CONSENSUS          ALPAPAFATTVTQLEPHDLELAALYEVATESICETAARLLFMAVKWAKSVPAFSTLPLQDQLILLEEAWRELFVLGAAQWAIPDACTLLAVASEANNANTDSQKLNADKIIAEIQALQEVVSRFRQLRLDATEFACLKAIVLFKAADAAAIAALQDEAQLTLNSYIHTRYPAPCRFGKLLLLLPALRSISPSTIEELFAITRLLSDMYK                                                                                                     


                                                                
                                                      
                                                                                                
                                                                                                                                                                   

HNF4_DROME         apGNGLSVISLVKAENESRQSK.kQFASINDVCESMKQQLLTLVEWAKQIPAFNELQLDDQVALLRAHAGEHLLLGLSRRSM.kDVLLLSN..NCVITRHCPDPLV.dISRIGARIIDELVTVMKDVGIDDTEFACIKALVFFDP.ePHRIKSLRHQILNNLEDYISDRQY.rGRFGEILLILPVLQSITWQMIEQIQ.iDSLLQEMLL                                                                                                     
O77099             stSNGLSVKFLLLAENRSRHFG.kRFASINDVCDSMKQQLLILVEWAKSIPAFAELQLDDQVALLRAHAGEHLLLGLSRRSM.eEMLLLGN..NCIITKQSPDSKM.dISRIGARIIDELVSAIKDIKLDDSELACIKALVFFDP.qPQKIKALRHQVLNNLEDYVSDKQY.rGRFGEILLLLPVLQSITWQMIQQIE.iDSLLQEMLL                                                                                                     
O77100             DTSNGLSVKFLLLAENRSRHFG.kRFASINDVCDSMKQQLLILVEWAKSIPAFAELQLDDQVALLRAHAGEHLLLGLSRRSM.EEMLLLGN..NCIITKQSPDSKM.dISRIGARIIDELVSAIKDIKLDDSELACIKALVFFDP.qPQKIKALRHQVLNNLEDYVSDKQY.rGRFGEILLLLPVLQSITWQMIQQIE.iDSLLQEMLL                                                                                                     
O46175             TQANGLSVVSLLNAELLSRKVI.rKLAKINDVCDSIKQQLLILVEWAKYIPAFTVLHLDDQVALLRAHAGEHLLLGCARRSL.KDILLLGN..NCIITKHNIDGRM.dISMIGMRVMDEIVKPLREIDIDDTEFACLKAIVFFDP.qPQKIKQLRYQIQINLEDYISDRQY.rGRFGELLLCLPPLQSITWQMIEQIQ.vDSLLQEMLL


RORB_HUMAN         dtEIDRIAQNIIKSHLETCQYT.sREALWQQCAIQITHAIQYVVEFAKRITGFMELCQNDQILLLKSGCLEVVLVRMCRAFN.nNTVLFE...GKYGGMQMFKALG..SDDLVNEAFD.FAKNLCSLQLTEEEIALFSSAVLISP.ePRKVQKLQEKIYFALQHVIQKNHLDDETLAKLIAKIPTITAVCNLHGEKLQ.fPPLYKELF.                                                                                                     
Q9BMC6             SHAEGDISKVLVKSLAEAHANT.tYEEMWLDCADKLTGMIQNIIEFAKLIPGFMKLTQDDQILLLKSGSFELAIVRLSRLID.rDQVLYG..DAVLSIRECVHARD.pRDVALVVGIFDAAKTIARLKLTETELALYQSLVLLWP.gNPEIQCLFNMSMAAMRHEIETNHAdVTVLDTLLAKIPTFRELSLMHLEALC.f.                                                                                                     
Q27547             WSRRSDISKVLVKSLAEAHANT.tYEAMWLDCADKLTTMIQSIIEFAKLMPGFMKLTQDDQILLLKSGSFELAIVRLSRLID.rDTVLYG..DVVLPIRDCVHARD.pRDMALIVGIFDAAKTIARLKLTETELALYQSLVHLWP.gNHEIQCLFNMSMTAMRHEIETNHhdVTVLDTLLAKLPTFRELSLMHLEALC.fPALYKELF.    


