MetaCyc Release Notes History

This document summarizes the release history of MetaCyc.

 

MetaCyc Statistics by Year

	2009	2008	2007	2006	2005	2004	2003	2002	2001	2000	1999	Description
Metabolic Pathways	1436	1203	1010	879	692	528	491	460	445	366	296	Number of metabolic pathways, excluding superpathways.
Reactions	8248	7312	6576	6113	5520	4955	4858	4294	4218	4002	3779	Number of biochemical reactions.
Enzymes	6056	5127	4582	3841	3029	1940	1618	1267	1115	344	82	Number of enzymes that catalyze biochemical reactions.
Genes	5709	4748	4161	3630	2931	1821	1673	600	0	0	0	Number of genes.
Chemical Compounds	8363	7234	6561	5978	4817	3551	3029	2404	2335	2180	1949	Number of chemical compounds.
Organisms	1834	1549	1077	902	601	302	222	174	158	131	NA	The number of distinct taxa that pathways in MetaCyc are labeled to occur in. [more]
Citations	21713	17916	15875	11934	8599	5050	3619	2718	2381	604	184	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.

   

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Release Notes for MetaCyc Version 13.6

Released on November 21, 2009

 

New and Updated Pathways

We have added 43_{[more info]} new pathways to MetaCyc since the last release.  In addition, we significantly revised 8 pathways by adding commentary and updated enzyme and gene information, for a total of 51 new and updated pathways.  Of the new pathways, 2 were contributed by PMN (Plant Metabolic Network) curators.  We also added 2 new superpathways.

Microbial Metabolism:  Among the additions to microbial metabolism are pathways for the biosynthesis of the indolocarbazole alkaloids rebeccamycin, K-252 and staurosporine. These actinobacterial secondary metabolites, along with related and derived compounds, are known to act as potent inhibitors of DNA topoisomerases and protein kinases. We also added several pathways for the degradation of lignin-derived compounds, including syringate, ferulate, vanillin, vanillate, 5,5'-dehydrodivanillate and guaiacylglycerol-β-guaiacyl ether. We completed our coverage of protocatechuate degradation by adding a third pathway that describes para-cleavage of this important intermediate of aromatic compounds degradation. In sulfur metabolism we added pathways for homotaurine degradation and tetrathionate oxidation. Other additions include a pathway used by marine bacteria that degrade acrylate, and yet another pathway for degradation of L-lysine.

In archaebacterial metabolism we added pathways for the biosynthesis of CDP-archaeol, the precursor of all archaebacterial phospholipids, and of the phospholipid archaetidylinositol.

Animal Metabolism:  We added several pathways that cover the metabolism of inositol phosphates, a group of compounds that includes several important secondary messengers and other compounds that play key roles in signal transduction. Several pathways describe the metabolism of 3-phosphoinositides, D-myo-inositol (1,4,5)-trisphosphate, D-myo-inositol (1,4,5,6)-tetrakisphosphate and D-myo-inositol (3,4,5,6)-tetrakisphosphate. Additional pathways describe several routes for the biosynthesis of D-myo-inositol hexakisphosphate (phytate) and of inositol pyrophosphate compounds.  We also included pathways for the degradation of L-dopa, noradrenaline and adrenaline, purines, and phenylalanine via decarboxylation or transamination of its side chain.

Plant Metabolism:  We continued to expand our coverage of plant secondary metabolites.  We added a pathway for the biosynthesis of echinatin, a retrochalcone that is one of several secondary metabolites present in licorice, a substance derived from the root and rhizome of the genus Glycyrrhiza. We also added a pathway for the biosynthesis of coumestrol, a coumestan isoflavone found in many leguminous plants, many of which act as phytoestrogens in mammals.  Other new pathways include the biosynthesis of flavonol glucosides, the protoberberine alkaloid dehydroscoulerine, the cytotoxic alkaloid camptothecin, phaselic acid, and benzoylanthranilate, the precursor of dianthranmides.  We also added a pathway for phosphate acquisition and updated a previously curated pathway for ethylene biosynthesis from methionine.

New External Database Links for Compounds:  To improve correlation with other databases, we have added the following numbers of new database links from MetaCyc compounds to external databases: 105 ChEBI compounds, 503 PubChem compounds and 504 KEGG compounds.  A total of 4311 MetaCyc compounds are now linked to KEGG.

New Pathways

3-phosphoinositide biosynthesis

3-phosphoinositide degradation

5,5'-dehydrodivanillate degradation

acetaldehyde biosynthesis I

acetaldehyde biosynthesis II

acrylate degradation

archaetidylinositol biosynthesis

benzoylanthranilate biosynthesis

camptothecin biosynthesis

CDP-archaeol biosynthesis

D-myo-inositol (1,3,4)-trisphosphate biosynthesis

D-myo-inositol (1,4,5)-trisphosphate biosynthesis

D-myo-inositol (1,4,5)-trisphosphate degradation

D-myo-inositol (1,4,5,6)-tetrakisphosphate biosynthesis

D-myo-inositol (3,4,5,6)-tetrakisphosphate biosynthesis

D-myo-inositol-5-phosphate metabolism

D-myo-inositol hexakisphosphate biosynthesis I

D-myo-inositol hexakisphosphate biosynthesis II (mammalian)

D-myo-inositol hexakisphosphate biosynthesis IV (Dictyostelium)

dehydroscoulerine biosynthesis

ferulate degradation

flavonol glucosylation I

guaiacylglycerol-β-guaiacyl ether degradation

homotaurine degradation

inositol pyrophosphates biosynthesis

K-252 biosynthesis

L-dopa degradation

lysine degradation X

noradrenaline and adrenaline degradation

ornithine degradation II (Stickland reaction)

phaselic acid biosynthesis

phenylalanine degradation IV (mammalian, via side chain)

phosphate acquisition

phosphinothricin tripeptide biosynthesis

protocatechuate degradation III (para-cleavage pathway)

purine degradation IV (aerobic)

rebeccamycin biosynthesis

staurosporine biosynthesis

syringate degradation

tetrathionate oxidation

vanillin and vanillate degradation

New Pathways from Plant Metabolic Network (PMN)

coumestrol biosynthesis

echinatin biosynthesis

New Superpathways

superpathway of D-myo-inositol (1,4,5)-trisphosphate metabolism

superpathway of inositol phosphate compounds

Updated Pathways

arginine, ornithine and proline interconversion

ethylene biosynthesis from methionine

gallate degradation II

lysine degradation VI

methylgallate degradation

protocatechuate degradation I (meta-cleavage pathway)

superpathway of sulfide oxidation (Acidithiobacillus ferrooxidans)

xylogalacturonan biosynthesis

 

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Release Notes for MetaCyc Version 13.5

Released on Oct 7th, 2009

MetaCyc KB Statistics

Pathways	1399
Reactions	8094
Enzymes	5857
Chemical Compounds	8221
Organisms	1795
Citations	20860

 

New and Updated Pathways

We have added 46_{[more info]} new pathways to MetaCyc since the last release.  In addition, we significantly revised 13 pathways by adding commentary and updated enzyme and gene information, for a total of 64 new and updated pathways.  Of the new pathways, 2 were contributed by PMN (Plant Metabolic Network) curators (www.plantcyc.org).  We also added 8 new superpathways.

Microbial Metabolism:  We added an RNA-dependent cysteine biosynthesis pathway found in the Euryarchaeota, two pathways for the salvage of adenosylcobalamin, several pathways describing biosynthesis of carotenoid compounds in bacteria, including neurosporin, zeaxanthin-β-D-diglucoside, synechoxanthin, myxol-2' fucoside and spheroidene, a pathway for the biosynthesis of the siderophore petrobactin, a novel pathway for the biosynthesis of the common electron carrier menaquinone, and a pathway for the biosynthesis of the fatty acid palmitoleate. We also created a superpathway describing the complete biosynthesis of fatty acids in E. coli and imported a pathway for methylthioadenosine degradation from EcoCyc.

Animal Metabolism:  We added a pathway for the biosynthesis of selenocysteine that is found in both eukaryotes and archaea.  We also covered thyroid hormone biosynthesis and metabolism, pathways for the degradation of tryptophan and serotonin, and pathways for the biosynthesis of phosphatidylethanolamine and cysteine.

Plant Metabolism:  We enhanced our coverage of glucosinolates, a class of nitrogen and sulfur containing secondary metabolites involved in plant pathogen defense.  New pathways included glucosinolate biosynthesis from di-, tri-, tetra-, penta- and hexahomomethionine, as well as two breakdown (activation) pathways of indole glucosinolates.  We also added a plant pathway for isoprene biosynthesis.  Isoprene emissions from trees and other plants have a major effect on atmospheric chemistry.  In addition, we curated a pathway for methyl indole-3-acetate interconversion showing one of several ways that plants can modulate the biological activity of this hormone.

Also in plant metabolism we covered the biosynthesis of 12 new plant sesquiterpenoids including the phytotoxin botrydial, plant defense compounds curcumene and bergamotene,  and compounds used in the flavor, fragrance and drug industries.  We also curated four new polyketide biosynthetic pathways and pathways for biosynthesis of the diterpenoid  phytoalexin casbene, the polyamine putrescine, the terpenophenolic compound olivetol involved in plant defense, and the hormone tuberonate glucoside.  In addition, we added an aldehyde oxidation pathway, a pathway for dihydroconiferyl aldehyde biosynthesis and we reviewed an existing homogalacturonan degradation pathway.

New External Database Links for Compounds and Reactions

To improve correlation with other databases, we have added the following numbers of new database links from MetaCyc compounds and reactions to external databases: 922 KEGG compounds, 304 ChEBI compounds, 900 PubChem compounds, and 3269 KEGG reactions.

We thank Dr. Daniel Kliebenstein of the University of California Davis for providing valuable feedback on glucosinolate pathway curation.

