While the order of SBs tends to be conserved, the lengths of corresponding SBs relative to each other vary greatly in homoeologous pairs (Fig. 2).
Proteasomal inhibition regained the truncated fragment of XIAP and no accumulation of the full-length XIAP could be detected, whereas zDEVD treatment could inhibit the cleaved fragment of XIAP and conserved the full-length XIAP.
In all insects analyzed so far sizes of the mature RNA are conserved, while the length of the overall repeat usually represents a multiple of a nucleosome length (core plus spacer).
Overall, the structure of the VP2 S domain appears well conserved, but the length of the β-strands and the loops constituting the P domain appear to be very different when compared to their IBDV and IPNV homologues.
In several cases, the homologous WDR proteins are highly conserved throughout the length of the proteins, and appear to operate in highly analogous mechanisms, with specificity in function conferred by changes in upstream signaling pathways and/or downstream effectors.
A-G repeat sequences are reported in Additional file 2. In BAP proteins found in wholly-sequenced A. baumannii genomes (Fig. 1), the NH2 region is conserved, the COOH region varies in length because either 2 or 4 copies of the EFG module are present (Additional file 2).
The conserved proteins are, on average, longer than the poorly conserved ones, and the length distributions for the poorly conserved proteins have a relatively narrow peak, in contrast to the conserved proteins whose lengths spread over a wider range of values.
Within ORFs, errors may result in frame-shifting and premature stop codons; those that conserve the ORF change the length of the protein, often (but not always) without major functional consequences.
Noticing the remarkable high conservation of some amino acids and even of the conserved (short) length of ICL1 within GPCRs, our results about the G-protein sensitivity of ICL1 might also be important for other GPCRs.
Two parameters must be selected to begin the analysis: 1) motif match length: the desired conserved sequence motif length to search for in the analysis, 2) mismatches: the number of base mismatches allowed between two nearly-conserved sequence motifs without disqualification.
