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Three cell lysis proteins were well-conserved including a murein-transglycosylase (conserved in 33 phages) and two holins (each conserved in 27 phages).
d Number of identified peptides contained in each conserved motif.
Constraints derived from this left null space basis are a fundamental part of kinetic modelling because the amount of each conserved moiety is time-invariant [41].
Each conserved moiety corresponds to a particular identifiable molecular substructure that is invariant with respect to the chemical transformations of that network.
The 7 kb proximal promoter sequences of genes in each conserved co-expression cluster were retrieved from the Promoser database (biowulf.bu.edu/zlab).
To test this possibility, we performed deletion analyses, where the contribution of each conserved motif to silencing of the white-reporter was determined in ectopic targeting experiments.
Each conserved non-coding sequence (CNS) plus the subsets of human- chimp- and mouse-specific accelerated regions were obtained from [19].
Where the current studies compare contiguous regions of gp120, this approach would generate individual scores for each conserved and variable region on the samples.
We compare it to estimates obtained either by assuming that each (conserved) gene has the same chance to be a target of a given factor or by assuming that each conserved sequence position has an equal chance to be a binding site of the factor.
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If a 50 nt margin was allowed for each conserved region, the number of conserved SO-IPAC, A-IPAC, and SE-IPAC increased to 379, 2115, and 3673, respectively (Additional file 1: Figure S8B).
Each conserved region is composed of three individual conserved sequence blocks (CSB-1, CSB-2, and CSB-3) each of which are broadly conserved [ 23].
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