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Table 6 Examples of COGs conserved in euryarchaea but missing in A. pernix

From: Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs)

COG number Phylogenetic pattern* Function Comments
0101 amtks-yqvdcebrhujwgpolinx Pseudouridylate synthase (tRNA psi55) This RNA modification enzyme hitherto has been considered ubiquitous and essential [54]
1549 amtks- - - - - - - - - - - - - - - - - - - - Archaeosine tRNA-ribosyltransferase, contains PUA domain See text
2036 amtks-y- - - - - - - - - - - - - - - - - - Histones H3 and H4 In the crenarchaeon Sulfolobus solfataricus, the role of histones in maintaining DNA supercoiling appears to be relegated to the DNA-binding protein Sso7d [55]. However, A. pernix does not encode an ortholog of this protein, and the mechanism of chromatin packaging remains unclear
1933 amtks- - - - - - - - - - - - - - - - - - - - Unique archaeal DNA polymerase, large subunit This DNA polymerase is highly conserved among the euryarchaea but so far has not been seen in other taxa [15]
1311 amtks-y- - - - - - - - - - - - - - - - - - Small subunit of DNA polymerase, predicted phosphatase (calcineurin-like superfamily) The absence of this subunit, which is represented by (predicted) active phosphatases in archaea and inactivated forms in eukaryotes [37] correlates with the absence of the large subunit
1111 amtks-y- - - - - - - - - - - - - - - - - ERCC4-like helicase A typical archaeal-eukaryotic repair protein, a predicted active helicase in euryarchaea and an inactivated form in eukaryotes [39]
1107 amtks- - - - - - - - - - - - - - - - - - - - Archaea-specific RecJ-like exonuclease, ontains DnaJ-type Zn finger domain  
1243 amtks-y-v- - - - - - - - - - - - - - - - Transcription elongation factor ELP3 Consists of an amino-terminal biotin-synthase-like domain and a carboxy-terminal histone acetylase domain (only the biotin-synthase-like domain is represented in some bacteria)
0206 amtks- -qvdcebrhuj-gpol-nx Cell division GTPase FtsZ A central component of bacterial and archaeal cell-division machinery which is homologous (although only weakly similar) and functionally analogous to eukaryotic tubulins [56]. So far, among prokaryotes, FtsZ has been found missing only in Chlamydia [57].
0455 amtks- -qvdcebr-uj- - -ol-n- ATPases involved in chromosome partitioning There may be a correlation between the absence of FtsZ and the presence of only one chromosome-partitioning ATPase (the ortholog of bacterial Mrp) in A. pernix
1149 amtks- - -v- - - - - - - - - - - - - - - MinD superfamily P-loop ATPases containing an inserted ferredoxin domain  
0065 amtks-yqvdcebrh-j- - - - - -n- 3-Isopropylmalate dehydratase large subunit A. pernix does not encode committed enzymes of leucine biosynthesis, indicating that, unlike all other free-living organisms whose genomes have been sequenced so far, it cannot produce leucine. It might depend on other archaea and/or bacteria as the source of leucine, or perhaps synthesize leucine by a distinct, completely uncharacterized pathway
0066 amtks-yqvdcebrh-j- - - - - -n- 3-isopropylmalate dehydratase small subunit  
0473 amtks-yqvdcebrh-j- - - - - -nx 3-isopropylmalate dehydrogenase  
0119 amtks-yqvdcebrh-j- - - - - -n- Isopropylmalate/homocitrate/citramalate synthase  
0015 amtks-yqvdcebrhuj- - - - - -n- Adenylosuccinate lyase Most of the enzyme of the de novo pathway of purine biosynthesis are missing in A. pernix. It appears likely that, in this organism, all purine nucleotides are produced via the salvage pathway.
0104 amtks-yqvdcebrhuj- - - - - -n- Adenylosuccinate synthase  
0034 amtks-yqvdcebrh-j- - - - - -n- Glutamine phosphoribosyl-pyrophosphate amidotransferase  
0151 amtks-yqvdcebrhuj- - - - - -n- Phosphoribosylamine-glycine ligase  
0150 amtks-yqvdcebrh-j- - - - - -n- Phosphoribosylamino-imidazol (AIR) synthetase PurM  
0152 amtks-yqvdcebrh-j- - - - - -nx Phosphoribosylamino-imidazolesuccino-carboxamide (SAICAR) synthase  
0041 amtks-yqvdcebrh-j- - - - - -n- Phosphoribosylcarboxy-aminoimidazole (NCAIR) mutase PurE  
0047 amtks-yqvdcebrh-j- - - - - -n- Phosphoribosylformyl-glycinamidine (FGAM) synthase, glutamine amidotransferase  
   domain  
0046 amtks-yqvdcebrh-j- - - - - -n- Phosphoribosylformyl-glycinamidine (FGAM) synthase, synthetase domain  
0340 amtks-yqvdcebrhuj- - - -linx Biotin-(acetyl-CoA carboxylase) ligase A. pernix apparently does not encode any enzymes of biotin synthesis or biotin-utilizing enzymes
0511 amtks-yqvdcebrhuj- - - -linx Biotin carboxyl carrier protein of acetyl-CoA carboxylase  
0157 amtks-yqv-cebrhu- - - - - - -n- Nicotinate-nucleotide pyrophosphorylase  
  1. *In the phylogenetic patterns, each letter indicates that a particular genome is represented in the given COG, and a dash indicates the absence of a representative from the corresponding genome. The one-letter code for genomes is as follows: a, Archeoglobus fulgidus; m, Methanococcus jannaschii; t, Methanobacterium thermoautotrophicum; k, Pyrococcus horikoshii; s, Pyrococcus abyssi; z, Aeropyrum pernix; y, Saccharomyces cerevisiae; q, Aquifex aeolicus; v, Thermotoga maritima; d, Deinococcus radiodurans; c, Synechocystis sp; e, Escherichia coli; b, Bacillus subtilis; r, Mycobacterium tuberculosis; h, Haemophilus influenzae; u, Helicobacter pylori; j, Campylobacter jejuni; w, Ureaplasma urealyticum; g, Mycoplasma genitalium; p, Mycoplasma pneumoniae; o, Borrelia burgdorferi; l, Treponema pallidum; i, Chlamydia trachomatis and C. pneumoniae; n, Neisseria meningitidis; x, Rickettsia prowazekii.