Elisa Corteggiani Carpinellielisacorteggiani.com/wp-content/uploads/2014/05/CVElisaCCResRepMay2014.pdfYFP by affinity chromatography; spectroscopic and electrophoretic analysis of

Elisa Corteggiani Carpinelli Citizenship: Italian ▪ Date of birth: 04 March 1982

Contact Website: elisacorteggiani.com e-mail: [email protected]

Key Skills

Enthusiastic scientist with great capability for design and management of scientific projects. Proficient or familiar with a vast array of laboratory techniques and with the fundamental data analysis tools. Skilled at scientific communication and teaching. Experienced in working in teams and in projects where a multidisciplinary approach is required.

Education

2007 to 2011 PhD in Biochemistry and Biotechnology (grade: A) University of Padua, Italy

2004 to 2006 Master Degree in Molecular Biology (110/110 with distinction) University of Padua, Italy

2001 to 2004 Bachelor Degree in Molecular Biology (110/110 with distinction) University of Padua, Italy

1996 to 2001 High school diploma (100/100) Liceo Classico F.A.Gualterio, Orvieto, Italy

Most relevant Post-graduate Schools, attended as student and/or as teacher

Teacher 2013 XVII International School of Pure and Applied Biophysics (Venice) Renewable energy and biofuels: a biophysical and biochemical approach

Student 2009 School on Next generation sequencing: available technologies and applications (Padova) Organized by the graduate school on Biochemistry and Biotechnology, teacher: Prof. Giorgio Valle

Student 2009 School on Proteomics and Mass Spectrometry: a theoretical and practical course (Padova) Organized by the graduate school on Biochemistry and Biophysics, teacher: Prof. Peter James

Student 2007 XI International School of Pure and Applied Biophysics (Venice) Advanced optical microscopy methods in biophysics

Post graduate Research

University of Padua, Padua, Italy Post Doctoral Fellowship Functional Genomics Research group (PI Prof. Giorgio Valle) May 2011 to May 2013 Topics: functional genomics and mutagenesis of the microalgae Nannochloropsis gaditana

metagenomic analysis of water samples from an highly polluted area Responsibilities: identification of scientific problems; design and realization of experiments; collaboration to various research projects of the group; realization of web facilities; education of undergraduate and master’s students

University of Padua, Padua, Italy PhD program Functional Genomics Research group (PI Prof. Giorgio Valle) January 2009 to April 2011 Topic: genomics and transcriptomics of the microalgae Nannochloropsis gaditana Responsibilities: identification of a scientific problem of interest and elaboration of a scientific project; design of the experimental strategies to tackle the chosen scientific problem; realization of some of the experiments; coordination of the work of the other researchers involved in the project; setting up of innovative laboratory procedures; education of undergraduate and master’s students

University of Padua, Padua, Italy PhD program Photosynthesis Research group (PI Prof. Giorgio Mario Giacometti) January 2007 to December 2008 Topics: functional and regulatory aspects of the photosynthetic apparatus of high plants and cyanobacteria

peroxidase activities in the photosynthetic compartments Responsibilities: design of the experimental strategies to tackle the assigned scientific problems; realization of the experiments; setting up of new laboratory procedures; troubleshooting; education of undergraduate and master students

Employments not in Academia

Various Private and Public Companies Short term contracts as Teacher Specialization courses about renewable energies for employees December 2013 to now

Various elementary and high schools Short term contracts as Teacher Laboratories experiences for school children and refresh course for life science’s teachers

2007 to 2012

Teaching Experience in Academia

University of Padua, Padua, Italy Teaching Assistant Laboratories of Molecular Biology Academic years 2006-2007; 2007-2008; 2010-2011 Program: production of a library of Lambda Phage DNA; Plasmid DNA preparation from E.coli; genomic DNA extraction from human saliva; PCR amplification; agarose and polyacrylamide gel electrophoresis.

University of Padua, Padua, Italy Teaching Assistant Laboratories of Structural Biochemistry Academic years 2008-2009; 2009-2010; 2011-2012 Program: growth and induction of E.coli strains transformed for the overexpression of a pH sensitive YFP; purification of the YFP by affinity chromatography; spectroscopic and electrophoretic analysis of the obtained fractions, fluorometric analysis of the purified proteins at different pH.

