|+|||+.|  +|.+++|
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             ccccCCcccCCChhHHHHHHhcCceeEEEEEEEEcCCccccCCCcccccccceeeEEeeccCCCCCCchhHHHHHHHHHH
Q 001235          310 LTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNDEEEEGDNTLPQKRKRLWGLVVCHNTTPRFVPFPLRYACEFLAQV  389 (1117)
Q Consensus       310 l~l~~~~lr~~~~~h~~yl~n~~v~asl~~~i~~~~~~~~~~~~~~~~~~~lWGl~~~hh~~p~~~~~~~r~~~~~l~~~  389 (1117)
                      +|||+|.|||+||||+|||+||||.||||||||+|              |+|||||+|||.|||++||++|.||||++|+
T Consensus       241 ~DLs~svLRSvSp~H~eYLrNMGV~ASmSISivv~--------------g~LWGLIACHH~sPk~ip~~vR~acef~gq~  306 (750)
T COG4251         241 LDLSYSVLRSVSPIHLEYLRNMGVGASMSISIVVD--------------GKLWGLIACHHQSPKVIPYEVRKACEFFGQV  306 (750)
T ss_pred             ccchHHHHhccChHHHHHHHhcCcceeeEEEEEEC--------------CeeEEeeeeccCCCccCCHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999              9999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH-HHHHHhhhcCC-CcccccCCcchhhhccCCEEEEEECCeEEEecCCCCHHHHHHH
Q 001235          390 FAIHVNKELELEYQILEKNILRTQ-TLLCDMLMRDA-PLGIVTQSPNIMDLVKCDGAALLYKNKIWRLGVTPNDFQLHDI  467 (1117)
Q Consensus       390 ~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~-~~~~~~~~~~~~~l~~~~g~a~~~~~~~~~~G~~p~~~~~~~l  467 (1117)
                      +|.+|+.+.+.+...........+ .++..|...++ ..+++...++|++|+.||||+||++|++.++|.||+.+++..|
T Consensus       307 ~s~~i~~~e~~~~~d~r~~l~~~~arl~~~ma~~~~~~d~L~~~~~dll~L~~adGaal~fg~~~~~vG~tP~~~~v~~L  386 (750)
T COG4251         307 LSMEISALEQSEDADYRVQLTEHHARLLRYMAHAADFVDGLIDHQDDLLDLMPADGAALCFGGRWHLVGETPPRPAVQRL  386 (750)
T ss_pred             HHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHhhhcchhhhhcCCchhhHhhccCCceEEEECCEEEEecCCCChHHHHHH
Confidence            999998654433222111122222 34444555554 5788999999999999999999999999999999999999999


Q ss_pred             HHHHHhccCCCceEeecccccccCCCccccccccccEEEEEeCC--CCEEEEeccCCccEEeeccCCCCCCCC-CCCCcc
Q 001235          468 VSWLSEYHMDSTGLSADSLYDAGYLGALALGDVVCGMAAVRISP--KDMIFWFRSQTASEVRWGGAKHEPDEK-DDGRKM  544 (1117)
Q Consensus       468 ~~~l~~~~~~~~~~~t~~l~~~~~p~~~~~~~~~~g~l~~~~~~--~~~l~wfR~e~~~~v~W~G~p~~~~~~-~~g~~l  544 (1117)
                      +.||.++... .+|+||+|+.. ||+++.++..||||||++|+.  ++||+|||||++++|+|||||+|+... ++|.||
T Consensus       387 l~wl~~~~~~-~vf~TdsL~q~-yPda~~~~~vAsGlLAI~is~~~s~~llWFRpEvv~tV~WGG~P~k~~e~~~~~~rL  464 (750)
T COG4251         387 LQWLAEREEG-DVFATDSLSQV-YPDAEDYASVASGLLAIPISRVKSNYLLWFRPEVVQTVNWGGDPEKPYEAGPMGIRL  464 (750)
T ss_pred             HHHHhcCCcc-cEEeecccccc-CcchhhhccccceeEEEEeeccccceEEEEchHHheeeccCCCCCCccccCCCCccc
Confidence            9999887655 79999999985 999999999999999999998  899999999999999999999999863 557899