NRH3_MOUSE         SPEQLGMIEKLVAAQQQCNRRS.aRQQRFAHFTELAIVSVQEIVDFAKQLPGFLQLSREDQIALLKTSAIEVMLLETSRRYN.sESITFLK..DFSYNREDFAKAG.LQVEFINPIFE.FSRAMNELQLNDAEFALLIAISIFSA.dQLQVERLQHTYVEALHAYVSINHP.rLMFPRMLMKLVSLRTLSSVHSEQVF.lPPLLSEIWD                                                                                                     
Q62735             TSTTKLCREKTELTVDQQTLLD.sAEENFLILTEMATSHVQILVEFTKRLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFN..KKLPAG...HADLLEERIRKSG.ISDEYITPMFS.FYKSVGELKMTQEEYALLTAIVILSP.dREAVEKLQEPLLDVLQKLCKIYQP.pQHFACLLGRLTELRTFNHHHAEMLM.fTPLLCEIWD                                                                                                     
Q91X41             SPEQLGMIEKLVAAQQQCNRRS.aRQQRFAHFTELAIVSVQEIVDFAKQLPGFLQLSREDQIALLKTSAIEVMLLETSRRYN.sESITFLK..DFSYNREDFAKAG.LQVEFINPIFE.FSRAMNELQLNDAEFALLIAISIFSA.dQLQVERLQHTYVEALHAYVSINHP.rLMFPRMLMKLVSLRTLSSVHSEQVF.lPPLLSEIWD                                                                                                     
Q92943             TSTTKSCREKTELTPDQQTLLH.sAEENFLILTEMATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFN..KKLPSG...HSDLLEERIRNSG.ISDEYITPMFS.FYKSIGELKMTQEEYALLTAIVILSP.dREAVEKLQEPLLDVLQKLCKIHQP.pQHFACLLGRLTELRTFNHHHAEMLM.fTPLLCEIWD                                                                                                     
Q60641             TSTTKFCREKTELTADQQTLLD.sAEENFLILTEMATSHVQILVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFN..KKLPAG...HADLLEERIRKSG.ISDEYITPMFS.FYKSVGELKMTQEEYALLTAIVILSP.dREAVEKLQEPLLDVLQKLCKMYQP.pQHFACLLGRLTELRTFNHHHAEMLM.fTPLLCEIWD                                                                                                     
Q96RI1             TSTTKSCREKTELTPDQQTLLH.sAEENFLILTEMATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFN..KKLPSG...HSDLLEERIRNSG.ISDEYITPMFS.FYKSIGELKMTQEEYALLTAIVILSP.dREAVEKLQEPLLDVLQKLCKIHQP.pQHFACLLGRLTELRTFNHHHAEMLM.fTPLLCEIWD


NR52_MOUSE         saSIPHLILELLKCEPDEPQVQ.eKLSAFGLLCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQV.kEGTIFLVTGEHVDYSTIISHT.EVAFNNLLSLAQELVVRLRSLQFDQREFVCLKFLVLFSS.nLQLVEGVQEQVNAALLDYTVCNYP.tEKFGQLLLRLPEIRAISKQAEDYLY.yNNLLIEML.                                                                        

Q9NB03             .......................cEVDLFELMCKVLDQNLFSQVDWARNTIFFKDLKVDDQMKLLQNSWSDMLVLDHIHQR...................dLLGLGLLGVPSLAEHFNELQNKLQELKFDVGDYICMKFLLLLNP.nRKTVVEGYENVQAALLDYTLTCYP.pDKFSKLLSIIPEIHAMAT........sQTLLMEMLH                                                                                                     
Q9VVS8             .......................vEVDLFELMCKVLDQNLFSQVDWARNTVFFKDLKVDDQMKLLQHSWSDMLVLDHLHHR...................nLMSLGLLGVPQLGDYFNELQNKLQDLKFDMGDYVCMKFLILLNP.nRKTVSEGHDNVQAALLDYTLTCYP.nDKFRGLVNILPEIHAMAVRGEDHLY.tQTLLMEMLH                                                                                                     
FTF1_DROME         .......................vEVDLFELmCKVLDQNLFSQVDWARNTVFFKDLKVDDQMKLLQHSWSDMLVLDHLHHR...................nLMSLGLLGVPQPGDYFNELQNKLQDLKFDMGDYVCMKFLILLNP.nRKTVSEGHDNVQAALLDYTLTCYP.nDKFRGLVNILPEIHAMAVRGEDHLI.sTVPAVRPPK                                                                                                     
Q24538             .......................vEVDLFELmCKVLDQNLFSQVDWARNTVFFKDLKVDDQMKLLQHSWSDMLVLDHLHHR...................nLMSLGLLGVPQPGDYFNELQNKLQDLKFDMGDYVCMKFLILLNP.nRKTVSEGHDNVQAALLDYTLTCYP.nDKFRGLVNILPEIHAMAVRGEDHLI.sTVPAVRPPK                                                                                                     
Q9Y0D1             .......................cEVDLFELMCKVLQQNLFAQVDWPRNSCFFKDLKVDDQMKLLQHSWSDLLILDHLHQR...................dLLSLALLGTTQFADRFHAILNKLRDLNFDISDFVCVKFIILLNP.dRRAVIAARPGATGIDGIYSQCLPR.sGEIQKLMDLLPELHFLAENGEKYLY.tQTLLMEMLH                                                                                                     
FTF1_BOMMO         .......................cEVDLFELMCKVLDQNLFSQVDWARNTVFFKYLKVDDQMKLLQDSWSVMLVLDHLHQR...................dLLCLGLLGVPSLADHFNELQNKLAELKFDVPDYICVKFMLLLNP.nVKCVREGYQTVQAALLDYPYLLST.qDKFGKLVMVVPEIHALRLGEKSTCT.qARHLPRLFS

