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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.)