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Conserved Residues in MPID-T2:

A Sequence logo is a graphical display of a multiple sequence 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 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).

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 sequence logos are currently available for peptides of length 8, 9, 10, 11, 12, 13, 14, 15, 16 and 20 amino acids. Peptides of length 8, 9, 10, 11, 12 and 13 are generally bound to MHC-I proteins and peptides of length 12, 13, 14, 15, 16, 18 and 20 are mostly bound to class II MHC molecules. The motifs presented here are derived using the web based application WebLogo (Crooks et al., 2004). The images of the motifs presented here are obtained using peptides extracted from available experimentally determined crystal 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.


Peptide conserved residues by peptide length:

Peptide conserved residues by species and peptide length:

Peptide conserved residues by MHC allele and peptide length:

Color Scheme:

Polar: GSTYC Amide: QN Basic: KRH Acidic: DE Hydrophobic: AVLIPWFM

Figure 1: Conserved residues of all 8-mer peptides available in MPID-T2.

Figure 2: Conserved residues of all 9-mer peptides available in MPID-T2.

Figure 3: Conserved residues of all 10-mer peptides available in MPID-T2.

Figure 4: Conserved residues of all 11-mer peptides available in MPID-T2.

Figure 5: Conserved residues of all 12-mer peptides available in MPID-T2.

Figure 6: Conserved residues of all 13-mer peptides available in MPID-T2.

Figure 7: Conserved residues of all 14-mer peptides available in MPID-T2.

Figure 8: Conserved residues of all 15-mer peptides available in MPID-T2.

Figure 9: Conserved residues of all 16-mer peptides available in MPID-T2.

Figure 10: Conserved residues of all 20-mer peptides available in MPID-T2.

Figure 11: Conserved residues of human 8-mer peptides available in MPID-T2.

Figure 12: Conserved residues of human 9-mer peptides available in MPID-T2.

Figure 13: Conserved residues of human 10-mer peptides available in MPID-T2.

Figure 14: Conserved residues of human 11-mer peptides available in MPID-T2.

Figure 15: Conserved residues of human 12-mer peptides available in MPID-T2.

Figure 16: Conserved residues of human 13-mer peptides available in MPID-T2.

Figure 17: Conserved residues of human 14-mer peptides available in MPID-T2.

Figure 18: Conserved residues of human 15-mer peptides available in MPID-T2.

Figure 19: Conserved residues of human 20-mer peptides available in MPID-T2.

Figure 20: Conserved residues of murine 8-mer peptides available in MPID-T2.

Figure 21: Conserved residues of murine 9-mer peptides available in MPID-T2.

Figure 22: Conserved residues of murine 10-mer peptides available in MPID-T2.

Figure 23: Conserved residues of murine 11-mer peptides available in MPID-T2.

Figure 24: Conserved residues of murine 12-mer peptides available in MPID-T2.

Figure 25: Conserved residues of murine 13-mer peptides available in MPID-T2.

Figure 26: Conserved residues of murine 14-mer peptides available in MPID-T2.

Figure 27: Conserved residues of murine 15-mer peptides available in MPID-T2.

Figure 28: Conserved residues of murine 16-mer peptides available in MPID-T2.

Figure 29: Conserved residues of rat 9-mer peptides available in MPID-T2.

Figure 30: Conserved residues of A*0201 9-mer peptides available in MPID-T2.

Figure 31: Conserved residues of A*0201 10-mer peptides available in MPID-T2.

Figure 32: Conserved residues of B*0801 8-mer peptides available in MPID-T2.

Figure 33: Conserved residues of B*2705 9-mer peptides available in MPID-T2.

Figure 34: Conserved residues of B*3501 9-mer peptides available in MPID-T2.

Figure 35: Conserved residues of DRB1*0101 13-mer peptides available in MPID-T2.

Figure 36: Conserved residues of DRB1*0101 15-mer peptides available in MPID-T2.

Figure 37: Conserved residues of H2-Db 9-mer peptides available in MPID-T2.

Figure 38: Conserved residues of H2-Db 10-mer peptides available in MPID-T2.

Figure 39: Conserved residues of H2-Kb 8-mer peptides available in MPID-T2.

Figure 40: Conserved residues of H2-Kb 9-mer peptides available in MPID-T2.