SUPERFAMILY 1.75 HMM library and genome assignments server

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SUPERFAMILY model 0047872

Seed sequence: 90389 d1kska4
Superfamily: 55120 Pseudouridine synthase
Comment: 1.73 all builds
Date built: 2008-09-10
Length: 172
Sequences: 2575
Other models: All models from the Pseudouridine synthase superfamily


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Hydrophobicity, emmission, insertion, deletion and amino acid plots

Graphical representation by Martin Madera (explanation below).





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Plot explanation

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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