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MetaCyc Release Notes History

This document summarizes the release history of MetaCyc.

 

MetaCyc Statistics by Year
2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2004 2003 2002 2001 Description
Metabolic Pathways 2642 2609 2507 2411 2255 2097 1928 1790 1642 1436 1203 1010 800 692 528 491 460 445 Number of metabolic pathways, excluding superpathways
Reactions 14971 14654 13924 13074 12074 11409 10481 9609 8988 8248 7312 6576 5871 5520 4955 4858 4294 4218 Number of biochemical reactions
Enzymes 11848 11680 11306 10789 10100 9148 8426 7611 6912 6056 5127 4582 3527 3029 1940 1618 1267 1115 Number of enzymes that catalyze biochemical reactions
Genes 12138 11962 11522 10928 10187 9119 8317 7509 6675 5709 4748 4161 3630 2931 1821 1673 600 0 Number of genes
Chemical Compounds 14847 14411 13585 12792 11681 10965 10157 9277 8869 8363 7234 6561 5254 4817 3551 3029 2404 2335 Number of chemical compounds
Organisms 2941 2914 2831 2740 2579 2460 2362 2216 2072 1834 1549 1077 729 601 302 222 174 158 The number of distinct taxa that pathways in MetaCyc are labeled to occur in [more]
Citations 56914 55666 51482 47838 43818 37570 36796 31145 26848 21713 17916 15875 10658 8599 5050 3619 2718 2381 Number of distinct references cited within MetaCyc

Note: The statistics for each year pertain to the last MetaCyc version released in that year.
NA = Not available.
Click here for information on the taxonomic distribution of MetaCyc pathways.

 

Release Notes for MetaCyc Version 22.0

MetaCyc KB Statistics
Pathways 2642
Reactions 14971
Enzymes 11848
Chemical Compounds 14847
Organisms 2941
Citations 56914
EC numbers 6093
Textbook Page Equivalency 9194

Released on Apr ?, 2018

New and Updated Pathways

We have added 41[more info] new pathways to MetaCyc since the last release. In addition, we significantly revised 43 pathways by modifying pathway diagrams, adding commentary, and updating enzyme and gene information, for a total of 84 new and updated pathways. We also added one new superpathway.

New Pathways

Cobamide biosynthesis: The cobamides are complex cobalt-containing cofators that are required for the enzymatic activity of many enzymes. Four of the six coordination sites of the cobalt ion are provided by the corrin ring, while the other two are provided by upper (Coβ) and lower (Coα) ligands. Most readers are likely familiar with adenosylcobalamin, the cofactor used by eukaryotic organisms in which the two ligands are 5'-deoxyadenosyl and 5,6-dimethylbenzimidazole, respectively. However, most bacteria utilize different forms of cobamides in which the upper ligand is often a methyl group while the lower ligand is one of 16 different compounds. We have added a large number of pathways that describe the biosynthesis of these bacterial cobamides, rearranged our current cobamide biosynthesis pathways, and added a few new cobamide salvage pathways.

Siderophore biosynthesis: Iron is an essential trace element. In the presence of oxygen, ferrous iron is rapidly oxidized to ferric iron, which tends to form insoluble compounds and becomes unavailable to organisms. As a result, the level of physiologically available iron can drop far below 1 μM and become growth-limiting for bacteria. To survive, many bacteria evolved specialized transport systems called siderophores, which are low molecular mass compounds that complex and retract iron ions.
We have added several new siderophore biosynthesis pathways (and revised an existing one), bringing the total of siderophore biosynthetic pathways in MetaCyc to 26.

Archeal pathways: We added two new pathways found in archaebacteria. One pathway describes methionine biosynthesis utilizing hydrogen sulfide as the sulfur source. The other pathway described sulfur reduction in the thermophile Pyrococcus furiosus.

Isonitrile compounds biosynthesis: Isonitrile-functionalized compounds are not very common, though analyses of metagenomic sequences suggest that the enzymes that produce them are much more prevalent than previously thought. We added pathways describing the biosynthesis of three such compounds. The first compound, 3-[(E)-2-isocyanoethenyl]-1H-indole, has antibacterial activity against Gram-positive bacteria. Paerucumarin is an iron-chelating compound whose function is not yet known, while rhabduscin, a potent inhibitor of insect tyrosinase (EC 1.14.18.1), is produced by bacterial symbionts of nematodes that infect insect larvae, and is used as a chemical weapon by the nematodes.

Hapalindole-type alkaloids biosynthesis: Hapalindole-type alkaloids are a group of hybrid isoprenoid-indole alkaloids produced solely by members of Subsection V of the cyanobacteria, such as the Fischerella and Hapalosiphon genera. These compounds often have antibacterial, antimycotic, or antialgal activities.

Protein glycosylation pathways: We added two new protein glycosylation pathways. One pathway describes the formation of the core M3 glycan on mammalian proteins, and the other describes the extension of core M3 to the complex glycan found on the α-dystroglycan protein.

Electron transfer pathways: We added two new bacterial anaerobic electron transfer pathways that utilize hydrogen peroxide as the electron acceptor via the activity of cytochrome c peroxidase (ccp). Other New Biosynthetic Pathways Other New Degradation Pathways

New Superpathways

Revised Pathways

Glycan pathways: Due to the size and complexity of complex glycans, pathways describing their biosynthesis and degradation are difficult to follow when using the full molecular detail of the molecules involved. The use of GlycoCT icons makes such diagrams much easier to follow. During this release we have updated many of our existing glycan pathways to use GylcoCT icons (Ceroni et al,Source Code Biol Med. 2007 Aug 7;2:3).

Glutathione-mediated detoxification: We have revised two existing pathway variants that describe a common route for detoxification and processing of xenobiotics, found in fungi, plants, and animals. The xenobiotics are conjugated to glutathione, followed by sequestration and degradation.

Other revised biosynthetic pathways

Other revised degradation pathways

Other Improvements

Update of EC Reactions:

During this quarter we have updated the Enzyme Commission (EC) definitions in MetaCyc with the latest information (as of March 2018) from the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) and the Joint Commission on Biochemical Nomenclature (JCBN), available from the ExplorEnz database. MetaCyc now contains 6093 EC numbers (including internal M numbers).


 

Release Notes for MetaCyc Version 21.5

MetaCyc KB Statistics
Pathways 2609
Reactions 14654
Enzymes 11680
Chemical Compounds 14411
Organisms 2914
Citations 55666
EC numbers 6044
Textbook Page Equivalency 8968

Released on Nov 28, 2017

New and Updated Pathways

We have added 37[more info] new pathways to MetaCyc since the last release. In addition, we significantly revised 8 pathways by modifying pathway diagrams, adding commentary, and updating enzyme and gene information, for a total of 46 new and updated pathways. We also added one new superpathway.

