Algorithms for matching partially labelled sequence graphs

Table 1 Proteins used as test data

PDB	Protein	Length	Domain ends
PDB	Protein	Used (full)	N–C (len)
1aoz	Ascorbate oxidase	434 (552)	9–126 (118)
			135–301 (167)
			378–526 (149)
1lci	Luciferase	404 (404)	24–186 (163)
			187–355 (164)
			359–435 ( 77)
1pkm	Pyruvate kinase	367 (390)	41–116 ( 76)
			117–388 (172)
			409–527 (119)
3ctz	Prolyl aminopeptidase	572 (617)	3–160 (158)
			161–319 (159)
			320–574 (255)
3vqt	Translation factor RF3	495 (495)	1–277 (250)
			278–389 (105)
			390–529 (140)
4rcn	Fatty-acid acyl-CoA carboxylase	401 (1972)	3–102 (100)
			103–345 (176)
			346–470 (125)

Against the protein name and PDB code, the length of the portion used is given with the length of the full chain in parentheses. The three domains used for each protein are specified by their residue numbers in the PDB entry and the length of the domain. (NB: because of missing segments in the PDB structure and omitted segments, the difference in the domain end-points does not necessarily equal the number of residues in the domain)

ISSN: 1748-7188