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Figure 4 | BMC Bioinformatics

Figure 4

From: Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL): adapting the Partial Phylogenetic Profiling algorithm to scan sequences for signatures that predict protein function

Figure 4

Structural alignment of crystallized ABC permeases with UrtB and UrtC. Primary sequence of HI1471 from H. influenzae and BtuC from E. coli were aligned by MUSCLE. The ten transmembrane helices (A-J) observed in the respective structures are indicated in yellow. Predictions of transmembrane helices of C. glutamicum UrtB and UrtC were carried out by MEMSAT3[14] and are also shown in yellow. The UrtB and UrtC sequences were added to the HI1471/BtuC alignment manually. Topology of the crystallized permeases is indicated in the last line (O:outside, I:inside). The four highest scoring SIMBAL subsequences at 15 amino acid length for UrtB and UrtC are indicated in red font. Note that all are partially or completely localized to the predicted inside (cytoplasmic) face of the membrane.

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BMC Bioinformatics

ISSN: 1471-2105

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