New Pathways of General Applicability

N-linked glycosylation is an important protein post-translational modification in eukaryotes and archaea, and very rarely, in bacteria. During this process certain oligosaccharides are attached to an L-asparagine residue in the polypeptide chain of target proteins. The composition and structure of the oligosaccharide varies greatly among kingdoms and to a lesser degree among species. N-linked glycosylation in eukaryotes consists of three stages: the initial synthesis of a high-mannose, dolichol phosphate-linked precursor tetradecasaccharide and its transfer from the dolichol phosphate anchor to a newly synthesized polypeptide; the trimming (processing) of these high-mannose structures by α-glucosidases and α-mannosidases, which occurs in the ER and Golgi complex; and the synthesis of complex branched oligosaccharide chains, carried out by Golgi glycosyltransferases. In the past MetaCyc only contained a pathway describing the first stage. We have now added pathways describing all stages of the process in multiple kingdoms, and revised an existing archaeal pathway. New and revised N-glycosylation pathways include:

Carotenoid metabolism: Carotenoids are isoprenoid pigments in the yellow to red color range. They are commonly produced by photosynthetic organisms, but also by some non-photosynthetic fungi and bacteria. In photosynthetic organisms cartenoids participate in light harvesting and provide protection against photooxidative stress through energy-dissipation of excess light absorbed by the antenna pigments. In non-photosynthetic organisms carotenoids serve multiple roles, such as antioxidants, virulence factors, and modulators of membrane function. Animals, including humans, cannot synthesize carotenoids, but require them for the synthesis of retinoids and vitamin A. We have reorganized and updated our coverage of carotenoid biosynthesis by adding all known pathways as of September 2017. New pathways include:

 

We also revised several existing carotenoid biosynthesis pathways including:

Bioluminescence: Throughout evolution, bioluminescence has been reinvented many times; some 30 different independent systems are still extant. We added two new pathways that describe bioluminescence in fungi and in the fire squid, bringing the total of MetaCyc bioluminescence pathways to seven.

Brominated compounds biosynthesis: Marine organisms, including bacteria, algae and invertebrates, produce many brominated compounds. In some marine sponges within the Dysideidae family polybrominated diphenyl ethers can exceed 10% of the sponge tissue by dry weight. In many cases the origin of the compounds was shown to be symbiotic bacteria. We have added several new pathways that describe bacterial biosynthesis of organobromine compounds.

New Animal Pathways

  • anandamide degradation (from HumanCyc)
  • dopamine degradation (from HumanCyc)
  • Updated Microbial Pathways

  • benzoyl-CoA degradation II (anaerobic)
  • benzoate degradation I (aerobic)
  • benzoyl-CoA degradation III (anaerobic)
  • D-arabitol degradation
  • heme biosynthesis I
  • heme biosynthesis II
  • lipoate biosynthesis and incorporation I
  • lysine degradation II
  • lysine fermentation to acetate and butyrate
  • methanogenesis from acetate
  • methanogenesis from methanol
  • NAD biosynthesis III
  • pentachlorophenol degradation
  • peptidoglycan biosynthesis I
  • pyruvate dehydrogenase complex pathway
  • ribitol degradation
  • xylitol degradation
  • New Pant Pathways

  • acetyl-CoA biosynthesis (from citrate)
  • artemisinin biosynthesis
  • capsanthin and capsorubin biosynthesis
  • cardiolipin biosynthesis
  • coumarin biosynthesis (via 2-coumarate)
  • ferulate and sinapate biosynthesis
  • glucosinolate breakdown
  • lactucaxanthin biosynthesis
  • morphine biosynthesis
  • salvianin biosynthesis
  • soybean saponin biosynthesis (via soyasapogenol B)
  • superpathway of acetyl-CoA biosynthesis
  • Updated Plant Pathways

  • abscisic acid biosynthesis
  • carotenoid biosynthesis
  • glucosinolate biosynthesis from homomethionine
  • glucosinolate biosynthesis from phenylalanine
  • glucosinolate biosynthesis from tryptophan
  • phospholipase pathway
  • triacylglycerol biosynthesis

  • Release Notes for MetaCyc Version 10.1

    Released on May 19, 2006.

    MetaCyc KB Statistics
    Pathways 759
    Reactions 5797
    Enzymes 3370
    Chemical Compounds 5095
    Organisms 686
    Citations 9799

    New and Updated Pathways

    47 new pathways were added to MetaCyc since the last release. In addition, we significantly revised 21 pathways, by adding commentary and updated enzyme and gene information, for a total of 68 updated pathways.

    In microbial/animal metabolism we added 11 new pathways, and significantly enhanced 13 pathways, for a total of 24 pathways.

    In central metabolism we have updated several pathways covering variants of the tricarboxylic acid (TCA) cycle (both complete and incomplete cycles), glycolysis, and pyruvate fermentation. We updated our coverage of amino-acid biosynthesis and degradation pathways with new pathways for the biosynthesis of isoleucine, arginine, and β-alanine, and for the degradation of tyrosine, phenylalanine and hydroxyproline. We also added a new variant of 2-oxobutanoate degradation, and a new pathway for 2-methylbutyrate biosynthesis.

    In plant metabolism we added 36 new pathways, and enhanced 8 pathways, for a total of 44 pathways.

    New plant primary metabolism pathways include several pathways of fatty acid and sugar-nucleotide metabolism.

    New plant secondary metabolism pathways include the biosynthesis of several anthocyanins and the degradation of chlorophyll. In addition, we added four new pathways describing the biosynthesis of geranyl diphosphate, geranylgeranyl diphosphate and trans,trans-farnesyl diphosphate, which simplify the metabolism of terpenoids. Moreover, four important biosynthetic pathways of Cannabis and hops (the latter being involved in the flavouring of beer) have been added to the database.

    We have also updated and revised several existing pathways: ascorbate biosynthesis; aurone biosynthesis; coenzyme A biosynthesis; isoflavonoid biosynthesis II; NAD/NADH phosphorylation and dephosphorylation; sulfate assimilation III; triacylglycerol degradation; and wighteone and luteone biosynthesis.

    Update of EC Reactions

    During this quarter we have updated the reactions in MetaCyc with the latest information (as of February 2006) from the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB), by  incorporating supplement 11 (see Enzyme Nomenclature Supplement 11).

    New Microbial/Animal Pathways

  • arginine biosynthesis III
  • β-alanine biosynthesis IV
  • biotin-carboxyl carrier protein
  • 4-hydroxyproline degradation II
  • isoleucine biosynthesis II
  • isoleucine biosynthesis III
  • isoleucine biosynthesis IV
  • isoleucine biosynthesis V
  • 2-methylbutyrate biosynthesis
  • 2-oxobutanoate degradation I
  • tyrosine degradation II

    Updated Microbial/Animal Pathways

  • acetyl-coa fermentation to butyrate
  • CMP-KDO biosynthesis I
  • fatty acids biosynthesis (initial steps)
  • glycolysis III
  • 4-hydroxyproline degradation I
  • incomplete reductive TCA cycle
  • isoleucine biosynthesis I
  • 2-oxobutanoate degradation I
  • phenylalanine degradation I
  • pyruvate fermentation to acetate and alanine
  • pyruvate fermentation to acetate and lactate
  • TCA cycle variation I
  • tyrosine degradation I

    New Plant Pathways

  • acacetin biosynthesis
  • acyl-ACP desaturation pathway
  • acyl-ACP thioesterase pathway
  • acyl-CoA synthetase pathway
  • acyl-CoA thioesterase pathway
  • anthocyanin biosynthesis (delphinidin 3-O-glucoside)
  • anthocyanin biosynthesis (pelargonidin 3-O-glucoside, cyanidin 3-O-glucoside)
  • bitter acids biosynthesis
  • cannabinoid biosynthesis
  • chlorophyll a degradation
  • CMP-KDO biosynthesis II (from D-arabinose 5-phosphate)
  • cohumulone biosynthesis
  • 6'-deoxychalcone metabolism
  • fatty acid β-oxidation II (plant, saturated)
  • fatty acid β-oxidation III (plant, unsaturated, odd number)
  • fatty acid β-oxidation IV (plant, unsaturated, even number)
  • GDP-L-galactose biosynthesis
  • geranyldiphosphate biosynthesis
  • geranylgeranyldiphosphate biosynthesis I (cytosolic)
  • geranylgeranyldiphosphate biosynthesis II (plastidic)
  • hesperitin glycoside biosynthesis
  • humulone biosynthesis
  • leucodelphinidin biosynthesis
  • lysine biosynthesis VI
  • naringenin glycoside biosynthesis
  • pelargonidin conjugates biosynthesis
  • phytol salvage pathway
  • ponciretin biosynthesis
  • rose anthocyanin biosynthesis
  • sakuranetin biosynthesis
  • sphingolipid biosynthesis (plants)
  • superpathway of fatty acid biosynthesis II (plant)
  • trans,trans-farnesyl diphosphate biosynthesis
  • trigonelline biosynthesis
  • UDP-D-apiose biosynthesis (from UDP-D-glucuronate)
  • xanthohumol biosynthesis

