CPSARST: an efficient circular permutation search tool applied to the detection of novel protein structural relationships

Table 1 Retrieved parent proteins of engineered CPs by CPSARST

PDB entry	Chain	Size	Function	Parent structure/recorded CP site	Retrieved structure/determined CP site	D (%)*
1AJK	A,B	214	Circularly permuted (1-3,1-4)-beta-D-glucan 4-glucanohydrolase H	2AYH/84	2AYH/84	0.00
1AJO	A,B	214	Circularly permuted (1-3,1-4)-beta-D-glucan 4-glucanohydrolase H	2AYH/127	2AYH/127	0.00
1ALQ		266	CP254 beta-lactamase	3BLM/254	3BLM/254	0.00
1BD7	A,B	176	Circularly permuted BB2-crystallin	1BLBC/87	1BLBC/87	0.00
1CPM		214	Glucanase	2AYH/59	2AYH/59	0.00
1CPN		208	Glucanase	2AYH/59	2AYH/59	0.00
1FW8	A	416	Phosphoglycerate kinase	3PGK/72	3PGK/73	0.24
1G2B	A	62	Spectrin alpha chain	1SHG/47	1SHG/47	0.00
1N02	A	102	Cyanovirin-N	2EZM/50	2EZM/51	0.98
1P5C	A-D	167	Lysozyme	1LW9A/12	1LW9A/12	0.00
1SWF	A-D	128	Circularly permuted core-streptavidin E51/A46	1STP/51	1STP/51	0.00
1SWG	A-D	128	Circularly permuted core-streptavidin E51/A46	1STP/51	1STP/51	0.00
1TUC		63	alpha-Spectrin	1SHG/20	1SHG/20	0.00
1TUD		62	alpha-Spectrin	1SHG/48	1SHG/48	0.00
1UN2	A	197	Thiol-disulfide interchange protein	1A2J/100	1A2J/100	0.00
Average						0.08

*Percentage distance of the retrieved permutation site to the exact one. See text for definition.

ISSN: 1474-760X