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

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