University of Padua, Padua, Italy Teaching Assistant Laboratories of Metabolic Biochemistry Academic year 2011-2012 Program: measure of the photosynthetic activity of leaf disks in a simple experimental system in response to different lights; purification of mitochondria from yeast and measure of the ATP production of the purified mitochondria using a fluorometric assay.

University of Padua, Padua, Italy Teaching Assistant Laboratories of Biochemistry Academic year 2012-2013 Program: introduction to absorbance spectroscopy, measure of the enzymatic kinetics of l-lactate dehydrogenase, mathematical formalisation of the data.

University of Padua, Padua, Italy Teaching Assistant Tutorials and Exercises of Metabolic Biochemistry Academic years 2009-2010; 2010-2011; 2011-2012 Program: principles of bioenergetics; glycolysis, gluconeogenesis and pentose phosphate pathway; citric acid cycle; metabolic regulation; fatty acid metabolism; amino acid metabolism; hormonal regulation of mammalian metabolism; biotechnological applications of the metabolic manipulation of various microorganisms.

University of Padua, Padua, Italy Teaching Assistant Practical Laboratories of Genomics Academic years 2010-2011; 2011-2012; 2012-2013 Programs of the three years:

! Library preparation of full-length transcripts using the In-Fusion Full Length library construction system, sequencing and bioinformatics analysis of the data;

! Introduction to PERL programming and realisation of a simple program for primer oligonucleotide design; experimental testing of the designed primers by PCR reaction and sequencing;

! Metagenomic analysis of a water sample: sampling, extraction of nucleic acids, library preparation, sequencing and data analysis

Technical skills

Molecular Biology Purification of nucleic acids from various organisms (plants, algae and bacteria); design and production of recombinant constructs for genome mutagenesis and protein overexpression; transformation of bacteria, cyanobacteria yeast and algae; enzymatic manipulation of nucleic acids; agarose and polyacrylamide electrophoresis; pulsed field gel electrophoresis (PFGE).

Genomics and Transcriptomics

Genomic DNA library preparation using the E.coli host system; preparation of mate-paired libraries for SOLiD sequencing; preparation of libraries for Ion Proton sequencing; some experience with genome assembly; mRNA enrichment and ribodepletion of Total RNA samples; preparation of full length cDNA libraries; enzymatic manipulation of RNA for 5’ end capturing.

Microscopy In vivo Fluorescent and Confocal Microscopy

Biochemistry Purification of active proteins and protein complexes from photosynthetic membranes; overexpression and purification of proteins in E.coli host system; native and denaturing protein electrophoresis, 2D gel electrophoresis; western blotting and immunodecoration; fplc and hplc for proteins and pigments analysis and purification; measures of oxygen evolution from photosynthetic samples; preparation of protein samples for analysis with mass-spectrometry.

Spectroscopy Absorbance spectroscopy; pulsed amplitude modulated (PAM) fluorometry for analysis of photosynthetic activity; fluorescence spectroscopy.

Language skills Italian (native language) English (speak fluently; read and

write with high proficiency) French (basic knowledge)

Informatics skills Basic knowledge of Perl programming,

proficient usage of many available biological databases and analysis tools

Proficient usage of spreadsheets and text editors, good capabilities with

digital graphic software

Proficient in the design and management of web pages and blogs

and in the use of socials

Publications in international journals ! A deep survey of alternative splicing in grape reveals changes in the splicing machinery related to tissue, stress

condition and genotype. Vitulo N, Forcato C, Corteggiani Carpinelli E, Telatin A, Campagna D, D’Angelo M, Zimbello R, Corso M, Vannozzi A, Bonghi C, Lucchin M and Valle G BMC Plant Biology. 14:99. doi:10.1186/1471-2229-14-99. Epub 2014 Apr 17.

