Exercises Pairwise alignment Homology search BLAST Multiple alignment
Exercises • • • Pairwise alignment Homology search (BLAST) Multiple alignment (CLUSTAL W) Iterative Profile Search: Profile Search – – Pfam Prosite PSI-BLAST SAM
Overview Exercises Query Sequence Unknown Blast Sequence to search for close homologs PFAM PROSITE Search p. FAM, Prosite for conserved motifs You detected homology with an annotated protein family Clustal. W Make a multiple sequence alignment HMMer, PSSM PSI-blast Generate profile or HMM Profile Search database for remote homologs
Terminal Oxidases Exercises • Unknown protein is a heme cupper oxidase • Enzyme that reduces O 2 to H 2 O in respiratory chain Cytc e. Fe Fe Fe OUT e. Fe IN I e- Fe Cu. B O 2 H 2 O • Subunit contains 2 hemes and a Cu prosthetic group • The residues that are ligands of these groups have been conserved in all types of terminal oxidase complexes
Terminal Oxidases Exercises Cytc NADH e- Nadh. dh succinate e- cytochrome c oxidase equinol O 2 H 2 O ? cytbc 1 e- succ. dh O 2 H 2 O ? quinol oxidase e- O 2 H 2 O H+ e- H+
Exercises Multiple Alignment
Multiple Alignment Exercises Multiple alignment: standard gap cost Prosite pattern Ligands Cu center Ligands hemes
Exercises Multiple alignment: large gap cost Prosite pattern Multiple Alignment Ligands Cu center Ligands hemes
Exercises Tree based on subselection Phylogenetic Tree
Exercises PROSITE
Exercises Prosite
Exercises Prosite
Exercises Prosite
Exercises Prosite
Exercises Prosite
Exercises
Exercises
Exercises Prosite
Exercises Prosite domain
Exercises
Exercises Pattern & profile
Exercises
Exercises
Exercises
Exercises p. FAM
Exercises Pfam
Exercises Pfam
Exercises Pfam
Exercises COX family Pfam
Exercises Pfam
Exercises Pfam
Exercises Pfam
Exercises Pfam
Exercises Pfam
Exercises Pfam
Exercises BLOCKS
Exercises • Blocks
Exercises
Exercises
Overview Exercises Query Sequence Unknown Blast Sequence to search for close homologs PFAM PROSITE Search p. FAM, Prosite for conserved motifs You detected homology with an annotated protein family Make a multiple sequence alignment HMMer, PSSM PSI-blast Generate profile or HMM Profile Search database for remote homologs
Exercises PSI-BLAST
Exercises PSI-BLAST • PSI BLAST – Start from a single sequence – Blast it against NCBI – Select high scoring hits – Perform multiple alignment – Construct profile – Iterate and find remote homologs • Usually cut the sequence in pieces • Avoid to give as input multi domain proteins
Exercises PSI-BLAST
Exercises PSI-BLAST
Exercises PSI-BLAST
Exercises PSI-BLAST
Exercises PSI-BLAST
Exercises PSI-BLAST
Exercises SAM
Exercises SAM http: //www. cse. ucsc. edu/research/compbio/HMM-apps/HMM-applications. html
Exercises SAM
Exercises SAM
Exercises
SAM Exercises Markov model short. t 2 k-w 0. 5. mod position Transition probabilities Emission probability per AA Insertion probability per AA
SAM Exercises input targets
Exercises SAM
Exercises SAM
Exercises SAM Hit with highest score! Hit with a protein family for which the 3 D structure has been determined
SAM Exercises Try to view the structure of the family
Exercises SAM
Exercises SAM
Exercises Logos of the secondary structure prediction SAM
Exercises SAM
HMMer Exercises Null model states Emission probability per AA Insertion probability per AA Transition probabilities
Exercises
Exercises
Exercises
Exercises
Exercises
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