    Updated Plant Pathways:

  • ascorbate biosynthesis
  • aurone biosynthesis
  • coenzyme A biosynthesis
  • isoflavonoid biosynthesis II
  • NAD/NADH phosphorylation and dephosphorylation
  • sulfate assimilation III
  • triacylglycerol degradation
  • wighteone and luteone biosynthesis


    Release Notes for MetaCyc Version 10.0

    Released on March 13, 2006.

    MetaCyc KB Statistics
    Pathways 719
    Reactions 5598
    Enzymes 3165
    Chemical Compounds 4907
    Organisms 638
    Citations 9149

    New and Updated Pathways

    47 new pathways were added to MetaCyc since the last release. In addition, we significantly revised 15 pathways, by adding commentary and updated enzyme and gene information, for a total of 62 updated pathways.

    In microbial/animal metabolism we added 19 new pathways, and significantly enhanced 9 pathways, for a total of 28 pathways.

    Among the topics that received special attention this quarter were amino acid degradation pathways, including the branched chain amino acids (leucine, isoleucine, and valine), glutamate, methionine, tryptophan, and phenylalanine. Two new degradation pathways of the aromatic pyridine ring were added: nicotinate degradation II, which is an aerobic pathway, and nicotinate degradation III, which is an anaerobic fermentation pathway. Nicotinate (also known as niacin, or vitamin B3) is important in both biological and industrial processes. Additionally, a superpathway of nicotinate degradation was created that includes all three pathway variants of nicotinate degradation.

    In plant metabolism we added 28 new pathways, and enhanced 6 pathways, for a total of 34 pathways.

    New plant primary metabolism pathways include biosynthesis of the the purine precursors of caffeine and theobromine, very long chain fatty acids, sorbitol, chlorophyll, gibberellin and its precursors, and phytyl-PP. A pathway involved in NAD/NADH phosphorylation and dephosphorylation was also added.

    New plant secondary metabolism pathways include the biosynthesis of an isoflavonoid (6,7,4'-trihydroxyisoflavone), a flavone (luteolin), a flavonol (pinobanskin), a stilbene (pinosylvin) and a cinnamic acid derivative (rosmarinic acid). In addition, four new pathways describe the biosynthesis of the purine alkaloids caffeine and theobromine.

    We have also updated and revised several existing pathways, including ureide degradation, resveratrol biosynthesis, biotin biosynthesis, sorbitol utilization, gibberellin inactivation, and chlorophyllide a biosynthesis.

    New microbial/animal pathways:

  • 1,6-anhydro-N-acetylmuramic acid recycling
  • 2-keto glutarate dehydrogenase complex
  • ADP-L-glycero-β-D-manno-heptose biosynthesis
  • branched-chain α-keto acid dehydrogenase complexes
  • gibberellin biosynthesis IV (Gibberella fujikuroi)
  • glutamate degradation VI (to pyruvate)
  • glutamate degradation VIII (to propionate)
  • glycogen biosynthesis II (from UDP-D-Glucose)
  • isoleucine degradation II
  • leucine degradation II
  • leucine degradation III
  • methionine degradation III
  • mevalonate degradation
  • nicotinate degradation II
  • nicotinate degradation III
  • phenylalanine degradation III
  • superpathway of nicotinate degradation
  • tryptophan degradation VIII (to tryptophol)
  • valine degradation II

    Updated microbial/animal pathways:

  • glutamate degradation I
  • glutamate degradation II
  • glutamate degradation VII
  • glycolysis II
  • isoleucine degradation I
  • leucine degradation I
  • pyruvate dehydrogenase complex
  • reductive tricarboxylic acid cycle
  • valine degradation I

    New plant pathways:

  • 6,7,4'-trihydroxyisoflavone biosynthesis
  • caffeine biosynthesis I
  • caffeine biosynthesis II (via paraxanthine)
  • chlorophyll a biosynthesis I
  • chlorophyll a biosynthesis II
  • chlorophyll cycle
  • ent-kaurene biosynthesis
  • GA12 biosynthesis
  • gibberellin biosynthesis I (non C-3, non C-13 hydroxylation)
  • gibberellin biosynthesis II (early C-3 hydroxylation)
  • gibberellin biosynthesis III (early C-13 hydroxylation)
  • luteolin biosynthesis
  • NAD/NADH phosphorylation and dephosphorylation
  • phytyl-PP biosynthesis
  • pinobanksin biosynthesis
  • pinosylvin metabolism
  • purine degradation
  • rosmarinic acid biosynthesis I
  • rosmarinic acid biosynthesis II
  • salvage pathways of purine nucleosides II (plant)
  • SAM cycle
  • sorbitol biosynthesis
  • superpathway of GA12 biosynthesis
  • superpathway of gibberellin biosynthesis
  • superpathway of rosmarinic acid biosynthesis
  • theobromine biosynthesis I
  • theobromine biosynthesis II (via xanthine)
  • very long chain fatty acid biosynthesis

    Updated plant pathways:

  • biotin biosynthesis II
  • chlorophyllide a biosynthesis
  • gibberellin inactivation
  • resveratrol biosynthesis
  • sorbitol utilization
  • ureide degradation


    Release Notes for MetaCyc Version 9.6

    Released on December 15, 2005.

    MetaCyc KB Statistics
    Pathways 692
    Reactions 5520
    Enzymes 3029
    Chemical Compounds 4817
    Organisms 601
    Citations 8599

    New and Updated Pathways

    81 new pathways were added to MetaCyc since the last release. In addition, we significantly revised 36 pathways, by adding commentary and updated enzyme and gene information, for a total of 117 updated pathways.

    In microbial/animal metabolism we added 29 new pathways, and significantly enhanced 33 pathways, for a total of 62 pathways.

    Topics that received special attention this quarter include nitrogen metabolism (citrulline, arginine, 4-aminobutyrate, urea, and polyamines), arsenic detoxification, and bacterial degradation of both naturally occurring compounds and xenobiotics. We expanded our coverage of thiol metabolism to include glutathione amide, glutathionylspermidine and trypanothione, and continued to enhance our coverage of amino acid metabolism with various pathways of arginine, cysteine, histidine, glutamate, and proline metabolism.

    In plant metabolism we added 52 new pathways, and enhanced 3 pathways, for a total of 55 pathways.

    New plant primary metabolism pathways include plant variants of amino acid metabolism (glutamate, methionine, and proline), and pathways of fatty acid and UDP-sugar metabolism.

