Table 1. Representative TyrA sequences for 58 Cohesion Groups

Cohesion Group	Source of TyrA sequence	Acronym^a	SEED: FIG & PEG #	gi # ^b	Taxon Group^c
TyrCG-1	Erwinia carotovora	Ecar	fig|218491.3.peg.2590	50122273*	Lower-gamma Proteobacteria (“subclass”)
TyrCG-2	Pseudomonas putida	Pput	fig|160488.1.peg.1756	26988501*	Upper-gamma_1 Proteobacteria (“subclass”)
TyrCG-3	Psychrobacter sp.	PSYC	fig|259536.4.peg.787	71038727*	Upper-gamma_2 Proteobacteria (“subclass”)
TyrCG-4	Xantomonas campestris	Xcam	fig|190485.1.peg.1454	21230932*	Upper-gamma_3 Proteobacteria (“subclass”)
TyrCG-5	Alkalilimnicola ehrlichei	Aehr	NA	114320089	Upper-gamma_4 Proteobacteria (“subclass”)
TyrCG-6	Marinobacter aquaeolei	Maqu	NA	77952716	Upper-gamma_5 Proteobacteria (“subclass”)
TyrCG-7	Burkholderia xenovorans	Bxen	fig|36873.1.peg.4890	91784814*	Beta_1 Proteobacteria (“subclass”)
TyrCG-8	Bordetella pertussis	Bper_1	fig|257313.1.peg.827	33592104*	Beta_2 Proteobacteria (“subclass”)
TyrCG-9	Neisseria gonorrhoeae	Ngon	fig|242231.4.peg.1532	59801853*	Beta_3 Proteobacteria (“subclass”)
TyrCG-10	Polaromonas sp.	POLA	fig|296591.1.peg.2815	91787673*	Beta_4 Proteobacteria (“subclass”)
TyrCG-11	Nitrosomonas europaea	Neur	fig|228410.1.peg.323	30248354*	Beta_5 Proteobacteria (“subclass”)
TyrCG-12	Bartonella henselae	Bhen	fig|283166.1.peg.1442	49476273*	Alpha_1 Proteobacteria (“subclass”)
TyrCG-13	Wolinella succinogenes	Wsuc	fig|273121.1.peg.325	34482497*	Epsilon Proteobacteria (Class) / Flavobacteria (Class)
TyrCG-14	Geobacter sulfurreducens	Gsul	fig|243231.1.peg.2590	39997701*	Desulfuromonadales (Order)
TyrCG-15	Desulfovibrio desulfuricans	Ddes	fig|207559.3.peg.3693	78358524*	Desulfovibrionales (Order)
TyrCG-16	Synechocystis sp.	SYNE_3	fig|1148.1.peg.1391	16330562*	Cyanobacteria (Phylum)
TyrCG-17	Thermobifida fusca	Tfus	fig|269800.4.peg.764	72161612*	Actinobacteridae (Subclass)
TyrCG-18	Lactobacillus plantarum	Lpla	fig|220668.1.peg.1693	28271503*	Bacilli (Class)
TyrCG-19	Clostridium difficile	Cdif	fig|1496.1.peg.2965	115250885*	Clostridia_1 (“subclass”)
TyrCG-20	Clostridium thermocellum	Cthe_5	fig|203119.1.peg.2939	67874921*	Clostridia_2 (“subclass”)
TyrCG-21	Moorella thermoacetica	Mthe_3	fig|264732.1.peg.2464	83590180*	Clostridia_3 (“subclass”)
TyrCG-22	Deinococcus radiodurans	Drad	fig|243230.1.peg.1305	6458858*	Deinococci (Class)
TyrCG-23	Bacteroides thetaiotaomicron	Bthe_9	fig|226186.1.peg.3931	29341249*	Bacteroidetes (Class)
TyrCG-24	Chlorobium tepidum	Ctep	fig|194439.1.peg.84	21672925*	Chlorobia (Class)
TyrCG-25	Petrotoga miotherma	Pmio	NA	NA	Phylogenetic mixture: Petrotoga (Genus), Dictyoglomi (Class)
TyrCG-26	Coxiella burnetii	Cbur	fig|227377.1.peg.935	29654299*	Phylogenetic mixture: Proteobacteria: Upper-gamma (Class), Sphingobacteria (Class), Proteobacteria: Alpha (Class)
TyrCG-27	Rhodopirellula baltica (Pirellula sp.)	Rbal	fig|243090.1.peg.3009	32473675*	Phylogenetic mixture: Planctomycetaceae (Family), Myxococcales (Order), Verrucomicrobia (Phylum)
TyrCG-28	Leptospira interrogans	Lint_1	fig|267671.1.peg.2379	45658293*	Phylogenetic mixture: Spirochaetes (Phylum), Fibrobacteres (Phylum)
TyrCG-29	Dehalococcoides ethenogenes	Deth	fig|243164.3.peg.722	57234714*	Chloroflexi (Phylum)
TyrCG-30	Rhodospirillum rubrum	2Rrub_1	fig|1085.1.peg.3401	83592308	Alpha_2 Proteobacteria (“subclass”)
TyrCG-31	Gemmata obscuriglobus	Gobs	NA	NA	Planctomyceteceae (Family)
TyrCG-O	Acidithiobacillus ferrooxidans	Afer_4	NA	NA	Upper-gamma Proteobacteria (“subclass”) orphan
TyrCG-O	Aquifex aeolicus	Aaeo	fig|224324.1.peg.1217	15606822*	Aquificae (Phylum) orphan
TyrCG-O	Azoarcuss sp.	AZOA	fig|76114.4.peg.1423	56475924*	Beta Proteobacteria (“subclass”) orphan
TyrCG-O	Chromobacterium violaceum	Cvio	fig|243365.1.peg.3407	34498862*	Beta Proteobacteria (“subclass”) orphan
