A comparative proteomics resource: proteins of Arabidopsis thaliana

Table 3 Comparison of PAT with other resources

(a) Coverage	PAT	PEDANT/MatDB	TAIR/GO	EBI Proteomes/InterPro
	94% A-E	30.9% PDB	38% ALL	77.3% InterPro
	84% A-D	26.7% SCOP	14% Non-IEA	0.07% PDB
	65% A-C
	46% A-B
	38% A
(b) Specific examples	Target	Other sources	PAT
			Results	Reliability
	AP2 domain (1gcc)	140 hits by BLAST against NR	155 hits	C (90% certainty) or above
	15239082 (At5g11550.1)	No hits by PSI-BLAST None from TAIR, PEDANT	1EE4	C
	15228210 (At3g47660)	FYVE/PHD zinc finger RCC1 like domain Sugar transporter signature (PROSITE)	FYVE/PHD zinc finger; RCC1 like domain; PH domain	A (99.9% certainty); B (99% certainty); C
	Cytochrome P450	238 (TAIR GO)	249 hits 256 hits	C or above D (50% certainty) or above
	Protein-kinase-like domain	1037 hits (PEDANT/MatDB) 951 hits (TAIR GO)	1,179 hits	C or above
Alpha/beta hydrolase fold	Arabidopsis	194 hits (PEDANT/MatDB, SCOP 3.65)	340 hits 200 hits	C or above A
	Human	69 hits (PEDANT/MatDB, SCOP c.69)	1,086 hits 1,18 hits	C or above A

(a) Percent coverage against specific data sources. (b) PDB sequence of 1gcc [22] was used to perform a standard BLAST search. The putative protein with gi number 15239082 (At5g11550.1) returns no hits using PSI-BLAST. The putative protein (gi number 15228210, locus id At3g47660) contains a FYVE/PHD zinc finger domain, and an RCC1 like domain (a regulator of chromosome condensation). TAIR also reported a sugar transporter signature for this protein from Prosite search. The term 'cytochrome P450' was used to search TAIR GO annotation (release). This was obtained using the search by keyword query feature, after we've loaded the TAIR GO data into our database. The cytochrome P450 fold in the SCOP hierarchy was used to retrieve the hits from PAT. Actual hits may vary between releases.

ISSN: 1474-760X