New Pathways

β-caryophyllene biosynthesis

β-cubebene biosynthesis

adenosylcobalamin salvage from cobalamin

adenosylcobalamin salvage from cobinamide II

aldehyde oxidation I

aloesone biosynthesis II

aromatic polyketides biosynthesis

barbaloin biosynthesis

bergamotene biosynthesis I

bergamotene biosynthesis II

botrydial biosynthesis

casbene biosynthesis

curcumene biosynthesis

cysteine biosynthesis II (RNA-dependent)

demethylmenaquinone-8 biosynthesis II

eudesmol biosynthesis

myxol-2' fucoside biosynthesis

neurosporene biosynthesis

olivetol biosynthesis

palmitoleate biosynthesis I

patchoulol biosynthesis

petrobactin biosynthesis

phosphatidylethanolamine biosynthesis III

plumbagin biosynthesis

putrescine biosynthesis IV

santalene biosynthesis

selenocysteine biosynthesis II (archaea and eukaryotes)

selinene biosynthesis

serotonin degradation

spheroidene and spharoidenone biosynthesis

synechoxanthin biosynthesis

thyroid hormone biosynthesis

thyroid hormone metabolism I (via deiodination)

thyroid hormone metabolism II (via conjugation and/or degradation)

tryptophan degradation X (mammalian, via tryptamine)

tuberonate glucoside biosynthesis

valencene and 7-epi-α-selinene biosynthesis

zeaxanthin-β-D-diglucoside biosynthesis

zerumbone biosynthesis

New Pathways from Plant Metabolic Network (PMN)

aliphatic glucosinolate biosynthesis, side chain elongation cycle

dihydroconiferyl aldehyde biosynthesis

glucosinolate biosynthesis from dihomomethionine

glucosinolate biosynthesis from hexahomomethionine

glucosinolate biosynthesis from pentahomomethionine

glucosinolate biosynthesis from tetrahomomethionine

glucosinolate biosynthesis from trihomomethionine

indole glucosinolate breakdown (active in intact plant cell)

indole glucosinolate breakdown (insect chewing induced)

isoprene biosynthesis

methyl indole-3-acetate interconversion

New Pathways from EcoCyc

methylthioadenosine degradation

New Superpathways

cysteine biosynthesis III (mammalia)

cysteine biosynthesis IV (fungi)

superpathway of flavones and derivatives biosynthesis

superpathway of menaquinone-8 biosynthesis II

superpathway of 5-aminoimidazole ribonucleotide biosynthesis

superpathway of unsaturated fatty acids biosynthesis (E. coli)

superpathway of fatty acids biosynthesis (E. coli)

tryptophan degradation XI (mammalian, via kynurenine)

Updated Pathways

(S)-reticuline biosynthesis I

abietic acid biosynthesis

astaxanthin biosynthesis

chorismate biosynthesis I

cysteine biosynthesis I

fluorene degradation I

galactose degradation I (Leloir pathway)

homogalacturonan degradation

jasmonic acid biosynthesis

phytyl diphosphate biosynthesis

proanthocyanidin biosynthesis from flavanols

superpathway of heme biosynthesis from uroporphyrinogen-III

ternatin C5 biosynthesis

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Release Notes for MetaCyc Version 13.1

Released on June 19, 2009

MetaCyc KB Statistics

Pathways	1355
Reactions	7837
Enzymes	5792
Chemical Compounds	7979
Organisms	1735
Citations	19994

 

New and Updated Pathways

We have added 56_{[more info]} new pathways to MetaCyc since the last release.  In addition, we significantly revised 10 pathways by adding commentary and updated enzyme and gene information, for a total of 66 new and updated pathways.  Of the new pathways, eight were contributed by PMN (Plant Metabolic Network) curators (www.plantcyc.org).  We also added six new superpathways, one of which was contributed by PMN.

During this release we have expanded our coverage of microbial pathways for the degradation of aromatic compounds, with an emphasis on chloro-substitution.  Other fields that received special attention were archaeal metabolic pathways and the biosynthesis of bacterial auto-inducer compounds.

In animal metabolism, we added pathways for the biosynthesis of dolichol and dolichyl-phosphate, creatine-phosphate, histamine and four pathways for the biosynthesis of CMP-sialic acid derivatives.  We also added a histamine degradation pathway.

In plant metabolism we curated pathways for biosynthesis of the plant hormones indole-3-acetyl amino acids, jasmonyl amino acids and hydroxyjasmonate sulfate, as well as the flavonoids quercetinsulphates, chrysoeriol and luteolin glycosides.  In addition, we added pathways for thiamine (vitamin B1) biosynthesis, serine racemization and calamenene terpenoid biosynthesis.

During this release period all MetaCyc compounds have been indexed in the NCBI PubChem database and 6,774 corresponding links from MetaCyc to PubChem have been either updated or added.

We thank Dr. Kuni Takayama from the William S. Middleton Memorial Veterans Hospital, Madison, WI for his useful advice concerning the Mycobacterium tuberculosis mycolate biosynthesis pathway.

New Pathways

2,4,5-trichlorophenoxyacetate degradation

2,4,6-trichlorophenol degradation

2,4-dichlorotoluene degradation

2,5-dichlorotoluene degradation

2-aminophenol degradation

2-chlorobenzoate degradation

3,4-dichlorobenzoate degradation

3,4-dichlorotoluene degradation

3-chlorobenzoate degradation II (via protocatechuate)

3-chlorobenzoate degradation III (via gentisate)

3-chlorocatechol degradation II (ortho)

3-chlossrocatechol degradation III (meta pashsway)

3-dehydroquinate biosynthesis I

3-dehydroquinate biosynthesis II (archaea)

4-chlorobenzoate degradation

4-methylcatechol degradation (ortho cleavage)

6-hydroxymethyl-dihydropterin diphosphate biosynthesis

archaetidylserine biosynthesis

autoinducer AI-1 biosynthesis

autoinducer AI-2 biosynthesis

autoinducer AI-2 biosynthesis II (Vibrio)

biphenyl degradation

chlorinated phenols degradation

chorismate biosynthesis from 3-dehydroquinate

cis-calamenene related sesquiterpenoids biosynthesis

CMP-2-keto-3-deoxy-D-glycero-D-galacto-nononate biosynthesis

CMP-N-acetylneuraminate biosynthesis I (eukaryotes)

CMP-N-acetylneuraminate biosynthesis II (bacteria)

CMP-N-glycoloylneuraminate biosynthesis

CMP-pseudaminate biosynthesis

creatine-phosphate biosynthesis

cysteine biosynthesis II (Archaea)

dolichol and dolichyl phosphate biosynthesis

flavin biosynthesis II (archaea)

flavin biosynthesis III (eukaryotes)

gentisate degradation

glycerol degradation II

glycerol degradation III

histamine biosynthesis

histamine degradation

lanosterol biosynthesis

methylsalicylate degradation

mevalonate pathway II (archaea)

salicylate degradation I

serine racemization

(S)-reticuline biosynthesis II

tetrahydromethanopterin biosynthesis

tyrosine biosynthesis IV

New Pathways from Plant Metabolic Network (PMN)

chrysoeriol biosynthesis

hydroxyjasmonate sulfate biosynthesis

indole-3-acetyl-amino acid biosynthesis

jasmonoyl-amino acid conjugates biosynthesis I

jasmonoyl-amino acid conjugates biosynthesis II

luteolin glycosides biosynthesis

quercetinsulphates biosynthesis

thiamine biosynthesis II

New Superpathways

alliin degradation

gluconeogenesis II (Methanobacterium thermoautotrophicum)

Methanobacterium thermoautotrophicum biosynthetic metabolism

superpathway of jasmonoyl amino acid biosynthesis

superpathway of salicylate degradation

superpathway of sialic acid and CMP-sialic acid biosynthesis

 Updated Pathways

γ-hexachlorocyclohexane degradation

coenzyme B biosynthesis

glutamate biosynthesis V

glycine degradation (creatine biosynthesis)

IAA biosynthesis I

IAA conjugate biosynthesis II

pentachlorophenol degradation

removal of superoxide radicals

S-adenosyl-L-methionine cycle II (eukaryotic)

(S)-reticuline biosynthesis I

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Release Notes for MetaCyc Version 13.0

Released on March 9, 2009

MetaCyc KB Statistics

Pathways	1289
Reactions	7686
Enzymes	5528
Chemical Compounds	7722
Organisms	1683
Citations	19155

 

The MetaCyc Web site has been redesigned to provide a new toolbar and new search commands. For quick instructions on how to use it, click here, or watch the webinar on how to use the new site.

New and Updated Pathways

We have added 92_{[more info]} new pathways to MetaCyc since the last release.  In addition, we significantly revised 17 pathways by adding commentary and updated enzyme and gene information, for a total of 109 new and updated pathways. Of the new pathways, 16 were contributed by PMN (Plant Metabolic Network) curators (www.plantcyc.org); four were contributed by MouseCyc (Mouse Genome Informatics) curator Alexei Evsikov (mousecyc.jax.org); two were contributed by the Rhodococcus Genome Project, Eltis laboratory (www.rhodococcus.ca); and one was contributed by SRI postdoctoral fellow Malabika Sarker.  We also added four new superpathways, one of which was contributed by PMN.

During this release we have significantly expanded our coverage of bacterial degradation pathways for chloro-aromatic compounds, important pollutants of the environment. Another field that received extensive curation concerns the metabolism of dimethylsulfide, the major contributor of sulfur to the atmosphere, and related compounds.  Other additions include new pathways for the biosynthesis of tyrosine, mannosylfructose, zymosterol, indican and indigo, as well as pathways for the degradation of pseudouridine, acetoin, citrate, 4-sulfocatechol, ethanedisulfonate, malonate, anthranilate, 4-ethylphenol and nitrilotriacetate.

A new pathway for mycolate biosynthesis in Mycobacterium tuberculosis H37Rv represents an important pathway for the design of anti-tubercular drugs.  Mycolic acids are components of the mycobacterial cell wall and are essential for survival of the organism.  They are responsible for the unusually low permeability and consequent resistance to common antibiotics, as well as for virulence and the persistence of the tubercle bacillus within infected organisms.  This pathway details the biosynthesis of mycolic acids and their processing into final products.

In animal metabolism, we added pathways for the biosynthesis of bile acids, 1,25-dihydroxyvitamin D3 and L-carnitine, as well as the mitochondrial L-carnitine shuttle pathway and a pathway for spermine and spermidine degradation.

In plant primary metabolism we focused our curation effort in the biosynthesis of ascorbate (vitamin C), various phospholipids, and the cell surface lipids cutin and wax. We created three new biosynthesis pathways for ascorbate, three for phosphatidylcholine, two for phosphatidylglycerol and one for phosphatidylethanolamine.  In addition, we updated five existing pathways for ascorbate, cutin, cuticular wax, glycolipid, and phospholipid biosynthesis.  We also continued our effort to further enhance the coverage of plant secondary metabolites with new pathways for the biosynthesis of vitexin, isovitexin, peonidin and their derivatives, flavonols, triterpenoids(one of which could be used as a source for potential hydrocarbon fuels), cinnamates and sterols.  We also added pathways for the biosynthesis of methylquercetin, the alkaloid capsiconiate, a  higher plant pathway for protein turnover in germinating seeds, and a plant pathway for 2,4,6-trinitrotoluene (TNT) degradation. In addition, we added two algal pathways for alginate biosynthesis.

