KEGG   PATHWAY: rop00680Help
Entry
rop00680                    Pathway                                

Name
Methane metabolism - Rhodococcus opacus
Description
Methane is metabolized principally by methanotrophs and methanogens in the global carbon cycle. Methanotrophs consume methane as the only source of carbon, while methanogens produce methane as a metabolic byproduct. Methylotrophs, which are microorganisms that can obtain energy for growth by oxidizing one-carbon compounds, such as methanol and methane, are situated between methanotrophs and methanogens. Methanogens can obtain energy for growth by converting a limited number of substrates to methane under anaerobic conditions. Three types of methanogenic pathways are known: CO2 to methane [MD:M00567], methanol to methane [MD:M00356], and acetate to methane [MD:M00357]. Methanogens use 2-mercaptoethanesulfonate (CoM; coenzyme M) as the terminal methyl carrier in methanogenesis and have four enzymes for CoM biosynthesis [MD:M00358]. Coenzyme B-Coenzyme M heterodisulfide reductase (Hdr), requiring for the final reaction steps of methanogenic pathway, is divided into two types: cytoplasmic HdrABC in most methanogens and membrane-bound HdrED in Methanosarcina species. In methanotrophs and methyltrophs methane is oxidized to form formaldehyde, which is at the diverging point for further oxidation to CO2 for energy source and assimilation for biosynthesis. There are three pathways that convert formaldehyde to C2 or C3 compounds: serine pathway [MD:M00346], ribulose monophosphate pathway [MD:M00345], and xylulose monophosphate pathway [MD:M00344]. The first two pathways are found in prokaryotes and the third is found in yeast. As a special case of methylotrophs, various amines can be used as carbon sources in trimethylamine metabolism [MD:M00563].
Class
Metabolism; Energy metabolism
BRITE hierarchy
Pathway map
Methane metabolism
rop00680

All organismsOrtholog table
Other DBs
BSID: 
GO: 
Organism
Rhodococcus opacus [GN:rop]
Gene
fdhA; glutathione-independent formaldehyde dehydrogenase [KO:K00148] [EC:1.2.1.46]
N; K17067 methanol:N,N-dimethyl-4-nitrosoaniline oxidoreductase [EC:1.2.99.4] [KO:K17067] [EC:1.2.99.4]
zinc-containing alcohol dehydrogenase; K00121 S-(hydroxymethyl)glutathione dehydrogenase / alcohol dehydrogenase [EC:1.1.1.284 1.1.1.1] [KO:K00121] [EC:1.1.1.1 1.1.1.284]
zinc-containing alcohol dehydrogenase; K00121 S-(hydroxymethyl)glutathione dehydrogenase / alcohol dehydrogenase [EC:1.1.1.284 1.1.1.1] [KO:K00121] [EC:1.1.1.1 1.1.1.284]
zinc-containing alcohol dehydrogenase; K00121 S-(hydroxymethyl)glutathione dehydrogenase / alcohol dehydrogenase [EC:1.1.1.284 1.1.1.1] [KO:K00121] [EC:1.1.1.1 1.1.1.284]
zinc-containing alcohol dehydrogenase; K00121 S-(hydroxymethyl)glutathione dehydrogenase / alcohol dehydrogenase [EC:1.1.1.284 1.1.1.1] [KO:K00121] [EC:1.1.1.1 1.1.1.284]
alcohol dehydrogenase; K00121 S-(hydroxymethyl)glutathione dehydrogenase / alcohol dehydrogenase [EC:1.1.1.284 1.1.1.1] [KO:K00121] [EC:1.1.1.1 1.1.1.284]
putative alcohol dehydrogenase; K00121 S-(hydroxymethyl)glutathione dehydrogenase / alcohol dehydrogenase [EC:1.1.1.284 1.1.1.1] [KO:K00121] [EC:1.1.1.1 1.1.1.284]