Q ss_pred             cccchhhhhhhhhccccCCCchHHHHHHHHHHHHHHHHHhhhccccccccchhhhhhhHHHHHHHHHHHHHHHHHHHHHh
Q 001235          545 HPRSSFKAFLEVVKTRSLPWKDYEMDAIHSLQLILRNAFKDVGTLDLDTKSIHSKLCDLKIEGMKELEAVTSEMVRLIET  624 (1117)
Q Consensus       545 ~PR~SF~~w~e~v~~~s~pW~~~El~aa~sL~liL~~~l~~l~~~~~~~~~~~~~l~~~~~~~~~eL~~~~~~l~~lie~  624 (1117)
                      +||+||+.|+|+|++++.||+..|++++..|+..+.+...+-                     .+++..           
T Consensus       465 ~PRkSFe~WkE~vRl~s~PWs~~ei~~A~~LR~aiv~ivl~~---------------------aeela~-----------  512 (750)
T COG4251         465 TPRKSFELWKETVRLQSQPWSEVEIEAALELRKAIVGIVLRH---------------------AEELAQ-----------  512 (750)
T ss_pred             CCcccHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHHHH---------------------HHHHHH-----------
Confidence            999999999999999999999999999999844333222000                     000000           


Q ss_pred             cCccEEEEeCCCcEEeecHHHHHHcCCCcccccCCccccccccCcHHHHHHHHHHHHcCCcceeeEEEEEeeccccCCce
Q 001235          625 ATVPILAVDVDGLVNGWNTKIAELTGLSVDKAIGKHFLTLVEDSSIDTVKRMLYLALQGQEEQNIQFEIKTHGSKINDDP  704 (1117)
Q Consensus       625 a~~gi~~~D~dG~I~~~N~a~~~l~G~s~eeliG~~~~dlv~~~~~~~~~~~l~~~l~g~~~~~~e~~~~~~~~~~dG~~  704 (1117)
                                                                                                      
T Consensus       513 --------------------------------------------------------------------------------  512 (750)
T COG4251         513 --------------------------------------------------------------------------------  512 (750)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             EEEEEEEEEeecCCCCEEEEEEEEEccchhhhhhhhHhhHHHHHHHHHhCCCCCCCCeeeeCCCCceeechhhHHHhcCC
Q 001235          705 ITLIVNACASRDLHDNVVGVCFVAQDITPQKTVMDKFTRIEGDYKAIVQNPNPLIPPIFGSDEFGWCCEWNPAMVKLTGW  784 (1117)
Q Consensus       705 ~~v~v~~~pi~d~~G~v~gv~~v~~DITerK~aE~~L~~se~~l~~i~~~~~~li~~I~~~D~~g~i~~~N~a~~~l~G~  784 (1117)
                                                                                                      
T Consensus       513 --------------------------------------------------------------------------------  512 (750)
T COG4251         513 --------------------------------------------------------------------------------  512 (750)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             ChhhHhhcchhhhhcCCchhhhhccChhHHHHHHHHHHHHhcCCCCceEeEEEEecCCcEEEEEEEEeeeeCCCCCEEEE
Q 001235          785 KREEVIDKLLLAEVFGTNMACCRLKNQEAFVNLGIVLNKAMSGQDPEKVPFGFFARNGKYAECLLCVNKKLDREGAVTGV  864 (1117)
Q Consensus       785 ~~eEliGk~l~~ei~~~~~~~~~l~~~d~~~~~~~~l~~~l~g~~~~~~e~~~~~~dG~~~~v~~~~~pi~d~~G~v~g~  864 (1117)
                                                                                                      
T Consensus       513 --------------------------------------------------------------------------------  512 (750)
T COG4251         513 --------------------------------------------------------------------------------  512 (750)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             EeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHhcC---CCCHHHHHHHHHHHHHHHHHH
Q 001235          865 FCFLQLASHELQQALHVQRLSEQTALKRLKALAYTKRQIRNPLSGIIFSRKMMEGT---ELGAEQKRLLHTSAQCQRQLH  941 (1117)
Q Consensus       865 v~i~~DITerk~~e~el~~~ae~~~~~k~~~la~isHEIrnPL~~I~~~~~LL~~~---~l~~~~~~~l~~i~~~~~~l~  941 (1117)
                                      +++..++.+....+|...++|++++||+.|.++.++|...   .++++.++++..+.+....|.
T Consensus       513 ----------------l~r~lersn~el~~f~yv~sHdlqePl~~I~~~a~lL~~~~~~~~d~~~~~~i~~~~~~~~~~~  576 (750)
T COG4251         513 ----------------LRRELERSNAELRAFAYVASHDLQEPLRQISNYAQLLSERYSDALDEEAKEFITFISRLTSLMQ  576 (750)
T ss_pred             ----------------HHHHHhhhhHHHHHHHHHhhhhhhHHHHHHHHHHHhhhhccccccChHHHHHHHHHHHHHHHHH
Confidence                            0011112222233456667999999999999999999864   578899999999999999999


