Conserved Residues in MPID-T:

A Sequence logo is a graphical display of a multiple alignment consisting of colour coded stacks of letters representing amino acids at successive positions. The height of a given letter increases with increasing frequency of the amino acid, and its height increases with increasing conservation of the aligned positions; hence, letters in the stacks with single residues(i.e.,representing conserved positions) are taller than those in stacks with multiple residues(i.e., where there is more variation).

Within stacks, the most frequently occurring residues are not only taller, but also occupy higher positions in the stack, so that the most prominent residue at the top is the one predicted to be the most likely to occur at that position. To address the problem of sequence redundancy within a block, which strongly biases residue frequencies, sequence weights are calculated using a position-specific scoring matrix (PSSM). This reduces the tendency for over-represented sequences to dominate stacks, and increases the representation of rare amino acids relative to common ones.

MHC allele specific peptide structures for peptide structures are currently available for peptides of length 8, 9, 10, 13 and 14. Peptides of length 8, 9 and 10 are bound to class I MHC molecules and peptides of length 13 and 14 are bound to class II MHC molecules. The motifs presented here are derived from available experimentally determined structures. Due to the absense of sufficient experimentally determined structures, motifs for some alleles may be uninformative and users are adviced to refer to SYFPEITHI for more detailed motifs.

Figure 1: Conserved residues of all 8-mer peptides available in MPID-T.

Figure 2: Conserved residues of all 9-mer peptides available in MPID-T.

Figure 3: Conserved residues of all 10-mer peptides available in MPID-T.

Figure 4: Conserved residues of all 13-mer peptides available in MPID-T.

Figure 5: Conserved residues of all 14-mer peptides available in MPID-T.

Figure 6: Conserved residues of human 8-mer peptides available in MPID-T.

Figure 7: Conserved residues of human 9-mer peptides available in MPID-T.

Figure 8: Conserved residues of human 10-mer peptides available in MPID-T.

Figure 9: Conserved residues of human 13-mer peptides available in MPID-T.

Figure 5: Conserved residues of human 14-mer peptides available in MPID-T.

Figure 10: Conserved residues of murine 8-mer peptides available in MPID-T.

Figure 11: Conserved residues of murine 9-mer peptides available in MPID-T.

Figure 12: Conserved residues of murine 10-mer peptides available in MPID-T.

Figure 13: Conserved residues of murine 13-mer peptides available in MPID-T.

Figure 5: Conserved residues of murine 14-mer peptides available in MPID-T.

Figure 14: Conserved residues of A*0201 9-mer peptides available in MPID-T.

Figure 15: Conserved residues of A*0201 10-mer peptides available in MPID-T.

Figure 16: Conserved residues of B*0801 8-mer peptides available in MPID-T.

Figure 17: Conserved residues of B*2705 9-mer peptides available in MPID-T.

Figure 18: Conserved residues of DRB1*0101 13-mer peptides available in MPID-T.

Figure 19: Conserved residues of H2-Db 9-mer peptides available in MPID-T.

Figure 20: Conserved residues of H2-Kb 8-mer peptides available in MPID-T.

Figure 21: Conserved residues of H2-Kb 9-mer peptides available in MPID-T.