SUPERFAMILY 1.75 HMM library and genome assignments server

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SUPERFAMILY model 0034788

Seed sequence: 42601 d16vpa_
Superfamily: 56548 Conserved core of transcriptional regulatory protein vp16
Comment: 1.69 all builds
Date built: 2005-09-08
Length: 356
Sequences: 20
Other models: All models from the Conserved core of transcriptional regulatory protein vp16 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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