SUPERFAMILY 1.75 HMM library and genome assignments server

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SUPERFAMILY model 0036294

Seed sequence: 43248 d1d6ma_
Superfamily: 56712 Prokaryotic type I DNA topoisomerase
Comment: 1.69 all builds
Date built: 2005-09-08
Length: 609
Sequences: 513
Other models: All models from the Prokaryotic type I DNA topoisomerase 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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