1. Rules of thumb when looking at a multiple alignment (MA)
Hydrophobic residues are internal
Gly (Thr, Ser) in loops
MA: hydrophobic block -> internal -strand
MA: alternating (1-1) hydrophobic/hydrophilic => edge -strand
MA: alternating 2-2 (or 3-1) periodicity => -helix
MA: gaps in loops
MA: Conserved column => functional? => active site

2. Rules of thumb when looking at a multiple alignment (MA) … cont.
Active site residues are together in 3D structure
Helices often cover up core of strands
Helices less extended than strands => more residues to cross protein
-- motif is right-handed in >95% of cases (with parallel strands)
MA: ‘inconsistent’ alignment columns and match errors!
Secondary structures have local anomalies, e.g. -bulges

3. Amino acid properties

4. Amino acid hydrophobicity scale
hydrophilic

7. Burried and Edge strands
Parallel -sheet
Anti-parallel -sheet

8. Periodicity patterns within secondary structures
Burried -strand
Edge -strand
-helix
= hydrophilic
= hydrophobic

9. TOPS diagrams
Circle = helix
Triangle = strand

10. -- motif is right-handed in >95% of casesLH RH

11. Flavodoxin-cheY example: 5()
1fx PKALIVYGSTTGNT-EYTAETIARQLANAG-YEVDSRDAASVEAGGLFEGFDLVLLGCSTWGDDSI------ELQDDFIPLF-DSLEETGAQGRKVACF
FLAV_DESDE MSKVLIVFGSSTGNT-ESIaQKLEELIAAGG-HEVTLLNAADASAENLADGYDAVLFgCSAWGMEDL------EMQDDFLSLF-EEFNRFGLAGRKVAAf
FLAV_DESVH MPKALIVYGSTTGNT-EYTaETIARELADAG-YEVDSRDAASVEAGGLFEGFDLVLLgCSTWGDDSI------ELQDDFIPLF-DSLEETGAQGRKVACf
FLAV_DESSA MSKSLIVYGSTTGNT-ETAaEYVAEAFENKE-IDVELKNVTDVSVADLGNGYDIVLFgCSTWGEEEI------ELQDDFIPLY-DSLENADLKGKKVSVf
FLAV_DESGI MPKALIVYGSTTGNT-EGVaEAIAKTLNSEG-METTVVNVADVTAPGLAEGYDVVLLgCSTWGDDEI------ELQEDFVPLY-EDLDRAGLKDKKVGVf
2fcr KIGIFFSTSTGNT-TEVADFIGKTLGA---KADAPIDVDDVTDPQALKDYDLLFLGAPTWNTG----ADTERSGTSWDEFLYDKLPEVDMKDLPVAIF
FLAV_AZOVI AKIGLFFGSNTGKT-RKVaKSIKKRFDDET-MSDA-LNVNRVS-AEDFAQYQFLILgTPTLGEGELPGLSSDCENESWEEFL-PKIEGLDFSGKTVALf
FLAV_ENTAG MATIGIFFGSDTGQT-RKVaKLIHQKLDG---IADAPLDVRRAT-REQFLSYPVLLLgTPTLGDGELPGVEAGSQYDSWQEFT-NTLSEADLTGKTVALf
FLAV_ANASP SKKIGLFYGTQTGKT-ESVaEIIRDEFGN---DVVTLHDVSQAE-VTDLNDYQYLIIgCPTWNIGEL QSDWEGLY-SELDDVDFNGKLVAYf
FLAV_ECOLI AITGIFFGSDTGNT-ENIaKMIQKQLGK---DVADVHDIAKSS-KEDLEAYDILLLgIPTWYYGE AQCDWDDFF-PTLEEIDFNGKLVALf
4fxn MK--IVYWSGTGNT-EKMAELIAKGIIESG-KDVNTINVSDVNIDELL-NEDILILGCSAMGDEVL EESEFEPFI-EEIS-TKISGKKVALF
FLAV_MEGEL MVE--IVYWSGTGNT-EAMaNEIEAAVKAAG-ADVESVRFEDTNVDDVA-SKDVILLgCPAMGSEEL EDSVVEPFF-TDLA-PKLKGKKVGLf
FLAV_CLOAB MKISILYSSKTGKT-ERVaKLIEEGVKRSGNIEVKTMNLDAVD-KKFLQESEGIIFgTPTYYAN ISWEMKKWI-DESSEFNLEGKLGAAf
3chy ADKELKFLVVDDFSTMRRIVRNLLKELGFN--NVEEAEDGVDALNKLQAGGYGFVI---SDWNMPNM DGLELL-KTIRADGAMSALPVLM T
1fx GCGDS-SY-EYFCGA-VDAIEEKLKNLGAEIVQD GLRIDGD--PRAARDDIVGWAHDVRGAI
FLAV_DESDE ASGDQ-EY-EHFCGA-VPAIEERAKELgATIIAE GLKMEGD--ASNDPEAVASfAEDVLKQL
FLAV_DESVH GCGDS-SY-EYFCGA-VDAIEEKLKNLgAEIVQD GLRIDGD--PRAARDDIVGwAHDVRGAI
FLAV_DESSA GCGDS-DY-TYFCGA-VDAIEEKLEKMgAVVIGD SLKIDGD--PE--RDEIVSwGSGIADKI
FLAV_DESGI GCGDS-SY-TYFCGA-VDVIEKKAEELgATLVAS SLKIDGE--PD--SAEVLDwAREVLARV
2fcr GLGDAEGYPDNFCDA-IEEIHDCFAKQGAKPVGFSNPDDYDYEESKS-VRDGKFLGLPLDMVNDQIPMEKRVAGWVEAVVSETGV------
FLAV_AZOVI GLGDQVGYPENYLDA-LGELYSFFKDRgAKIVGSWSTDGYEFESSEA-VVDGKFVGLALDLDNQSGKTDERVAAwLAQIAPEFGLS--L--
FLAV_ENTAG GLGDQLNYSKNFVSA-MRILYDLVIARgACVVGNWPREGYKFSFSAALLENNEFVGLPLDQENQYDLTEERIDSwLEKLKPAV-L------
FLAV_ANASP GTGDQIGYADNFQDA-IGILEEKISQRgGKTVGYWSTDGYDFNDSKA-LRNGKFVGLALDEDNQSDLTDDRIKSwVAQLKSEFGL------
FLAV_ECOLI GCGDQEDYAEYFCDA-LGTIRDIIEPRgATIVGHWPTAGYHFEASKGLADDDHFVGLAIDEDRQPELTAERVEKwVKQISEELHLDEILNA
4fxn G-----SY-GWGDGKWMRDFEERMNGYGCVVVET PLIVQNE--PDEAEQDCIEFGKKIANI
FLAV_MEGEL G-----SY-GWGSGEWMDAWKQRTEDTgATVIGT AIVNEM--PDNA-PECKElGEAAAKA
FLAV_CLOAB STANSIAGGSDIA---LLTILNHLMVKgMLVYSG----GVAFGKPKTHLGYVHINEIQENEDENARIfGERiANkVKQIF
3chy VTAEAKK--ENIIAA AQAGAS GYVV-----KPFTAATLEEKLNKIFEKLGM------ G
Iteration 0 SP= AvSP= SId= AvSId= 0.313

12. Building flavodoxin RH