Genome Property Definition Page

Namemethanogenesis marker set
DescriptionMembers of this genome property are, at least for now, largely uncharacterized proteins that appear to represent marker proteins for methanogenic archaea, as detected by our novel algorithm, partial phylogenetic profiling. Substrates that can be reduced wih H2 to methane may include methanol only, as in Methanosphaera stadtmanae, or carbon dioxide and other compounds. This Genome Property represents proteins that both are universal in the first ten completed genomes of archaeal methanogens and can serve as markers for methanogenesis (are found nowhere else). These markers have the same phylogenetic distribution, among completely sequenced genomes, as the enzyme methyl-coenzyme M reductase, whose components (for now) are represented in a separate Genome Property, GenProp0719. This analysis was performed without the availability of an anaerobic methane-oxidizing archaeal genome sequence, and it is unclear how such a genome would affect the results.
JCVI RoleMethanogenesis
Parent PropertyGenProp0011: methanogenesis
Literature References
[ 1 ]Fricke WF, Seedorf H, Henne A, Kruer M, Liesegang H, Hedderich R, Gottschalk G, Thauer RK  The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis.  J Bacteriol. 2006 Jan;188(2):642-58.  PMID 16385054

Step NameStep NumRequiredEvidence (Method)Evidence Go Terms
CoB--CoM heterodisulfide reductase, subunit Bme_hdrBYESTIGR03288 (HMM): CoB--CoM heterodisulfide reductase, subunit B
CoB--CoM heterodisulfide reductase, subunit Cme_hdrCYESTIGR03290 (HMM): CoB--CoM heterodisulfide reductase, subunit C
methyl coenzyme M reductase system, component A2me_mcr2YESTIGR03269 (HMM): methyl coenzyme M reductase system, component A2
methyl-coenzyme M reductase, alpha subunitme_mcrAYESTIGR03256 (HMM): methyl-coenzyme M reductase, alpha subunit
methyl-coenzyme M reductase, beta subunitme_mcrBYESTIGR03257 (HMM): methyl-coenzyme M reductase, beta subunit
methyl-coenzyme M reductase I operon protein Cme_mcrCYESTIGR03264 (HMM): methyl-coenzyme M reductase I operon protein C
methyl-coenzyme M reductase operon protein Dme_mcrDYESTIGR03260 (HMM): methyl-coenzyme M reductase operon protein D
methyl-coenzyme M reductase, gamma subunitme_mcrGYESTIGR03259 (HMM): methyl-coenzyme M reductase, gamma subunit
tetrahydromethanopterin S-methyltransferase, subunit Ame_mtrAYESTIGR01111 (HMM): tetrahydromethanopterin S-methyltransferase, subunit A
tetrahydromethanopterin S-methyltransferase, subunit Bme_mtrBYESTIGR04166 (HMM): tetrahydromethanopterin S-methyltransferase, subunit B
tetrahydromethanopterin S-methyltransferase, subunit Cme_mtrCYESTIGR01148 (HMM): tetrahydromethanopterin S-methyltransferase, subunit C
tetrahydromethanopterin S-methyltransferase, subunit Dme_mtrDYESTIGR01112 (HMM): tetrahydromethanopterin S-methyltransferase, subunit D
tetrahydromethanopterin S-methyltransferase, subunit Eme_mtrEYESTIGR01113 (HMM): tetrahydromethanopterin S-methyltransferase, subunit E
tetrahydromethanopterin S-methyltransferase, subunit Fme_mtrFYESTIGR02507 (HMM): tetrahydromethanopterin S-methyltransferase, F subunit
tetrahydromethanopterin S-methyltransferase, subunit Gme_mtrGYESTIGR01149 (HMM): tetrahydromethanopterin S-methyltransferase, subunit G
tetrahydromethanopterin S-methyltransferase, subunit Hme_mtrHYESTIGR01114 (HMM): N5-methyltetrahydromethanopterin:coenzyme M methyltransferase subunit H
methanogenesis marker protein 1meth_01YESTIGR03266 (HMM): putative methanogenesis marker protein 1
methanogenesis marker protein 2meth_02YESTIGR03267 (HMM): putative methanogenesis marker protein 2
methanogenesis marker protein 3meth_03YESTIGR03268 (HMM): putative methanogenesis marker protein 3
methanogenesis marker protein 4meth_04YESTIGR03270 (HMM): putative methanogen marker protein 4
methanogenesis marker protein 5meth_05YESTIGR03271 (HMM): putative methanogenesis marker protein 5
methanogenesis marker protein 6meth_06YESTIGR03272 (HMM): putative methanogenesis marker protein 6
methanogenesis marker protein 7meth_07YESTIGR03274 (HMM): putative methanogenesis marker protein 7
methanogenesis marker protein 8meth_08YESTIGR03275 (HMM): putative methanogenesis marker protein 8
methanogenesis marker domain 9meth_09YESTIGR03277 (HMM): putative methanogenesis marker domain 9
methanogenesis radical SAM marker proteinmeth_10YESTIGR03278 (HMM): methanogenesis marker radical SAM protein
methanogenesis imperfect marker 11meth_11YESTIGR03280 (HMM): methanogenesis imperfect marker protein 11
methanogenesis marker protein 12meth_12YESTIGR03281 (HMM): putative methanogenesis marker protein 12
methanogenesis marker 13 metalloproteinmeth_13YESTIGR03282 (HMM): putative methanogenesis marker 13 metalloprotein
methanogenesis marker protein 14meth_14YESTIGR03285 (HMM): putative methanogenesis marker protein 14
methanogenesis marker protein 15meth_15YESTIGR03286 (HMM): putative methanogenesis marker protein 15
methanogenesis marker 16 metalloproteinmeth_16YESTIGR03287 (HMM): putative methanogenesis marker 16 metalloprotein
methanogenesis marker protein 17meth_17YESTIGR03291 (HMM): putative methanogenesis marker protein 17

Parent Properties

Sibling Properties
GenProp0288tetrahydromethanopterin S-methyltransferase complex
GenProp0719methyl-coenzyme M reductase