We thank Dr. Carol Bult and Dr. Alexei Evsikov from the Jackson Laboratory for their contribution of pathways from the MouseCyc database (mousecyc.jax.org).

We thank Dr. Lindsay Eltis and Dr. Hao-Ping Chen from the University of British Columbia for their contribution of pathways from the Rhodococcus jostii RHA1 database (www.rhodococcus.ca).

We thank Malabika Sarker from SRI International for her contribution of the Mycobacterium tuberculosis mycolate biosynthesis pathway, by far the largest pathway in our database.

Update of EC Reactions

During this quarter we have updated the reactions in MetaCyc with the latest information (as of January 2009) from the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB), by incorporating the final version of supplement 14 (see Enzyme Nomenclature Supplement 14).

Compound Protonation and Reaction Balancing

Starting with version 13.0, all MetaCyc compounds have been adjusted to a consistent protonation state for a reference pH of 7.3, common in the cellular cytosol. This adjustment was performed using the Marvin computational chemistry software (ChemAxon, Ltd). In addition, all reactions that had a mass-imbalance due only to hydrogen atoms were computationally balanced by adding or removing protons from the appropriate side of the reaction.

 These updated compounds and reactions will be propagated into all BioCyc PGDBs, and to other PGDBs created using Pathway Tools, making it easier to apply flux-balance analysis (FBA) techniques to these databases. This change results in certain differences between some MetaCyc reactions and the comparable reactions in other databases, such as the Enzyme Database . However, we believe that the representation of reactions in MetaCyc is more consistent and, within the limits of the cytosolic pH of 7.3, more accurate.

New Pathways

• 1,2,4,5-tetrachlorobenzene degradation
• 1,2,4-trichlorobenzene degradation
• 1,2-dichlorobenzene degradation
• 1,25-dihydroxyvitamin D₃ biosynthesis
• 1,3-dichlorobenzene degradation
• 2,4-dichlorophenoxyacetate degradation
• 3,4,6-trichlorocatechol degradation
• 3,4-dichlorocatechol degradation
• 3,5-dichlorocatechol degradation
• 3-chlorobenzoate degradation (aerobic)
• 3-chlorocatechol degradation
• 3-chlorotoluene degradation I
• 3-chlorotoluene degradation II
• 4-chloro-2-methylphenoxyacetate degradation
• 4-chlorocatechol degradation
• 4-ethylphenol degradation (anaerobic)
• 4-sulfocatechol degradation
• 5-chloro-3-methyl-catechol degradation
• acetoin degradation
• alginate biosynthesis I
• alginate biosynthesis II
• anthranilate degradation I (aerobic)
• anthranilate degradation II (aerobic)
• avenacin biosynthesis
• bile acid biosynthesis, neutral pathway
• C30 botryococcene biosynthesis
• capsiconiate biosynthesis
• cardenolide biosynthesis
• cardenolide glucosides biosynthesis
• ceramide biosynthesis
• chlorobenzene degradation
• chlorogenic acid biosynthesis II
• chlorogenic acid biosynthesis I
• chlorosalicylate degradation
• citrate degradation
• dammara-18(28),21-diene biosynthesis
• dimethylsulfide degradation I
• dimethylsulfide degradation II (oxidation)
• dimethylsulfide degradation III (oxidation)
• dimethylsulfone degradation
• dimethylsulfoniopropionate biosynthesis I (Wollastonia)
• dimethylsulfoniopropionate biosynthesis II (Spartina)
• dimethylsulfoniopropionate biosynthesis III (algae)
• dimethylsulfoniopropionate degradation I (cleavage)
• dimethylsulfoniopropionate degradation II (cleavage)
• dimethylsulfoniopropionate degradation III (demethylation)
• dimethylsulfoxide degradation
• diploterol and cycloartenol biosynthesis
• ethanedisulfonate degradation
• glycerol-3-phosphate shuttle
• indican biosynthesis
• indigo biosynthesis
• L-carnitine biosynthesis
• malonate degradation II (biotin-dependent)
• mangrove triterpenoid biosynthesis
• mannosylfructose biosynthesis
• methanesulfonate degradation
• methylthiopropionate degradation I (cleavage)
• methylthiopropionate degradation II (demethylation)
• mitochondrial L-carnitine shuttle pathway
• mycolate biosynthesis
• nitrilotriacetate degradation
• pseudoeuridine degradation
• seed germination protein turnover
• serotonin and melatonin biosynthesis
• spermine and spermidine degradation
• sphingomyelin metabolism
• sphingosine and sphingosine-1-phosphate metabolism
• tyrosine biosynthesis III
• zymosterol biosynthesis

New Pathways from Plant Metabolic Network (PMN)

• 2,3-cis-flavanols biosynthesis
• 2,3-trans-flavanols biosynthesis
• 2,4,6-trinitrotoluene degradation
• ascorbate biosynthesis II (L-gulose pathway)
• ascorbate biosynthesis III (VTC2 cycle)
• ascorbate biosynthesis IV (extended VTC2 cycle)
• isovitexin and isovitexin glycosides biosynthesis
• methylquercetin biosynthesis
• peonidin and derivatives biosynthesis
• phosphatidylcholine biosynthesis II
• phosphatidylcholine biosynthesis III
• phosphatidylcholine biosynthesis IV
• phosphatidylglycerol biosynthesis I
• phosphatidylglycerol biosynthesis II
• phosphatidylethanolamine biosynthesis II
• vitexin and detivatives biosynthesis

New Pathways from MouseCyc

• ceramide biosynthesis
• serotonin and melatonin biosynthesis
• sphingomyelin metabolism
• sphingosine and sphingosine-1-phosphate metabolism

New Pathways from the Rhodococcus jostii RHA1 database

• biphenyl degradation
• phthalate degradation

New Superpathways

• superpathway of dimethylsulfone degradation
• superpathway of dimethylsulfoniopropionate degradation
• superpathway of mycolate biosynthesis
• superpathway of phosphatidylcholine biosynthesis

Updated Pathways

• 1,4-dichlorobenzene degradation
• ascorbate biosynthesis I (galactose pathway)
• ascorbate biosynthesis VI
• cuticular wax biosynthesis
• cutin biosynthesis
• ergosterol biosynthesis
• ethylbenzene degradation (anaerobic)
• glycolipid biosynthesis
• histidine biosynthesis
• lupeol biosynthesis
• malonate degradation I (biotin-independent)
• phospholipid biosynthesis II
• proanthocyanidin biosynthesis from flavanols
• superpathway of ergosterol biosynthesis
• thiamin biosynthesis I
• tyrosine biosynthesis II
• uridine-5'-phosphate biosynthesis

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Release Notes for MetaCyc Version 12.5

Released on October 15, 2008

MetaCyc KB Statistics

Pathways	1203
Reactions	7312
Enzymes	5127
Chemical Compounds	7234
Organisms	1549
Citations	17916

New and Updated Pathways

We have added 72_{[more info]} new pathways to MetaCyc since the last release.  In addition, we significantly revised seven pathways by adding commentary and updated enzyme and gene information, for a total of 79 new and updated pathways. Of the new pathways, 12 were contributed by PMN (Plant Metabolic Network) curators (http://plantcyc.org), two were contributed by SGD (Saccharomyces Genome Database) curator Cynthia Krieger (http://pathway.yeastgenome.org/biocyc/) and 13 were imported from EcoCyc, as shown below.  We also added three new superpathways.  The superpathway of linamarin and lotaustralin biosynthesis was also contributed by PMN.

During this period we have significantly revised our coverage of fatty acid biosynthesis. Detailed pathways now describe the biosynthesis of the basic long chain saturated fatty acids palmitate and stearate.  Additional pathways cover the biosynthesis of common unsaturated fatty acids such as palmitoleate, cis-vaccenate, oleate, linoleate, α-linolenate and γ-linolenate. Other additions include new pathways for the biosynthesis of trehalose, acetoin, L-asparagine, butanediol, CDP-diacylglycerol, glycine betaine, and molybdopterin guanine dinucleotide.  We also added pathways for the degradation of sulfoacetaldehyde, and nitrate assimilation in cyanobacteria.  In the area of microbial secondary metabolism we added pathways for the biosynthesis of aflatoxins, geosmin, and the antibiotics rifamycin B and gramicidin S.

In plant metabolism, we continued to focus on further enhancing our coverage of plant secondary metabolites.  New pathways were added for the biosynthesis of the triterpenoids thalianal, marneral, baruol and arabidiol; the flavone apigenin; the sorghum allelochemical compound sorgoleone; the flavor and aroma-related compounds furaneol and cinnamate esters; and acridone alkaloids which are potential chemopreventive agents.  We also added pathways for the degradation of the cyanogenic glycosides lotasutraline, amygdalin and prunasin; and dhurrin degradation which involves hydrolysis of cyanogenic glucosides.  In primary metabolism, we curated pathways for the biosynthesis of xylogalacturonan - a pectic polysaccharide; the unusual fatty acids crepenynic acid and vernolic acid; the metal ion chelator nicotianamine; and lupinate which may stabilize plant hormone metabolism.  We also added a plant wound healing and defense pathway involving wound-induced proteolysis.  In addition we curated two transport pathways, one involving long distance transport of nicotianamine (NA) and one involving transport of ammonia for metabolic processes.

Update of EC Reactions

During this quarter we have updated the reactions in MetaCyc with the latest information (as of August 2008) from the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB), by incorporating supplement 14 (see Enzyme Nomenclature Supplement 14).