TyrCG-O	Dechloromonas aromatica	Daro	fig|159087.4.peg.933	71906873*	Beta Proteobacteria (“subclass”) orphan
TyrCG-O	Desulfitobacterium hafniense	Dhaf	fig|49338.1.peg.2227	89334457*	Clostridia (“subclass”) orphan
TyrCG-O	Magnetococcuss sp.	MAGN_1	fig|156889.1.peg.1669	NA	Unclassified Proteobacteria orphan
TyrCG-O	Methylobacillus flagellatus	Mfla_5	fig|265072.1.peg.206	91775427*	Beta Proteobacteria (“subclass”) orphan
TyrCG-O	Methylococcus capsulatus	Mcap_1	fig|243233.4.peg.782	53804254*	Upper-gamma Proteobacteria (“subclass”) orphan
TyrCG-O	Microbulbifer degradans	Mdeg	fig|203122.1.peg.1111	90021791*	Upper-gamma Proteobacteria (“subclass”) orphan
TyrCG-O	Nitrosococcus oceani	Noce_1	fig|323261.3.peg.7	77163714*	Upper-gamma Proteobacteria (“subclass”) orphan
TyrCG-O	Pelagibacter ubique^a	Pubi	fig|335992.3.peg.1115	71082920*	Alpha Proteobacteria (“subclass”) orphan
TyrCG-O	Symbiobacterium thermophilum	Sthe	fig|292459.1.peg.1361	51856245*	Actinobacteridia (Class) orphan
TyrCG-O	Syntrophobacter fumaroxidans	Sfum_1	NA	71548230*	Syntrophobacterales (Order) orphan
TyrCG-O	Syntrophomonas wolfei	Swol_1	NA	114566874*	Clostridia (“subclass”) orphan
TyrCG-O	Thermodesulfobacterium commune	Tcom	NA	NA	Thermodesulfobacteria (Phylum) orphan
TyrCG-O	Thermotoga maritima	Tmar	fig|243274.1.peg.339	15643112*	Thermotogae (Genus) orphan
TyrCG-O	Thiobacillus denitrificans	Tden	fig|292415.3.peg.543	74316971*	Beta Proteobacteria (“subclass”) orphan
TyrCG-80	Methanococcoides burtonii	Mbur	fig|259564.1.peg.2246	91773934*	Euryarchaea (Phylum)
TyrCG-81	Haloarcula marismortui	Hmar_2	fig|272569.1.peg.498	55377389*	Euryarchaea; Halobacteria (Class)
TyrCG-82	Ferroplasma acidarmanus	Faci_1	fig|97393.1.peg.324	68141176*	Euryarchaea; Thermoplasmata (Class)
TyrCG-83	Methanospirillum hungatei	Mhun	NA	8602324*	Euryarchaea; Methanomicrobia (Class)
TyrCG-84	Sulfolobus solfataricus	Ssol	fig|273057.1.peg.273	15897245*	Crenarchaeota; Sulfolobales (Order)
TyrCG-85	Pyrobaculum aerophilum	Paer_2	fig|178306.1.peg.1339	18312982*	Phylogenetic mixture: Crenarchaeota; Thermoprotei (Class), Euryarchaea; Thermococcaceae (Family)
TyrCG-86	Archaeoglobus fulgidus	Aful_1	fig|224325.1.peg.224	11497843*	Phylogenetic mixture: Euryarchaea; Archaeoglobi (Class), Nanoarchaeota (Phylum)
TyrCG-95	Arabidopsis thaliana	1Atha	fig|3702.1.peg.1877	15218283*	Eukaryota; Viridiplantae (Kingdom)
TyrCG-98	Saccharomyces cerevisiae	Scer	fig|4932.3.peg.431	6319643*	Eukaryota; Fungi (Kingdom)

^aOrganism acronyms consist of four letters: the first letter of the Genus name followed by the first three letters of the Species name. If underscore/number designations follow the acronym proper, these are used to distinguish potential ambiguities (as implemented at AroPath http://www.aropath.lanl.gov/Organisms/Acronyms_sorted_by_species.html). Multiple TyrA species in a single organism are distinguished by numbers preceding the acronym.

^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 Class, but wide deviations occur in either direction (see text). Lower-gamma and upper-gamma Proteobacteria (our designation) can be thought of as Sub-class designations of the Proteobacteria Class. The designation “subsystem” indicates cohesion groups that partition within a formal class. Thus, for example, the Beta Proteobacteria (a formal class) partition into five cohesion groups which do not correspond to formal taxon subdivisions. For detailed information the organism names are hyper-linked to the Taxonomy Browser at NCBI.

^dPelagibacter ubique is labeled as Candidatus Pelagibacter ubique in many databases (“Candidatus” refers to an organism that cannot be maintained in a culture collection) preceding the genus/species designation.