Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development

Table 1 Reference enzyme information.

	REFERENCE PROTEIN				BLAST THRESHOLD AND SEQUENCES USED
Gene	Enzyme	Organism	Accession Number	Reference	BLASTp e-value	Chosen enzymes for the probe design
phnA1a	Putative alpha subunit of ring-hydroxylating dioxygenase	Sphingomonas sp. CHY-1	Q65AT1	[24]	1e-40	B2Z3Z2, A2TC87, A4XDY3, 085843, A9Y004, B5L7S0, B5L7R9, Q1HCP6, Q7WUA0
phnA2a	Putative beta subunit of ring-hydroxylating dioxygenase	Sphingomonas sp. CHY-1	Q65AT0	[24]	1e-30	A2TC88, A4XDY2, 085842, B5L7R8
ahdA1c	Putative large subunit of oxygenase	Sphingomonas sp. P2	Q83VL2	[27, 32]	1e-40	A2TC29, A9XZZ2, Q65AS5
ahdA2c	Putative small subunit of oxygenase	Sphingomonas sp. P2	Q83VL1	[27, 32]	1e-30	A9XZZ3, Q65AS6, A4XDV1, 085992, A2TC30, Q9Z4T6
bphB	Putative 1,2-dihydrodiol-l,2-dihydroxy-dehydrogenase	Sphingobium xenophagum	Q9X9Q9	[25]	1e-40	Q14RW3, 085972
bphC	Putative biphenyl-2,3-diol 1,2-dioxygenase	Sphingobium xenophagum	P74836	[25]	1e-40	PI 1122, Q6LCU9, Q7DG81, A4XDU9, 085990, A9XZZ5, Q65AS8, Q9KWI2
bphA3	Putative ferredoxin component of dioxygenase	Sphingomonas yanoikuyae	A2TC31	[24, 32]	1e-20	034128, Q65AS7, A9XZZ4, A4XDV0, 085991, Q83VL0
ahdA4	Putative ferredoxin reductase component of dioxygenase	Sphingomonas yanoikuyae	A2TC59	[24, 32]	1e-40	Q83VI9, A4XDS3, 085962

Organism name and source, accession number and bibliographic reference for each reference protein. BLASTp expected threshold values used and selected sequences for multiple alignments for the probe design are given.

ISSN: 1471-2105