The film interested me because of many comparable similarities today and because the father of close childhood friends of mine had been included on the Hollywood-blacklist.
We also manually examined the BLAST results to ensure that there were no hits to other species at comparable similarities.
In addition, comparable similarities are observed to very different type I PKS enzymes, such as those involved in the secondary metabolism (e.g. 32% identity of POR_0548 with AnaF from the anatoxin-a synthetase gene cluster).
The results obtained with ECFP4 (Additional file 1: Table S2), demonstrate that this fingerprint was not helpful to identify and classify data sets by their structural diversity, giving comparable similarity values.
BLAST (tblastn) analysis groups SiMA closest to the S. uberis lactoferrin binding protein, Lbp (32% identity, 49% positive) [30] and the S. dysgalactiae subsp. dysgalactiae (GCS) M-like protein, DemA (31% identity, 51% positive) [31], though SiMA has near comparable similarity to a number of other streptococcal M family proteins (Fig. 1A).
In addition to a significant speed improvement, our method produced comparable similarity scores to the established method.
The discrepancy of gene and species tree may be caused by the overall comparable similarity of the GbX proteins which ranges from 70%to88%8% (based on BLOSUM62).
Comparable similarity scores, e.g. scores expressed as a percentage, so users can easily assess how close a suggested match is to their data, and decide on a cut-off to automatically accept matches.
To obtain comparable similarity values for molecules of arbitrary sizes the result S A, B) of the OA is normalized to a range of [0,1] by Equation 3. (3) S OA (A, B ) = S (A, B ) S (A, A ) S (B, B ) An example of an OA of two molecular graphs is visualized in Figure 1a.
Several iterations of SORTA-user interviews resulted in the identification of the following user requirements: Comparable similarity scores, e.g. scores expressed as a percentage, so users can easily assess how close a suggested match is to their data, and decide on a cut-off to automatically accept matches.
For example, residues 335 467 of yPrp3CTF spatially align with cow AcyP (PDB ID 2ACY; Figure 3 figure supplement 2C) with a RMSD of 2.5 Å over 90 common Cα atoms (Z-score 10.1) and show a comparable similarity to the BLUF domain of the BlrB photoreceptor from Rhodobacter sphaeroides (PDB ID 2BYC; RMSD of 2.0 Å for 84 common Cα atoms; Z-score of 10.0; Figure 3 figure supplement 2D).
