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Figure 7 | BMC Bioinformatics

Figure 7

From: RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs

Figure 7

RIO output for the A. thaliana protein F12M16_14 analyzed against the Pfam ldh domain alignment (PF00056) The "Sequence" column identifies sequences in the Pfam alignment either by their SWISS-PROT "ID" or their TrEMBL "AC" [36] with added species information (the numbers after the dash are the Pfam domain boundaries added by HMMER). "Description" is the "DE" information either from SWISS-PROT or TrEMBL. The number of observed orthologies ("o"), subtree-neighborings ("n"), and super-orthologies ("s") to the query in the 100 bootstrapped trees are indicated (in %) for the sequences in the Pfam alignment. Furthermore the evolutionary distances (average number of amino acid replacements per residue calculated by maximum likelihood based on the BLOSUM 62 matrix) between the query and the sequences in the Pfam alignment are shown. For space reasons some lines of the output are not shown ("...") (the complete output is available at http://www.genetics.wustl.edu/eddy/forester/rio_analyses/RIO_paper/AT_LDH_MDH/). The output is sorted by orthology values. According to this RIO analysis the query sequence is likely to be orthologous and a subtree-neighbor to the plant sequences MDHM_BRANA and Q9SPB8_SOYBN. In addition, the query is likely to be super-orthologous to MDHM_BRANA. The bacterial sequences MDH_ECOLI and MDH_SALTY are also possibly orthologs but no subtree-neighbors. Hence, F12M16_14 is very likely to be a malate dehydrogenase and possibly mitochondrial.

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