Alignment of the sequences

Fig. 5. Structure-based alignment of the sequences of the water-soluble Rieske fragment from bovine heart bci complex (ISF), the water-soluble Rieske fragment from spinach b f complex (RFS), and of the Rieske domain of naphthalene dioxygenase (NDO) and of the metal binding loops of rubredoxin (RXN) and transcriptional factor TFIIS (TFI). The numbering of the j3 strands is the same for the ISF and RFS. The metal binding ligands are highlighted the asterisks indicate those residues that are fully conserved between the three Rieske proteins.

With the structure of ascorbate oxidase in hand, a new structurally based alignment of the sequences of ascorbate oxidase, laccase, and ceruloplasmin has been performed (Messerschmidt and Huber, 1990). In brief, while gene triplication for ceruloplasmin is still revelant, its sequence can be further subdivided into two domains per unit of triplicated sequence, or six domains in total. Each of these sequences bears some resemblance to each of the three domains of ascorbate oxidase, as does each of the two domains in laccase. The coppers of the trinuclear site of ceruloplasmin then are predicted to be bound between domains 1 and 6, with a type I site also lying in both domains 6 and 4 (see Huber, 1990). The relative orientation of each of these domains is not predicted by this alignment, but it turns out that the structure of nitrite reductase may shed some light on this (see Section V,C). 

Figure 6.6. Global and local alignments. Two alignments of the sequences X and Y are shown a global PSA on the left and a local PSA on the right. Below each alignment is its score as calculated using the scheme of Figure 6.5.

Figure 7.16. Sequence Alignment of Internal Repeats. (A) An alignment of the sequences of the two repeats of the TATA-hox-binding protein. The amino-terminal repeat is shown in green and the carboxyl-terminal repeat in blue. (B) Structure of the TATA-hox-binding protein. The amino-terminal domain is shown in green and the carboxyl-terminal domain in blue.

Table 3. Alignment of the sequences of the catalytic domain of selected human matrix metallo proteases (Matrixins). The sequences have been colored according to the secondary structure, with the zinc-chelating residues shown in white and the catalytic glutamic acid shown in red. Yellow residues identify amino acids discussed in the text.

Fig. 13. BLAST2Sequences problem 2 alignment view at the junction. The sequence between the nucleotides 655..752 is missing in the alignment of the sequence to itself. The nucleotides at the junction of the two alignments are highlighted by rectangles.

Figure 7. Alignment of the sequences of the serine pioteinases shown in Figure 6. TRP, CHT, ELA, and MCP correspond to trypsin, chymotrypsin, elastase, and mast-cell proteinase, respectively. The shaded texes designate identical or highly conserved residues, and the bold horizontal lines represent structurally-conserved regions of these proteins derived from the structural overlay presented in Figure 6.

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