New Pathways

• α-linolenate biosynthesis
• γ-linolenate biosynthesis I (plants)
• γ-linolenate biosynthesis II (animals)
• (1'S,5'S)-averufin biosynthesis
• 3-amino-5-hydroxybenzoate biosynthesis
• cis-vaccenate biosynthesis
• acetoin biosynthesis II
• acridone alkaloid biosynthesis
• acyl carrier protein metabolism
• aflatoxins B₁ and G₁ biosynthesis
• aflatoxins B₂ and G₂ biosynthesis
• ammonium transport
• asparaginyl-tRNA^asn biosynthesis via transamidation
• butanediol biosynthesis
• CDP-diacylglycerol biosynthesis III
• cinnamate esters biosynthesis
• dhurrin degradation
• fatty acid biosynthesis initiation II
• fatty acid biosynthesis initiation III
• fatty acids biosynthesis (yeast)
• Fe(II)-NA phloem transport
• furaneol biosynthesis
• geosmin biosynthesis
• glycine betaine biosynthesis V (from glycine)
• gramicidin S biosynthesis
• kanosamine biosynthesis
• linoleate biosynthesis I (plants)
• linoleate biosynthesis II (animals)
• lupinate biosynthesis
• molybdenum cofactor (sulfide) biosynthesis
• molybdopterin guanine dinucleotide biosynthesis
• nicotianamine biosynthesis
• nitrate reduction VI (assimilatory)
• oleate biosynthesis II (animals)
• palmitate biosynthesis I (animals)
• palmitate biosynthesis II (bacteria and plants)
• rifamycin B biosynthesis
• stearate biosynthesis I (animals)
• stearate biosynthesis II (plants)
• sterigmatocystin biosynthesis
• sulfoacetaldehyde degradation II
• trehalose biosynthesis VI
• trehalose biosynthesis VII
• versicolorin B biosynthesis
• wound-induced proteolysis

New Pathways from PMN (http://plantcyc.org)

• amygdalin and prunasin degradation
• apigenin glycosides biosynthesis
• arabidiol biosynthesis
• baruol biosynthesis
• crepenynic acid biosynthesis
• lotaustralin biosynthesis
• lotaustralin degradation
• marneral biosynthesis
• sorgoleone biosynthesis
• thalianol and derivatives biosynthesis
• vernolic acid biosynthesis
• xylogalacturonan biosynthesis

New Pathways from EcoCyc

• biosynthesis of 4-amino-4-deoxy-L-arabinose-modified lipid A
• formate to dimethyl sulfoxide electron transfer
• formate to nitrate electron transfer
• formate to trimethylamine N-oxide electron transfer
• NADH to cytochrome bd oxidase electron transfer
• NADH to cytochrome bo oxidase electron transfer
• NADH to dimethyl sulfoxide reductase electron transfer
• NADH to fumarate electron transfer
• NADH to nitrate reductase electron transfer
• NADH to trimethylamine N-oxide reductase electron transfer
• oleate β-oxidation
• succinate to cytochrome bd oxidase electron transfer
• succinate to cytochrome bo oxidase electron transfer

New Pathways from SGD (http://pathway.yeastgenome.org/biocyc/)

• acetoin biosynthesis III
• butanediol degradation

New Superpathways

• superpathway of aflatoxin biosynthesis
• superpathway of rifamycin B biosynthesis
• superpathway of linamarin and lotaustralin biosynthesis

Updated Pathways

• fatty acid biosynthesis initiation I
• petroselinate biosynthesis
• palmitoleate biosynthesis
• CDP-diacylglycerol biosynthesis I
• CDP-diacylglycerol biosynthesis II
• oleate biosynthesis I (plants)
• superpathway of fatty acid biosynthesis II (plant)

 

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Release Notes for MetaCyc Version 12.1

Released on June 27, 2008

MetaCyc KB Statistics

Pathways	1138
Reactions	7114
Enzymes	4986
Chemical Compounds	7140
Organisms	1505
Citations	17340

 

New and Updated Pathways

We have added 101_{[more info]} new pathways to MetaCyc since the last release.  In addition, we significantly revised 13 pathways by adding commentary and updated enzyme and gene information, for a total of 114 new and updated pathways. The N-acetylneuraminate and N-acetylmannosamine degradation pathway was imported from EcoCyc. We also created 20 new superpathways.

We have undertaken a major effort to enhance the curation of quinone biosynthesis to cover the different varieties of quinones found in prokaryotic and eukaryotic organisms. These include menaquinones, demethylmenaquinones and ubiquinones of different tail length, phylloquinone, plastoquinone and rhodoquinones, as well as the plant quinones alizarin, lawsone and juglone.

We also covered the microbial biosynthesis of CDP-3,6-dideoxyhexoses CDP-abequose, CDP-ascarylose, CDP-paratose and CDP-tyvelose which are important O-antigens of several enterobacterial species. In the area of microbial secondary metabolism, we added pathways for the biosynthesis of staphyloxanthin, tuberculosinol and the antibiotics albaflavenone, puromycin, streptomycin, terpentecin and validamycin A.

In plant metabolism we continue to expand our coverage of secondary metabolite biosynthesis including alkaloids, quinones (see above), terpenoids and isoflavonoid glycosides. We have added pathways for the biosynthesis of metabolites significant in plant defense such as maysin. We also added pathways of medical significance, including the biosynthesis of cocaine, quinine, hyperforin, hypericin and colchicine. Newly added pathways of industrial significance included rubber, urushiol and various scent volatiles. Pathways of primary metabolism include the biosynthesis of plant cell wall polysaccharides such as xylan and xyloglucan, several auxin metabolism pathways and biosynthetic pathways for wax esters, hypusine and homospermidine. We also curated two pathways involved in the production of phytosiderophores, as well as pathways involving iron chelation and transport.

New Pathways

• (-)-(4S)-limonene degradation
• (+)-(4R)-limonene degradation
• (4R)-carveol and (4R)-dihydrocarveol degradation
• (4R)-carvone biosynthesis
• (4S)-carveol and (4S)-dihydrocarveol degradation
• 1,4-dihydroxy-2-naphthoate biosynthesis I
• 1,4-dihydroxy-2-naphthoate biosynthesis II (plants)
• 2'-(5'-phosphoribosyl)-3'-dephospho-CoA biosynthesis II (malonate decarboxylase)
• 2,3-dihydroxybenzoate biosynthesis
• 2'-deoxymugineic acid phytosiderophore biosynthesis
• 2-keto-L-gulonate biosynthesis
• 3-hydroxypropionate/4-hydroxybutyrate cycle
• 4-hydroxyphenylpyruvate biosynthesis
• afrormosin conjugates interconversion
• albaflavenone biosynthesis
• alizarin biosynthesis
• all trans undecaprenyl diphosphate biosynthesis
• beta-carboline biosynthesis
• bornyl diphosphate biosynthesis
• CDP-3,6-dideoxyhexose biosynthesis
• CDP-abequose biosynthesis
• CDP-ascarylose biosynthesis
• CDP-paratose biosynthesis
• CDP-tyvelose biosynthesis
• cinchona alkaloids biosynthesis
• cocaine biosynthesis
• colchicine biosynthesis
• dalcochinin biosynthesis
• dalpatein and dalnigrein biosynthesis
• decaprenyl diphosphate biosynthesis
• demethylmenaquinone-6 biosynthesis
• demethylmenaquinone-8 biosynthesis
• demethylmenaquinone-9 biosynthesis
• dodecaprenyl diphosphate biosynthesis
• ephedrine biosynthesis
• epoxypseudoisoeugenol-2-methylbutyrate biosynthesis
• eugenol and isoeugenol biosynthesis
• Fe(III)-phytosiderophore transport
• Fe(III)-reduction and Fe(II) transport
• geraniol and geranial biosynthesis
• geranyl acetate biosynthesis
• glutaminyl-tRNA^gln biosynthesis via transamidation
• heliocides biosynthesis
• heme degradation
• heptaprenyl diphosphate biosynthesis
• homospermidine biosynthesis
• hydroxylated mugineic acid phytosiderophore biosynthesis
• hyperforin biosynthesis
• hypericin biosynthesis
• hypoglycin biosynthesis
• hypusine biosynthesis
• IAA conjugate biosynthesis III
• IAA degradation V
• IAA degradation VI
• IAA degradation VII
• juglone biosynthesis
• lacinilene C biosynthesis
• lawsone biosynthesis
• linear furonocoumarin biosynthesis II
• magnoflorine biosynthesis
• malonate degradation
• maysin biosynthesis
• menaquinone-10 biosynthesis
• menaquinone-11 biosynthesis
• menaquinone-12 biosynthesis
• menaquinone-13 biosynthesis
• menaquinone-6 biosynthesis
• menaquinone-7 biosynthesis
• menaquinone-9 biosynthesis
• N-acetylneuraminate and N-acetylmannosamine degradation
• nonaprenyl diphosphate biosynthesis
• octaprenyl diphosphate biosynthesis
• oligomeric urushiol biosynthesis
• phycocyanobilin biosynthesis
• phycoerythrobilin biosynthesis
• puromycin biosynthesis
• rhodoquinone-10 biosynthesis
• rhodoquinone-9 biosynthesis
• rubber biosynthesis
• simple coumarins biosynthesis
• staphyloxanthin biosynthesis
• streptomycin biosynthesis
• t-anethole biosynthesis
• TCA cycle variation IV
• terpentecin biosynthesis
• trichloroethylene degradation
• tridecaprenyl diphosphate biosynthesis
• tuberculosinol biosynthesis
• ubiquinone-10 biosynthesis (eukaryotic)
• ubiquinone-10 biosynthesis (prokaryotic)
• ubiquinone-7 biosynthesis (eukaryotic)
• ubiquinone-7 biosynthesis (prokaryotic)
• ubiquinone-8 biosynthesis (eukaryotic)
• ubiquinone-9 biosynthesis (eukaryotic)
• ubiquinone-9 biosynthesis (prokaryotic)
• usnate biosynthesis
• validamycin A biosynthesis
• wax esters biosynthesis I
• wax esters biosynthesis II
• xylan biosynthesis
• xyloglucan biosynthesis

New superpathways

• bacillibactin biosynthesis
• butanediol biosynthesis I
• butanediol biosynthesis II
• heme biosynthesis I
• heme biosynthesis II
• superpathway of carotenoid biosynthesis
• superpathway of CDP-3,6-dideoxyhexose biosynthesis
• superpathway of demethylmenaquinone-6 biosynthesis
• superpathway of demethylmenaquinone-8 biosynthesis
• superpathway of demethylmenaquinone-9 biosynthesis
• superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate)
• superpathway of menaquinone-10 biosynthesis
• superpathway of menaquinone-11 biosynthesis
• superpathway of menaquinone-12 biosynthesis
• superpathway of menaquinone-13 biosynthesis
• superpathway of menaquinone-6 biosynthesis
• superpathway of menaquinone-7 biosynthesis
• superpathway of menaquinone-8 biosynthesis
• superpathway of phylloquinone biosynthesis
• superpathway of plastoquinone biosynthesis

Updated pathways

• 1,4-dihydroxy-2-naphthoate biosynthesis II (plants)
• 2'-(5''-phosphoribosyl)-3'-dephospho-CoA biosynthesis I (citrate lyase)
• calystegine biosynthesis
• de novo biosynthesis of pyrimidine deoxyribonucleotedes
• enterobactin biosynthesis
• geranylgeranyldiphosphate biosynthesis
• IAA degradation IV
• NAD biosynthesis III
• photosynthesis, light reactions
• plastoquinone biosynthesis
• sanguinarine and macarpine biosynthesis
• secologanin and strictosidine biosynthesis
• superpathway of geranylgeranyldiphosphate biosynthesis II (via MEP)

 

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Release Notes for MetaCyc Version 12.0

Released on April 1, 2008

MetaCyc KB Statistics

Pathways	1036
Reactions	6739
Enzymes	4731
Chemical Compounds	6719
Organisms	1108
Citations	16335

New and Updated Pathways

We have added 51_{[more info]} new pathways 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 66 new and updated pathways.

