Figure 3.

Sequences detected in a PSI-BLAST simulated checkpoint search based on a HMM trained using the six repeats of the Thermotoga putative clamp protein. The transition probability pairs used to obtain the HMM parameters from secondary structure propensities are as for Figure 1. The NCBI non-redundant database was searched. Sequences with pairwise significant internal repeats, coiled-coil regions and compositionally biased regions were eliminated from the search and are not shown (see Materials and Methods).