KEGG   PATHWAY: byi00680Help
Entry
byi00680                    Pathway                                

Name
Methane metabolism - Burkholderia sp. YI23
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
byi00680

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BSID: 
GO: 
Organism
Burkholderia sp. YI23 [GN:byi]
Gene
hypothetical protein; K16256 mxaA protein [KO:K16256]
von Willebrand factor; K16257 mxaC protein [KO:K16257]
mxaL; putative MxaL-like protein [KO:K16258]
mxaL; putative MxaL-like protein [KO:K16259]
formaldehyde dehydrogenase; K00148 glutathione-independent formaldehyde dehydrogenase [EC:1.2.1.46] [KO:K00148] [EC:1.2.1.46]
formaldehyde dehydrogenase; K00148 glutathione-independent formaldehyde dehydrogenase [EC:1.2.1.46] [KO:K00148] [EC:1.2.1.46]
S-(hydroxymethyl)glutathione dehydrogenase/class III 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]
S-(hydroxymethyl)glutathione dehydrogenase/class III 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]
S-formylglutathione hydrolase; K01070 S-formylglutathione hydrolase [EC:3.1.2.12] [KO:K01070] [EC:3.1.2.12]
molybdopterin oxidoreductase Fe4S4 region; K00123 formate dehydrogenase major subunit [EC:1.2.1.2] [KO:K00123] [EC:1.2.1.2]
formate dehydrogenase subunit alpha; K00123 formate dehydrogenase major subunit [EC:1.2.1.2] [KO:K00123] [EC:1.2.1.2]
NAD-dependent formate dehydrogenase subunit alpha; K00123 formate dehydrogenase major subunit [EC:1.2.1.2] [KO:K00123] [EC:1.2.1.2]
NADH dehydrogenase (quinone); K00124 formate dehydrogenase iron-sulfur subunit [KO:K00124]
formate dehydrogenase subunit beta; K00124 formate dehydrogenase iron-sulfur subunit [KO:K00124]
NAD-dependent formate dehydrogenase; K00127 formate dehydrogenase subunit gamma [KO:K00127]
formate dehydrogenase subunit gamma; K00127 formate dehydrogenase subunit gamma [KO:K00127]
formate dehydrogenase delta subunit; K00126 formate dehydrogenase subunit delta [EC:1.2.1.2] [KO:K00126] [EC:1.2.1.2]
(2Fe-2S)-binding domain-containing protein; K03518 carbon-monoxide dehydrogenase small subunit [EC:1.2.99.2] [KO:K03518] [EC:1.2.99.2]
2Fe-2S iron-sulfur cluster binding domain-containing protein; K03518 carbon-monoxide dehydrogenase small subunit [EC:1.2.99.2] [KO:K03518] [EC:1.2.99.2]
2Fe-2S iron-sulfur cluster binding domain-containing protein; K03518 carbon-monoxide dehydrogenase small subunit [EC:1.2.99.2] [KO:K03518] [EC:1.2.99.2]
aldehyde oxidase and xanthine dehydrogenase molybdopterin binding protein; 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]
oxidoreductase; K03519 carbon-monoxide dehydrogenase medium subunit [EC:1.2.99.2] [KO:K03519] [EC:1.2.99.2]
molybdopterin dehydrogenase FAD-binding protein; K03519 carbon-monoxide dehydrogenase medium subunit [EC:1.2.99.2] [KO:K03519] [EC:1.2.99.2]
molybdopterin dehydrogenase FAD-binding protein; K03519 carbon-monoxide dehydrogenase medium subunit [EC:1.2.99.2] [KO:K03519] [EC:1.2.99.2]
molybdopterin dehydrogenase; K03519 carbon-monoxide dehydrogenase medium subunit [EC:1.2.99.2] [KO:K03519] [EC:1.2.99.2]