Among the new microbial pathways curated in MetaCyc during the last quarter are a newly discovered autotrophic CO₂ fixation pathway (comprising the 3-hydroxypropionate cycle and glyoxylate assimilation pathway), several pathways for the degradation of s-triazine herbicides such as atrazine, the biosynthesis of several GDP-sugars, and the biosynthesis and degradation pathways of itaconate.  In the area of antibiotic biosynthesis we added a pathway for (5R)-carbapenem which is a member of the carbapenem class of beta-lactam antibiotics, and pathways for the biosynthesis of fosfomycin and the phenazine compounds phenazine-1-carboxylate and 2-hydroxyphenazine.  We also added a CDP-diacylglycerol biosynthesis pathway from EcoCyc, and created a superpathway of atrazine degradation..

We also added a pathway for 4-hydroxybenzoate biosynthesis in higher and lower eukaryotes.  In addition, we  imported 9 new pathways from YeastCyc (part of the Saccharomyces Genome Database) that describe pathways found in that organism.

In plant metabolism we curated a variety of new pathways for the biosynthesis of plant secondary metabolites.  These include:  the sesquiterpenoids farnesene, germacrene and costunolide; the toxic terpenoid gossypol found in cotton; three triterpene saponin glycosylation pathways; the alkaloids capsaicin, hemlock poisons gamma-coniciene and coniine, and piperine (which gives black pepper its pungent flavor); rotenoid; and the isoflavans vestitol and sativan.  We also added a superpathway of formononetin derivative biosynthesis showing the formation of two of the many isoflavonoids derived from this compound, as well as the production of a storage form of formononetin.  In general these plant secondary metabolites are involved in plant defense and/or stress responses and many have potential applications in medicine and agriculture.  Also in the area of plant secondary metabolism we curated new pathways for the degradation of ethiin, alliin and isoalliin, and we updated the pathway for hyoscyamine and scopolamine biosynthesis.

In addition, we curated biosynthetic pathways for the plant scent volatiles phenylethanol and trimethoxybenzene.  In the area of plant energy metabolism we added a pathway for the Rubisco shunt, a bypass of glycolysis providing an efficient way for plants to convert carbohydrates into seed storage oil.

Update of EC Reactions

During this quarter we have updated the reactions in MetaCyc with the latest information (as of January 2008) from the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB), by  incorporating supplement 13 (see Enzyme Nomenclature Supplement 13).

We would like to welcome a new curator,  Dr. A. Karthikeyan (Karthik) from the Carnegie Institution, to the MetaCyc team.

New pathways:

• β-alanine biosynthesis V
• γ-coniciene and coniine biosynthesis
• (5R)-carbapenem biosynthesis
• 1,3,5-trimethoxybenzene biosynthesis
• 2-hydroxyphenazine biosynthesis
• 2-methylcitrate cycle II
• 3-hydroxypropionate cycle
• 4-hydroxybenzoate biosynthesis I (eukaryotes)
• 4-hydroxybenzoate biosynthesis II
• alliin degradation
• atrazine degradation II
• atrazine degradation III
• capsaicin biosynthesis
• costunolide biosynthesis
• deethylsimazine degradation
• ethiin degradation
• ethylmalonyl pathway
• farnesene biosynthesis
• fosfomycin biosynthesis
• GDP-α-D-perosamine biosynthesis
• GDP-6-deoxy-D-talose biosynthesis
• GDP-L-colitose biosynthesis
• germacrene biosynthesis
• glutamate degradation X
• glycogen degradation II
• glyoxylate assimilation
• gossypol biosynthesis
• isoalliin degradation
• isopropylamine degradation
• itaconate biosynthesis
• itaconate degradation
• phenazine-1-carboxylate biosynthesis
• phenylethanol biosynthesis
• piperine biosynthesis
• pyruvate fermentation to acetate VIII
• rotenoid biosynthesis
• Rubisco shunt
• saponin biosynthesis II
• saponin biosynthesis III
• saponin biosynthesis IV
• vestitol and sativan biosynthesis

Imported pathways

• 4-aminobutyrate degradation III
• 4-hydroxybenzoate biosynthesis III (yeast)
• CDP-diacylglycerol biosynthesis I
• glycine biosynthesis III
• glycine biosynthesis IV
• hexaprenyl diphosphate biosynthesis
• NAD salvage pathway III
• phosphatidylcholine biosynthesis
• tyrosine degradation III
• ubiquinone-6 biosynthesis

Superpathways

• superpathway of atrazine degradation
• Superpathway of formononetin derivative biosynthesis

Updated pathways:

• 2-methylcitrate cycle I
• 4-aminobutyrate degradation III
• arginine degradation IX (arginine:pyruvate transaminase pathway)
• arginine degradation IX (arginine:pyruvate transaminase pathway)
• atrazine degradation I (aerobic)
• cyanurate degradation
• glycine biosynthesis I
• glyoxylate cycle
• hexaprenyl diphosphate biosynthesis
• hyoscyamine and scopolamine biosynthesis
• nicotinate degradation III
• peptidoglycan biosynthesis I
• polyisoprenoid biosynthesis (E. coli)
• tyrosine degradation III
• ubiquinone-6 biosynthesis

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Release Notes for MetaCyc Version 11.6

Released on December 5, 2007

MetaCyc KB Statistics

Pathways	1010
Reactions	6576
Enzymes	4582
Chemical Compounds	6561
Organisms	1077
Citations	15875

New and Updated Pathways

79 new pathways (including one superpathway) were added to MetaCyc since the last release. In addition, we significantly revised 30 pathways, by adding commentary and updated enzyme and gene information, for a total of 109 new and updated pathways.

Major additions include a much better coverage for the microbial degradation of nitroaromatic compounds, urate and allantoin metabolism, and acetate metabolism. We have added pathways for the biosynthesis of bacteriochlorophyll a, several GDP-sugars, the compatible solutes glucosyl- and mannosyl-glycerate, the enzyme cofactor tetrahydrobiopterin, and several naturally occurring β-lactam antibiotics, including the penam, ceph-3-em and clavam classes. We also significantly enhanced coverage of nitrate reduction, and added pathways for propylene degradation, sorbitol biosynthesis, and many other miscellaneous pathways.

In plant metabolism we curated six new secondary metabolic pathways. The new pathways include biosynthesis of the fragrance compound linalool and the flavor compounds of vanilla, garlic, onion and chive, biosynthesis of the toxic metabolites α-solanine and α-chaconine, which are found in potatoes, and biosynthesis of two terpenoid drugs: the important anticancer drug taxol, which is produced in yew trees, and the multi-use drug ginseng.

We would like to welcome new members to the MetaCyc team: Drs. Lukas Mueller and Anuradha Pujar from Cornell University, and Dr. Kate Dreher from the Carnegie Institution.

New pathways:

• 2,4-dinitrotoluene degradation
• 2,6-dinitrotoluene degradation
• 2-nitrobenzoate degradation I
• 2-nitrobenzoate degradation II
• 2-nitrophenol degradation
• 2-nitrotoluene degradation
• 4-chloronitrobenzene degradation
• 4-nitrotoluene degradation II
• acetate conversion to acetyl-CoA
• acetate formation from acetyl-CoA I
• acetate formation from acetyl-CoA II
• acetate formation from acetyl-CoA III (succinate)
• acetone degradation II (to acetoacetate)
• acetyl-CoA fermentation to butyrate II
• adenosine 5'-monophosphate recycling
• allantoin degradation IV (anaerobic)
• allantoin degradation to glyoxylate I
• allantoin degradation to glyoxylate II
• allantoin degradation to glyoxylate III
• bacteriochlorophyll a biosynthesis
• cardiolipin biosynthesis I
• cephalosporin C biosynthesis
• cephamycin C biosynthesis
• chlorophyllide a biosynthesis II
• clavulanate biosynthesis
• CO₂ fixation into oxaloacetate
• cysteine sulfoxides degradation
• de novo biosynthesis of uridine-5'-monophosphate
• deacetylcephalosporin C biosynthesis
• epoxysqualene biosynthesis
• fructose degradation
• GDP-glucose biosynthesis
• GDP-mannose biosynthesis I
• GDP-mannose biosynthesis II
• ginsenoside biosynthesis
• glucosylglycerate biosynthesis
• isopenicillin N biosynthesis
• linalool biosynthesis
• L-lactaldehyde degradation (aerobic)
• L-lactaldehyde degradation (anaerobic)
• mannosylglycerate biosynthesis I
• mannosylglycerate biosynthesis II
• nitrate reduction III (dissimilatory)
• nitrate reduction IV (dissimilatory)
• nitrate reduction V (assimilatory)
• nitrobenzene degradation I
• nitrobenzene degradation II
• penicillin K biosynthesis
• phosphatidyl-ethanolamine biosynthesis
• propylene degradation
• pyrimidine ribonucleotides interconversion
• pyruvate fermentation to acetate V
• pyruvate fermentation to acetate VI
• pyruvate fermentation to acetate VII
• shikonin biosynthesis
• sorbitol biosynthesis II
• steroidal glycoalkaloid biosynthesis
• succinate fermentation to butyrate
• sulfolipid biosynthesis
• taxol biosynthesis
• TCA cycle variation III (higher eukaryotes)
• tetrahydrobioprein biosynthesis I
• tetrahydrobioprein biosynthesis II
• tryptophan degradation IX
• urate biosynthesis
• urate degradation to allantoin
• urea degradation I
• urea degradation II
• vanilla biosynthesis