    New microbial/animal pathways:

  • 4-aminobutyrate degradation II
  • arginine degradation IX (D-arginine dehydrogenase pathway)
  • arginine degradation XI
  • arsenate detoxification I
  • arsenate detoxification II
  • arsenate reduction (respiratory)
  • arsenite oxidation (respiratory)
  • biotin biosynthesis III
  • citrulline-nitric oxide cycle
  • creatinine degradation II
  • creatinine degradation III
  • glutathione amide metabolism
  • glutathionylspermidine biosynthesis
  • histidine degradation II
  • histidine degradation III
  • histidine degradation V
  • IAA biosynthesis IV
  • IAA biosynthesis V
  • imidazole-lactate degradation
  • proline biosynthesis V (from arginine)
  • protein citrullination
  • putrescine biosynthesis I
  • putrescine biosynthesis II
  • putrescine biosynthesis III
  • putrescine degradation III
  • putrescine degradation IV
  • putrescine degradation V
  • superpathway of citrulline metabolism
  • urea cycle
  • Updated microbial/animal pathways:

  • 3-phenylpropionate degradation
  • 4-aminobutyrate degradation I
  • 4-hydroxymandelate degradation
  • aerobactin biosynthesis
  • arginine degradation I
  • arginine degradation II
  • arginine degradation III
  • arginine degradation IV
  • arginine degradation V
  • biotin biosynthesis I
  • citrulline degradation
  • creatinine degradation I
  • cysteine biosynthesis II
  • gallate degradation I
  • gallate degradation II
  • glutamate degradation I
  • glutamate degradation II
  • heme biosynthesis II
  • methylgallate degradation
  • nicotinate degradation
  • nopaline degradation
  • octopine degradation
  • proline degradation I
  • putrescine degradation I
  • putrescine degradation II
  • quinate degradation
  • shikimate degradation
  • spermidine biosynthesis
  • spermine biosynthesis
  • toluene degradation II
  • toluene degradation III
  • toluene degradation V
  • trypanothione biosynthesis
  • New plant pathways:

  • 6-methoxymellein biosynthesis
  • aerobic respiration -- electron donor III
  • aloesone biosynthesis
  • benzoxazinoid glucosides biosynthesis
  • β-pyrazole-1-ylalanine biosynthesis
  • canavanine biosynthesis
  • canavanine degradation
  • coniferin metabolism
  • curcumin glucoside biosynthesis
  • cyclopropane and cyclopropene fatty acid biosynthesis
  • DIBOA / DIMBOA biosynthesis
  • DIMBOA-Glc degradation
  • fatty acid biosynthesis - initial steps II
  • GDP-L-fucose biosynthesis I (from GDP-D-mannose)
  • GDP-L-fucose biosynthesis II (from L-fucose)
  • gibberellin inactivation pathway I
  • gibberellin inactivation pathway II (early-13-hydroxylation GAs)
  • glutamate biosynthesis V
  • glutamate degradation X
  • glycerol degradation IV
  • inositol oxidation pathway
  • kievitone biosynthesis
  • lathyrine biosynthesis
  • lipid-dependent phytate biosynthesis I (via Ins(1,4,5)P3)
  • lipid-dependent phytate biosynthesis II (via Ins(1,3,4)P3)
  • lipid-independent phytate biosynthesis
  • lupeol biosynthesis
  • methionine salvage pathway II
  • mimosine biosynthesis
  • monolignol glucosides biosynthesis
  • pentaketide chromone biosynthesis
  • phylloquinone biosynthesis
  • phytate degradation I
  • phytate degradation II
  • proline biosynthesis IV
  • proline degradation III
  • resveratrol biosynthesis
  • sorbitol degradation II
  • superpathway of isoflavonoids (via naringenin)
  • superpathway of pterocarpan biosynthesis (via daidzein)
  • superpathway of pterocarpan biosynthesis (via formononetin)
  • tetrahydroxyxanthone biosynthesis (from 3-hydroxybenzoate)
  • tetrahydroxyxanthone biosynthesis (from benzoate)
  • UDP-D-galacturonate biosynthesis I (from UDP-D-glucuronate)
  • UDP-D-galacturonate biosynthesis II (from D-galacturonate)
  • UDP-D-xylose biosynthesis
  • UDP-L-arabinose biosynthesis I (from UDP-xylose)
  • UDP-L-arabinose biosynthesis II (from L-arabinose)
  • volatile benzenoid ester biosynthesis
  • volatile cinnamoic ester biosynthesis
  • wighteone and luteone biosynthesis
  • willardiine and isowillardiine biosynthesis
  • Updated plant pathways

  • asparagine biosynthesis II
  • gibberellin biosynthesis
  • sinapate ester biosynthesis

  • Release Notes for MetaCyc Version 9.5

    Released on September 30, 2005.

    MetaCyc KB Statistics
    Pathways 621
    Reactions 5428
    Enzymes 2698
    Chemical Compounds 4620
    Organisms 506
    Citations 7369

     

    New and Updated Pathways

    During this quarter we have added 30 new pathways to MetaCyc, and updated the information in 15 additional pathways, for a total of 45 new or modified pathways .

    In microbial metabolism, we focused primarily on the biochemistry of the important thiols glutathione and mycothiol, the transformations of choline, γ-butyrobetaine, glycine betaine and carnitine, and the biosynthesis and degradation of the amino acids methionine and cysteine. In addition, we added pathways covering the degradation of butanediol and the biosynthesis of the enzyme cofactor lipoate. We also rewrote the pathway for the biosynthesis of teichoic acid, an important component of the cell wall of Gram-positive bacteria.

    In plant metabolism , we have added many new pathways involved in the primary metabolism of plants. Main topics were carbohydrate (galactose, mannitol, and sucrose) metabolism, membrane phospholipids (choline I and II) biosynthesis, enzyme cofactors (tetrahydrofolate, formyltetrahydrofolate and biotin) biosynthesis, asparagine degradation, and biosynthesis of the abiotic stress response secondary metabolite, β-alanine betaine. We also added  two biosynthetic pathways of plant alkaloids (berberine and (S)-reticuline), and covered the biosynthesis of β-alanine and pantothenate.

    Update of EC Reactions

    During this quarter we have updated the reactions in MetaCyc with the latest information (as of January 2005) from the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB), by  incorporating supplement 10 (see Enzyme Nomenclature Supplement 10).

    New Cellular Location Ontology

    We have introduced an improved and expanded cellular component ontology that is used both for specifying enzyme cellular locations, and for describing the compartments involved in transport reactions. Our vocabulary of cellular component terms was expanded from 35 to over 150 terms, which are now organized into classes, subclasses and instances. The terms are also related to each other using multiple relationships such as 'component-of' and 'surrounded-by'. For example, the term "inner membrane (sensu Gram-negative bacteria)" is surrounded by the terms "periplasmic space (sensu Gram-negative bacteria)" and "cell wall (sensu Gram-negative bacteria)", and surrounds the terms "cytoplasm" and "cytosol". These new relationships between cellular locations will allow us to introduce more robust querying, and a better graphical display of protein locations. Whenever possible, the new ontology terms have a cross-reference to the Gene Ontology Consortium's (GO) cellular component ontology.

    More Chemical Structures

    We also continued the addition of chemical structures to our compound library. We have added 724 new structures during this period, and now have 4316 compounds with structures.

    Pathway Tools Software Enhancements

    There have been many enhancements to the Pathway Tools software which is used to query MetaCyc. Please see the Pathway Tools Release Notes for more details.

