Table 1. Representative TyrA sequences for 58 cohesion groups

 

Cohesion

group

Source of TyrA sequence

Acronyma

SEED: fig & peg

number

gib

number

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

Xantomonas 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) & Proteobacteria: (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

Azoarcuss 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

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*

Betaproteobacteria (“subclass”) orphan

TyrCG-O

Methylococcus capsulatus

Mcap_1

fig|243233.4.peg.782

53804254*

upper-Gammaproteobacteria (“subclass”) orphan

TyrCG-O

Microbulbifer degradans

Mdeg

fig|203122.1.peg.1111

90021791*

upper-Gammaproteobacteria (“subclass”) orphan

TyrCG-O

Nitrosococcus oceani

Noce_1

fig|323261.3.peg.7

77163714*

upper-Gammaproteobacteria (“subclass”) orphan

TyrCG-O

Pelagibacter ubiquea

Pubi

fig|335992.3.peg.1115

71082920*

Alphaproteobacteria (“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*

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

8602324*

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  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).   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.