Superpathways

• superpathway of penicillin, cephalosporin and cephamycin biosynthesis

Updated pathways:

• 4-nitrobenzoate degradation
• 4-nitrotoluene degradation I
• 4-toluenecarboxylate degradation
• 4-toluenesulfonate degradation I
• acetyl-CoA fermentation to butyrate II
• acetylene degradation
• cardiolipin biosynthesis II
• chlorophyll cycle
• chlorophyllide a biosynthesis I
• de novo biosynthesis of pyrimidine ribonucleotides
• fatty acid β-oxidation IV (plant, unsaturated, even number)
• fatty acid activation
• glutamate degradation V (via hydroxyglutarate)
• incomplete reductive TCA cycle
• methionine biosynthesis I
• methionine salvage pathway
• NAD/NADH phosphorylation and dephosphorylation
• nitrate reduction I (denitrification)
• octane oxidation
• superpathway of allantoin degradation (E. coli)
• superpathway of allantoin degradation in plants
• superpathway of allantoin degradation in yeast
• superpathway of C1 compounds oxidation to CO₂
• superpathway of purines degradation in plants
• superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae)
• taurine biosynthesis
• thiocyanate degradation I
• thiocyanate degradation II
• ureide biosynthesis
• very long chain fatty acid biosynthesis

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Release Notes for MetaCyc Version 11.5

Released on August 15, 2007

MetaCyc KB Statistics

Pathways	977
Reactions	6483
Enzymes	4332
Chemical Compounds	6375
Organisms	1029
Citations	15199

New and Updated Pathways

10 new pathways were added to MetaCyc since the last release. In addition, we significantly revised 5 pathways, by adding commentary and updated enzyme and gene information, for a total of 15 new and updated pathways.

In microbial metabolism we curated 7 new pathways, incorporated one new pathway from EcoCyc, and significantly enhanced 5 existing pathways, for a total of 13 pathways.

We have updated our coverage of the biosynthesis of adenosylcobalamin (vitamin B12), one of the most structurally complex small molecules made in nature. MetaCyc pathways describe both the aerobic and anaerobic biosynthetic routes, and the synthesis of one of its precursors, 5,6-dimethylbenzimidazole (DMB). We also added a pathway for biosynthesis of the important vitamin L-ascorbate (vitamin C) in bacteria, a pathway for the biosynthesis of the amino sugar donor UDP-N-acetyl-D-galactosamine, and pathways for degradation of the pentose sugars arabinose and xylose.

In mammalian metabolism we curated two new pathways: a pathway for biosynthesis of L-ascorbate (vitamin C) in higher animals, and a pathway for degradation of the sugar acid glucuronate.

New microbial pathways:

• 5,6-dimethylbenzimidazole biosynthesis
• L-ascorbate biosynthesis II
• D-arabinose degradation III
• L-arabinose degradation II
• L-arabinose degradation III
• UDP-N-acetyl-D-galactosamine biosynthesis II
• xylose degradation II

New  microbial pathway from EcoCyc:

• chitobiose degradation

New Mammalian pathways:

• L-ascorbate biosynthesis III
• glucuronate degradation

Updated microbial pathways:

• adenosylcobalamin biosynthesis I (early cobalt insertion)
• adenosylcobalamin biosynthesis II (late cobalt incorporation)
• adenosylcobalamin salvage from cobinamide and cobalamin
• xylitol degradation
• Superpathway of pentose and pentitol degradation

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Release Notes for MetaCyc Version 11.1

Released on May 25, 2007

MetaCyc KB Statistics

Pathways	966
Reactions	6464
Enzymes	4271
Chemical Compounds	6354
Organisms	1023
Citations	14937

New and Updated Pathways

39 new pathways were added to MetaCyc since the last release. In addition, we significantly revised 31 pathways, by adding commentary and updated enzyme and gene information. We also created 1 new superpathway, for a total of 71 new and updated pathways.

In microbial metabolism we curated 20 new pathways, incorporated 6 new EcoCyc pathways, and significantly enhanced 31 existing pathways, for a total of 57 pathways.

Several topics received special attention during this release. We have reorganized and significantly expanded our coverage of fermentation pathways, the metabolism of the amino acids glutamate, glutamine, aspartate and asparagine, the degradation of the pesticide parathion and related compounds, and the metabolism of the vitamins B6 and B12. In addition we added or revised many pathways covering a wide range of topics, including purine degradation, the reductive monocarboxylate cycle, and polyhydroxybutyrate biosynthesis, to name a few.

In plant metabolism we added 13 new pathways and one superpathway.  Five well-known alkaloid biosynthesis pathways complete the coverage of this domain. In addition, we added two biosynthetic pathways of hydroxycinnamic acid amides. The serotonin amides are reported to be antioxidants, and the tyramine amides, widespread in plants, are cell wall constituents playing a role in cell wall reinforcement and protection of plants against pathogen infections. Finally, we curated six new  pathways for the biosynthesis of phenylpropenoids belonging to the class of lignans and hydrolyzable tannins, a group of compounds reported to have, amongst other things, antioxidant and antitumor properties.  A superpathway of hydrolyzable tannins was also created.

Special thanks: We bid a fond farewell to our colleagues Drs. Sue Rhee, Peifen Zhang, Hartmut Foerster, and Chris Tissier of the Carnegie Institution. The Carnegie group has curated a large number of plant pathways and enzymes into MetaCyc, making it the most comprehensive existing database on plant metabolism.  Thank you for your many contributions to MetaCyc, and to the curation procedures and software behind it.

New microbial pathways:

• adenosylcobalamin biosynthesis from cobyrinate a,c-diamide I
• adenosylcobalamin biosynthesis from cobyrinate a,c-diamide II
• adenosylcobalamin biosynthesis I (early cobalt insertion)
• diethylphosphate degradation
• glycolysis V
• methanol oxidation to formaldehyde
• methyl parathion degradation
• p-nitrophenol degradation I
• p-nitrophenol degradation II
• paraoxon degradation
• purine degradation II (anaerobic)
• pyruvate fermentation to acetate II
• pyruvate fermentation to acetate III
• pyruvate fermentation to acetate IV
• pyruvate fermentation to ethanol I
• pyruvate fermentation to ethanol II
• pyruvate fermentation to lactate
• pyruvate fermentation to propionate II (acrylate pathway)
• reductive monocarboxylic acid cycle
• UDP-N-acetyl-D-galactosamine biosynthesis

     New  microbial pathways from EcoCyc:

• 2-O-α-mannosyl-D-glycerate degradation
• aminopropylcadaverine biosynthesis
• arginine dependent acid resistance
• glutamate dependent acid resistance
• L-galactonate degradation
• melibiose degradation

 Updated microbial pathways:

• adenosylcobalamin biosynthesis II (late cobalt incorporation)
• asparagine biosynthesis I
• asparagine degradation I
• aspartate biosynthesis
• aspartate degradation I
• aspartate degradation II
• Bifidobacterium shunt
• cyclohexanol degradation
• formaldehyde assimilation III (dihydroxyacetone cycle)
• glutamate biosynthesis II
• glutamate biosynthesis IV
• glutamine biosynthesis I
• glutamine degradation I
• glutamine degradation II
• glycine biosynthesis II
• glycine cleavage complex
• heterolactic fermentation I
• hexitol fermentation to lactate, formate, ethanol and acetate
• homolactic fermentation
• L-alanine fermentation to propionate and acetate
• methionine biosynthesis I
• N-acetylneuraminate degradation
• parathion degradation
• polyhydroxybutyrate biosynthesis
• purine degradation III (anaerobic)
• pyruvate fermentation to acetate I
• pyruvate fermentation to propionate I
• reductive acetyl coenzyme A pathway
• superpathway of glutamate and glutamine biosynthesis
• UDP-N-acetyl-D-glucosamine biosynthesis II
• vitamin B₆ degradation

New plant pathways:

• bisbenzylisoquinoline alkaloid biosynthesis
• cornusiin E biosynthesis
• gallotannin biosynthesis
• gramine biosynthesis
• hydroxycinnamic acid serotonin amides biosynthesis
• hydroxycinnamic acid tyramine amides biosynthesis
• laudanine biosynthesis
• lupanine biosynthesis
• matairesinol biosynthesis
• palmatine biosynthesis
• pentagalloylglucose biosynthesis
• podophyllotoxin and 6-methoxypodophyllotoxin biosynthesis
• sesamin biosynthesis

New Superpathways

• superpathway of hydrolyzable tannin biosynthesis

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Release Notes for MetaCyc Version 11.0

Released on March 16, 2007

MetaCyc KB Statistics

Pathways	935
Reactions	6262
Enzymes	3995
Chemical Compounds	6218
Organisms	952
Citations	12729

New and Updated Pathways

47 new pathways were added to MetaCyc since the last release. In addition, we significantly revised 26 pathways, by adding commentary and updated enzyme and gene information. We also created 12 new superpathways, for a total of 85 new and updated pathways.

In microbial metabolism we curated 16 new pathways, incorporated 4 new EcoCyc pathways and one ScoCyc pathway, and significantly enhanced 20 existing pathways, for a total of 41 pathways.

Topics that were covered include the metabolism of the toxic compounds methylglyoxal and phenylmercury acetate, the degradation of the amino acids alanine and threonine, and the degradation of miscellaneous aromatic and non-aromatic compounds including phenol, benzene, catechol, toluene, naphthalene, xylene, acrylonitrile, 4-hydroxyphenylacetate, and acetone. We also modified several pathways of sugar metabolism. In addition, we incorporated 4 new pathways from EcoCyc, describing the degradation of purine and pyrimidine nucleosides, and a Streptomyces coelicolor A3(2) pathway for the biosynthesis of the polyketide antibiotic actinorhodin, which was submitted by Veronica Armendarez of the  John Innes Centre. Thank you Veronica!

In plant metabolism we added 26 new pathways, and enhanced 6 pathways, for a total of 32 pathways.

