Akula S , Thorpe M , Boinapally V , Hellman L .

	Fig 1. The chymase locus.The genes encoding serine proteases are depicted in double height to easily locate them in the maps. The bordering genes are included to trace the origin of the locus and to also define changes that have occurred upstream or downstream of the locus. Gene names for the serine proteases, as given in the database, particularly in fish and amphibians do not match their closest homologs in mammals, and can sometimes be quite misleading. The α-chymase related genes are depicted in light blue, the β-chymases in slightly darker blue, cathepsin G in green, the M8 family in a darker green, the granzymes in dark blue and the duodenases in red. The Chinese alligator locus and the two individual contigs that appears most closely related to the mammalian chymase locus genes are marked with red stars and the genes are depicted in light or dark blue. One of the Xenopus genes that also cluster with these genes (Fig 6) are also shown in dark blue. The genes from the other loci in reptiles, birds and frogs that are more distantly related to the mammalian chymase locus genes are shown in light brown.
	Fig 2. The fish chymase locus.The locus that harbors chymase-related genes in fish and do not show homology to neither the chymase locus nor the met-ase locus of mammals. The genes encoding serine proteases are depicted in double height to easily locate them in the maps. The different fish chymase locus-related genes are shown in dark brown.
	Fig 3. The met-ase locus.A. The genes encoding serine proteases are depicted in double height to easily locate them in the maps. The bordering genes are included to trace the origin of the locus and to also define changes that have occurred upstream or downstream of the locus. Gene names, as given in the database, particularly in fish and amphibians do not match their closest homologs in mammals, and can sometimes be quite misleading. CFD is depicted in orange, granzyme M in red, PRSS57 in blue, N-elastase, azurocidin and proteinase 3 in various shades of green. The fish chymase locus-related genes in the met-ase locus are shown in dark brown. The granzyme A/K genes located in the cichlid met-ase locus are marked by red stars.
	Fig 4. The second locus encoding complement factor D in fish.The genes encoding serine proteases are depicted in double height to easily locate them in the maps. This locus encodes only CFD in most fish species. The only exception so far is in the spotted gar, which has one copy in the met-ase locus (Fig 3). The CFD gene is depicted in orange.
	Fig 5. The granzyme A/K locus.The genes encoding serine proteases are depicted in double height to easily locate them in the maps. The bordering genes are included to easily trace the origin of the locus and to also define changes that have occurred upstream or downstream of the locus. Gene names in the database as A or K in fish and amphibians do not always match their closest homologs in mammals. The granzyme A and K genes from mammals, birds and reptiles form distinct sub-branches and are therefore depicted in dark and light blue respectively. The color coding in fish is not so distinct but the genes have been coded light and dark blue as named in the database. However, as seen in Fig 6E, they cluster together and not within the mammalian sub-branches for A and K. Three genes of the cichlid GzmA/Ks that have specificity triplets as the chymases, SGG, have been marked by red stars.
	Fig 6. Phylogenetic analysis using the MrBayes algorithm.The original tree includes many members that cannot easily be displayed on one page. The individual parts of the tree have therefore been enlarged and presented separately (Figs 7–10) for the chymase locus-related genes, the fish chymase-related genes, the met-ase locus genes and the granzyme A/K locus genes, respectively. The chymase locus-related fish genes that are found within the met-ase locus (Fig 10) are marked by green instead of blue. Human and mouse coagulation factor X and complement factor B have been used as outgroups to get a more distinct topology of the tree. The three catfish serine proteases that are under more detailed biochemical analyses are marked by red stars in Fig 9. They represent three of the four major sub-branches of fish chymase-locus related serine protease genes. The posterior probability values are shown at each branch point in the tree.
	Fig 7. The branch of the phylogenetic tree containing the mammalian chymase locus genes.The triplets constituting the amino acid positions 189, 216 and 226 (S1 pocket), chymotrypsinogen numbering are shown after each of the individual proteases in the tree. A question mark has been inserted when the sequence is not complete, indicating the gene is a pseudogene. The posterior probability values are shown at each branch point in the tree.
	Fig 8. The branch of the phylogenetic tree containing the fish chymase locus related genes.The triplets constituting the amino acid positions 189, 216 and 226 (S1 pocket), chymotrypsinogen numbering are shown after each of the individual proteases in the tree. The posterior probability values are shown at each branch point in the tree.
	Fig 9. The branch of the phylogenetic tree containing the met-ase locus genes.All the mammalian met-ase locus genes are found within this branch. However, some of the met-ase locus genes in fish are found in the fish chymase locus branch and some in the granzyme A/K branch. The triplets constituting the amino acid positions 189, 216 and 226, chymotrypsinogen numbering are shown after each of the individual proteases in the tree. The posterior probability values are shown at each branch point in the tree.
	Fig 10. The branch of the phylogenetic tree containing the T cell tryptase locus genes (granzyme A/K locus).The genes originating from the met-ase locus are shown in light blue. The triplets constituting the amino acid positions 189, 216 and 226, chymotrypsinogen numbering, are shown after each of the individual proteases in the tree. The posterior probability values are shown at each branch point in the tree.
	Fig 11. Human chymase structure with inhibitor highlighting the catalytic triad and S1 pocket.The PDB structure 3N7O was used to visualize specificity-conferring triplet (S1 pocket) of residues 189, 216 and 226, chymotrypsinogen numbering, highlighted in red. The catalytic triad residues His57, Asp102 and Ser195 and shown in blue. The bound inhibitor is highlighted in green in both ribbon and space-filling models to visualize how it sits into the S1 pocket. UCSF Chimera program was used to construct the image with further annotation in Adobe Illustrator (CS6).

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