putative carbon monoxide dehydrogenase; K03519 carbon-monoxide dehydrogenase medium subunit [EC:1.2.99.2] [KO:K03519] [EC:1.2.99.2]
dehydrogenase/oxidase; K03520 carbon-monoxide dehydrogenase large subunit [EC:1.2.99.2] [KO:K03520] [EC:1.2.99.2]
xanthine dehydrogenase; K03520 carbon-monoxide dehydrogenase large subunit [EC:1.2.99.2] [KO:K03520] [EC:1.2.99.2]
xanthine dehydrogenase; K03520 carbon-monoxide dehydrogenase large subunit [EC:1.2.99.2] [KO:K03520] [EC:1.2.99.2]
aldehyde oxidase and xanthine dehydrogenase molybdopterin binding protein; K03520 carbon-monoxide dehydrogenase large subunit [EC:1.2.99.2] [KO:K03520] [EC:1.2.99.2]
aldehyde oxidase and xanthine dehydrogenase molybdopterin binding protein; K03520 carbon-monoxide dehydrogenase large subunit [EC:1.2.99.2] [KO:K03520] [EC:1.2.99.2]
glycine hydroxymethyltransferase; K00600 glycine hydroxymethyltransferase [EC:2.1.2.1] [KO:K00600] [EC:2.1.2.1]
serine hydroxymethyltransferase; K00600 glycine hydroxymethyltransferase [EC:2.1.2.1] [KO:K00600] [EC:2.1.2.1]
serine hydroxymethyltransferase; K00600 glycine hydroxymethyltransferase [EC:2.1.2.1] [KO:K00600] [EC:2.1.2.1]
serine--glyoxylate transaminase; K00830 alanine-glyoxylate transaminase / serine-glyoxylate transaminase / serine-pyruvate transaminase [EC:2.6.1.44 2.6.1.45 2.6.1.51] [KO:K00830] [EC:2.6.1.51 2.6.1.45 2.6.1.44]
D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding protein; K00018 glycerate dehydrogenase [EC:1.1.1.29] [KO:K00018] [EC:1.1.1.29]
phosphopyruvate hydratase; K01689 enolase [EC:4.2.1.11] [KO:K01689] [EC:4.2.1.11]
phosphopyruvate hydratase; K01689 enolase [EC:4.2.1.11] [KO:K01689] [EC:4.2.1.11]
phosphopyruvate hydratase; K01689 enolase [EC:4.2.1.11] [KO:K01689] [EC:4.2.1.11]
phosphoenolpyruvate carboxylase; K01595 phosphoenolpyruvate carboxylase [EC:4.1.1.31] [KO:K01595] [EC:4.1.1.31]
malate dehydrogenase; K00024 malate dehydrogenase [EC:1.1.1.37] [KO:K00024] [EC:1.1.1.37]
fructose-bisphosphate aldolase; K01623 fructose-bisphosphate aldolase, class I [EC:4.1.2.13] [KO:K01623] [EC:4.1.2.13]
fructose-bisphosphate aldolase; K01624 fructose-bisphosphate aldolase, class II [EC:4.1.2.13] [KO:K01624] [EC:4.1.2.13]
fructose-bisphosphate aldolase; K01624 fructose-bisphosphate aldolase, class II [EC:4.1.2.13] [KO:K01624] [EC:4.1.2.13]
inositol phosphatase/fructose-16-bisphosphatase; K03841 fructose-1,6-bisphosphatase I [EC:3.1.3.11] [KO:K03841] [EC:3.1.3.11]
inositol phosphatase/fructose-16-bisphosphatase; K03841 fructose-1,6-bisphosphatase I [EC:3.1.3.11] [KO:K03841] [EC:3.1.3.11]
6-phosphofructokinase; K16370 6-phosphofructokinase 2 [EC:2.7.1.11] [KO:K16370] [EC:2.7.1.11]
amine dehydrogenase; K15228 methylamine dehydrogenase light chain [EC:1.4.9.1] [KO:K15228] [EC:1.4.9.1]
amine dehydrogenase; K15229 methylamine dehydrogenase heavy chain [EC:1.4.9.1] [KO:K15229] [EC:1.4.9.1]
formylmethanofuran dehydrogenase subunit A; K00200 formylmethanofuran dehydrogenase subunit A [EC:1.2.99.5] [KO:K00200] [EC:1.2.99.5]
