Table 2

Detailed analysis of non-transposable element, repeated sequences in three P. triticina BAC clones
ORF Size bp Pgtrepeats Conserved domain % Ident Exp* Dominant peptide Notes
1F16-a 757 35 194-443 51 no 9.2% Lys 216-252-40.3% CI Winged helix DNA/RNA binding
1F16-b 458 98 97-458 40 no 11.8% Lys Highly helical
1F16-c 462 98 all 40 no 13.2% Lys 6-91-60.3% CI ubiquitin ligase
1F-16-d 489 44 344-485 48 no 10.8% Lys 3 alpha helices and 7 beta sheets in conserved domain
13.0% Ser
1F16-f 651 80 51-245 74 yes 9.2% Lys 38-163-38.7% CI oxidoreductase
HSP02-a 658 19 all 31 no 9.7% Lys
HSP02-b 299 80 35-94 68 no 9.4% Lys 32-73-80% CI metal binding protein
11.7% Ser 145-256-80% CI protease hydrolase inhibitor
HSP02-c 252 50 33-127 52 yes 11.1% Lys 33-95 53% CI DNA binding domain
10.7% Glu
HSP02 243 35 all yes 11.9% Ala Alignment in Pgt are to DNA, not protein
13.6% Ser
11.5% Thr
HSP04-a 952 74 256-470 48 no 9.9% Ala
HSP04-b 484 76 300-454 74 no none
HSP04-c 442 69 all 34 yes 9.0% Lys
HSP04-d 679 81 10-351 68 no 9.3% Lys 11 alpha helices in conserved region
HSP04-e 420 131 55-386 55 yes 9.5% ala 216-388-51% identical in Mlp
HSP04-f 262 474 20-189 44 no 11.5% ser EST sequence hits
HSP04-g 543 96 all 69 yes 11.4% Lys Highly helical
9.0% ser
HSP04-h 262 66 199-258 65 yes 12.6% Lys P-loop NTPase/DEAD box
HSP04-i 326 20 127-242 34 yes 12.8% Lys Highly helical
11.0% Glu
HSP04-j 309 69 191-303 35 no 9.7% Lys 2-191-99.7% CI Recombinant DNA binding/ RAD54 like
10.7% Ser

Each was evaluated for number of repeated homologs in the Pgt genome, region of conservation, alignment identity, expression in infected tissue, the dominant peptides, and their best detected fit to a protein structural model.

* Exp - expression in infected tissue 6 dpi.

** PHYRE 2.0 confidence interval (CI) of protein segment matching a structural model with the listed function [35].

Fellers et al.

Fellers et al. BMC Genomics 2013 14:60   doi:10.1186/1471-2164-14-60

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