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Table 1. Sources & properties of representative sequences for TyrA cohesion groups
Cohesion group	Source of TyrA sequence	Acronyma	SEED: fig & peg number	gi numberb	Taxon placement of non-LGT membersc
TyrCG-1 β	Erwinia carotovora	Ecar	fig|218491.3.peg.2590	50122273*	lower-Gammaproteobacteria (4 Orders)
TyrCG-2 α	Pseudomonas putida	Pput	fig|160488.1.peg.1756	26988501*	upper-Gamma_1proteobacteria (Pseudomonadaceae Family)
TyrCG-3 α	Psychrobacter sp.	PSYC	fig|259536.4.peg.787	71038727*	upper-Gamma_2proteobacteria (Moraxellaceae Family)
TyrCG-4 β	Xanthomonas campestris	Xcam	fig|190485.1.peg.1454	21230932*	upper-Gamma_3proteobacteria (Xanthomonadaceae Family)
TyrCG-5 α	Alkalilimnicola ehrlichei	Aehr	fig|187272.6.peg.896	114320089	upper-Gamma_4proteobacteria (Chromatiales Order)
TyrCG-6 α	Marinobacter aquaeolei	Maqu	NA	77952716	upper-Gamma_5proteobacteria (2 Orders)
TyrCG-7 α	Burkholderia xenovorans	Bxen	fig|36873.1.peg.4890	91784814*	Beta_1proteobacteria (Burkholderiaceae Family)
TyrCG-8 α	Bordetella pertussis	Bper_1	fig|257313.1.peg.827	33592104*	Beta_2proteobacteria (Alcaligenaceae Family)
TyrCG-9 α	Neisseria gonorrhoeae	Ngon	fig|242231.4.peg.1532	59801853*	Beta_3proteobacteria (Neisseriaceae Family)
TyrCG-10 α	Polaromonas sp.	POLA	fig|296591.1.peg.2815	91787673*	Beta_4proteobacteria (Comamonadaceae Family)
TyrCG-11 α	Nitrosomonas europaea	Neur	fig|228410.1.peg.323	30248354*	Beta_5proteobacteria (Nitrosomonadaceae Family)
TyrCG-12 α	Bartonella henselae	Bhen	fig|283166.1.peg.1442	49476273*	Alpha_1proteobacteria (Most Orders)
TyrCG-13 α	Wolinella succinogenes	Wsuc	fig|273121.1.peg.325	34482497*	Flavobacteria Class
TyrCG-14 α	Geobacter sulfurreducens	Gsul	fig|243231.1.peg.2590	39997701*	Delta_1proteobacteria (Desulfuromonadales Order)
TyrCG-15 β	Desulfovibrio desulfuricans	Ddes	fig|207559.3.peg.3693	78358524*	Delta_2proteobacteria (Desulfovibrionales Order)
TyrCG-16 α	Synechocystis sp.	SYNE_3	fig|1148.1.peg.1391	16330562*	Cyanobacteria Phylum
TyrCG-17 α	Thermobifida fusca	Tfus	fig|269800.4.peg.764	72161612*	Actinobacteridae Subclass
TyrCG-18 α	Lactobacillus plantarum	Lpla	fig|220668.1.peg.1693	28271503*	Bacilli Class
TyrCG-19 α	Clostridium difficile	Cdif	fig|1496.1.peg.2965	115250885*	Clostridia_1 (Clostridiales Order)
TyrCG-20 α	Clostridium thermocellum	Cthe_5	fig|203119.1.peg.2939	67874921*	Clostridia_2 (2 Orders)
TyrCG-21 α	Moorella thermoacetica	Mthe_3	fig|264732.1.peg.2464	83590180*	Clostridia_3 (2 Orders)
TyrCG-22 α	Deinococcus radiodurans	Drad	fig|243230.1.peg.1305	6458858*	Deinococci Class
TyrCG-23 β	Bacteroides thetaiotaomicron	Bthe_9	fig|226186.1.peg.3931	29341249*	Bacteroidetes Class
TyrCG-24 α	Chlorobium tepidum	Ctep	fig|194439.1.peg.84	21672925*	Chlorobia Class
TyrCG-25 α	Petrotoga miotherma	Pmio	NA	NA	Unresolved phylogenetic mixture
TyrCG-26 β	Coxiella burnetii	Cbur	fig|227377.1.peg.935	29654299*	Unresolved phylogenetic mixture
TyrCG-27 α	Rhodopirellula baltica (Pirellula sp.)	Rbal	fig|243090.1.peg.3009	32473675*	Unresolved phylogenetic mixture
TyrCG-28 α	Leptospira interrogans	Lint_1	fig|267671.1.peg.2379	45658293*	Unresolved phylogenetic mixture
TyrCG-29 β	Dehalococcoides ethenogenes	Deth	fig|243164.3.peg.722	57234714*	Chloroflexi Phylum
TyrCG-30 β	Rhodospirillum rubrum	2Rrub_1	fig|1085.1.peg.3401	83592308*	Alpha_2proteobacteria (2 Orders)
TyrCG-31 α	Gemmata obscuriglobus	Gobs	NA	NA	Planctomyceteceae Family
TyrCG-O α	Acidithiobacillus ferrooxidans	Afer_4	NA	NA	upper-Gammaproteobacteria orphan
TyrCG-O α	Aquifex aeolicus	Aaeo	fig|224324.1.peg.1217	15606822*	Aquificae orphan
TyrCG-O α	Azoarcus sp.	AZOA	fig|76114.4.peg.1423	56475924*	Betaproteobacteria orphan
TyrCG-O α	Chromobacterium violaceum	Cvio	fig|243365.1.peg.3407	34498862*	Betaproteobacteria orphan