    New microbial pathways:

  • carnitine degradation II
  • carnitine degradation III
  • choline degradation II
  • γ-butyrobetaine degradation
  • γ-glutamyl cycle
  • glutathione redox reactions I
  • glutathione-mediated detoxification
  • glycine betaine biosynthesis II (Gram-positive bacteria)
  • glycine betaine degradation
  • putrescine degradation II (from EcoCyc)
  • Updated microbial pathways:

  • butanediol biosynthesis
  • choline degradation I
  • formaldehyde oxidation III (mycothiol-dependent)
  • glycine betaine biosynthesis I (Gram-negative bacteria)
  • glycine betaine biosynthesis IV (from glycine)
  • glutathione redox reactions II
  • L-cysteine degradation I
  • lipoate biosynthesis and incorporation  (from EcoCyc)
  • methionine biosynthesis III
  • methionine biosynthesis IV
  • methionine degradation I
  • mycothiol biosynthesis
  • mycothiol-mediated detoxification
  • mycothiol oxidation
  • teichoic acid (poly-glycerol) biosynthesis
  • New plant pathways

  • aerobic respiration
  • asparagine degradation II
  • asparagine degradation III
  • β-alanine betaine biosynthesis
  • β-alanine biosynthesis I
  • β-alanine biosynthesis II
  • β-alanine biosynthesis III
  • berberine biosynthesis
  • biotin biosynthesis III
  • choline biosynthesis II
  • choline biosynthesis III
  • formylTHF biosynthesis I
  • galactose degradation III
  • mannitol biosynthesis
  • mannitol degradation II
  • pantothenate biosynthesis II
  • pantothenate biosynthesis III
  • (S)-reticuline biosynthesis
  • sucrose degradation to ethanol and lactate (anaerobic)
  • tetrahydrofolate biosynthesis I

  • Release Notes for MetaCyc Version 9.1

    Released on May 23, 2005.

    MetaCyc KB Statistics
    Pathways 601
    Reactions 5273
    Enzymes 2458
    Chemical Compounds 4496
    Organisms 456
    Citations 6566

     

    This last quarter has been very productive at MetaCyc. We have added a total of 62 new pathways, and updated the information in 20 additional pathways!

    In microbial metabolism, we added 20 new pathways. These pathways include expanded coverage of the metabolism of the amino acids lysine, isoleucine and tryptophan, the biosynthesis of the important redox cofactor nicotinamide adenine dinucleotide (NAD), a superpathway that ties together the different pathways for aerobic degradation of aromatic compounds found in Pseudomonas, the metabolism of the sugar trehalose, and a few new pathways for the degradation of xenobiotic compounds.

  • aromatic compound degradation (aerobic)
  • benzoate degradation I (aerobic)
  • indole-3-acetate degradation to anthranilate
  • isethionate degradation
  • lysine biosynthesis II
  • lysine biosynthesis III
  • lysine biosynthesis V
  • NAD biosynthesis II (from tryptophan)
  • NAD salvage pathway I
  • superpathway of isoleucine biosynthesis
  • superpathway of NAD biosynthesis in eukaryotes
  • trehalose biosynthesis IV
  • trehalose biosynthesis V
  • trehalose degradation II (high osmolarity)
  • trehalose degradation III
  • trehalose degradation IV
  • trehalose degradation V
  • tryptophan degradation V (via indole-3-acetamide)
  • tryptophan degradation VI (side chain pathway)
  • tryptophan degradation VII (via tryptamine)
  • In plant metabolism we added 38 new pathways. New plant pathways include plant variants of amino acid metabolism, pathways of fatty acid metabolism, plant hormone biosynthesis (brassinosteroids and cytokinins), and secondary metabolism (isoflavonoids, phenylpropanoids, nitrogen-containing glucosides and terpenoids).

  • ammonia assimilation cycle II
  • biochanin A conjugates interconversion
  • brassinosteroid biosynthesis II
  • capsidiol biosynthesis
  • choline biosynthesis
  • cis-zeatin biosynthesis
  • cytokinins 7-N-glucoside biosynthesis
  • cytokinins 9-N-glucoside biosynthesis
  • cytokinins degradation
  • cytokinins-O-glucoside biosynthesis
  • diterpene phytoalexins precursors biosynthesis
  • dTDP-L-rhamnose biosynthesis II
  • fatty acid oxidation pathway II
  • fatty acid oxidation pathway III
  • flavonol biosynthesis
  • formononetin conjugates interconversion
  • glucosinolate biosynthesis from phenylalanine
  • glutamate degradation IX
  • glyceollin biosynthesis I
  • glyceollin biosynthesis II
  • linamarin biosynthesis
  • linamarin degradation
  • maackiain biosynthesis
  • maackiain conjugates interconversion
  • medicarpin biosynthesis
  • medicarpin conjugates interconversion
  • menthol biosynthesis
  • phaseollin biosynthesis
  • phenylalanine biosynthesis III
  • pisatin biosynthesis
  • plant monoterpene biosynthesis
  • proline biosynthesis III
  • sesquiterpenoid phytoalexins biosynthesis
  • sinapate ester biosynthesis
  • sterol biosynthesis
  • trans-zeatin biosynthesis
  • tyrosine biosynthesis II
  • UDP-L-rhamnose biosynthesis
  • In mammalian metabolism we have added a cholesterol biosynthesis pathway from HumanCyc. This pathway describes the biosynthesis of cholesterol from farnesyl diphosphate in an extensive series of 22 reactions.  Combined with the existing mevalonate pathway, which is linked to it, MetaCyc now covers the complete biosynthesis of cholesterol from acetyl-CoA.

  • cholesterol biosynthesis
  • We have also incorporated the following new yeast pathways which were curated by our friends at SGD. Thank you Eurie Hong and Rama Balakrishnan!

  • allantoin degradation II
  • glutamate biosynthesis from glutamine
  • superpathway of NAD biosynthesis in eukaryotes
  • Additional yeast-specific information, provided by SGD, was added to the following existing MetaCyc pathways:

  • glutamate biosynthesis III
  • NAD biosynthesis II (from tryptophan)
  • NAD salvage pathway I
  • Besides entering new pathways, we have been working on adding commentary and updated enzyme and gene information to existing pathways. The following pathways have been revised to reflect current knowledge and to provide better commentary:

  • 1,8-cineole degradation
  • anthocyanin biosynthesis
  • arginine biosynthesis I
  • arginine biosynthesis II
  • brassinosteroid biosynthesis I
  • dolichyl-diphosphooligosaccharide biosynthesis
  • glycine degradation II
  • isoflavonoid biosynthesis II
  • lysine biosynthesis I
  • lysine degradation III
  • NAD biosynthesis I
  • NAD salvage II
  • NAD salvage III
  • nylon-6 oligomer degradation
  • sophorosyloxydocosanoate biosynthesis
  • sophorosyloxydocosanoate degradation
  • sucrose degradation II
  • trehalose biosynthesis I
  • trehalose biosynthesis II
  • trehalose degradation I
  • In addition, we continue to expand our chemical compound library and add chemical structures to the compounds. Over 93% of our 4496 compounds have structures.


    Release Notes for MetaCyc Version 9.0

    Released on February 25, 2005.

    MetaCyc KB Statistics
    Pathways 547
    Reactions 5046
    Enzymes 2062
    Chemical Compounds 3945
    Organisms 341
    Citations 5468

     

  • A total of 20 new pathways have been added to MetaCyc in this release.

    In bacterial metabolism, we have expanded our coverage of ammonia oxidation and folate metabolism by adding new pathways and improving the annotation of existing ones. We have expanded our coverage of the Entner-Doudoroff pathway to include the interesting variations found in different species of archaebacteria, added a new pathway and more information about nitro-aromatic compounds degradation, and added a pathway for the biosynthesis of myo-inositol.

