TABLE 1.
Distribution of PPX proteins encoded by 67 completed genomes
| Taxonomy | Organisma | Accession no. for PPX proteinb |
|---|---|---|
| Archaea (Crenarchaeota) | Aeropyrum pernix | |
| Archaea (Crenarchaeota) | Pyrobaculum aerophilum | |
| Archaea (Crenarchaeota) | Sulfolobus solfataricus | NP_342652 (417) |
| Archaea (Crenarchaeota) | Sulfolobus tokodaii | NP_377507 (417) |
| Archaea (Euryarchaeota) | Archaeoglobus fulgidus | NP_069590 (322) |
| Archaea (Euryarchaeota) | Halobacterium sp. strain NRC-1 | |
| Archaea (Euryarchaeota) | Methanococcus jannaschii | NP_247590 (307) |
| Archaea (Euryarchaeota) | Methanothermobacter thermoautotrophicus | |
| Archaea (Euryarchaeota) | Pyrococcus abysii | |
| Archaea (Euryarchaeota) | Pyrococcus horikoshii | |
| Archaea (Euryarchaeota) | Thermoplasma acidophilum | |
| Archaea (Euryarchaeota) | Thermoplasma volcanium | |
| Aquificales | Aquifex aeolicus | NP_213602.1 (312) |
| Cyanobacteria | Nostoc sp. strain PCC 7120 | NP_487592 (550) |
| Cyanobacteria | Synechocystis sp. strain PCC 6803 | NP_442969 (540) |
| Planctomyces or Chlamydia | Chlamydia trachomatis | |
| Firmicutes (low G+C) | Staphylococcus aureus | NP_372443 (309)c |
| Firmicutes (low G+C) | Bacillus subtilis | NP_391935 (309)d |
| Firmicutes (low G+C) | Bacilus halodurans | NP_242259 |
| Firmicutes (low G+C) | Clostridium acetobutylicum | NP_347258 (499), NP_348756 (310) |
| Firmicutes (low G+C) | Clostridium perfringens | NP_562578 (502) |
| Firmicutes (low G+C) | Lactococcus lactis | NP_267969 (314)d |
| Firmicutes (low G+C) | Listeria innocua | NP_470822 (308)c |
| Firmicutes (low G+C) | Listeria monocytogenes | NP_464973 (308)c |
| Firmicutes (low G+C) | Mycoplasma genitalium | |
| Firmicutes (low G+C) | Mycoplasma pneumoniae | |
| Firmicutes (low G+C) | Mycoplasma pulmonis | |
| Firmicutes (low G+C) | Streptococcus pneumoniae | NP_358982 (311)d |
| Firmicutes (low G+C) | Streptococcus pyogenes | NP_268701 (311)d |
| Firmicutes (low G+C) | Ureaplasma urealyticum | |
| Firmicutes (high G+C) | Mycobacterium leprae | NP_302578 (339), NP_301313 (317) |
| Firmicutes (high G+C) | Mycobacterium tuberculosis | NP_335491 (319), NP_334925 (344) |
| Spirochaetales | Borrelia burgdorferi | |
| Spirochaetales | Treponema pallidum | |
| Thermotogales | Thermotoga maritima | NP_228010 (288)d |
| Thermus or Deinococcus | Deinococcus radiodurans | NP_285509 (515), NP_296296 (314) |
| α Proteobacteria | Agrobacterium tumefaciens | NP_531842 (507), NP_531319 (341) |
| α Proteobacteria | Brucella melitensis | NP_541576 (473), NP_540121 (512) |
| α Proteobacteria | Caulobacter crescentus | NP_420516 (499), NP_420425 (391) |
| α Proteobacteria | Mesorhizobium loti | NP_108461 (372), NP_108317 (511) |
| α Proteobacteria | Rickettsia conorii | NP_36029 (473) |
| α Proteobacteria | Rickettsia prowazekii | NP_220678 (470) |
| α Proteobacteria | Sinorhizobium meliloti | NP_384861 (446), NP_385294 (507) |
| β Proteobacteria | Neisseria meningitidis | NP_274476 (502) |
| β Proteobacteria | Ralstonia solanacearum | NP_519658 (527) |
| ɛ Proteobacteria | Campylobacter jejuni | NP_281544 (486) |
| ɛ Proteobacteria | Helicobacter pylori 26695 | NP_207076 (484) |
| γ Proteobacteria | Escherichia coli K-12 | NP_416997 (513), NP_418226 (494) |
| γ Proteobacteria | Haemophilus influenzae | NP_438855 (323) |
| γ Proteobacteria | Pasteurella multocida | NP_246746 (516) |
| γ Proteobacteria | Pseudomonas aeruginosa | NP_253928 (506) |
| γ Proteobacteria | Salmonella enterica | NP_457037 (513), NP_457833 (493) |
| γ Proteobacteria | Salmonella enterica serovar Typhimurium | NP_461437 (513), NP_462804 (493) |
| γ Proteobacteria | Vibrio cholerae | NP_230371 (523), NP_229959 (497), NP_231323 (301) |
| γ Proteobacteria | Xylella fastidiosa | NP_299867 (508) |
| γ Proteobacteria | Yersinia pestis | NP_406345 (519) |
| Eucarya (Arthropoda) | Drosophila melanogaster | AAF45743 (405) |
| Eucarya (Ascomycota) | Saccharomyces cerevisiae | NP_0111262 (588), NP_012071 (397) |
| Eucarya (Ascomycota) | Schizosaccharomyces pombe | NP_594390 (384) |
| Eucarya (Nematoda) | Caenorhabditis elegans | |
| Eucarya (Microsporidia) | Encephalitozoon cuniculi | |
| Eucarya (Chordata) | Homo sapiens | |
| Eucarya (Chordata) | Mus musculus | |
| Eucarya (Chordata) | Rattus norvegicus | |
| Eucarya (Chordata) | Danio rerio (zebra fish) | |
| Eucarya (Chordata) | Fugu rubripes (torafugu fish) | |
| Eucarya (Embryophyta) | Arabidopsis thaliana | AAC24085 (568) |
a
Genomes are available at NCBI Genome Entrez (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db = Genome). One constraint imposed was that the alignment must stretch over approximately the entire sequence length retrieved.
b
Most of the PPX proteins listed are putative. Accession numbers are from the NCBI database. The reciprocal best-hit relationship between each protein and the PPX families was confirmed for all sequences. The total lengths of the amino acid sequences are given in parentheses.
c
More divergent sequences were obtained from a BlastP search against the A. fulgidus PPX sequence for an amino acid expect (e) value of ≤10−50.
d
More divergent sequences were obtained from COG 0248 and COG1227 of the clusters of orthologous groups of proteins (COG) database at NCBI.