Table 3

Distribution of urea amidolyase and related proteins in eubacterial species.a

Enzymesb


Phylum or Class

Species

UA

UC

Ac

Ureased


Alphaproteobacteria

Caulobacter crescentus NA1000

-

1

1*

-

Asticcacaulis excentricus CB 48

-

1

1*

-

Sinorhizobium medicae WSM419

-

-

-

α,β,γ

Betaproteobacteria

Achromobacter piechaudii ATCC 43553

-

1

1*

-

Bordetella pertussis Tohama I

-

-

-

α,β,γ

Nitrosomonas europaea ATCC 19718

-

1

-

-

Neisseria meningitidis FAM18

-

-

-

-

Burkholderia sp. CCGE1001

-

1

1*

α,β,γ

Gammaproteobacteria

Escherichia coli O111:H- str. 11128

-

-

-

α,β,γ

Yersinia pestis Angola

-

-

-

α,β

Haemophilus influenzae 86-028NP

-

-

-

α,β,γ

Pantoea ananatis LMG 20103

1

1

(1)

-

Pantoea sp. At-9b

-

2

1*

-

Shewanella oneidensis MR-1

-

-

-

-

Pseudomonas aeruginosa LESB58

-

-

-

α,β,γ

Coxiella burnetii Dugway 5J108-111

-

-

-

-

Pectobacterium carotovorum subsp. carotovorum PC1

-

2

1*

-

Xanthomonas campestris pv. campestris str. B100

-

-

-

-

Cellvibrio japonicus Ueda107

-

2

1*

-

Teredinibacter turnerae T7901

-

1

1*

α,β,γ

Marinomonas sp. MED121

-

1

1*

α,γ

Klebsiella pneumoniae 342

-

1

1*

α,β,γ

Pseudomonas fluorescens SBW25

-

-

-

α,β,γ

Deltaproteobacteria

Geobacter sp. M21

-

-

-

-

Sorangium cellulosum 'So ce 56'

-

1

-

α,β/γ

Epsilonproteobacteria

Helicobacter pylori B38

-

-

-

α,β/γ

Wolinella succinogenes DSM 1740

-

1

1+

-

Acidobacteria

Acidobacterium capsulatum ATCC 51196

-

-

-

-

Solibacter usitatus Ellin6076

-

1

1*

-

Cyanobacteria

Synechococcus sp. PCC 7002

-

-

-

α,β,γ

Gloeobacter violaceus PCC 7421

-

1

1+

-

Cyanothece sp. PCC 7425

-

1

1

α,β,γ

Deinococcus-Thermus

Thermus thermophilus HB8

-

-

-

-

Deinococcus deserti VCD115

-

-

-

-

Chloroflexi

Dehalococcoides ethenogenes 195

-

-

-

-

Aquificae

Aquifex aeolicus VF5

-

-

-

-

Thermotogae

Thermotoga maritima MSB8

-

-

-

-

Fusobacteria

Fusobacterium nucleatum subsp. Nucleatum ATCC 25586

-

-

-

-

Verrucomicrobia

Verrucomicrobium spinosum DSM 4136

-

1

1*

α,β,γ

Chlamydiae

Chlamydophila pneumoniae CWL029

-

-

-

-

Chlamydia trachomatis B/TZ1A828/OT

-

-

-

-

Bacterioidetes

Porphyromonas gingivalis W83

-

-

-

-

Chlorobi

Chlorobium limicola DSM 245

-

-

-

-

Fibrobacteres

Fibrobacter succinogenes subsp. succinogenes S85

-

-

-

-

Actinobacteria

Mycobacterium tuberculosis F11

-

-

-

α,β,γ

Corynebacterium aurimucosum ATCC 700975

-

-

-

-

Streptomyces avermitilis MA-4680

-

1

1*

α,β,γ; α,β/γ

Bifidobacterium longum subsp. infantis ATCC 15697

-

-

-

α,β/γ

Spirochaetes

Borrelia burgdorferi ZS7

-

-

-

-

Treponema denticola ATCC 35405

-

-

-

-

Planctomycetes

Rhodopirellula baltica SH 1

-

-

-

-

Firmicutes

Clostridium botulinum A2 str. Kyoto

-

-

-

-

Mycoplasma hyopneumoniae 7448

-

-

-

-

Streptococcus pneumoniae 70585

-

-

-

-

Bacillus anthracis str. CDC 684

-

-

-

-

Roseburia intestinalis L1-82

-

1

1*

-


aSee Additional file 7 for the sequence sources.

bSee Figure 1 for the enzyme name abbreviations. The number of sequences found from each genome is shown. '-' indicates that no similar sequence was found.

cThe amidase gene located next to (within 200 bp) the urea carboxylase gene is indicated with *. The amidase gene located close to (within 6,500 bp) but not next to the urea carboxylase gene is indicated with +. See Additional file 8 for the distance between the genes. The amidase sequences that are a part of the urea amidolyase sequences are shown in parentheses.

dFor urease, the search results for three subunits (α, β, or γ) are shown. β/γ indicates that the β and γ subunits are fused into one gene.

Strope et al. BMC Evolutionary Biology 2011 11:80   doi:10.1186/1471-2148-11-80

Open Data