TyrCG-O α	Dechloromonas aromatica	Daro	fig|159087.4.peg.933	71906873*	Betaproteobacteria orphan
TyrCG-O α	Desulfitobacterium hafniense	Dhaf	fig|49338.1.peg.2227	89334457*	Clostridia orphan
TyrCG-O α	Magnetococcus sp.	MAGN_1	fig|156889.1.peg.1669	NA	Unclassified Proteobacteria orphan
TyrCG-O α	Methylobacillus flagellatus	Mfla_5	fig|265072.1.peg.206	91775427*	Betaproteobacteria orphan
TyrCG-O α	Methylococcus capsulatus	Mcap_1	fig|243233.4.peg.782	53804254*	upper-Gamma Proteobacteria orphan
TyrCG-O α	Microbulbifer degradans	Mdeg	fig|203122.1.peg.1111	90021791*	upper-Gamma Proteobacteria orphan
TyrCG-O α	Nitrosococcus oceani	Noce	fig|323261.3.peg.7	77163714*	upper-Gamma Proteobacteria orphan
TyrCG-O α	Pelagibacter ubiqued	Pubi	fig|335992.3.peg.1115	71082920*	Alphaproteobacteria orphan
TyrCG-O α	Symbiobacterium thermophilum	Sthe	fig|292459.1.peg.1361	51856245*	Firmicutes orphan
TyrCG-O β	Syntrophobacter fumaroxidans	Sfum_1	fig|335543.6.peg.3883	71548230*	Syntrophobacterales orphan
TyrCG-O α	Syntrophomonas wolfei	Swol_1	NA	114566874*	Clostridia orphan
TyrCG-O β	Thermodesulfobacterium commune	Tcom	NA	NA	Thermodesulfobacteria orphan
TyrCG-O α	Thermotoga maritima	Tmar	fig|243274.1.peg.339	15643112*	Thermotogae orphan
TyrCG-O α	Thiobacillus denitrificans	Tden	fig|292415.3.peg.543	74316971*	Betaproteobacteria orphan
TyrCG-80 β	Methanococcoides burtonii	Mbur	fig|259564.1.peg.2246	91773934*	Euryarchaea Phylum
TyrCG-81 β	Haloarcula marismortui	Hmar_2	fig|272569.1.peg.498	55377389*	Halobacteria Class
TyrCG-82 β	Ferroplasma acidarmanus	Faci_1	fig|97393.1.peg.324	68141176*	Thermoplasmata Class
TyrCG-83 β	Methanospirillum hungatei	Mhun	fig|323259.5.peg.1087	88602324*	Methanomicrobia Class
TyrCG-84 β	Sulfolobus solfataricus	Ssol	fig|273057.1.peg.273	15897245*	Sulfolobales Order
TyrCG-85 β	Pyrobaculum aerophilum	Paer_2	fig|178306.1.peg.1339	18312982*	Unresolved phylogenetic mixture
TyrCG-86 β	Archaeoglobus fulgidus	Aful_1	fig|224325.1.peg.224	11497843*	Unresolved phylogenetic mixture
TyrCG-95 β	Arabidopsis thaliana	1Atha	fig|3702.1.peg.1877	15218283*	Viridiplantae Kingdom
TyrCG-98 β	Saccharomyces cerevisiae	Scer	fig|4932.3.peg.431	6319643*	Fungi Kingdom
α for cohesion groups that belong to the TyrAα sub-homology group as shown in the TyrA CG tree.					TyrA tree
β for cohesion groups that belong to the TyrAβ sub-homology group as shown in the TyrA CG tree.					TyrA tree
aOrganism acronyms consist of four letters: the first letter of the genus name followed by the first three letters of the species name. Any underscore-number designations that follow the acronym proper are used to distinguish potential ambiguities, multiple TyrA species in a single organism are distinguished by numbers preceding the acronym (as implemented at AroPath).
bGene identification number. A red asterisk indicates that sequencing of the genome is essentially complete.
cAn attempt is made to describe each cohesion group at the hierarchical level at which all organisms having the sequence occupy the same taxon. NCBI’s taxonomy page is used as a resource for this. Typically, cohesion groups gather at about the level of Family or Class, but wide deviations occur in either direction (see text). In our treatment, Gammaptoteobacteria are clearly divided into two groups, with lower-Gammaproteobacteria and upper-Gammaproteobacteria being the equivalent of "Superorder" taxon designation. Thus, for example, the Betaproteobacteria (a formal class) partition into five cohesion groups which do not correspond to formal taxon subdivisions. The organism names and gi numbers are hyper-linked to the Taxonomy Browser at NCBI, the fig/peg numbers are hyperlinked to Protein Pages at the SEED.
dPelagibacter ubique is labeled as Candidatus Pelagibacter ubique in many databases. (“Candidatus” refers to an organism that cannot be maintained in a culture collection.)