A special focus was given to the metabolism of betalains, which constitute chromo-alkaloid pigments that replace anthocyanins in the plant order Caryophyllales.  The lipoxygenase (LOX) pathway, which leads to the biosynthesis of a wide variety of compounds such as jasmonic acid, volatile aldehydes and alcohols, alpha ketols, and divinyl ethers, has been extensively overhauled. MetaCyc now contains the 9-LOX, 13-LOX and their corresponding AOS (allene oxide synthase), HPL (hydroperoxide lyase) and DES (divinyl ether synthase) branches curated in separate pathways.  An exhaustive list of pathways involved in the biosynthesis of oleoresin compounds found in coniferous plants have been added to the database.  Finally, a number of new pathways concerning various compound classes, such as terpenoids (DMNT and crocetin biosynthesis) have also been added.

We have also extensively updated pathways relating to glycolysis and related pathways (starch biosynthesis and TCA cycle) in plants by adding a comprehensive list of cytosolic and plastidic enzymes, as well as pathways concerning homomethonine and jasmonic acid biosynthesis.

Update of EC Reactions

During this quarter we have updated the reactions in MetaCyc with the latest information (as of January 2007) from the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB), by  incorporating supplement 12 (see Enzyme Nomenclature Supplement 12).

 

New microbial pathways:

• acetone degradation (to methylglyoxal)
• aminopropanol biosynthesis
• aminopropanol phosphate biosynthesis
• benzene degradation
• catechol degradation to 2-oxopent-4-enoate II
• methylglyoxal degradation III
• methylglyoxal degradation IV
• methylglyoxal degradation V
• methylglyoxal degradation VII
• methylglyoxal degradation VIII
• m-xylene degradation to m-toluate
• naphthalene degradation
• phenol degradation I (aerobic)
• p-xylene degradation to p-toluate
• threonine degradation I
• threonine degradation IV

     New  microbial pathways from EcoCyc:

• degradation of purine deoxyribonucleosides
• degradation of purine ribonucleosides
• degradation of pyrimidine deoxyribonucleosides
• degradation of pyrimidine ribonucleosides

     A new microbial pathway from ScoCyc:

• actinorhodin biosynthesis

Updated microbial pathways:

• acrylonitrile degradation
• alanine degradation II
• alanine degradation III
• alanine degradation IV
• β-alanine biosynthesis III
• D-lactate fermentation to propionate and acetate
• Entner-Doudoroff pathway III (semi-phosphorylative)
• galactonate degradation
• galactose degradation I
• GDP-D-rhamnose biosynthesis
• glucose degradation (oxidative)
• glycolysis I
• 4-hydroxyphenylacetate degradation
• methylglyoxal degradation II
• phenylmercury acetate degradation
• superpathway of methylglyoxal degradation in E. coli
• superpathway of threonine metabolism
• threonine degradation II
• threonine degradation III (to methylglyoxal)
• toluene degradation to benzoate

New plant pathways:

• 13-LOX and 13-HPL pathway
• 9-LOX and 9-AOS pathway
• 9-LOX and 9-HPL pathway
• abietic acid biosynthesis
• amaranthin biosynthesis
• betacyanin biosynthesis
• betacyanin biosynthesis (via dopamine)
• betalain biosynthesis (to betalamic acid)
• betanidin degradation
• betaxanthin biosynthesis
• betaxanthin biosynthesis (via dopamine)
• betaxanthin biosynthesis (via dopaxanthin)
• crocetin biosynthesis
• crocetin esters biosynthesis
• dehydroabietic acid biosynthesis
• divinyl ether biosynthesis I (9-LOX)
• divinyl ether biosynthesis II (13-LOX)
• DMNT biosynthesis
• isopimaric acid biosynthesis
• levopimaric acid biosynthesis
• neoabietic acid biosynthesis
• oleoresin monoterpene volatiles biosynthesis
• oleoresin sesquiterpene volatiles biosynthesis
• palustric acid biosynthesis
• S-methylmethionine cycle

Updated plant pathways:

• glycolysis IV
• homomethionine biosynthesis
• jasmonic acid biosynthesis
• phospholipid biosynthesis II
• starch degradation
• sucrose degradation III

New Superpathways

• superpathway of betalain biosynthesis
• superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle
• superpathway of diterpene resin acids biosynthesis
• superpathway of lipoxygenase
• superpathway of methionine biosynthesis (by sulfhydrylation)
• superpathway of methionine degradation
• superpathway of oleoresin turpentine biosynthesis
• superpathway of sulfide oxidation (Acidithiobacillus ferrooxidans)
• superpathway of sulfur metabolism (Desulfocapsa sulfoexigens)
• superpathway of sulfur oxidation (Acidianus ambivalens)
• superpathway of thiosulfate metabolism (Desulfovibrio sulfodismutans)

---

Release Notes for MetaCyc Version 10.6

Released on January 10, 2007

MetaCyc KB Statistics

Pathways	879
Reactions	6113
Enzymes	3841
Chemical Compounds	5978
Organisms	902
Citations	11934

New and Updated Pathways

93 new pathways were added to MetaCyc since the last release. In addition, we significantly revised 32 pathways, by adding commentary and updated enzyme and gene information, for a total of 125 updated pathways.

In microbial metabolism we added 37 new pathways, and significantly enhanced 27 pathways, for a total of 64 pathways.

We expanded our coverage of lysine degradation by adding five new pathways from bacteria, yeasts, fungi and mammals. We also added a new superpathway that provides an overview of the many different initial reactions in lysine degradation. Additional degradation topics covered in this release include new and modified pathways for the degradation of phenylalanine, ornithine, nitroethane, orthanilate, sucrose, carbon tetrachloride, 2-nitropropane and carbon disulfide. New and modified biosynthetic pathways include homocysteine, siroheme amide, dolichyldiphosphooligosaccharide and phenylalanine. Other pathways include new variants for hydrogen oxidation and the reductive TCA cycle, an improved Calvin cycle, and an expanded methanogenesis from carbon dioxide pathway.

We significantly expanded our coverage of microbial sulfur metabolism, adding and modifying pathways for the oxidation, reduction and disproportionation of sulfur compounds, including the inorganic compounds sulfide, elemental sulfur, thiosulfate, tetrathionate, sulfite and sulfate, as well as organosulfur compounds such as homocysteine, methionine, sulfoacetaldehyde and benzenesulfonate.

In plant metabolism we added 52 new pathways, and enhanced 5 pathways, for a total of 57 pathways.

Eight new plant alkaloid biosynthesis pathways have been added to this release, improving the comprehensiveness of well-characterized alkaloid pathways in the MetaCyc collection. In addition, nine biosynthetic pathways of unusual fatty acids found in certain plant seed oils have been reviewed. Several metabolic pathways of carbohydrates (e.g. the raffinose series , including stachyose, ajugose, etc), carotenoid and anthocyanin pigments (e.g. astaxanthin, bixin, shisonin, gentiodelphin and anthocyanidin) and flavonols (e.g. the pharmaceutically important syringetin or the food aroma compound raspberry ketone) have been introduced. Finally, we added a pathway for the biosynthesis of the molybdenum cofactor (moco), which binds the transition element molybdenum.

We have also updated pathways in the areas of flavonoid, phytoalexins and lipid biosynthesis.

In animal metabolism we imported 3 new pathways from HumanCyc, and curated one new pathway, for a total of 4 pathways.

Our coverage of cholesterol biosynthesis was expanded by adding two new pathways and a superpathway from HumanCyc.  The new pathways show other biosynthetic intermediates that can occur, and the superpathway provides an overview of these routes. Another new pathway describes the degradation of L-cysteine in mammals.

Special thanks: We would like to thank Dr. Ruth Welti for her help in updating the glycolipid and phospholipid desaturation pathways.

New microbial pathways:

• carbon disulfide oxidation II (aerobic)
• carbon tetrachloride degradation I
• carbon tetrachloride degradation II
• carbon tetrachloride degradation III
• homocysteine biosynthesis
• hydrogen oxidation II (aerobic)
• lysine degradation IV
• lysine degradation V
• lysine degradation VI
• lysine degradation VII
• lysine degradation VIII
• lysine degradation IX
• nitroethane degradation
• reductive TCA cycle II
• siroheme amide biosynthesis
• sucrose degradation IV
• sulfate activation for sulfonation
• sulfide oxidation II (sulfide dehydrogenase)
• sulfide oxidation IV (sulfur dioxygenase)
• sulfite oxidation I (sulfite oxidoreductase)
• sulfite oxidation II
• sulfite oxidation III
• sulfite oxidation IV
• sulfur disproportionation II (aerobic)
• sulfur reduction I
• sulfur reduction II (via polysulfide)
• tetrathionate oxidation
• tetrathionate reduction I (to thiosulfate)
• tetrathionate reductiuon II (to trithionate)
• thiosulfate disproportionation I (thiol-dependent)
• thiosulfate disproportionation II (non thiol-dependent)
• thiosulfate disproportionation III (rhodanese)
• thiosulfate oxidation II (multienzyme complex)
• thiosulfate oxidation III (via tetrathionate)

New animal pathways:

• cholesterol biosynthesis II (via 24,25-dihydrolanosterol)
• cholesterol biosynthesis III (via desmosterol)
• L-cysteine degradation III

Updated microbial pathways:

• benzenesulfonate degradation
• Calvin cycle
• carbon disulfide oxidation I (anaerobic)
• dolichyldiphosphooligosaccharide biosynthesis
• homocysteine degradation
• hydrogen oxidation I (aerobic)
• interconversion of arginine, ornithine and proline (Stickland reaction)
• L-cysteine degradation I
• lysine degradation I
• methanogenesis from CO₂
• methionine degradation I (to homocysteine)
• 2-nitropropane degradation
• ornithine degradation (proline biosynthesis)
• orthanilate degradation
• phenylalanine biosynthesis I
• phenylalanine degradation II
• sucrose degradation I
• sulfate reduction I (assimilatory)
• sulfate reduction II (assimilatory)
• sulfate reduction III (dissimilatory)
• sulfate reduction IV (dissimilatory)
• sulfide oxidation I (sulfide-quinone reductase)
• sulfoacetaldehyde degradation
• sulfur disproportionation I (anaerobic)
• sulfur oxidation I (aerobic)
• sulfur oxidation II (Fe⁺³-dependent)
• thiosulfate oxidation I (to tetrathionate)

New plant pathways:

