SUPERFAMILY model 0040406
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Hydrophobicity, emmission, insertion, deletion and amino acid plots
Graphical representation by Martin Madera (explanation below).
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The top plot (blue line) is the average hydrophobicity, calculated as the sum
over all amino acids of (match emmission probability) * (delta-G
surface-buried). The transfer energies in kcal/mol are taken from Table 8,
Miller et al, J. Mol. Biol. (1987) 196, 641-56.
The middle plot shows match emmission probabilities. The amino acids in each
column are ordered from most hydrophilic (top) to most hydrophobic (bottom). The size
of each column is proportional to the difference between the match emmission
distribution and the generic background distribution:
The columns are partitioned between amino-acids according to the ratio of their
probabilities; only letters larger than a threshold size are shown. The columns are
aligned at the bottom of A (alanine).
The bottom plot gives the probability that there is an insertion (light green) or
a deletion (red) at that position in the HMM. The dark green curve gives the
probability P of an insert-insert transition; assuming there is an insertion at that
node, 1/(1-P) gives its expected length.
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