putative zinc-containing alcohol dehydrogenase; K00121 S-(hydroxymethyl)glutathione dehydrogenase / alcohol dehydrogenase [EC:1.1.1.284 1.1.1.1] [KO:K00121] [EC:1.1.1.1 1.1.1.284]
zinc-containing alcohol dehydrogenase; K00121 S-(hydroxymethyl)glutathione dehydrogenase / alcohol dehydrogenase [EC:1.1.1.284 1.1.1.1] [KO:K00121] [EC:1.1.1.1 1.1.1.284]
zinc-containing alcohol dehydrogenase; K00121 S-(hydroxymethyl)glutathione dehydrogenase / alcohol dehydrogenase [EC:1.1.1.284 1.1.1.1] [KO:K00121] [EC:1.1.1.1 1.1.1.284]
oxidoreductase; K00123 formate dehydrogenase major subunit [EC:1.2.1.2] [KO:K00123] [EC:1.2.1.2]
oxidoreductase; K00123 formate dehydrogenase major subunit [EC:1.2.1.2] [KO:K00123] [EC:1.2.1.2]
oxidoreductase iron-sulfur subunit; K03518 carbon-monoxide dehydrogenase small subunit [EC:1.2.99.2] [KO:K03518] [EC:1.2.99.2]
oxidoreductase iron-sulfur subunit; K03518 carbon-monoxide dehydrogenase small subunit [EC:1.2.99.2] [KO:K03518] [EC:1.2.99.2]
ndhB; nicotine dehydrogenase small subunit [KO:K03518] [EC:1.2.99.2]
carbon monoxide dehydrogenase small subunit; K03518 carbon-monoxide dehydrogenase small subunit [EC:1.2.99.2] [KO:K03518] [EC:1.2.99.2]
carbon monoxide dehydrogenase small subunit; K03518 carbon-monoxide dehydrogenase small subunit [EC:1.2.99.2] [KO:K03518] [EC:1.2.99.2]
kdhB; ketone dehydrogenase small subunit [KO:K03518] [EC:1.2.99.2]
kdhM; ketone dehydrogenase medium subunit [KO:K03519] [EC:1.2.99.2]
carbon monoxide dehydrogenase medium subunit; K03519 carbon-monoxide dehydrogenase medium subunit [EC:1.2.99.2] [KO:K03519] [EC:1.2.99.2]
oxidoreductase FAD-binding subunit; K03519 carbon-monoxide dehydrogenase medium subunit [EC:1.2.99.2] [KO:K03519] [EC:1.2.99.2]
carbon monoxide dehydrogenase medium subunit; K03519 carbon-monoxide dehydrogenase medium subunit [EC:1.2.99.2] [KO:K03519] [EC:1.2.99.2]
carbon monoxide dehydrogenase large subunit; K03520 carbon-monoxide dehydrogenase large subunit [EC:1.2.99.2] [KO:K03520] [EC:1.2.99.2]
carbon monoxide dehydrogenase large subunit; K03520 carbon-monoxide dehydrogenase large subunit [EC:1.2.99.2] [KO:K03520] [EC:1.2.99.2]
glyA; serine hydroxymethyltransferase [KO:K00600] [EC:2.1.2.1]
glyA; serine hydroxymethyltransferase [KO:K00600] [EC:2.1.2.1]
serine hydroxymethyltransferase; K00600 glycine hydroxymethyltransferase [EC:2.1.2.1] [KO:K00600] [EC:2.1.2.1]
glyA; serine hydroxymethyltransferase [KO:K00600] [EC:2.1.2.1]
eno; phosphopyruvate hydratase [KO:K01689] [EC:4.2.1.11]
ppc; phosphoenolpyruvate carboxylase [KO:K01595] [EC:4.1.1.31]
mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
dak; dihydroxyacetone kinase [KO:K00863] [EC:2.7.1.29]
fbaA; fructose-bisphosphate aldolase [KO:K01624] [EC:4.1.2.13]
aldolase; K01624 fructose-bisphosphate aldolase, class II [EC:4.1.2.13] [KO:K01624] [EC:4.1.2.13]
glpX; fructose 1,6-bisphosphatase II [KO:K02446] [EC:3.1.3.11]
6-phosphofructokinase; K00850 6-phosphofructokinase 1 [EC:2.7.1.11] [KO:K00850] [EC:2.7.1.11]
methylamine dehydrogenase; K00317 dimethylamine/trimethylamine dehydrogenase [EC:1.5.8.1 1.5.8.2] [KO:K00317] [EC:1.5.8.2 1.5.8.1]
histamine dehydrogenase; K00317 dimethylamine/trimethylamine dehydrogenase [EC:1.5.8.1 1.5.8.2] [KO:K00317] [EC:1.5.8.2 1.5.8.1]