formylmethanofuran dehydrogenase subunit B; K00201 formylmethanofuran dehydrogenase subunit B [EC:1.2.99.5] [KO:K00201] [EC:1.2.99.5]
formylmethanofuran dehydrogenase; K00202 formylmethanofuran dehydrogenase subunit C [EC:1.2.99.5] [KO:K00202] [EC:1.2.99.5]
tetrahydromethanopterin formyltransferase; K00672 formylmethanofuran--tetrahydromethanopterin N-formyltransferase [EC:2.3.1.101] [KO:K00672] [EC:2.3.1.101]
methenyltetrahydromethanopterin cyclohydrolase; K01499 methenyltetrahydromethanopterin cyclohydrolase [EC:3.5.4.27] [KO:K01499] [EC:3.5.4.27]
methylene-tetrahydromethanopterin dehydrogenase; K10714 methylene-tetrahydromethanopterin dehydrogenase [EC:1.5.1.-] [KO:K10714] [EC:1.5.1.-]
formaldehyde-activating protein; K10713 5,6,7,8-tetrahydromethanopterin hydro-lyase [EC:4.2.1.147] [KO:K10713] [EC:4.2.1.147]
formaldehyde-activating protein; K10713 5,6,7,8-tetrahydromethanopterin hydro-lyase [EC:4.2.1.147] [KO:K10713] [EC:4.2.1.147]
acetate kinase; K00925 acetate kinase [EC:2.7.2.1] [KO:K00925] [EC:2.7.2.1]
phosphate acetyltransferase; K00625 phosphate acetyltransferase [EC:2.3.1.8] [KO:K00625] [EC:2.3.1.8]
phosphate acetyltransferase; K00625 phosphate acetyltransferase [EC:2.3.1.8] [KO:K00625] [EC:2.3.1.8]
AMP-dependent synthetase and ligase; K01895 acetyl-CoA synthetase [EC:6.2.1.1] [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]
AMP-dependent synthetase and ligase; K01895 acetyl-CoA synthetase [EC:6.2.1.1] [KO:K01895] [EC:6.2.1.1]
AMP-dependent synthetase and ligase; K01895 acetyl-CoA synthetase [EC:6.2.1.1] [KO:K01895] [EC:6.2.1.1]
phosphoenolpyruvate synthase; K01007 pyruvate, water dikinase [EC:2.7.9.2] [KO:K01007] [EC:2.7.9.2]
phosphoenolpyruvate synthase; K01007 pyruvate, water dikinase [EC:2.7.9.2] [KO:K01007] [EC:2.7.9.2]
phosphoglycerate mutase; K01834 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase [EC:5.4.2.11] [KO:K01834] [EC:5.4.2.11]
phosphoglycerate mutase; K15634 probable phosphoglycerate mutase [EC:5.4.2.12] [KO:K15634] [EC:5.4.2.12]
putative phosphoglycerate mutase; K15634 probable phosphoglycerate mutase [EC:5.4.2.12] [KO:K15634] [EC:5.4.2.12]
putative phosphoglycerate mutase family protein; K15634 probable phosphoglycerate mutase [EC:5.4.2.12] [KO:K15634] [EC:5.4.2.12]
D-isomer specific 2-hydroxyacid dehydrogenase; K00058 D-3-phosphoglycerate dehydrogenase [EC:1.1.1.95] [KO:K00058] [EC:1.1.1.95]
D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding protein; K00058 D-3-phosphoglycerate dehydrogenase [EC:1.1.1.95] [KO:K00058] [EC:1.1.1.95]
D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding protein; K00058 D-3-phosphoglycerate dehydrogenase [EC:1.1.1.95] [KO:K00058] [EC:1.1.1.95]
D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding protein; K00058 D-3-phosphoglycerate dehydrogenase [EC:1.1.1.95] [KO:K00058] [EC:1.1.1.95]
phosphoserine aminotransferase; K00831 phosphoserine aminotransferase [EC:2.6.1.52] [KO:K00831] [EC:2.6.1.52]
serB; phosphoserine phosphatase SerB [KO:K01079] [EC:3.1.3.3]
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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