The default BLAST Expectation thresholds used were lowered to 100 to show weaker matches.
Further weaker matches were found for bone marrow suppression (Supplemental Figure 4).
Among these, 32% show a close match to the p63 consensus (strong motif) while the remaining 41.3% are a weaker match (Additional file 1: Figure S1).
The match scores and conserved residues found within the Msx sequence of Amphimedon queenslandica (a sponge) reveal strong matches to the MH3/4 domains and much weaker matches to the MH1 and MH2 domains, that lack canonical cores amino acids.
Two DM containing proteins were confidently predicted to contain EH1-like motifs – human DMRT2 (bit score 11.6), and Drosophila dmrt11e (bit score 11.2) – these are likely orthologs; a C. elegans protein, C27C12.6 contained a weaker match (bit score 6.6).
The baculovirus Spodoptera litura NPV appears to be the most similar viral species overall in GenBank, as there were strong matches to ribonucleotide reductase subunits RR1 and RR2 and weaker matches to a number of other peptides of this viral species.
Interestingly, the sequence of the binding site for Rap1 at the silencers is distinct from the genome-wide binding profile of Rap1, being a weaker match to the consensus, and indeed is bound with low affinity relative to the consensus sequence.
Human DUSP27 is on chromosome 1q24 and, like its zebrafish ortholog, is adjacent to a gene encoding POU class 2 homeobox 1. Zebrafish dusp27 has a weaker match (43% identity over 169 amino acids) to the human gene dual specificity phosphatase and pro isomerase domain containing 1 (DUPD1, HUGO #23481, GenBank NM_001003892 on chr. 10q22).
(Percentages do not add up to 100% because of a very small number of probe sets with weak matching to multiple clones53).
Weak matching rules for a quasicrystalline tiling are local rules that ensure that fluctuations in "perp-space" are uniformly bounded.
