Six of these variants place a high affinity (H), low affinity (L) or deleted (X) Pho4-binding site in the positions corresponding to UASp1 and UASp2 in Figure 7A.
While considerably divergent from these earlier-characterized versions, both families are predicted to bind double-stranded substrates based on the strong conservation of residues at positions corresponding to nucleic acid binding sites in the classical PIWI modules in both of the novel families (see Figures 1, 2, and 4).
Detailed information on the piRNA mRNA pair and a link to the Genome Browser will be displayed in the search result, and the genomic positions corresponding to the piRNA-binding sites can be viewed in the Genome Browser by clicking on the link.
They found that the Alu counterparts of the p53 binding motifs contain the CG dimers in the positions corresponding to CA and TG in the p53 sites.
While the majority of amino acid residues in the binding pocket were highly conserved, a clear divergence existed at two amino acid positions corresponding to S. cerevisiae residues Gln324 and Thr340 (Table 2).
Previous studies on SGLT1 [8] and the recently resolved structure of vSGLT [9] suggest that the amino acid at positions corresponding to 457 in SGLT1 plays a direct role in sugar binding and transport.
In addition, the aromatic and hydrophobic moieties of bosentan, including the 2-pyrimidyl group, the 4-t-butylphenyl group, and the 5-methoxyphenoxy group, occupy the positions corresponding to the side chains of Ile19, Ile20, and Trp21 of ET-1, respectively, and essentially the same residues of the ETB receptor are involved in binding these ligands (Supplementary Fig. 7c).
Further evidence for FilGAP's use of a similar binding motifs are: 1) Phe726, Leu732, and Val734 in the FilGAP binding site are identical to the corresponding amino acids of GPIbα, which make strong hydrophobic contacts with FLNa [14]; and 2) the amino acid positions corresponding to Thr728 and Gly730 in FilGAP vary between GPIbα and integrin β.
Control sequences, comprising all BCO and RCO binding sequences in the consensus subtype B HIV-1 pol, were constructed by ligating 10 short (<100 nt) oligonucleotides (Table S6) with degenerate positions corresponding to the mutations of interest (Figure 3A).
The binary index s has m positions corresponding to the m drugs; "1" in a given position denotes resistance to the corresponding drug, while "0" means susceptibility.