                                                                                                    


The sequences showed similarity with NR52_MOUSE, but we had problem aligning helix 1 and sheet regions. Also we are not sure about helix 12 of FTF1_DROME, Q24538 and FTF1_DROME. 


RXRG_XENLA         atSEEMPVERILEAELAVDPKI.sTNDPVTNICHAADKQLFTLVEWAKRIPYFSDLPLEDQVILLRAGWNELLIASFSHRSV.qDGILLAT..GLHVHRSSAHNAG..VGSIFDRVLTELVSKMKDMDMDKSELGCLRAIVLFNP.nAAEVEALREKVYATLESYTKQKYP.pGRFAKLLLRLPALRSIGLKCLEHLF.iDTFLMEML.                                                                                                     
TR4_HUMAN          .......................pEYLNVHYICESASRLLFLSMHWARSIPAFQALGQDCNTSLVRACWNELFTLGLAQCA..qVMSLST...ILAAIVNHLQNS..kQVMEHIWKLQEFCNSMAKLDIDGYEYAYLKAIVLFSP.sTSQIEKFQEKAQMELQDYVQKTYS.tYRLARILVRLPALRLMSSNITEELF...........                                                                                                     
TR4_MOUSE          .......................pEYLNVHYICESASRLLFLSMHWARSIPAFQALGQDCNTSLVRACWNELFTLGLAQCA..qVMSLST...ILAAIVNHLQNS..kQVMEHIWKLQEFCNSMAKLDIDGYEYAYLKAIVLFSP.gTSQIEKFQEKAQMELQDYVQKTYS.tYRLARILVRLPALRLMSSNITEELF...........                                                                                                     
TR4_RAT            .......................pEYLNVHYICESASRLLFLSMHWARSIPAFQALGQDCNTSLVRACWNELFTLGLAQCA..qVMSLST...ILAAIVNHLQNS..kQVMEHIWKLQEFCNSMAKLDIDGHEYAYLKAIVLFSP.gTSQIEKFQEKAQMELQDYVQKTYS.tYRLARILVRLPALRLMSSNITEELF...........                                                                                                     
Q15625             .......................pEYLNVHYIGESASRLLFLSMHWALSIPSFQALGQENSISLVKAYWNELFTLGLAQCW..qVMNVAT...ILATFVNCLHNS..kLLMEHIFKLQEFCNSMVKLCIDGYEYAYLKAIVLFSP.nMELIEKFQEKAYVEFQDYITKTYP.tYRLSRLLLRLPALRLMNATITEELF...........                                                                                                     
Q62152             .......................pEYLNAHYIGESASRLLFLSMHWALSIPSFQALGQENSISLVKAYWNELFTLGLAQCW..qVMNVAT...ILATFVNCLHSS..kSLMEHIFKLQEFCNSMVKLCIDGHEYAYLKAIVLFSP.nMELIERFQEKAYVEFQDYITRTYP.tYRLSRLLLRLPALRLMNATITEELF...........                                                                                                     
Q26622             .......................pQFLNVHYICESASRLLFLSMHWARSLPAFQVLSADTHTSMVQKCWSELFTLGLAQCA..qAMALST...ILTAIVNHLQTS..kAVMEHIWKLQEFVTTTSKLDVDQTEFAYLKTIVLFSP.nVRQIEKFQEMAISELHDYEAQTYP.lNRFSKLLLRLPTLRLLSPAIMEELF...........                                                                                                     
O61227             .......................pPYLNIHYICESGSRLLFLSIHWTRNIPAFQYLTTETQITLLRGCWAELFTLGLAQCS..qTLSLST...ILSALISHLHTL..kQVSDHIVKLQDYANTMNRLNVDEHEYAYLKAITLFSA.lRKHVEKLQEKSFQALKTYVHNSFP.tDRFPRLLLRLPPLRGLEPLVLEELF...........             



Aligning helix 1 and helix 12 was impossible. Helix 12 region contains no recognizable LXXLL motif.

The top layer shows the consensus sequence. Residues are coloured after their physico-chemical properties. (GPX black; positive blue; negative red; CM yellow; H dark purple; NQ light purple; all others
green).