hypothetical protein; K00441 coenzyme F420 hydrogenase subunit beta [EC:1.12.98.1] [KO:K00441] [EC:1.12.98.1]
ackA; acetate kinase [KO:K00925] [EC:2.7.2.1]
pta; phosphate acetyltransferase [KO:K13788] [EC:2.3.1.8]
acs; acetate--CoA ligase [KO:K01895] [EC:6.2.1.1]
acetate--CoA ligase; K01895 acetyl-CoA synthetase [EC:6.2.1.1] [KO:K01895] [EC:6.2.1.1]
acs; acetate--CoA ligase [KO:K01895] [EC:6.2.1.1]
acetate--CoA ligase; K01895 acetyl-CoA synthetase [EC:6.2.1.1] [KO:K01895] [EC:6.2.1.1]
acs; acetyl-CoA synthetase [KO:K01895] [EC:6.2.1.1]
hypothetical protein; K01007 pyruvate, water dikinase [EC:2.7.9.2] [KO:K01007] [EC:2.7.9.2]
hypothetical protein; K01007 pyruvate, water dikinase [EC:2.7.9.2] [KO:K01007] [EC:2.7.9.2]
gpmA; phosphoglyceromutase [KO:K01834] [EC:5.4.2.11]
phosphoglycerate mutase family protein; K01834 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase [EC:5.4.2.11] [KO:K01834] [EC:5.4.2.11]
phosphoglycerate mutase family protein; K15634 probable phosphoglycerate mutase [EC:5.4.2.12] [KO:K15634] [EC:5.4.2.12]
phosphoglycerate mutase family protein; K15634 probable phosphoglycerate mutase [EC:5.4.2.12] [KO:K15634] [EC:5.4.2.12]
phosphatase; K15634 probable phosphoglycerate mutase [EC:5.4.2.12] [KO:K15634] [EC:5.4.2.12]
2; K15634 probable phosphoglycerate mutase [EC:5.4.2.12] [KO:K15634] [EC:5.4.2.12]
bifunctional RNase H/acid phosphatase; K15634 probable phosphoglycerate mutase [EC:5.4.2.12] [KO:K15634] [EC:5.4.2.12]
serA; D-3-phosphoglycerate dehydrogenase [KO:K00058] [EC:1.1.1.95]
dehydrogenase; K00058 D-3-phosphoglycerate dehydrogenase [EC:1.1.1.95] [KO:K00058] [EC:1.1.1.95]
hprA; glycerate dehydrogenase [KO:K00058] [EC:1.1.1.95]
serC; phosphoserine aminotransferase [KO:K00831] [EC:2.6.1.52]
serB; phosphoserine phosphatase [KO:K01079] [EC:3.1.3.3]
hypothetical protein; K14941 2-phospho-L-lactate guanylyltransferase [EC:2.7.7.68] [KO:K14941] [EC:2.7.7.68]
fbiA; LPPG:FO 2-phospho-L-lactate transferase [KO:K11212] [EC:2.7.8.28]
fbiB; F420-0--gamma-glutamyl ligase [KO:K12234] [EC:6.3.2.34 6.3.2.31]
Compound
C00011  
CO2
C00022  
Pyruvate
C00024  
Acetyl-CoA
C00033  
Acetate
C00036  
Oxaloacetate
C00037  
Glycine
C00048  
Glyoxylate
C00058  
Formate
C00065  
L-Serine
C00067  
Formaldehyde
C00074  
Phosphoenolpyruvate
C00085  
D-Fructose 6-phosphate
C00101  
Tetrahydrofolate
C00111  
Glycerone phosphate
C00118  
D-Glyceraldehyde 3-phosphate
C00132  
Methanol
C00143  
5,10-Methylenetetrahydrofolate
C00149  
(S)-Malate
C00168  
Hydroxypyruvate
C00184  
Glycerone
C00197  
3-Phospho-D-glycerate
C00199  
D-Ribulose 5-phosphate
C00218  
Methylamine
C00227  
Acetyl phosphate
C00231  
D-Xylulose 5-phosphate
C00237  
CO
C00258  
D-Glycerate
C00322  
2-Oxoadipate
C00354  
D-Fructose 1,6-bisphosphate
C00543  
Dimethylamine
C00565  
Trimethylamine
C00593  
Sulfoacetaldehyde
C00631  
2-Phospho-D-glycerate
C00862  
Methanofuran
C00876  
Coenzyme F420
C01001  
Formylmethanofuran
C01005  
O-Phospho-L-serine
C01031  
S-Formylglutathione
C01046  
N-Methyl-L-glutamate
C01080  
Reduced coenzyme F420
C01104  
Trimethylamine N-oxide
C01179  
3-(4-Hydroxyphenyl)pyruvate
C01217  
