TABLE 1.
Definitions of terms used
| Term | Description |
|---|---|
| Finished genomes | Organisms whose genomes have been fully sequenced; also referred to as “complete genomes” |
| LGT | Lateral gene transfer; any transfer of genetic material between cells which do not have a direct parent-offspring relationship; the term “horizontal gene transfer” is also frequently used |
| Character state | Phylogenetic term for a heritable trait (character) that can have different states; thus, prephenate dehydrogenase is a “character” that can have alternative “states” of being present or absent, of being fused with another protein or not fused with another protein, or of having either a lysine or an arginine residue at position 73, etc. |
| Substrate ambiguity | Descriptive of an enzyme having broad substrate specificity, i.e., able to utilize two or more related compounds as alternative substrate reactants |
| Homologs | Genes descended from a common ancestor; three types of homologs include paralogs, which originate in a common cell via gene duplication, orthologs, which originate by speciation, and xenologs, which originate via LGT |
| Phylogenetic tree | Multiple branches extend divergently from the nodes of a phylogenetic tree; if a single branch is used to represent the tree at a node position, it is said to be collapsed; restoration is achieved by expansion of the tree at that node position |
| Lower Gammaproteobacteria | Informal superorder designation for the class Gammaproteobacteria that is based upon many varied character states of aromatic amino acid biosynthesis; so far, this includes the orders Enterobacterales, Pasteurellales, and Vibrionales and all of the Alteromonadales (except for the family Alteromonadaceae) |
| Upper Gammaproteobacteria | Informal superorder designation for the class Gammaproteobacteria that is based upon many varied character states of aromatic amino acid biosynthesis; so far, this includes the orders Chromatiales, Oceanospirillales, Pseudomonadales, and Xanthomonadales and the family Alteromonadaceae of the Alteromonadales |
| Indels | Collective term for insertions or deletions that account for unmatched regions when amino acid sequence alignments are performed |
| Cohesion group | Collection of a given protein from various organisms whose amino acid sequences assemble as a compact cluster on a phylogenetic tree; the protein tree of adequately populated cohesion groups will generally parallel a section of a 16S rRNA phylogenetic tree, thus rigorously supporting a vertical genealogy (derivation from a common ancestor); organisms having occasional cohesion group members that are inconsistent with the 16S rRNA expectations have been the recipient of LGT originating from some organismal source represented by the cohesion group lineage |
| Supercohesion group | For each of many organisms, the sequences of multiple proteins in a biochemical pathway (e.g., the seven Trp pathway proteins) can be joined together in the same order (concatenated) prior to multiple alignment in order to provide a more powerful basis for cohesion group analysis |
| Xenolog intruder | Sequence member of a cohesion group encoded by a gene which arrived in its host organism via LGT; the donor organism can be assumed to be somewhere within the specific lineage defined by the cohesion group members |
| TyrA protein family | Dehydrogenase enzyme family, members of which function almost exclusively for l-tyrosine biosynthesis; the family exhibits widely variable substrate and cofactor specificities |
| TyrAα and TyrAβ | Two assemblages of TyrA cohesion groups which comprise distinct subhomology groups of the global TyrA protein tree |
| TyrAa | TyrA enzyme that is specific for l-arogenate (arogenate dehydrogenase) |
| TyrAp | TyrA enzyme that is specific for prephenate (prephenate dehydrogenase) |
| TyrAc | TyrA enzyme that can accept either prephenate or l-arogenate as substrate (cyclohexadienyl dehydrogenase) |