    In plant metabolism we continue to cover secondary metabolism, with new pathways covering the metabolism of phenylpropanoid acid, the biosynthesis of pterocarpan, and the interconversion of genistein and daidzein conjugates.

    In mammalian metabolism we added four human pathways: A pathway for the biosynthesis of the catecholamine neuro transmitters (norepinephrine, epinephrine and dopamine), a pathway for the degradation of the antidepressant drug bupropion, and two pathways that cover the various routes used in the metabolism of nicotine.

    We have also included three new yeast pathways, which were originally created for YeastCyc (SGD). Two of these pathways cover the biosynthesis of major constituents of the fungal plasma membrane (ergosterol and sphingolipid), and the third one describes a variant pathway for lysine biosynthesis.

    The following pathways have been curated in MetaCyc since the last release:

  • ammonia oxidation III
  • ascorbate glutathione cycle
  • daidzein conjugates interconversion
  • Entner-Doudoroff pathway II (non-phosphorylative)
  • Entner-Doudoroff pathway III (semi-phosphorylative)
  • folate polyglutamylation II
  • folate transformations
  • genistein conjugates interconversion
  • myo-inositol biosynthesis
  • 4-nitrobenzoate degradation
  • phenylpropanoid acid pathway
  • pterocarpan biosynthesis
  • The following new pathway has been imported from the EcoCyc database:

  • folate polyglutamylation I
  •  

    The following new yeast pathways have been provided by the YeastCyc database, ands were curated by Eurie L. Hong. Thank you for this contribution!

  • ergosterol biosynthesis
  • lysine biosynthesis II
  • sphingolipid metabolism
  • The following new human pathways have been imported from the HumanCyc database. We thank Teresa Steininger and Tom Kilduff for curation of the catecholamine biosynthesis pathway:

  • bupropion degradation
  • catecholamine biosynthesis
  • nicotine degradation II
  • nicotine degradation III
  • The following existing pathways have been revised to reflect current knowledge and to provide better commentary:

  • ammonia oxidation I (aerobic)
  • ammonia oxidation II (anaerobic)
  • 4-nitrotoluene degradation
  • phospholipid biosynthesis I
  • tetracholroethene degradation
  • In addition, we have continued adding chemical structures to compounds in our chemical compound library. The number of compounds with structures is now 3592.


    Release Notes for MetaCyc Version 8.6

    Released on November 8, 2004.

    MetaCyc KB Statistics
    Pathways 528
    Reactions 4955
    Enzymes 1940
    Chemical Compounds 3551
    Organisms 302
    Citations 5050

    The following new pathways have been added since the last release:

    New bacterial pathways mainly focus on C1 metabolism, specifically the different pathways employed by the methylotrophs, while new plant pathways mostly cover the different pathways employed in the metabolism of the plant hormone indole-3-acetate (IAA), and isoflavonoid biosynthesis.

    Several pathways have been modified. In particular, the plant pathways for anthocyanin and flavonoid biosynthesis, and the bacterial pathways covering glycerol metabolism, formaldehyde assimilation, the degradation of β-alanine, and the degradation of lactose. Modified pathways include:

    In addition, we have added chemical structures to many of the compounds in our chemical compound library. The number of compounds with structures is now 3258.


    Release Notes for MetaCyc Version 8.5

    Released on September 17, 2004.

    MetaCyc KB Statistics
    Pathways 513
    Reactions 4924
    Enzymes 1840
    Chemical Compounds 3467
    Organisms 262
    Citations 4662

    In this upgrade we introduced stereochemistry to our compound library. While not all structures have been updated yet, we are continuously adding stereochemistry information to our library of compounds.

    Another change you would notice is the labeling of genes and proteins in graphical diagrams with the initials of the organism's genus and species names. For example, the trpA gene from E. coli would now appear as Ec-trpA, and the tryptophan synthase protein will appear as tryptophan synthase (Ec). This was done to make it easier to tell genes and proteins appart, such as when genes and proteins from multiple organisms are present in a single pathway.

    In addition, we are continuing our on-going curation of new and existing pathways in MetaCyc. Editing existing pathways involves adding descriptive comments, references, and enzymes, and updating the pathway to reflect the latest available information.

    The following new pathways have been added since the last release:

    The following existing pathways were edited extensively:

    We also continue our effort of adding chemical structures for metabolites and other small molecules to MetaCyc. Currently 3074 of our compounds have a full molecular structure.


    Release Notes for MetaCyc Version 8.1

    Released on June 23, 2004.

    MetaCyc KB Statistics
    Pathways 506
    Reactions 4912
    Enzymes 1813
    Chemical Compounds 3091
    Organisms 243
    Citations 4455

    We are continuing our on-going curation of new and existing pathways in MetaCyc. Editing existing pathways involves adding descriptive comments, references, and enzymes.

    The following new pathways were curated:

    The following existing pathways were edited extensively:

    Many miscellaneous corrections and updates were applied. For example, the pathway for phenylalanine degradation was divided into two pathways, phenylalanine degradation II (anaerobic), which includes the reactions from phenylalanine to phenylacetate and phenylacetate degradation (anaerobic), which includes the reactions from phenylalanine to benzoyl-CoA. One enzyme in phenylacetate degradation (anaerobic) was newly curated.

    In addition a new superpathway was created, β-ketoadipate pathway, which is comprised of the following two pathways: catechol degradation II (ortho-cleavage pathway) and protocatechuate degradation II (ortho-cleavage pathway).

    Chemical structures for metabolites and other small molecules are being continiously added to MetaCyc. Currently 2737 of our compounds have a full molecular structure.


    Release Notes for MetaCyc Version 8.0

    Released on March 12, 2004.

    MetaCyc KB Statistics
    Pathways 496
    Reactions 4873
    Enzymes 1665
    Chemical Compounds 3051
    Organisms 231
    Citations 3771

    We are continuing our on-going curation of new and existing pathways in MetaCyc. Editing existing pathways involves adding descriptive comments, references, and enzymes.

    The following existing pathway was edited extensively:

    Many miscellaneous corrections and updates were applied. For example, the reactions within the superpathway of arginine degradation were reorganized into three separate subpathways:

    Chemical structures for metabolites and other small molecules have been added to MetaCyc.

    The set of enzyme inhibition categories that are represented in MetaCyc has been extended and revised. The new set includes: noncompetitive inhibitors, uncompetitive inhibitors and irreversible inhibitors, in addition to the previously existing categories of competitive inhibitors and allosteric inhibitors. A new category, inhibitors of unknown mechanism replaces two old categories that distinguished between mechanisms that were unknown because they had not been extensively curated versus ones that remained unknown after a substantial literature search, and the new category, other inhibitors, replaces a similar category in previous versions for all inhibitors that were neither competitive nor allosteric.

    Categories of enzyme activation were similarly reexamined, and documentation was updated. Although no new activation categories were added, the two categories for activators whose mechanism was unknown after a minimal versus a substantial literature search were combined into a single category for activators of unknown mechanism.

    See the PTools release notes for additional information on revising the enzyme inhibition and activation categories.

    Enhancements to MetaCyc over the last two years are described in the article, MetaCyc: a multiorganism database of metabolic pathways and enzymes, which was recently published in the Nucleic Acids Research 2004 Database issue.


    Release Notes for MetaCyc Version 7.6

    Released on November 4, 2003.

