Sequence alignment of proteins

Thompson and Goldstein [89] improve on the calculations of Stolorz et al. by including the secondary structure of the entire window rather than just a central position and then sum over all secondary strucmre segment types with a particular secondary structure at the central position to achieve a prediction for this position. They also use information from multiple sequence alignments of proteins to improve secondary structure prediction. They use Bayes rule to fonnulate expressions for the probability of secondary structures, given a multiple alignment. Their work describes what is essentially a sophisticated prior distribution for 6 i(X), where X is a matrix of residue counts in a multiple alignment in a window about a central position. The PDB data are used to form this prior, which is used as the predictive distribution. No posterior is calculated with posterior = prior X likelihood. 

Fig. 1 Blocks of multiple sequence alignment of protein sequences of carboxypeptidases from B. taurus, Mus musculus, Rattus norvegicus, Neurospora crassa, Schizosaccharomyces pombe, Drosophila melanogaster, and Homo sapiens along with protein sequence from H. pylori (Uniprot accession code HPAG1 0372 from strain HPAG1). Numbers on the top correspond to amino acid residue number of the carboxypeptidase enzyme from B. taurus. Gray vertical columns indicate conserved residues. Amino acid residues corresponding to Glu-182 and His-306, which coordinate to zinc, are conserved, whereas another Zn-coordinating amino acid residue corresponding to His-179 is substituted by Gin in the Helicobacter sequence. Functionally important residues corresponding to Arg-237 are also conserved...

Fig. 7 Sequence alignment of GPR motifs. Consensus amino acids are red chemically similar amino acids are blue. Consensus I refers to the conserved sequence defined with die family of AGS3-related proteins. Consensus II refers to the conserved sequence defined widi all known GPR proteins. Consensus II amino acid groupings are. =any, +=positive (HKR), —negative (DE), h=hydrophobic (ACFILMVWY), u=tiny (AGS), p=polar (CDEHKNQRST), and l=aliphatic (ILV). (C.e. C. elegans, D.m. D. melanogaster, A.t.. A. thaliand) The core GPR motif is as defined in Peterson et al. 2002. This figure is ad ted from die thesis of Dr. Yuri Peterson.

FIGURE 3-30 Aligning protein sequences with the use of gaps. subtilis. Introduction of a gap in the B. subtilis sequence allows a bet-Shown here is the sequence alignment of a short section of the EF-Tu ter alignment of amino acid residues on either side of the gap. Iden-... 

Fig. 4. Amino acid sequence alignment of the MT-like domains of the putative plant MTs (Fig. 3) with the a and (5 domains of Equine MT and the single domain of N. crassa MT. The numbers refer to the residue positions within the complete protein.

Multiple alignment Multiple sequence alignment involves the simultaneous comparison of several distinct sequences. If these sequences represent a single protein across multiple species, the alignment will indicate evolutionary relatedness. Alternatively, alignment of proteins within a single... 

---