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Valine, glutamate and threonine were present in the P3 position of multiple positive clones that exhibited strong reporter gene activity.
The end-sequences of multiple positive clones recovered from the screens were aligned on to the sequenced genome in order to identify and confirm the precise configuration of the loci involved [14].
The quality of the PWD BAC library was verified by hybridization with seven unique probes that identified multiple positive clones.
Category A and B consist of interactions supported by multiple positive clones with different (A) or identical (B) inserts.
Ten amino acids were represented in the P2 site of positive clones, but serine and threonine were particularly prominent, as they were present in multiple positive clones that exhibited strong reporter gene activity.
Out of 96 contigs anchored with SSR markers, 60 contigs could be unambiguously assigned to genomic regions, since multiple positive clones identified with a single marker or set of markers were assembled to an individual/unique contig.
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Category A and Category B comprised interactions supported by multiple positive prey clones with different (A) or identical (B) inserts.
Candidates were subcultured and verified using Southern analysis and multiple vials of positive clones were frozen in 15% glycerol at −80°C.
Positive clones were multiple re-streaked on medium and high stringency selection media (SD medium lacking Trp, Leu, His and Ade, supplemented with 2.5 mM 3-AT and 4 mg/ml X-α-gal) before purification and sequencing of the harboured plasmids.
In each set of positive clone candidates only a few clones are truly positive (TP) clones; the rest are false positive clones at multiple intersections generated when more than a single positive RP and CP are obtained by Illumina GoldenGate screening.
Among the positive clones, we found multiple cDNAs encoding for Gabarap and Gabarapl1, which we confirmed to be devoid of self-activation (Fig. 1A, and data not shown), suggesting that MAPK15 was able to interact with these proteins.
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