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For a peptidase, such as the lysosomal cysteine peptidase cathepsin B, no clear sequence motif for substrate binding has emerged, despite the identification of hundreds of cleavages sites in substrates (7).
No clear sequence preference was observed, similar to previous observations with the isolated PWWP domain of Dnmt3b but with one order of magnitude weaker affinity.
The metazoan fourth subunits are ∼3 fold larger and bear no clear sequence similarity to the fourth subunit previously identified in yeast.
MVB-12 is conserved among metazoans, but is ∼3 fold larger and bears no clear sequence similarity to the yeast protein Mvb12p.
For the 42 SNO sites that can be mapped into PDB structures, we found no clear sequence motif around the sites (shown at the center of the window of 21 residues) (Figure 5).
These results suggest that although the fourth yeast protein is ∼3 fold smaller and exhibits no clear sequence homolog with its metazoan counterparts, there may be some commonalities in function between the yeast and metazoan fourth subunits.
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Although we identified no clear sequence-based marker for the first two infection types, we could conservatively estimate the fraction of extrachromosomal prophages by identifying plasmid partition genes (ParA and ParB, Davis et al., 1992; Saint Girons et al., 2000; see Figure 3 figure supplement 1 for an example of a putative extrachromosomal prophage displaying ParA-ParB genes).
Because of the complex nature of the translocations and deletions of both alleles in the second case, no clear sequencing product on genomic DNA could be obtained.
No clear sequences matching the iron responsive element (IRE) motifs, commonly found in mammalian SLC11A2, were identified in any of the 3' regions of either slc11a2-α or slc11a2-β.
Interestingly, this show about logic is installed in a maze of nooks and compartments that have no clear, directive sequence.
While no clear consensus sequence, structure or mechanism has been reported yet among the potyviral elements, more thorough studies are needed to fill in the gap of knowledge.
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