Figure 5

Examples of the structures of key elementary functional loops in the clusters of arCOGs. (Cluster 1) the profile 292, signature -GxKMSKSxG- (PDB ID: 1FFY, chain A, residues 588–633) two lysines are shown as sticks; (cluster 2) the profile 251 -WxFGDGx(11)Y- (PDB ID: 1B4R, chain A: 38–58) structural repeat comprising Ig-like fold of PKD; (cluster 3) the profile 423 (IAx(9)Vx(6)LxxxGxV) Catabolite gene activator protein (PDB ID: 1RUN, chain A) in complex with DNA; (cluster 4) the profile 280 with the signature -Px(2)GxGxGxxRL- represents one of the three characteristic motifs in aminoacyl tRNA synthetases Class II core domains. The EFL corresponding to the profile 280 is shown for the structure PDB ID: 1E24, chain A, which is Lysyl-tRNA synthetase together with Lysine (blue), ATP (green), and Mn²⁺ ions (magenta); (cluster 5) “Helicases”: the profile 45 -Lx(3)Px(3)GKTLxAExA- (PDB ID: 2DR3 chain A: 9–51) recA family protein with ADP bound; (cluster 6) the profile 429 (VxGxDx(8)A) PDB ID: 1BC5 chain A chemotaxis receptor methyltransferase with S-adenosyl-L-homocysteine (SAM-analogue); (cluster 7) the profile 225 (Gx(6)GxxGxGKTT), the profile 195 (LSGGxxQRxxxAxxLxxxPxxxxxDEPxxxLD), profile 294 (GxxxQx(12)N); (cluster 8) the profile 14, signature -GMxCxxCxxxVx(8)GV- (PDB ID: 1KOV chain A:10–37). The copper ion is coordinated by Met and two Cys (shown in sticks representation) in the elementary functional loop.