For the BLAST scans, functionally validated KAP-β sequences [9][15][16] and their S. cerevisiae or H. sapiens orthologues (identified as reciprocal best BLAST hits) were used as queries in BLASTp scans of the predicted proteome panel.
Components of the annotation process included Blast analyses against several databases (e.g., UniProt, Ensembl D. melanogaster-specific and An. gambiae-specific databases, Le. major genome (v4.0), an in-house "all bacterial DNA sequences" database), followed by Interpro scans of the predicted Lutzomyia proteins to identify motifs/domains.
A fingerprint scan analysis of the predicted proteins identified 2/2 motifs that define the KCNK sub-family of two-pore channels, and 3/3 motifs defining the 5 members of the TASK channel sub-family (KCNK3, KCNK5, KCNK6, KCNK15, and KCNK17) in lizard, chicken, and finch.
During this analysis, careful consideration was taken in scanning the upstream regions of the predicted translational start site to ensure proteins were not mis-annotated.
By means of Differential Scanning Calorimetry method, the predicted results were verified experimentally and the agreement between the measured and predicted values was satisfactory.
In other works, it has been shown that ϵ effect scan changes the predicted probability of collapse by 20%to30%0% for benchmark project located in the south of downtown Los Angeles (Goulet et al. 2006).
PLACE [ 31] (http://www.dna.affrc.go.jp/PLACE/signalscan.html) was employed to scan the cis-acting elements of the predicted promoter sequences for every GmPHT1 genes.
Perl regular expressions were developed to identify and measure the lengths of individual LRRs of the LRIM-like proteins and to scan the predicted protein-coding genes of each mosquito species as well as those of A. mellifera, Bombyx mori (silk moth), D. melanogaster, and Tribolium castaneum (flour beetle).
Systematic cysteine-scanning mutagenesis showed the predicted TMD of one candidate MIP, DHRS3, to be a partially buried amphipathic alpha-helix in both lipid droplet monolayers and the cytoplasmic leaflet of endoplasmic reticulum membrane bilayers.
The predicted scans will be compared directly to the reference, in order to assess the quality of the prediction.