• abscisic acid glucose ester biosynthesis
• ajmaline and sarpagine biosynthesis
• ajugose biosynthesis I (galactinol-dependent)
• ajugose biosynthesis II (galactinol-independent)
• α-amyrin biosynthesis
• α-eleostearic acid biosynthesis
• anthocyanidin sophoroside metabolism
• arachidonate and eicosapentaenoate biosynthesis
• astaxanthin biosynthesis
• bixin biosynthesis
• calendic acid biosynthesis
• calystegine biosynthesis
• canthaxanthin biosynthesis
• chalcone 2'-O-glucoside biosynthesis
• chrysin biosynthesis
• chrysophanol biosynthesis
• coumarin metabolism (to melilotic acid)
• Δ5-eicosenoate biosynthesis
• A series fagopyritols biosynthesis
• B series fagopyritols biosynthesis
• Δ6-hexadecenoate biosynthesis
• dimorphecolate biosynthesis
• esculetin biosynthesis
• galactosylcyclitol biosynthesis
• gentiodelphin biosynthesis
• hyoscyamine and scopolamine biosynthesis
• kaempferol glucoside biosynthesis (Arabidopsis)
• kaempferol triglucoside biosynthesis
• linear furanocoumarin biosynthesis
• methylthiopropionate biosynthesis
• molybdenum cofactor biosynthesis
• N-glucosylnicotinate metabolism
• nicotine biosynthesis
• N-methyl-Δ¹-pyrrolinium cation biosynthesis
• palmitoleate biosynthesis
• petroselinate biosynthesis
• phaseic acid biosynthesis
• punicic acid biosynthesis
• pyridine nucleotide cycling (plants)
• quercetin glucoside biosynthesis (Arabidopsis)
• raspberry ketone biosynthesis
• rutin biosynthesis
• sanguinarine and macarpine biosynthesis
• secologanin and strictosidine biosynthesis
• shisonin biosynthesis
• stachyose biosynthesis
• syringetin biosynthesis
• ternatin C5 biosynthesis
• vindoline and vinblastine biosynthesis

Updated plant pathways:

• aurone biosynthesis
• camalexin biosynthesis
• flavonol biosynthesis
• glycolipid desaturation pathway
• phospholipid desaturation pathway

New Superpathways

• superpathway of anthocyanin biosynthesis (from delphinidin-3-O-glucoside)
• superpathway of anthocyanin biosynthesis (from pelargonidin-3-O-glucoside)
• superpathway of anthocyanin biosynthesis (from cyanidin and cyanidin-3-O-glucoside)
• superpathway of cholesterol biosynthesis
• superpathway of lysine degradation
• superpathway of sulfide oxidation (Starkeya novella)

---

Release Notes for MetaCyc Version 10.5

Released on September 8, 2006

MetaCyc KB Statistics

Pathways	800
Reactions	5871
Enzymes	3527
Chemical Compounds	5253
Organisms	729
Citations	10658

 

New and Updated Pathways

44 new pathways were added to MetaCyc since the last release. In addition, we significantly revised 24 pathways, by adding commentary and updated enzyme and gene information, for a total of 68 updated pathways.

In microbial metabolism we added 30 new pathways, and significantly enhanced 17 pathways, for a total of 47 pathways.

New pathways include the biosynthesis of cell components such as tetrapyrroles, lipids and peptidoglycan, and the degradation of several aromatic compounds, including cyanurate, melamine, N-cyclopropylmelamine, and 4-toluenesulfonate.

We significantly expanded our coverage of methanogenesis, adding pathways for the biosynthesis of several methanogenic cofactors including coenzyme B, coenzyme M, factor 420, factor 430, and methanofuran, a pathway for the regeneration of coenzyme B and coenzyme M from their heterosulfide, seven new pathways for methanogenesis from different substrates, and a lactate biosynthetic pathway from the methanogen Methanocaldococcus jannaschii, in which lactate is used as a precursor for factor 420.

We also added two new superpathways for aerobic toluene degradation and the degradation of pentoses and pentitols, and imported 4 new pathways from EcoCyc, covering lipoate biosynthesis and incorporation, lipopolysaccharide biosynthesis, and the degradation of ethylene glycol.

In addition to creating new pathways, we updated pre-existing pathways in the following areas: heme biosynthesis; lipoate biosynthesis; NAD biosynthesis; pentitol degradation; benzoyl-CoA degradation; other aromatic compounds degradation; and lysine degradation and fermentation.

Finally, we reorganized some of our existing pathways, breaking them into several shorter conserved pathways which are linked to each other. Doing so decreases redundancy in MetaCyc, and will improve future pathway predictions by our PathoLogic software. Reorganized pathways include biosynthesis of tetrapyrrole-derived molecules, including heme, chlorophyll and cobalamine, and degradative pathways of aromatic compounds that proceed through the intermediates 2-oxopent-4-enoate and glutaryl-CoA.

In plant metabolism we added 12 new pathways, and enhanced 7 pathways, for a total of 19 updated pathways.

A variety of new plant pathways have been added to the database. They include acetyl-CoA biosynthesis, mitochondrial membrane lipid cardiolipin biosynthesis, activation of the secondary metabolite glucosinolate, and biosynthesis of the medicinal alkaloid morphine. Biosynthetic pathways of the phenylpropenoids ferulate, sinapate and coumarin have also been added. The former two compounds are precursors to UV-protecting hydroxycinnamyl esters in plants, whereas coumarins are recognized for their pharmacological and therapeutic properties in humans. Other new additions include the biosynthetic pathways of the important terpenoids artemisinin (the most potent anti-malaria drug) and soybean saponin, as well as salvianin, a major anthocyanin in the Labiatae family that contributes to flower coloration.

We have also updated a number of existing pathways including abscisic acid and carotenoid biosyntheses, and several glucosinolate biosynthesis pathways.

In animal metabolism we imported 2 new pathways from HumanCyc, covering the degradation of anandamide, a member of the endocannabinoid class of signaling lipids, and of dopamine, a neurotransmitter and physiological regulator.

We would like to express our gratitude to Drs. Maor Bar-Peled, Ed Cahoon, Clint Chapple, Peter Facchini, Jonathan Page and David Seigler for their invaluable contribution to the identification and curation of many of the plant pathways in the last two MetaCyc releases.  We would also like to thank Dr. Rob Gunsalus for his suggestions concerning methanogenesis.

New microbial pathways:

• coenzyme B/coenzyme M regeneration
• cyanurate degradation
• ethylene glycol degradation (from EcoCyc)
• factor 420 biosynthesis
• factor 420 polyglutamylation
• factor 430 biosynthesis
• glutaryl-CoA degradation
• KDO₂-lipid A biosynthesis I (from EcoCyc)
• lactate biosynthesis
• Lipid A-core biosynthesis (from EcoCyc)
• lipoate biosynthesis and incorporation II (from EcoCyc)
• melamine degradation
• methanofuran biosynthesis
• methanogenesis from dimethylamine
• methanogenesis from dimethylsulfide
• methanogenesis from methanethiol
• methanogenesis from methylamine
• methanogenesis from methylthiopropionate
• methanogenesis from tetramethylammonium
• methanogenesis from trimethylamine
• methyl-coenzyme M oxidation to CO₂
• N-cyclopropylmelamine degradation
• 2-oxopent-4-enoate degradation
• peptidoglycan biosynthesis II
• siroheme biosynthesis
• super pathway of aerobic toluene degradation
• superpathway of pentose and pentitol degradation
• tetrapyrrole biosynthesis I
• tetrapyrrole biosynthesis II
• 4-toluenesulfonate degradation II

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 plant 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.

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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:

• aurone biosynthesis
• β-alanine degradation II
• formaldehyde oxidation II (GSH-dependent)
• formaldehyde oxidation IV (tetrahydrofolate pathway)
• formaldehyde oxidation V (H₄MPT pathway)
• formate oxidation to CO₂
• IAA biosynthesis II
• IAA biosynthesis III
• IAA conjugate biosynthesis I
• IAA conjugate biosynthesis II
• IAA degradation I
• IAA degradation II
• IAA degradation III
• IAA degradation IV
• isoflavonoid biosynthesis
• isoflavonoid biosynthesis, initial reactions
• methane oxidation to methanol
• methanol and methylamine oxidation to formaldehyde
• superpathway of C1 compounds oxidation to CO₂

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:

• glycerol and glycerphosphodiester degradation
• glycerol degradation II
• glycerol fermentation to 1,3-propanediol
• formaldehyde assimilation I (serine pathway)
• formaldehyde assimilation II (RuMP Cycle)
• β-alanine degradation I
• lactose degradation II
• lactose degradation III

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:

• oxidative ethanol degradation I
• oxidative ethanol degradation II
• oxidative ethanol degradation III
• plastoquinone biosynthesis
• superpathway of taurine degradation
• formaldehyde assimilation I (serine pathway)
• formaldehyde assimilation II (RuMP cycle)

The following existing pathways were edited extensively:

• protocatechuate degradation I (meta cleavage pathway)
• D-camphor degradation
• adamantanone transformation
• galena oxidation
• taurine degradation I
• taurine degradation II
• taurine degradation III
• nitrite oxidation
• ammonia oxidation I (aerobic)
• formaldehyde oxidation I
• formaldehyde oxidation II

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.

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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:

• benzoyl-CoA degradation (aerobic)
• betaine biosynthesis V
• fluorene degradation II
• sulfoacetaldehyde degradation
• taurine degradation I
• taurine degradation II
• vitamin E biosynthesis

The following existing pathways were edited extensively:

• fluorene degradation I
• lignin biosynthesis
• protocatechuate degradation II (ortho-cleavage pathway)
• taurine degradation III

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:

• lactose and galactose degradation I

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

• arginine degradation XII, which includes the reactions from arginine to putrescine
• putrescine degradation, which includes the reactions from putrescine to 4-aminobutyrate
• 4-aminobutyrate degradation, which includes the reactions from 4-aminobutyrate to succinate

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.

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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:

• carbon disulfide oxidation
• glycolysis IV
• glucosinolate biosynthesis from homomethionine
• homogalacturonan biosynthesis
• homogalacturonan degradation
• homomethionine biosynthesis
• suberin biosynthesis
• xanthophyll cycle

The following pathways were imported from EcoCyc:

• PPRP biosynthesis I
• PPRP biosynthesis II

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

• coenzyme M biosynthesis
• glucosinolate biosynthesis from tryptophan
• stachydrine degradation

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

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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.

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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

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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.

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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

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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

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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

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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.

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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.