Table 1. Representative TyrA sequences for 58 cohesion groups
Cohesion group Source of TyrA sequence Acronyma SEED: fig & peg number gi numberb Taxon groupc
TyrCG-1 Erwinia carotovora Ecar fig|218491.3.peg.2590 50122273* lower-Gammaproteobacteria (“class”)
TyrCG-2 Pseudomonas putida Pput fig|160488.1.peg.1756 26988501* upper-Gamma_1proteobacteria (“subclass”)
TyrCG-3 Psychrobacter sp. PSYC fig|259536.4.peg.787 71038727* upper-Gamma_2proteobacteria (“subclass”)
TyrCG-4 Xanthomonas campestris Xcam fig|190485.1.peg.1454 21230932* upper-Gamma_3proteobacteria (“subclass”)
TyrCG-5 Alkalilimnicola ehrlichei Aehr NA 114320089 upper-Gamma_4proteobacteria (“subclass”)
TyrCG-6 Marinobacter aquaeolei Maqu NA 77952716 upper-Gamma_5proteobacteria (“subclass”)
TyrCG-7 Burkholderia xenovorans Bxen fig|36873.1.peg.4890 91784814* Beta_1proteobacteria (“subclass”)
TyrCG-8 Bordetella pertussis Bper_1 fig|257313.1.peg.827 33592104* Beta_2proteobacteria (“subclass”)
TyrCG-9 Neisseria gonorrhoeae Ngon fig|242231.4.peg.1532 59801853* Beta_3proteobacteria (“subclass”)
TyrCG-10 Polaromonas sp. POLA fig|296591.1.peg.2815 91787673* Beta_4proteobacteria (“subclass”)
TyrCG-11 Nitrosomonas europaea Neur fig|228410.1.peg.323 30248354* Beta_5proteobacteria (“subclass”)
TyrCG-12 Bartonella henselae Bhen fig|283166.1.peg.1442 49476273* Alpha_1proteobacteria (“subclass”)
TyrCG-13 Wolinella succinogenes Wsuc fig|273121.1.peg.325 34482497* Epsilonproteobacteria (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: upper-Gammaproteobacteria (“subclass”) & Sphingobacteria (Class) & Alphaproteobacteria (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_2proteobacteria (“subclass”)
TyrCG-31 Gemmata obscuriglobus Gobs NA NA Planctomyceteceae (Family)
TyrCG-O Acidithiobacillus ferrooxidans Afer_4 NA NA upper-Gammaproteobacteria (“subclass”) orphan
TyrCG-O Aquifex aeolicus Aaeo fig|224324.1.peg.1217 15606822* Aquificae (Phylum) orphan
TyrCG-O Azoarcus sp. AZOA fig|76114.4.peg.1423 56475924* Betaproteobacteria (“subclass”) orphan
TyrCG-O Chromobacterium violaceum Cvio fig|243365.1.peg.3407 34498862* Betaproteobacteria (“subclass”) orphan
TyrCG-O Dechloromonas aromatica Daro fig|159087.4.peg.933 71906873* Betaproteobacteria (“subclass”) orphan
TyrCG-O Desulfitobacterium hafniense Dhaf fig|49338.1.peg.2227 89334457* Clostridia (“subclass”) orphan
TyrCG-O Magnetococcus sp. MAGN_1 fig|156889.1.peg.1669 NA Unclassified Proteobacteria orphan
TyrCG-O Methylobacillus flagellatus Mfla_5 fig|265072.1.peg.206 91775427* Betaproteobacteria (“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 fig|323261.3.peg.7 77163714* upper-Gamma Proteobacteria (“subclass”) orphan
TyrCG-O Pelagibacter ubiqued Pubi fig|335992.3.peg.1115 71082920* Alphaproteobacteria (“subclass”) orphan
TyrCG-O Symbiobacterium thermophilum Sthe fig|292459.1.peg.1361 51856245* Actinobacteria (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* Betaproteobacteria (“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* Halobacteria (Class)
TyrCG-82 Ferroplasma acidarmanus Faci_1 fig|97393.1.peg.324 68141176* Thermoplasmata (Class)
TyrCG-83 Methanospirillum hungatei Mhun NA 88602324* Methanomicrobia (Class)
TyrCG-84 Sulfolobus solfataricus Ssol fig|273057.1.peg.273 15897245* Sulfolobales (Order)
TyrCG-85 Pyrobaculum aerophilum Paer_2 fig|178306.1.peg.1339 18312982* Phylogenetic mixture: Thermoprotei (Class) & Thermococcaceae (Family)
TyrCG-86 Archaeoglobus fulgidus Aful_1 fig|224325.1.peg.224 11497843* Phylogenetic mixture: Archaeoglobi (Class) & Nanoarchaeota (Phylum)
TyrCG-95 Arabidopsis thaliana 1Atha fig|3702.1.peg.1877 15218283* Viridiplantae (Kingdom)
TyrCG-98 Saccharomyces cerevisiae Scer fig|4932.3.peg.431 6319643* 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. Multiple TyrA species in a single organism are distinguished by numbers preceding the acronym. .
http://www.aropath.lanl.gov/Organisms/Acronyms_sorted_by_species.html)
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). In our treatment, Gammaptoteobacteria can be
thought of as the equivalent of a Superclass, with lower-Gammaproteobacteria and upper-Gammaproteobacteria being elevatd to the taxon level of Class. The designation “subclass”
indicates cohesion groups that partition within a formal class. Thus, for example, the Betaproteobacteria (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.