The variants are numbered very simply:

1 - pathway is present
-1 - pathway is not present


------------------------------------------

The PyrI and PyrII situation is described by Swiss Prot as follows (in a description
of a bifunctional version:

DE PyrR bifunctional protein [Includes: Pyrimidine operon regulatory
DE protein; Uracil phosphoribosyltransferase (EC 2.4.2.9) (UPRTase)].
CC -!- FUNCTION: Regulates transcriptional attenuation of the pyrimidine
CC nucleotide (pyr) operon by binding in a uridine-dependent manner
CC to specific sites on pyr mRNA. This disrupts an antiterminator
CC hairpin in the RNA and favors formation of a downstream
CC transcription terminator, leading to a reduced expression of
CC downstream genes (By similarity).
CC -!- FUNCTION: Displays also a weak uracil phosphoribosyltransferase
CC activity which is not physiologically significant (By similarity).
CC -!- CATALYTIC ACTIVITY: UMP + diphosphate = uracil + 5-phospho-alpha-
CC D-ribose 1-diphosphate.


===========================


Note that

Carbamoyl-phosphate synthase small chain (EC 6.3.5.5)
and Carbamoyl-phosphate synthase large chain (EC 6.3.5.5)

are missing in

272844.1 Pyrococcus abyssi GE5
and 70601.1 Pyrococcus horikoshii OT3

although they are both present in Pyrococcus furiosus DSM 3638. It is also worth noting that they are
absent in Aeropyrum pernix K1 (another crenarcheae)


=========
Note that Carbamoyl-phosphate synthase large chain (EC 6.3.5.5)
(pyrAB) has two sections that are homologous. Sometimes, the two
copies occur as separate genes. I have not yet decided what is the
right way to represent the situation. At this point, we sometimes
have versions that are only half as long as the more normal version.
For now, I think that it makes sense to just label everything as "long
chain", even if it contains only one copy of the diverged duplicates.

============

The basic de novo pyrimidine biosynthesis pathway requires

Uracil phosphoribosyltransferase (EC 2.4.2.9)

as a last step. There are a number of archaea in which all of the
steps are cleary present except for this last one. In particular,

Methanocaldococcus jannaschii DSM 2661
Methanopyrus kandleri AV19
Methanosarcina acetivorans C2A
Methanosarcina barkeri
Methanosarcina mazei Go1
Thermoplasma acidophilum DSM 1728
Thermoplasma volcanium GSS1
Ferroplasma acidarmanus
Archaeoglobus fulgidus DSM 4304

On the other hand, many archaeal genomes do contain genes performing
this function:

Pyrococcus furiosus DSM 3638
Pyrococcus abyssi GE5
Methanococcus maripaludis S2
Sulfolobus solfataricus P2
Pyrobaculum aerophilum str. IM2
Sulfolobus tokodaii str. 7
Methanothermobacter thermautotrophicus str. Delta H
Halobacterium sp. NRC-1

So, I believe that it is reasonable to argue that this constitutes a
missing gene that might not be too hard to find.


If one seeks genes in M.jannaschii that act as signatures between
these two sets of organisms, there are no solidly discriminating
signatures. The best are as follows


MJ1097 1.350 diaminopimelate decarboxylase (lysA)
MJ0778 1.350 metal-dependent phosphohydrolase
MJ1113 1.181 Phospho-N-acetylmuramoyl-pentapeptide-transferase (EC 2.7.8.13)
MJ1312 1.181 Fe-S OXIDOREDUCTASE (1.8.-.-)
MJ0225 1.181 conserved hypothetical protein
MJ0655 1.181 LSU ribosomal protein L34E
MJ0657 1.181 LSU ribosomal protein L14E
MJ0151 1.067 transcriptional regulator, putative
MJ0206 1.067 conserved hypothetical protein
MJ0728 1.067 carbon monoxide dehydrogenase, catalytic subunit (cooS)

Of these, I believe that MJ0778 (NP_247763.1,gi|15668959,kegg|mja:MJ0778,uni|Q58188) is the
best candidate.

There is weak functional clustering to

Carbamoyl-phosphate synthase large chain (EC 6.3.5.5)

The clustering occurs in the following genomes:

Methanosarcina barkeri
Methanosarcina acetivorans C2A
Methanocaldococcus jannaschii DSM 2661
Methanococcoides burtonii DSM 6242
Methanococcus maripaludis S2
Methanosarcina mazei Go1

=
=====================================

The

Carbamoyl-phosphate synthase large chain (EC 6.3.5.5)

is split into two pieces in a number of genomes. It was first noted in M.jannaschii,
and it is split in a few other archaea. However, it is also split in a number of bacteria.
I have elected to call the pieces

Carbamoyl-phosphate synthase large chain A (EC 6.3.5.5)
and
Carbamoyl-phosphate synthase large chain B (EC 6.3.5.5)