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 [KO:K16256]
von Willebrand factor [KO:K16257]
mxaL; putative MxaL-like protein [KO:K16258]
mxaL; putative MxaL-like protein [KO:K16259]
formaldehyde dehydrogenase, glutathione-independent [KO:K00148] [EC:1.2.1.46]
formaldehyde dehydrogenase, glutathione-independent [KO:K00148] [EC:1.2.1.46]
S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase [KO:K00121] [EC:1.1.1.1 1.1.1.284]
S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase [KO:K00121] [EC:1.1.1.1 1.1.1.284]
alcohol dehydrogenase [KO:K00121] [EC:1.1.1.1 1.1.1.284]
S-formylglutathione hydrolase [KO:K01070] [EC:3.1.2.12]
molybdopterin oxidoreductase Fe4S4 region [KO:K00123] [EC:1.2.1.2]
formate dehydrogenase, alpha subunit [KO:K00123] [EC:1.2.1.2]
NAD-dependent formate dehydrogenase, alpha subunit [KO:K00123] [EC:1.2.1.2]
NADH dehydrogenase (quinone) [KO:K00124]
formate dehydrogenase, beta subunit [KO:K00124]
NAD-dependent formate dehydrogenase, gamma subunit [KO:K00127]
formate dehydrogenase, gamma subunit [KO:K00127]
formate dehydrogenase delta subunit [KO:K00126] [EC:1.2.1.2]
(2Fe-2S)-binding domain protein [KO:K03518] [EC:1.2.7.4]
2Fe-2S iron-sulfur cluster binding domain-containing protein [KO:K03518] [EC:1.2.7.4]
2Fe-2S iron-sulfur cluster binding domain-containing protein [KO:K03518] [EC:1.2.7.4]
aldehyde oxidase and xanthine dehydrogenase molybdopterin binding protein [KO:K03518] [EC:1.2.7.4]
carbon-monoxide dehydrogenase small subunit [KO:K03518] [EC:1.2.7.4]
oxidoreductase, medium chain [KO:K03519] [EC:1.2.7.4]
molybdopterin dehydrogenase FAD-binding protein [KO:K03519] [EC:1.2.7.4]
molybdopterin dehydrogenase FAD-binding protein [KO:K03519] [EC:1.2.7.4]
molybdopterin dehydrogenase [KO:K03519] [EC:1.2.7.4]
putative carbon monoxide dehydrogenase, middle subunit [KO:K03519] [EC:1.2.7.4]
dehydrogenase/oxidase [KO:K03520] [EC:1.2.7.4]
xanthine dehydrogenase, molybdenum binding subunit apoprotein [KO:K03520] [EC:1.2.7.4]
xanthine dehydrogenase, molybdenum binding subunit apoprotein [KO:K03520] [EC:1.2.7.4]
aldehyde oxidase and xanthine dehydrogenase molybdopterin binding protein [KO:K03520] [EC:1.2.7.4]
aldehyde oxidase and xanthine dehydrogenase molybdopterin binding protein [KO:K03520] [EC:1.2.7.4]
glycine hydroxymethyltransferase [KO:K00600] [EC:2.1.2.1]
serine hydroxymethyltransferase [KO:K00600] [EC:2.1.2.1]
serine hydroxymethyltransferase [KO:K00600] [EC:2.1.2.1]
Serine--glyoxylate transaminase [KO:K00830] [EC:2.6.1.51 2.6.1.45 2.6.1.44]
D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding protein [KO:K00018] [EC:1.1.1.29]
Hydroxypyruvate reductase [KO:K11529] [EC:2.7.1.165]
hypothetical protein [KO:K11529] [EC:2.7.1.165]
phosphopyruvate hydratase [KO:K01689] [EC:4.2.1.11]
phosphopyruvate hydratase [KO:K01689] [EC:4.2.1.11]
phosphopyruvate hydratase [KO:K01689] [EC:4.2.1.11]
phosphoenolpyruvate carboxylase [KO:K01595] [EC:4.1.1.31]
malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
fructose-bisphosphate aldolase [KO:K01623] [EC:4.1.2.13]
fructose-bisphosphate aldolase, class II, Calvin cycle subtype [KO:K01624] [EC:4.1.2.13]
fructose-bisphosphate aldolase, class II, Calvin cycle subtype [KO:K01624] [EC:4.1.2.13]
inositol phosphatase/fructose-16-bisphosphatase [KO:K03841] [EC:3.1.3.11]
Inositol phosphatase/fructose-16-bisphosphatase [KO:K03841] [EC:3.1.3.11]
6-phosphofructokinase [KO:K16370] [EC:2.7.1.11]
amine dehydrogenase [KO:K15228] [EC:1.4.9.1]
amine dehydrogenase [KO:K15229] [EC:1.4.9.1]
formylmethanofuran dehydrogenase subunit A [KO:K00200] [EC:1.2.99.5]
formylmethanofuran dehydrogenase, subunit B [KO:K00201] [EC:1.2.99.5]
formylmethanofuran dehydrogenase, subunit C [KO:K00202] [EC:1.2.99.5]
tetrahydromethanopterin formyltransferase [KO:K00672] [EC:2.3.1.101]
methenyltetrahydromethanopterin cyclohydrolase [KO:K01499] [EC:3.5.4.27]
methylene-tetrahydromethanopterin dehydrogenase [KO:K10714] [EC:1.5.1.-]
formaldehyde-activating enzyme [KO:K10713] [EC:4.2.1.147]
formaldehyde-activating protein [KO:K10713] [EC:4.2.1.147]
acetate kinase [KO:K00925] [EC:2.7.2.1]
phosphate acetyltransferase [KO:K00625] [EC:2.3.1.8]
phosphate acetyltransferase [KO:K00625] [EC:2.3.1.8]
AMP-dependent synthetase and ligase [KO:K01895] [EC:6.2.1.1]
acetate/CoA ligase [KO:K01895] [EC:6.2.1.1]
AMP-dependent synthetase and ligase [KO:K01895] [EC:6.2.1.1]
AMP-dependent synthetase and ligase [KO:K01895] [EC:6.2.1.1]
phosphoenolpyruvate synthase [KO:K01007] [EC:2.7.9.2]
phosphoenolpyruvate synthase [KO:K01007] [EC:2.7.9.2]
phosphoglycerate mutase 1 family [KO:K01834] [EC:5.4.2.11]
Phosphoglycerate mutase [KO:K15634] [EC:5.4.2.12]
putative phosphoglycerate mutase [KO:K15634] [EC:5.4.2.12]
putative phosphoglycerate mutase family protein [KO:K15634] [EC:5.4.2.12]
D-isomer specific 2-hydroxyacid dehydrogenase [KO:K00058] [EC:1.1.1.95]
D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding protein [KO:K00058] [EC:1.1.1.95]
D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding protein [KO:K00058] [EC:1.1.1.95]
D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding protein [KO:K00058] [EC:1.1.1.95]
phosphoserine aminotransferase [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
C00082  
L-Tyrosine
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
C00483  
Tyramine
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  
Coenzyme M
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
C20926  
gamma-Glutamyltyramine
C20954  
(5-Formylfuran-3-yl)methyl phosphate
C21068  
[5-(Aminomethyl)furan-3-yl]methyl phosphate
C21069  
[5-(Aminomethyl)furan-3-yl]methyl diphosphate
C21070  
(4-{4-[2-(gamma-L-Glutamylamino)ethyl]phenoxymethyl}furan-2-yl)methanamine
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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