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Table 1 Reference enzyme information.

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

  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
  1. 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.
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BMC Bioinformatics

ISSN: 1471-2105

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