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Examination of surface conservation among 10077a d revealed well-defined clusters of surface residues (Figure 5), including Val10, Thr13, Glu14, Asp15, Lys18, Val19, Ala22, Asn25, Ile63, Asp65, Ala67, Arg68, Lys86, Gln87, Ala89, Asn95, Ile104, Pro125, Thr127, Gly130 (using 10077a residue numbering).
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When the sequence conservation of OTUD orthologs from species annotated in the Ensembl project (www.ensembl.org; Data S1) is mapped onto the surface of OTUD1, OTUD2, and OTUD3, the putative sitesite comprising Cys and His loops emerged as regions of highest surface conservation greater than the S1 Ub-binding site.
(C ) Surface conservation of the output domain.
(C ) Surface conservation of CsgS9Output and LapG interaction interface.
The notion of geometric compatibility, as opposed to an increase in specific per-residue interactions as a predominant driver for high-affinity LapG binding, is supported by the overall low surface conservation of LapD orthologs.
The two first requirements suggest basing the procedure on flame surface conservation instead of on chemical reaction rates.
(D ) Surface conservation map of ANK repeats viewed from the side.
For the phylogeny based identification of functionally important residues on DDX3X surface, conservation scores were obtained by likelihood based approach using Jules-Thornton-Taylor Jules-Thornton-Taylor Jules-Thornton-TaylorBLAST E-value cut-off = 0.001; Iterations = 3) [19].
Surface conservation and surface potential of the Ron kinase domain were illustrated.
In light of the findings of surface charge conservation and from the mutation studies, we propose a model in which E18 in the α2-region of RF1 is not only involved in establishing the negatively charged surface patch important for interaction with the positively charged counterpart in RF3 but also involved in a specific interaction with RF3.
(D ) TBCC β-helix surface conservation showing the high conservation of the Arl2 catalytic site on one side of the TBCC β-helix domain.
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