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Figure 2 | BMC Bioinformatics

Figure 2

From: Mathematical model for empirically optimizing large scale production of soluble protein domains

Figure 2

Design of domain fragments. (a) Snap shot of the ProteoMix for the Kazusa HUGE KIAA1131 sequence. The results of PASS (domain predictions, Domain), DLiP and DLP (domain linker predictions, Linker), HMMTOP and MEMSAT (transmembrane predictions, Transmembrane), and BLAST to PDB sequences (homology to structurally known sequences, Blast_to_PDB) are shown. (b) Domain fragment design scheme. For each dissected domain, the corresponding linker or the N- or C-terminus of the full-length sequence that is in the N- or C-terminal end of the domain is used to determine the termini of the fragments. Three cleavage sites are defined along the linker region. The first one is at the end of the predicted linker on the PASS-predicted domain side (cleavage site 1), the second one is located in the middle of the linker region (cleavage site 2), and the third one is at the end of the linker region, opposite from the domain side (cleavage site 3). In addition, we designed a cleavage site at the terminal ends of the PASS-predicted domain (cleavage site 0) and at either the N or C terminus of the protein (cleavage site 4, in case it was close to the C- or N- terminus of the domain). Some cleavage sites were not defined: for example, when the length of a linker was too short to determine its center, the central cleavage site was omitted. The number of generated fragments was regarded as sufficient for assessing the presence of a cleavable site and for estimating the model's parameters.

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