Pathways Knowlegdes

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Pathway DOIs Note
sulfide oxidation IV (metazoa)

Accession ID: BioCyc:HUMAN_PWY-7927		 -
thiosulfate disproportionation I (thiol-dependent)

Accession ID: BioCyc:META_PWY-5277
  • 10.1023/a:1024255830925
 Frederiksen TM, Finster K. Sulfite-oxido-reductase is involved in the oxidation of sulfite in Desulfocapsa sulfoexigens during disproportionation of thiosulfate and elemental sulfur. Biodegradation. 2003 Jun;14(3):189–98. doi: 10.1023/a:1024255830925. PMID: 12889609.
succinate to cytochrome bo oxidase electron transfer

Accession ID: BioCyc:META_PWY0-1329		 -
glycerol-3-phosphate to cytochrome bo oxidase electron transfer

Accession ID: BioCyc:META_PWY0-1561
  • 10.1016/s0021-9258(17)38171-1
  • 10.1128/jb.115.3.816-823.1973
 Schryvers A, Lohmeier E, Weiner JH. Chemical and functional properties of the native and reconstituted forms of the membrane-bound, aerobic glycerol-3-phosphate dehydrogenase of Escherichia coli. Journal of Biological Chemistry. 1978 Feb;253(3):783–8. doi: 10.1016/s0021-9258(17)38171-1.; Freedberg WB, Lin ECC. Three Kinds of Controls Affecting the Expression of the glp Regulon in Escherichia coli. J Bacteriol. 1973 Sep;115(3):816–23. doi: 10.1128/jb.115.3.816-823.1973.
NADH to cytochrome bo oxidase electron transfer I

Accession ID: BioCyc:META_PWY0-1335		 -
assimilatory sulfate reduction II

Accession ID: BioCyc:META_SULFMETII-PWY
  • 10.1023/a:1007058421714
  • 10.1093/jxb/erh185
 Kopriva S, Koprivova A. Plant adenosine 5'-phosphosulphate reductase: the past, the present, and the future. J Exp Bot. 2004 Aug;55(404):1775–83. doi: 10.1093/jxb/erh185. PMID: 15208336.; Neumann S, Wynen A, Trüper HG, Dahl C. Characterization of the cys gene locus from Allochromatium vinosum indicates an unusual sulfate assimilation pathway. Mol Biol Rep. 2000 Mar;27(1):27–33. doi: 10.1023/a:1007058421714. PMID: 10939523.
superpathway of sulfate assimilation and cysteine biosynthesis

Accession ID: BioCyc:META_SULFATE-CYS-PWY		 -
4,4'-disulfanediyldibutanoate degradation

Accession ID: BioCyc:META_PWY-7898
  • 10.1099/mic.0.036178-0
 Wübbeler JH, Bruland N, Wozniczka M, Steinbüchel A. Biodegradation of the xenobiotic organic disulphide 4,4'-dithiodibutyric acid by Rhodococcus erythropolis strain MI2 and comparison with the microbial utilization of 3,3'-dithiodipropionic acid and 3,3'-thiodipropionic acid. Microbiology (Reading). 2010 Apr;156(Pt 4):1221–33. doi: 10.1099/mic.0.036178-0. PMID: 19959574.
sulfide oxidation I (sulfide-quinone reductase)

Accession ID: BioCyc:META_P222-PWY
  • 10.1007/s002030050615
 Reinartz M, Tschäpe J, Brüser T, Trüper HG, Dahl C. Sulfide oxidation in the phototrophic sulfur bacterium Chromatium vinosum. Arch Microbiol. 1998 Jul;170(1):59–68. doi: 10.1007/s002030050615. PMID: 9639604.
parathion degradation