Q ss_pred             HHHhh-ccccccccCcccceeEEeeHHHHHHHHHHHHHhhhcccCcEEEEeecCCCcceeEEecHHHHHHHHHHHHHHHh
Q 001235          942 KILDD-SDLDSIIDGYLDLEMVEFTLNEVLVASISQVMMKSNAKGIRIVNETAEQIMSETLYGDSIRLQQVLADFLSISI 1020 (1117)
Q Consensus       942 ~ii~d-Ld~skie~g~~~l~~~~~~L~~li~~v~~~~~~~~~~~~i~i~~~~~~~~~~~~v~~D~~~L~qVL~nLl~NAi 1020 (1117)
                      .||++ +.++++  |.......+.++.++++.++..+.....+.++++.+..   +|  .+.+|+.++.|++.||+.||+
T Consensus       577 ~lidd~l~~s~l--~~~~~~l~~td~~~vv~~vl~~l~~ri~dtgaei~i~~---lp--~v~~d~~~l~qv~~NLi~Nai  649 (750)
T COG4251         577 QLIDDLLTYSKL--GLTEAPLQPTDVQKVVDKVLLELSQRIADTGAEIRIAP---LP--VVAADATQLGQVFQNLIANAI  649 (750)
T ss_pred             HHHHHHhhhhhh--ccccCCCCCcchHHHHHHHHHhcccccccccceEEecc---cc--eeecCHHHHHHHHHHHHhhhe
Confidence            99999 599987  45555666999999999999999999999999998864   43  799999999999999999999


Q ss_pred             hccCC-CCeEEEEEEecccccccccceeEEEEEEeecCCCCChhhhhhccCCCC------CCCCccccHHHHHHHHHHcC
Q 001235         1021 NFVPN-GGQLMVSSSLTKDQLGQSVHLAYLELRITHAGGGIPEPLLDQMFGSEG------DTSEEGISLLISRKLVKLMN 1093 (1117)
Q Consensus      1021 k~~~~-~g~I~I~v~~~~~~~~~~~~~~~l~i~V~D~G~GI~~e~~~~iFe~f~------~~~GtGLGL~ivr~iVe~~g 1093 (1117)
                      ||..+ ..+|.|+....++         .+.|.|.|||+||++...++||..|.      .+.|+|+||+|||+|++.|+
T Consensus       650 k~~~~e~~~i~I~~~r~ed---------~~t~sV~dng~Gi~~a~~~riF~iFqRl~s~~~y~gtG~GL~I~kkI~e~H~  720 (750)
T COG4251         650 KFGGPENPDIEISAERQED---------EWTFSVRDNGIGIDPAYFERIFVIFQRLHSRDEYLGTGLGLAICKKIAERHQ  720 (750)
T ss_pred             ecCCCCCCceEEeeeccCC---------ceEEEecCCCCCcCHHHHHHHHHHHHhcCchhhhcCCCccHHHHHHHHHHhC
Confidence            99866 4899999777776         79999999999999999999999983      44599999999999999999


Q ss_pred             CEEEEEeeCCe-EEEEEEEeccCC
Q 001235         1094 GDVQYLREAGK-STFIVSVELAAA 1116 (1117)
Q Consensus      1094 G~I~v~s~~g~-ttF~i~LPl~~a 1116 (1117)
                      |+||++|.+|. +||.|++|...+
T Consensus       721 G~i~vEs~~gEgsTF~f~lp~~~~  744 (750)
T COG4251         721 GRIWVESTPGEGSTFYFTLPVGGE  744 (750)
T ss_pred             ceEEEeecCCCceeEEEEeecCCc
Confidence            99999999988 999999998764

