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SIMBAL heat map for the rhombosortase SO_2504 of Shewanella oneidensis MR-1.

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posted on 14.12.2011, 00:55 by Daniel H. Haft, Neha Varghese

Values are calculated for all possible subsequences with lengths from 204 (full length) at the apex of the triangular heat map to 6 along the base. Horizonal numbering represents sequence position, marking the center of each subsequence. represented SIMBAL scores are calculated as the negative log of the probability, according to the binomial distribution, that a BLAST hits list (at an optimized E-value cutoff) for a subsequence from SO_2504 could so strongly favor matches to rhomboid family proteases from species with GlyGly-CTERM sequences of rhomboid family proteases from species without. The peak score, 57.7, occurs for the fifteen-residue peptide QLLGYVGLSGMLHGL, containing the active residue, Ser-119, and represents the most extreme red color in the heat map. The positions of several key sequence motifs are indicated. The WRxxS/T motif, in loop L1, falls within a hexapeptide centered at 54.5 with a locally high SIMBAL score of 23.6. The sequence Ser-Gly-Met-Leu-His,, where Ser-119 is the active site residue and His-123 is the stacking residue for the active site His, belongs to transmembrane helix TM4. The region 176–184 shows the conserved TM6 motif AHxxGxxxG, with the catalytic His and the GxxxG transmembrane dimerization motif [10].

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