Fig. 3. Bar diagram comparisons and sequence alignments for the nht, rye, mia and sa predicted proteins. In bar diagrams: predicted histone fold domains are red; other conserved regions are blue. In multiple sequence alignments the colours are: yellow, hydrophobic; green, polar + Tyr; purple, charged; red, proline; orange, Phe. Red horizontal bars indicate alpha helices of the HFDs, shown above the alignment for the TAFs and below the alignment for the histones; blue or light blue horizontal bars indicate other conserved regions. (A,B) Structural comparisons of nht protein with TAF4 homologs from yeast to human. dTAF4: generally expressed Drosophila homolog of nht. Sequence alignments (B) show the histone fold domain (HFD) compared to histone H2a, the C-terminal CCTD region, and in between two additional regions with a conserved pattern of polar, charged and hydrophobic residues (dark-blue bars). (C,D) Structural comparisons of rye protein with TAF12 homologs from a range of metazoans. dTAF12: generally expressed Drosophila homolog of rye. Histone fold domain (HFD) also compared to histone H2b in (D). (E,F) Structural comparisons of mia protein with TAF6 homologs from yeast to human. dTAF6: generally expressed Drosophila homolog of mia. Sequence alignments (F) show the histone fold domain (HFD) compared to histone H4. The TAF6 domain is the extended region C-terminal to the HFD with a conserved pattern of polar, charged and hydrophobic residues. In B,D,F, residues with >15% of overall structure exposed (as predicted by DeepView software) in the hTAF4:hTAF12 or dTAF6 and dTAF9 heterodimers, based on their crystal structures (Werten et al., 2002; Xie et al., 1996) are marked `e'. Residues making heterodimeric bonds between hTAF4 and hTAF12, or between dTAF6 and dTAF9, analyzing all residues of opposing chains within 5 Å, are designated above the sequence alignment by the following symbols: 1 = binding to alpha-1 helix of heterodimer partner; 2 = binding to alpha-2 helix of heterodimer partner; 3 = binding to alpha-3 helix of heterodimer partner; i = forming an acid-base bond with heterodimeric partner. From the crystal structure of the nucleosome (Luger et al., 1997), regions of histones that form symmetrical tetrameric bonds are marked with an asterisk; regions of histones forming non-symmetrical tetrameric bonds (H2B-H4) are marked (8). (G,H) Comparisons of sa and TAF8 homologs from yeast to human. The histone fold domain predicted by PFAM family HMMer search is shown as a red bar, and the predicted alpha helices as green cylinders: secondary structure predictions show the helix-loop-helix-loop-helix pattern characteristic of histone fold domains. Significant region of homology just downstream of the predicted HFD marked with a light-blue bar.