Table 1.

Abbreviations, definitions, and key URL link to supplemental files^a

Abbreviation or term	Definition
EBs	Infectious elementary body developmental form of chlamydiae
RBs	Proliferative reticulate body developmental form of chlamydiae
Persistence	Quiescent aberrant body developmental form of chlamydiae
LGT	Lateral gene transfer
Trp	l-Tryptophan
PEP	Phosphoenolpyruvate
PRPP	Phosphoribosyl pyrophosphate
IDO	Indoleamine dioxygenase
IFN-γ	Gamma interferon
KDO	2-Keto-3-deoxyoctulosonic acid
LPS	Lipopolysaccharide
PMPs	Polymorphic membrane proteins
Trp content	Percentage of Trp residues in a given protein
p/P Trp ratio	Ratio of the Trp content of a given protein to that of the proteome
p/bdh-P Trp ratio	Ratio of the Trp content of a given protein to that fraction of the proteome that shares a best-hit homolog with another proteome to which it is being compared
Trp burden	Absolute number of Trp residues per given protein. Where an entire pathway is under consideration, the Trp burdens of individual proteins contribute to a cumulative Trp burden with respect to that pathway.
Trp hurdle	A particular step(s) in a multistep pathway that is conspicuous for having a high Trp content
Bidirectional best-hit pairs	Protein homologs from two different genomes where each is mutually the best BLAST hit returned when one is used as the query against the proteome of the other
Up-Trp selection	Evolutionary selection for increased Trp content in a given protein
Down-Trp selection	Evolutionary selection for decreased Trp content in a given protein
Achilles heel step	An enzyme in a multistep pathway whose Trp content renders the entire pathway vulnerable to Trp limitation
Master-slave mechanisms	Indirect effect of Trp content upon the expression of “slave” proteins that are dependent upon a “master” protein of high Trp content

^aSupplemental material for this article may be found at http://semiglobe.lanl.gov/supplement.php.