According to the classification of the MCF secondary structure region (Additional file 1), TR has the most conservative sequence with an identity of 70.44%, while the average identities of LOOP135 (loop3, loop5, loop5) and NCLOOP24 (n, c, loop2, loop4) (Additional file 1) are only 42.24% and 19.25%, respectively.
Since murine desmin, compared to human desmin, lacks a serine at position 82 (Fig. S1a), murine R349 is the ortholog of human R350 (both proteins further differ in 11 conservative amino acid changes; sequence identity is 97%%).
To assign functional conservation by 7-nt seed sequence identity is a conservative strategy.
We clustered the M. abscessus homologous genes using orthoMCL [ 28] on the translated protein sequences of all predicted genes with a conservative parameter value of 50% sequence identity.
As our dataset comprises relatively closely related organisms we chose a conservative parameter value of 50% sequence identity for the clustering.
Using orthoMCL [ 28] with a conservative parameter value of 50% sequence identity, we categorized these 70,309 proteins into 6,153 orthologous protein groups, including 3,947 core-genome groups and 55 strain-specific groups.> The average percentage of amino-acid sequence identity (AAI) of core proteins was determined as previously described [ 29].
Human ILBP binds bile acid derivatives in a well-characterised 2 1 ligand:protein complex, however, we show that the highly homologous rabbit ILBP (82% sequence identity) with seven conservative substitutions preferentially binds multiple conjugated deoxycholate ligands in a novel 3 1 binding mode essentially within the same β-clam shell structure.
However, we favor a more conservative approach since the correlation of sequence identity and hybridization signal ratios is known to become weaker with increasing sequence divergence [ 42, 47] resulting in impaired biological relevance of data from spots with low hybridization signals.
Since these cases are hard to detect automatically, we used a conservative approach by considering a threshold of 50% sequence identity.
Other significant partial hits (i.e., alignment of fragments of 60 120 residues with ~30% sequence identity and 40 60% identity plus conservative substitution with minimal to modest gapping) include FMLP receptors (human and mouse), LSH receptor (human and pig), melanocortin-3 receptor (rat), and metabotropic glutamate receptor 5 (rat).