>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

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

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

>PRK13557 histidine kinase; Provisional	Back alignment and domain information

>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; 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

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

>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; 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

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

>PRK13559 hypothetical protein; Provisional	Back alignment and domain information

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

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

>PRK09303 adaptive-response sensory kinase; Validated	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

>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

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

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

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

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

>COG3290 CitA Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]	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

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

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

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

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

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

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

>PRK10337 sensor protein QseC; Provisional	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

>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

>COG4192 Signal transduction histidine kinase regulating phosphoglycerate transport system [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

>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

>PRK10935 nitrate/nitrite sensor protein NarQ; Provisional	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

>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

>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

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

>COG4585 Signal transduction histidine kinase [Signal transduction mechanisms]	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

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

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

>PRK11091 aerobic respiration control sensor protein ArcB; Provisional	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

>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

>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

>PRK04184 DNA topoisomerase VI subunit B; Validated	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

>PRK13559 hypothetical protein; Provisional	Back alignment and domain information

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

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

>PRK14868 DNA topoisomerase VI subunit B; Provisional	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

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

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

>PRK13557 histidine kinase; Provisional	Back alignment and domain information

>TIGR01925 spIIAB anti-sigma F factor	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

>TIGR01052 top6b DNA topoisomerase VI, B subunit	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

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

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

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

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

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

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

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

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

>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL	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

>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

>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

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

>PF14501 HATPase_c_5: GHKL domain	Back alignment and domain information

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

>COG5002 VicK Signal transduction histidine kinase [Signal transduction mechanisms]	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

>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

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

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

>PF12860 PAS_7: PAS fold	Back alignment and domain information

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

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

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

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

>KOG0787 consensus Dehydrogenase kinase [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

>PRK11006 phoR phosphate regulon sensor protein; Provisional	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

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

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

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional	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

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

>COG1389 DNA topoisomerase VI, subunit B [DNA replication, recombination, and repair]	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

>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / 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

>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

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

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

>PF12860 PAS_7: PAS fold	Back alignment and domain information

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

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

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

>PRK10820 DNA-binding transcriptional regulator TyrR; 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

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

>smart00388 HisKA His Kinase A (phosphoacceptor) domain	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

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

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

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

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

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

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

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional	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

>smart00091 PAS PAS domain	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

>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A	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

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

>COG5385 Uncharacterized protein conserved in bacteria [Function unknown]	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

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

>PRK05559 DNA topoisomerase IV subunit B; Reviewed	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

>TIGR02373 photo_yellow photoactive yellow protein	Back alignment and domain information

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

>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [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

>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

>TIGR01059 gyrB DNA gyrase, B subunit	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

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

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

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

>TIGR02373 photo_yellow photoactive yellow protein	Back alignment and domain information

>smart00091 PAS PAS domain	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

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

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

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

>PRK05218 heat shock protein 90; 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

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

>TIGR02851 spore_V_T stage V sporulation protein T	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

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

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

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

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

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

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]	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		1117
2vea_A		520	The Complete Sensory Module Of The Cyanobacterial P		9e-63
3zq5_A		520	Structure Of The Y263f Mutant Of The Cyanobacterial		3e-62
4gw9_A		655	Structure Of A Bacteriophytochrome And Light-Stimul		2e-51
3g6o_A		505	Crystal Structure Of P. Aeruginosa Bacteriophytochr		4e-40
3c2w_A		505	Crystal Structure Of The Photosensory Core Domain O		2e-39
3ibr_A		505	Crystal Structure Of P. Aeruginosa Bacteriophytochr		1e-37
4e04_A		327	Rpbphp2 Chromophore-binding Domain Crystallized By		2e-35
2ool_A		337	Crystal Structure Of The Chromophore-Binding Domain		7e-35
2o9b_A		342	Crystal Structure Of Bacteriophytochrome Chromophor		5e-29
3s7n_A		343	Crystal Structure Of The Alternate His 207 Conforma		1e-28
3s7q_A		343	Crystal Structure Of A Monomeric Infrared Fluoresce		3e-28
1ztu_A		341	Structure Of The Chromophore Binding Domain Of Bact		9e-28
2lb5_A		208	Refined Structural Basis For The Photoconversion Of		1e-16
2k2n_A		172	Solution Structure Of A Cyanobacterial Phytochrome		1e-16

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