    MetaCyc KB Statistics
    Pathways 491
    Reactions 4858
    Enzymes 1618
    Chemical Compounds 3029
    Organisms 222
    Citations 3619

    The following pathways were newly curated in MetaCyc:

    The following pathways were imported from EcoCyc:

    The following pathways, which already existed in MetaCyc, were edited extensively:

    Many other miscellaneous corrections and updates have been applied.

    Chemical structures for metabolites and other small molecules have been added to MetaCyc.


    Release Notes for MetaCyc Version 7.5

    Released on August 29, 2003.

    MetaCyc KB Statistics
    Pathways 492
    Reactions 4831
    Enzymes 1571
    Chemical Compounds 2994
    Organisms 214
    Citations 3337

    New pathways have been added to MetaCyc either from recent curation or from importing them from other Pathway/Genome Databases. Existing pathways also have been extensively edited.

    The following pathways were newly curated in MetaCyc:

    • ascorbate biosynthesis
    • cellulose biosynthesis
    • salicylic acid biosynthesis
    • sulfide oxidation II

    The following pathways were imported from EcoCyc:

    • cyclopropane fatty acid (CFA) biosynthesis
    • fructoselysine degradation
    • lipoate biosynthesis and modification
    • lipoate salvage and modification
    • lysine degradation I

    The following pathways were imported from CauloCyc:

    • alanine degradation IV
    • PHB biosynthesis

    The following existing pathways were edited extensively in MetaCyc:

    • coenzyme B biosynthesis
    • thiocyanate degradation I

    MetaCyc display windows now feature full lists of references in addition to links to abstracts that have been supplied previously. The list of references associated with each database object (e.g., pathway, polypeptide, etc.) is located at the bottom of the display window.

    The pathway class hierarchy has been updated and improved to facilitate browsing of metabolic pathways within the BioCyc databases. The pathway hierarchy may be viewed here.

    The Pathway Tools software now supports association of evidence codes with information in BioCyc databases. Evidence codes are used to indicate the type of evidence that supports assertions within these databases. For example, an evidence code can be used to describe whether a pathway was predicted computationally or elucidated experimentally. The presence of a computer icon or a flask icon, respectively, indicate computational versus experimental evidence for an assertion. Click on these icons to obtain more details about the evidence for a given entity. Evidence information will be available in subsequent MetaCyc releases. For more information see the Pathway Tools 7.5 release notes.

    Many other miscellaneous corrections and updates have been applied.

    Chemical structures for metabolites and other small molecules have been added to MetaCyc


    Release Notes for MetaCyc Version 7.1

    Released on May 20, 2003.

    MetaCyc KB Statistics
    Pathways 484
    Reactions 4460
    Enzymes 1520
    Chemical Compounds 2942
    Organisms 201
    Citations 3029

    The following pathways were newly curated in MetaCyc:

    • fructan biosynthesis
    • fructan degradation
    • glycolate degradation II
    • glycosylglyceride desaturation pathway
    • methionine biosynthesis from homoserine II
    • phospholipid desaturation pathway
    • starch degradation
    • thiocyanate degradation II

    The following existing pathways were edited extensively in MetaCyc:

    • triacylglycerol biosynthesis
    • TCA cycle variation IX (TCA cycle in Helicobacter pylori)

    Chemical structures for 27 metabolites and other small molecules have been added to MetaCyc

    Note: The pathway classification hierarchy in MetaCyc is undergoing significant revision. Please be aware that some pathways may be assigned to inappropriate locations in the hierarchy in the version 7.1 release. These assignments will be corrected in the next release.


    Release Notes for MetaCyc Version 7.0

    Released on February 28, 2003.

    MetaCyc KB Statistics
    Pathways 477
    Reactions 4429
    Enzymes 1470
    Chemical Compounds 2921
    Organisms 190
    Citations 2974

    • New pathways have been added to MetaCyc either from recent curation or from importing them from other Pathway/Genome Databases. Existing pathways also have been extensively edited.

      The following pathways were newly curated in MetaCyc:

      • anaerobic ethylbenzene degradation
      • auxin biosynthesis
      • lipoxygenase pathway
      • starch biosynthesis
      • sucrose degradation III

      The following pathways were imported from EcoCyc:

      • L-ascorbate degradation
      • ethanol degradation
      • de novo biosynthesis of purine nucleotides
      • de novo biosynthesis of pyrimidine deoxyribonucleotides
      • de novo biosynthesis of pyrimidine ribonucleotidesribitol degradation
      • glycerol degradation I
      • phenylacetate degradation, aerobic
      • salvage pathways of adenine, hypoxanthine, and their nucleosides
      • salvage pathways of guanine, xanthine, and their nucleosides
      • salvage pathways of pyrimidine deoxyribonucleotides
      • salvage pathways of pyrimidine ribonucleotides

      The following pathways were imported from AraCyc:

      • abscisic acid biosynthesis
      • athocyanin biosynthesis
      • brassinosteroid biosynthesis
      • camalexin biosynthesis
      • carotenoid biosynthesis
      • chlorophyll biosynthesis
      • flavonoid biosynthesis
      • flavonoid biosynthesis II
      • gibberellin biosynthesis
      • indolylmethyl glucosinolate biosynthesis
      • jasmonic acid biosynthesis
      • phenylpropanoid pathway
      • polyamine biosynthesis III
      • proanthocyanidin biosynthesis from flavanols

      The following pathways were imported from MtbRvCyc:

      • mycothiol biosynthesis
      • mycothiol oxidation
      • mycothiol-dependent detoxification pathway
      • mycothiol-dependent formaldehyde detoxification

      The following existing pathways were edited extensively in MetaCyc:

      • asparagine biosynthesis II
      • dibenzo-p-dioxin degradation
      • dibenzofuran degradation
      • ethylene biosynthesis from methionine
      • lipase pathway
      • phospholipid biosynthesis II
      • orcinol degradation
      • resorcinol degradation
      • sucrose biosynthesis
      • sulfate assimilation III
      • tetrachloroethene degradation
      • ureide biosynthesis
      • ureide degradation

    • 400 new chemical structures for metabolites and other small molecules have been added to MetaCyc

    Release Notes for MetaCyc Version 6.5

    Released on August 30, 2002.

    MetaCyc KB Statistics
    Pathways 460
    Reactions 4294
    Enzymes 1267
    Chemical Compounds 2404
    Organisms 174
    Citations 2718

    This release contains several new changes:

    • SRI has started a collaboration with TAIR (The Arabidopsis Information Resource) at the Carnegie Institution. TAIR is responsible for adding new and editing existing plant-specific pathways to MetaCyc.
    • The following pathways were added since the last release. Please note they include both microbial and plant pathways.
      • anaerobic toluene degradation
      • anaerobic m-xylene degradation
      • anaerobic cyclohexane-1-carboxylate degradation
      • C4 photosynthetic carbon assimilation cycle
      • carotenoid biosynthesis
      • cutin biosynthesis
      • epicuticular wax biosynthesis
      • glycosylglyceride biosynthesis
      • lignin biosynthesis
      • nitrate assimilation pathway
      • photorespiration
      • photosynthesis, light reaction
    • In addition to adding new pathways to MetaCyc, we have also edited existing ones. We have added chemical structures, enzymes, reactions, comments and literature citations to existing pathways. The following pathways have been enhanced significantly.
      • glutamate fermentation-the methylaspartate pathway
      • glutamate fermentation-the hydroxyglutarate pathway
      • methionine salvage pathway
      • anaerobic benzoyl-CoA degradation II
    • Genes have been added to MetaCyc for some enzymes.


    Release Notes for MetaCyc Version 6.0

    Released on February 25, 2002.

