The most functionally informative innovation of FunnyBase is the process of culling through numerous primary similarity search results in order to identify links to systematic functional databases in GO and KEGG.
Despite diverse pigment content, primary sequence similarities indicate that all these antenna proteins originated from a common ancestral gene with one transmembrane helix [1].
This was somewhat surprising since (as already discussed) the mode of action and substrate preferences of the shrimp nuclease is much more similar to DNase I than to the DNA/RNA nonspecific nucleases which it shares primary structure similarities.
As a consequence of this immunologic "arms race," primary sequences similarities between the herpes recombinases and the RAG proteins have been selected against and thus are not readily evident, while functional similarities in the regulation, structure, and function of the respective recombinases have been relatively preserved.
In addition, in this work it is shown that some residual primary sequence similarities may still be evident between the DBP and RAG-1 protein, particularly in functional domains of the two proteins that have a high "information content" in contrast to the less conserved non-functional or spacer regions of the proteins.
Many families of AMPS have been reported from such secretions and members of each are classified on the basis of their primary structural similarities and/or the presence of well-defined structural motifs [ 1– 9].
Approximately 90% of these NFs shared primary sequence similarities to arthropod proteins, among which 26 families (NFa; 212 sequences) were found to be homologous only to sequences from arthropods but not to any proteins from non-nematode and non-arthropod species at a BLAST e-value cutoff of 1.0e-03 1.0e-03ditional file 2).
Based on primary sequence similarities, conservation patterns and phylogenetic analyses, RedCAPs formed a distinct family within the extended LHC protein superfamily that was neither more closely related to other three-helix families, like LHC, LHC-like or LHL4, nor to the four-helix PSBS family.
Based on the primary sequence similarity between RIP3 and RIP1 proteins and the conformational similarity between RIP1 and B-Raf proteins, we tested 10 commercially available protein kinase inhibitors in this assay, including eight B-Raf/B-RafV600E inhibitors, necrostatin-1 (Rinhibitoritor) and SU11248 (tyrosine protein kinase inhibitor; Table 1 and Supplementary Figure 2b).
Searching for U-snRNA candidates from Giardia based on primary sequence similarity failed, as expected, due to the observed low sequence similarity between Giardia and other well studied eukaryotes.
However, the primary sequence similarity of 10 45 50 bp introns present within or shortly downstream of E. gracilis presequences, and the similarity between the 86 bp intron in the Lhcb and the 93 bp intron in the PsbO presequences, suggest exon-shuffling rather than 'semi-exon shuffling' as a likely mechanism for the acquisition of presequences or their parts in E. gracilis.