Accession ID: BioCyc:META_PARATHION-DEGRADATION-PWY
  • 10.1128/aem.31.1.63-69.1976
  • 10.1139/m73-138
 Munnecke DM, Hsieh DP. Pathways of microbial metabolism of parathion. Appl Environ Microbiol. 1976 Jan;31(1):63–9. doi: 10.1128/aem.31.1.63-69.1976.; Sethunathan N, Yoshida T. A Flavobacterium sp. that degrades diazinon and parathion. Can J Microbiol. 1973 Jul;19(7):873–5. doi: 10.1139/m73-138. PMID: 4727806.
L-methionine biosynthesis III

Accession ID: BioCyc:META_HSERMETANA-PWY
  • 10.1016/0076-6879(87)43080-2
 Soda K. Microbial sulfur amino acids: an overview. Methods Enzymol. 1987;143():453–9. doi: 10.1016/0076-6879(87)43080-2. PMID: 3309561.
L-methionine biosynthesis IV (archaea)

Accession ID: BioCyc:META_PWY-7977
  • 10.1021/acs.biochem.5b00118
 Allen KD, Miller DV, Rauch BJ, Perona JJ, White RH. Homocysteine is biosynthesized from aspartate semialdehyde and hydrogen sulfide in methanogenic archaea. Biochemistry. 2015 May 26;54(20):3129–32. doi: 10.1021/acs.biochem.5b00118. PMID: 25938369.
superpathway of L-methionine biosynthesis (by sulfhydrylation)

Accession ID: BioCyc:META_PWY-5345
  • 10.1128/jb.181.18.5833-5837.1999
 Vermeij P, Kertesz MA. Pathways of Assimilative Sulfur Metabolism in Pseudomonas putida. J Bacteriol. 1999 Sep 15;181(18):5833–7. doi: 10.1128/jb.181.18.5833-5837.1999.
L-cysteine biosynthesis VIII (Thermococcus kodakarensis)

Accession ID: BioCyc:META_PWY-8009
  • 10.1021/acschembio.7b00064
  • 10.1038/ncomms13446
 Nagata R, Fujihashi M, Kawamura H, Sato T, Fujita T, Atomi H, Miki K. Structural Study on the Reaction Mechanism of a Free Serine Kinase Involved in Cysteine Biosynthesis. ACS Chem Biol. 2017 Jun 16;12(6):1514–23. doi: 10.1021/acschembio.7b00064. PMID: 28358477.; Makino Y, Sato T, Kawamura H, Hachisuka S, Takeno R, Imanaka T, Atomi H. An archaeal ADP-dependent serine kinase involved in cysteine biosynthesis and serine metabolism. Nature Communications. 2016 Nov 18;7(1):13446. doi: 10.1038/ncomms13446.
carbon disulfide oxidation I (anaerobic)

Accession ID: BioCyc:META_PWY-1164
  • 10.1038/nature10464
 Smeulders MJ, Barends TR, Pol A, Scherer A, Zandvoort MH, Udvarhelyi A, Khadem AF, Menzel A, Hermans J, Shoeman RL, Wessels HJ, van den Heuvel LP, Russ L, Schlichting I, Jetten MS, Op den Camp HJ. Evolution of a new enzyme for carbon disulphide conversion by an acidothermophilic archaeon. Nature. 2011 Oct 19;478(7369):412–6. doi: 10.1038/nature10464. PMID: 22012399.
superpathway of sulfide oxidation (Starkeya novella)

Accession ID: BioCyc:META_PWY-5335
  • 10.1074/jbc.275.18.13202
  • 10.1099/mic.0.26212-0
 Rohwerder T, Sand W. The sulfane sulfur of persulfides is the actual substrate of the sulfur-oxidizing enzymes from Acidithiobacillus and Acidiphilium spp. Microbiology (Reading). 2003 Jul;149(Pt 7):1699–710. doi: 10.1099/mic.0.26212-0. PMID: 12855721.; Kappler U, Bennett B, Rethmeier J, Schwarz G, Deutzmann R, McEwan AG, Dahl C. Sulfite:Cytochrome c oxidoreductase from Thiobacillus novellus. Purification, characterization, and molecular biology of a heterodimeric member of the sulfite oxidase family. J Biol Chem. 2000 May 05;275(18):13202–12. doi: 10.1074/jbc.275.18.13202. PMID: 10788424.
sulfate activation for sulfonation

