A comparative proteomics resource: proteins of Arabidopsis thaliana

Li, Wilfred W; Quinn, Greg B; Alexandrov, Nickolai N; Bourne, Philip E; Shindyalov, Ilya N

doi:10.1186/gb-2003-4-8-r51

Table 4 Sampling of known Arabidopsis protein structures in PAT

From: A comparative proteomics resource: proteins of Arabidopsis thaliana

(a) PDB structures from Arabidopsis mapped to FOLDLIB entries	PDB ID	SCOP family	SCOP superfamily	GI number	Name	Domain found	Reliability	Number of unknown or putative proteins with similar domain : total number*
	1dj2	Nitrogenase iron protein-like	P-loop containing nucleotide triphosphate hydrolases	15230358	Adenylosuccinate synthetase	1dj2 (48-490)	A	1:2
	1dcf	The receiver domain of the ethylene receptor	CheY-like	15219629	The receiver domain of the ethylene receptor	1dcf (605-736)	A	19:33
	1jh7	Cyclic nucleotide phospho-diesterase	Cyclic nucleotide phospho-diesterase	15234068	Putative protein	1fsi (1-181)	A	2:2
	2aak	Ubiquitin conjugating enzyme	Ubiquitin conjugating enzyme	15223746	Ubiquitin conjugating enzyme	1a3s (1-151)	A	6:12
	1vok	TATA-box binding protein (TBP), carboxy-terminal domain	TATA-box binding protein-like	15231241	TATA sequence-binding protein 1	1ais (12-198)	A	0:2
	3nul	Profilin (actin-binding protein)	Profilin (actin-binding protein)	15224838	Profilin 1	3nul (2-131)	A	0:4
	1ibj	Cystathionine synthase-like	PLP-dependent transferases	15230203	Cystathionine beta-lyase precursor	1ibj (1-464)	A	41:54
(b) PDB structures not found in FOLDLIB	PDB ID	SCOP family	SCOP superfamily	GI number	Name	Domain found	Reliability	Method
	1gp4,6	Penicillin synthase-like	Clavaminate synthase-like	15235853	Putative leucoantho-cyanidin dioxygenase	1hjg (43-350)	A	123D
	1e6b (88-220)	Glutathione S-transferases, carboxy-terminal domain	Pseudo SCOP entry by PAT (glutathione S-transferases, carboxy-terminal domain)	15226952	Putative glutathione S-transferase	1fw1 (89-193)	A	WU-BLAST
		Thioredoxin-like (glutathione S-transferases, carboxy-terminal domain)				1fw1 [1-218]	A	123D
						1fw1 [11-215]	A	WU-BLAST
	1e6b (8-87)	Thioredoxin-like				1fw1 (11-89)	A	WU-BLAST

a) The known Arabidopsis PDB ids are obtained from NCBI pdbaa FASTA file (9/1/02 release). Each PDB id is used as a query using the PAT id search field. The 'Domain found' column lists some of the domains found in the protein. Use the GI number to search the PAT web site to see all possible domain assignments. If there are multiple domain boundaries specified, only the longest possible domain boundary is listed. *Non-NR entries were also excluded in the statistics collected in the last column of the table. Only predictions with higher than C reliability (90% certainty) are included. The non-NR entries (contributed by Ceres, Inc) were absent from NR of NCBI at the time of analysis. 1gp4, 1gp6, and 1e6b were not in SCOP release 1.55 or the FOLDLIB in this study (see Table 1b). 1j6y was an NMR structure and was excluded. (b) The sequences of the three structures not in the FOLDLIB were analyzed as unknown proteins. The assignment by SCOP release 1.59 is enclosed in parenthesis. In the case of 1e6b, two distinct domains are classified by SCOP 1.59. The two regions are listed after the PDB id. In the case of 1gp4 or 1gp6, only 123D produced an A prediction correctly. In the case of 1e6b, the template is predicted correctly by both 123D and WUBLAST, but WUBLAST produced multiple domains, two of which coincides with SCOP release 1.59 assignment.

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