The Proteome and Lipidome of Thermococcus kodakarensis across the Stationary Phase

Table 3

Screening criteria used to consider whether upregulated proteins might play a role in tetraether lipid formation.

Genome accession	Annotated name	Number of screened archaeal genomes with a homologue present	Homologue present or absent in genome of N. equitans	Demonstrating identity to a squalene epoxidase	Number of predicted transmembrane helices by 3 different methods
YP_182427	Oxetanocin	9	Absent	No	0, 0, 0
YP_182519	Diphthine synthase	15	Present	No	0, 1, 0
YP_182619	Hypothetical protein TK0206	0	Absent	No	0, 1, 0
YP_182835	tRNA (guanine-N2)-dimethyltransferase	7	Present	No	0, 0, 0
YP_182912	Zinc-dependent protease	14	Absent	to P32476	0, 1, 1
YP_182969	Methylthioribose-1-phosphate isomerase	16	Absent	No	0, 2, 1
YP_182979	RNA helicase	16	Absent	No	0, 1, 0
YP_183072	Ribose ABC transporter permease	4	Absent	No	10, 9, 6
YP_183167	tRNA(Met) cytidine acetyltransferase	10	Present	No	0, 1, 1
YP_183265	Hypothetical protein TK0853	15	Absent	No	0, 2, 1
YP_183284	Ornithine carbamoyltransferase	16	Absent	No	0, 0, 0
YP_183321	Glutamyl-tRNA(Gln) amidotransferase subunit D	16	Present	No	0, 1, 0
YP_183327	3-Hydroxy-3-methylglutaryl-CoA reductase	13	Absent	No	0, 2, 1
YP_183397	Alanyl-tRNA editing protein AlaX	15	Present	No	0, 0, 0
YP_183662	Hypothetical protein TK1249	13	Absent	No	0, 0, 0
YP_183694	Endonuclease	16	Present	No	0, 0, 0
YP_183697	Peptidase	10	Absent	No	0, 0, 0
YP_183806	Glycerol 3-phosphate dehydrogenase	5	Absent	to Q75W20	0, 2, 1
YP_183841	Hypothetical protein TK1428	16	Present	No	0, 1, 0
YP_183917	30S ribosomal protein S11	16	Present	No	0, 0, 0
YP_183924	Hypothetical protein TK1511	3	Absent	No	0, 0, 0
YP_183938	50S ribosomal protein L6	16	Present	No	0, 0, 0
YP_183954	50S ribosomal protein L4P	16	Present	No	0, 0, 0
YP_184170	Peptide ABC transporter ATPase	16	Absent	No	0, 0, 0
YP_184182	Transcriptional regulator	8	Absent	No	0, 1, 0
YP_184227	L-Tyrosine decarboxylase	9	Absent	No	0, 3, 1
YP_184316	DNA polymerase II large subunit	9	Present	No	0, 2, 0
YP_184329	Apolipoprotein N-acyltransferase	11	Absent	No	1, 2, 1
YP_184398	Hypothetical membrane protein	0	Absent	No	0, 2, 1
YP_184506	NADH-quinone oxidoreductase	16	Absent	No	0, 0, 0
YP_184539	Protein kinase	16	Present	No	0, 0, 0
YP_184653	Lysyl-tRNA synthetase	10	Present	No	0, 0, 0

Sixteen different archaeal genomes were screened (refer to Materials and Methods) and a homologue was considered to be present for proteins with an -value < and coverage across > 30% of the protein.
More stringent criteria (-value < and coverage across > 60% of the protein) were used for determining the presence of homologues in N. equitans in order not to discard any potentially relevant proteins unnecessarily.
The potential level of similarity between a tetraether related enzyme and a squalene epoxidase is completely unknown; therefore, an -value of < was considered to be of interest, across any level of coverage in the protein.
Number of transmembrane helices predicted by TMHMM, TMbase, and SPLIT (given in that order in the table). See Materials and Methods for details on transmembrane prediction tools.