There were only five enzymes in which we found a motif conforming to the sequence FXFP; four of these were in kinases (PI 3-kinase δ, PI 4-kinase α, Ins(1,4,5 P3 3-kinase B, and Ins(1,3,4,5,6) 2-kinase) and only a single one was found in a phosphatase (PTEN).
Salanti et al [25] noted that this gene differs from the other var genes in that some of its domains do not conform to the sequence motif spacing-based classification schemes for CIDR and DBL domains used in other PfEMP1 proteins [26].
Two distinct binding sites are present on the AP-1 complex for target proteins: a site on the "hemi-complex" formed by the γ and σ subunits that binds to dileucine-based signals which conform to the sequence E/DxxxLφ, and a site on the μ1 subunit that binds to tyrosine-based signals which conform to the sequence Yxxφ, where φ represents a bulky hydrophobic residue [11], [12].
For other predicted precursors for which matching small RNA reads were recovered, the vast majority of reads conform to the sequences indicated in Table 1 [see also Additional File 1: Supplemental figure S3], consistent with the primary requirement for the annotation of plant miRNA sequences [ 30].
A TGGTACATATGTTCTA sequence conforming to the consensus sequence of the SOS box, which was described as a LexA binding site in C. glutamicum[ 27], was found to overlap with the −10 region of P4.
Analysis of the CRTR-1 amino acid sequence identified 2 potential sites for sumoylation, FK30QE and LK464AE, conforming to the consensus sequence, ψKXE (where ψ is a hydrophobic amino acid and X is any amino acid) [15].
An in silico analysis of upstream regions in the A1 and E2 genes demonstrates the presence of several potential forkhead binding sites conforming to the consensus sequence t(g/a TTT(g/a)(t/c) (Overdier et al., 1997; Fig. 7).
It is generally agreed that there are two major classes of PDZ domains – class I PDZ domains recognize and bind the C-termini of proteins conforming to the consensus sequence X-(S/T -X- V/I/L -COOH, while claS/T -X- V/I/L -COOHnteract with the C-terminal conS/T -X- V/I/L -COOH, where X iS/T -X- V/I/L -COOHd Φ stands for hydrophobic residue [16].
Thus it is not clear which are the negative determinant(s) preventing the phosphorylation of S511 despite its both conforming to the consensus sequence of CK2 and occupying an exposed position in NBD1 (11).
Moreover, also using Equation 2, we can obtain an overall likelihood of conforming to the event sequence, which should be useful for detecting misdiagnoses or choosing the most likely diagnosis from a selection of models for different diseases.
By analyzing the clusters described by Thomas and Emerson in their Supplemental data 1 (supp1.xls), we were struck by the fact that the reported number of zinc finger domains conforming to the consensus sequence were different from our results [ 2] and from those of the PFAM database.