5,6,7,8-Tetrahydromethanopterin
C01274  
5-Formyl-5,6,7,8-tetrahydromethanopterin
C01438  
Methane
C03232  
3-Phosphonooxypyruvate
C03576  
2-Mercaptoethanesulfonate
C03920  
2-(Methylthio)ethanesulfonate
C04330  
5,10-Methenyltetrahydromethanopterin
C04348  
L-Malyl-CoA
C04377  
5,10-Methylenetetrahydromethanopterin
C04488  
5-Methyl-5,6,7,8-tetrahydromethanopterin
C04628  
Coenzyme B
C04732  
5-Amino-6-(1-D-ribitylamino)uracil
C04832  
Coenzyme M 7-mercaptoheptanoylthreonine-phosphate heterodisulfide
C05528  
3-Sulfopyruvate
C06019  
D-arabino-Hex-3-ulose 6-phosphate
C11536  
(2R)-O-Phospho-3-sulfolactate
C11537  
(2R)-3-Sulfolactate
C14180  
S-(Hydroxymethyl)glutathione
C16583  
(R)-(Homo)2-citrate
C16588  
2-Oxopimelate
C16589  
2-Oxosuberate
C16590  
7-Oxoheptanoic acid
C16593  
7-Mercaptoheptanoic acid
C16594  
7-Mercaptoheptanoylthreonine
C16597  
(-)-threo-Iso(homo)2-citrate
C16598  
(R)-(Homo)3-citrate
C16600  
(-)-threo-Iso(homo)3-citrate
C19151  
Coenzyme F420-3
C19152  
Coenzyme F420-1
C19153  
Coenzyme F420-0
C19154  
7,8-Didemethyl-8-hydroxy-5-deazariboflavin
C19155  
(2S)-Lactyl-2-diphospho-5'-guanosine
C19156  
(2S)-2-Phospholactate
C20581  
cis-(Homo)2-aconitate
C20582  
cis-(Homo)3-aconitate
Reference
  Authors
Graham DE, Xu H, White RH
  Title
Identification of coenzyme M biosynthetic phosphosulfolactate synthase: a new family of sulfonate-biosynthesizing enzymes.
  Journal
J Biol Chem 277:13421-9 (2002)
Reference
  Authors
Deppenmeier U
  Title
The membrane-bound electron transport system of Methanosarcina species.
  Journal
J Bioenerg Biomembr 36:55-64 (2004)
Reference
  Authors
Hallam SJ, Putnam N, Preston CM, Detter JC, Rokhsar D, Richardson PM, DeLong EF
  Title
Reverse methanogenesis: testing the hypothesis with environmental genomics.
  Journal
Science 305:1457-62 (2004)
Reference
  Authors
Welander PV, Metcalf WW
  Title
Loss of the mtr operon in Methanosarcina blocks growth on methanol, but not methanogenesis, and reveals an unknown methanogenic pathway.
  Journal
Proc Natl Acad Sci U S A 102:10664-9 (2005)
Reference
  Authors
Yurimoto H, Kato N, Sakai Y
  Title
Assimilation, dissimilation, and detoxification of formaldehyde, a central metabolic intermediate of methylotrophic metabolism.
  Journal
Chem Rec 5:367-75 (2005)
Reference
  Authors
Fricke WF, Seedorf H, Henne A, Kruer M, Liesegang H, Hedderich R, Gottschalk G, Thauer RK.
  Title
The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis.
  Journal
J Bacteriol 188:642-58 (2006)
Reference
  Authors
Kato N, Yurimoto H, Thauer RK
  Title
The physiological role of the ribulose monophosphate pathway in bacteria and archaea.
  Journal
Biosci Biotechnol Biochem 70:10-21 (2006)
Reference
  Authors
Thauer RK, Kaster AK, Seedorf H, Buckel W, Hedderich R
  Title
Methanogenic archaea: ecologically relevant differences in energy conservation.
  Journal
Nat Rev Microbiol 6:579-91 (2008)
Reference
  Authors
Liffourrena AS, Salvano MA, Lucchesi GI
  Title
Pseudomonas putida A ATCC 12633 oxidizes trimethylamine aerobically via two different pathways.
  Journal
Arch Microbiol 192:471-6 (2010)
KO pathway
 

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