SUPERFAMILY 1.75 HMM library and genome assignments server

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SUPERFAMILY model 0048472

Seed sequence: 92374 d1nzea_
Superfamily: 101112 Oxygen-evolving enhancer protein 3,
Comment: 1.73 all builds
Date built: 2008-09-10
Length: 112
Sequences: 116
Other models: All models from the Oxygen-evolving enhancer protein 3, 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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