Accession ID: BioCyc:YEAST_PWY-5340		 -
cyanide detoxification I

Accession ID: BioCyc:ARA_ASPSYNII-PWY
  • 10.1007/s11103-005-6217-9
  • 10.1074/jbc.m007890200
  • 10.1104/pp.123.3.1163
 Piotrowski M, Volmer JJ. Cyanide metabolism in higher plants: cyanoalanine hydratase is a NIT4 homolog. Plant Mol Biol. 2006 May;61(1-2):111–22. doi: 10.1007/s11103-005-6217-9. PMID: 16786295.; Piotrowski M, Schönfelder S, Weiler EW. The Arabidopsis thaliana isogene NIT4 and its orthologs in tobacco encode beta-cyano-L-alanine hydratase/nitrilase. J Biol Chem. 2001 Jan 26;276(4):2616–21. doi: 10.1074/jbc.m007890200. PMID: 11060302.; Hatzfeld Y, Maruyama A, Schmidt A, Noji M, Ishizawa K, Saito K. beta-Cyanoalanine synthase is a mitochondrial cysteine synthase-like protein in spinach and Arabidopsis. Plant Physiol. 2000 Jul;123(3):1163–71. PMID: 10889265; PMCID: PMC59079.
L-cysteine biosynthesis I

Accession ID: BioCyc:ARA_CYSTSYN-PWY
  • 10.1016/j.jplph.2005.11.013
  • 10.1016/s0378-1119(00)00261-4
  • 10.1074/jbc.273.49.32739
  • 10.1104/pp.104.045377
  • 10.1124/jpet.106.118612
 Wu BJ, Di Girolamo N, Beck K, Hanratty CG, Choy K, Hou JY, Ward MR, Stocker R. Probucol [4,4'-[(1-Methylethylidene)bis(thio)]bis-[2,6-bis(1,1-dimethylethyl)phenol]] Inhibits Compensatory Remodeling and Promotes Lumen Loss Associated with Atherosclerosis in Apolipoprotein E-Deficient Mice. The Journal of Pharmacology and Experimental Therapeutics. 2007 May;321(2):477–84. doi: 10.1124/jpet.106.118612.; Wirtz M, Hell R. Functional analysis of the cysteine synthase protein complex from plants: structural, biochemical and regulatory properties. J Plant Physiol. 2006 Feb;163(3):273–86. doi: 10.1016/j.jplph.2005.11.013. PMID: 16386330.; Kawashima CG, Berkowitz O, Hell R, Noji M, Saito K. Characterization and expression analysis of a serine acetyltransferase gene family involved in a key step of the sulfur assimilation pathway in Arabidopsis. Plant Physiol. 2005 Jan;137(1):220–30. PMID: 15579666; PMCID: PMC548853.; Jost R, Berkowitz O, Wirtz M, Hopkins L, Hawkesford MJ, Hell R. Genomic and functional characterization of the oas gene family encoding O-acetylserine (thiol) lyases, enzymes catalyzing the final step in cysteine biosynthesis in Arabidopsis thaliana. Gene. 2000 Aug 08;253(2):237–47. doi: 10.1016/s0378-1119(00)00261-4. PMID: 10940562.; Noji M, Inoue K, Kimura N, Gouda A, Saito K. Isoform-dependent Differences in Feedback Regulation and Subcellular Localization of Serine Acetyltransferase Involved in Cysteine Biosynthesis from Arabidopsis thaliana. Journal of Biological Chemistry. 1998 Dec;273(49):32739–45. doi: 10.1074/jbc.273.49.32739.
sulfate reduction I (assimilatory)

Accession ID: BioCyc:VCHO_SO4ASSIM-PWY		 -