    MetaCyc KB Statistics
    Pathways 449
    Reactions 4218
    Enzymes 1147
    Chemical Compounds 2339
    Organisms 158
    Citations 2597

    New pathways in this release:

    • dhurrin biosynthesis
    • homoserine degradation I
    • methylglyoxal catabolism
    • mevalonate pathway
    • proline utilization 2
    • purine synthesis 2
    • trehalose biosynthesis 2


    Release Notes for MetaCyc Version 5.6

    Released on June 15, 2001.

    MetaCyc KB Statistics
    Pathways 445
    Reactions 4218
    Chemical Compounds 2335
    Organisms 158
    Citations 2383
    • Each reaction in MetaCyc that has an EC number now contains WWW links to all proteins in the PIR database that have the same EC number.
    • Each reaction in MetaCyc that has an EC number now contains all enzyme names associated with that EC number by the Enzyme Commission.
    • The following pathways were added to MetaCyc since the last release:
      • (+)-camphor degradation
      • 2-nitropropane degradation
      • 3-methylquinoline degradation
      • 4-aminobutyrate degradation II
      • 4-nitrotoluene catabolism
      • myo-inositol degradation
      • p-cymene degradation
      • acetate fermentation
      • acetyl-CoA assimilation
      • acrylonitrile degradation
      • adamantanone catabolism
      • aldoxime metabolism
      • alkanesulfonate monooxygenase two-component system
      • anaerobic ammonium oxidation
      • anaerobic benzoate degradation
      • APS pathway of sulfate reduction
      • arsonoacetate degradation
      • atrazine catabolism II
      • atrazine catabolism III
      • betaine biosynthesis II
      • betaine biosynthesis III
      • bifidum pathway
      • bisulfite reduction
      • butanediol fermentation
      • caprolactam degradation
      • carbon tetrachloride degradation
      • cobalamin biosynthesis, aerobic pathway
      • coenzyme B biosynthesis
      • coenzyme M biosynthesis
      • cyanide degradation
      • degradation of 3-phenylpropionic acid
      • degradation of urate
      • diacetyl fermentation
      • dibenzo-p-dioxin degradation
      • dibenzofuran degradation
      • dibenzothiophene desulfurization
      • disproportionation of elemental sulfur
      • dissimilation of catechol, meta-cleavage
      • dissimilation of protocatechuate, meta-cleavage
      • ethanol-acetate fermentation
      • Formation of acetate from pyruvate
      • gallate degradation, anaerobic
      • glutamate degradation IX
      • glycolysis 2
      • heterofermentative lactate fermentation
      • homocysteine and cysteine interconversion
      • hydrogen oxidation
      • ketogluconate metabolism
      • L-sorbose metabolism
      • lysine degradation III
      • maleamate pathway
      • methionine degradation 2
      • methionine recycling
      • N-acetylneuraminate catabolism
      • nitrite oxidation
      • orcinol metabolism
      • oxidation of galena
      • oxidation of sulfide or sulfur to sulfite
      • phenylmercury acetate degradation
      • phospholipid biosynthesis II
      • phosphonoacetate metabolism
      • propionate catabolism, 2-methylcitrate cycle
      • purine fermentation
      • reductive tricarboxylic acid pathway
      • resorcinol metabolism
      • rhizobactin 1021 biosynthesis
      • RuMP cycle and formaldehyde assimilation
      • serine-isocitrate lyase pathway
      • sorbitol metabolism
      • stachydrine catabolism
      • succinate-propionate fermentation pathway
      • sulfate assimilation 2
      • sulfide oxidation
      • TCA cycle, variation 1
      • TCA cycle, variation 2
      • TCA cycle, variation 3
      • TCA cycle, variation 4
      • TCA cycle, variation 5
      • TCA cycle, variation 6
      • TCA cycle, variation 7
      • TCA cycle, variation 8
      • thiocyanate metabolism
      • threonine biosynthesis from homoserine
      • xylulose-monophosphate cycle

    Release Notes for MetaCyc Version 5.4

    Released on Sept 1, 2000.

    MetaCyc KB Statistics
    Pathways 366
    Reactions 4002
    Chemical Compounds 2180
    Organisms 131
    Citations 604

    The following new pathways are contained in this version of MetaCyc:

    • ureide biosynthesis
    • lipoxygenase pathway I
    • threonine biosynthesis from homoserine
    • nicotine degradation
    • phosphonotase pathway
    • 4-toluenesulfonate degradation pathway
    • sophorosyloxydocosanoate degradation
    • phenol degradation
    • pentachlorophenol degradation pathway
    • tetrachloroethene degradation pathway
    • octane oxidation
    • atrazine catabolism
    • γ-hexachlorocyclohexane degradation pathway
    • cyclohexanol oxidation
    • central benzoyl-CoA pathway
    • aromatic compound degradation
    • 7α-dehydroxylation pathway
    • 4-toluenecarboxylate degradation
    • 2-aminobenzoate degradation
    • 1,4-dichlorobenzene degradation pathway
    • 1,2-dichloroethane degradation pathway
    • sucrose biosynthesis
    • acetylene degradation, anaerobic
    • anaerobic oxidation of phenylalanine
    • ethylene biosynthesis from methionine
    • glyceraldehyde 3-phosphate catabolism
    • pyruvate metabolism
    • pentose phosphate pathway, Mycoplasma pneumoniae
    • glucose fermentation
    • carbon monoxide dehydrogenase pathway
    • interconversion of arginine, ornithine and proline
    • anaerobic glycolysis
    • sophorosyloxydocosanoate biosynthesis
    • trypanothione biosynthesis
    • polyamine biosynthesis, Bacillus subtilis
    • ureide degradation
    • triglyceride biosynthesis
    • phytoalexin biosynthesis
    • galactolipid biosynthesis
    • lipoxygenase pathway II
    • lipases biosynthesis
    • glycerol biosynthesis
    • flavonoid biosynthesis
    • biotin biosynthesis II
    • starch and cellulose biosynthesis
    • phenylalanine biosynthesis IV
    • phenylalanine biosynthesis, Bacillus subtilis
    • asparagine biosynthesis II
    • arginine biosynthesis, Bacillus subtilis
    • ectoine synthesis
    • polythionate oxidation
    • sulfur oxidation
    • sulfur degradation II
    • Fe3+-dependent sulfur oxidation pathway
    • desulfonation of 2-aminobenzenesulfonate, benzenesulfonate and 4-toluenesulfonate
    • 2-aminobenzenesulfonate desulfonation pathway
    • nitroglycerin metabolism
    • denitrification pathway
    • oxidation of ammonia
    • UDP-glucose conversion
    • purine salvage, Halobacterium salinarium
    • purine and pyrimidine metabolism in Mycoplasma pneumoniae

    Release Notes for MetaCyc Version 5.0

    Released on June 1, 1999.

    MetaCyc KB Statistics
    Pathways 296
    Reactions 3779
    Chemical Compounds 1949
    Citations 184

    This first release of the MetaCyc Metabolic Encyclopedia is called version 5.0 so that its version numbers are synchronized with the version numbering of EcoCyc and of Pangea's Pathway Tools software.


    More About New Pathways Numbers

    The MetaCyc Statistics by Year table is updated at each release. The discrepancy between the numbers of new pathways reported in the release notes and those computed by the software in the Statistics by Year table results from curation activities such as interconversions of some pre-existing base pathways and superpathways, deletion of pathways, splitting of some pre-existing large pathways into smaller segments and renaming of database objects.