! Chromosome scale genome assembly and transcriptome profiling of Nannochloropsis gaditana in nitrogen depletion. Corteggiani Carpinelli E, Telatin A, Vitulo N, Forcato C, D’Angelo M, Schiavon R, Vezzi A, Giacometti GM, Morosinotto T, Valle G. Mol. Plant (2014) 7 (2): 323-335. doi: 10.1093/mp/sst120. First published online: August 21, 2013

! Acclimation of Nannochloropsis gaditana to different illumination regimes: Effects on lipids accumulation. Simionato D, Sforza E, Corteggiani Carpinelli E, Bertucco A, Giacometti GM, Morosinotto T. Bioresour Technol. 2011 May;102(10):6026-32. doi: 10.1016/j.biortech.2011.02.100. Epub 2011 Mar 2.

! Going ultradeep to unravel the secret recipe of biofuel. Elisa Corteggiani Carpinelli LAP Pubblishing. 2011

Communication at Scientific Conferences in Italian Institutions

XVII School of Pure and Applied Biophysics, Venice, Italy Lecture Annual International School for PhD Students "Renewable energy and biofuels: a biophysical and biochemical approach"

January 2013

Topic of the talk: Introduction to genomics and transcriptomics. Case study: the genome and transcriptome of the microalgae N. gaditana: what did we leant? Presentation of Bioinformatics tools to interrogate the genomic data.

Italian National Academy “Accademia dei Lincei”, Rome, Italy Oral communication International Conference on renewable energy: “Biological processes as a possible source for renewable energy”

November 2009

Topic of the talk: recent achievements on genomics and transcriptomics of the microalgae N. gaditana

Lectures and web

Collaboration with the “Fenice Green Energy Park” for didactic laboratories for school children about biofuels and for the setting up of a photobioreactor

2013 to now

Realization of web pages and video-tutorials for students and teachers (see http://elisacorteggiani.com/ section portfolio)

Since 2008 and until now

Cultural Association, Orvieto, Italy Communication at Public Conference Lectures for the 150 anniversary of “the origin of species” May 2009 Topic of the lecture: what Darwin didn’t know yet: evidences and elements that genetics and molecular biology added to Darwin’s theory of evolution by natural selection.

Hall of Residence for University Students “Marianum”, Padova, Italy Communication at Public Conference Lecture for the students of the residence January 2012 Topic of the lecture: Let’s talk about bioethics (the method used for the lecture and many of the contents were inspired by “Justice with Michel Sandel”, and I added specific references to some topics of Bioethics)

“F.A.Gualterio” High School, Orvieto, Italy Invited Author for the School Journal Editorials about the scientific literature and the wonder for nature, with suggested readings

School years 2007-2008; 2008-2009

! 1!

Going ultra deep to unravel the secret recipe of biofuel Genomic, transcriptomic and biochemical analysis of the metabolism of the microalga Nannochloropsis gaditana in order to understand and increase its oil productivity During the first two years of my PhD I was involved in various projects of biochemical characterization of the photosynthetic apparatus and of the proteins involved in its regulation. In this period I manifested a growing interest for some recent studies concerning the culturing of photosynthetic microorganisms to harness the energy of sunlight for powering human activities and I was therefore given the opportunity to contribute to a new project of the group concerning the production of biodiesel from microalgal biomass. I started working at the culturing of various oleaginous microalgae, measuring their physiological parameters and their growth kinetics and setting up the protocols for nucleic acid and protein extractions. Some of the results of this work are reported in (Simionato et al. 2011). The project envisioned the realization of efficient production plants where microalgae were used as factories of substrates for biofuel production. The plants would have been the result of the collaboration between biologists and engineers. The work in this interdisciplinary team and the discussions that we shared during the periodical meetings represented for me an excellent scientific experience and contributed to enlarge my vision of the biotechnological task. After attending a course for graduated students about next-generation sequencing, I had a proposal for my colleagues: I wanted to start a project of genome and transcriptome sequencing of a oleaginous microalga to pinpoint the genes responsible for the accumulation of oil inside the cell and to open up the perspective of genetic manipulation of the microorganism in order to boost its productivity. My supervisor agreed that the idea was interesting and gave me the chance to carry out the project on my own responsibility. In 2009 I started working on the sequencing of the genome and the transcriptome of the microalga Nannochloropsis gaditana in close collaboration with the group of Professor Giorgio Valle (Genomics Unit of the University of Padova) and of Doctor Tomas Morosinotto (Unity of Microalgal Biophysiology of the University of Padova). After three years work, the results of my research were: the complete! sequence of the genome of Nannochloropsis gaditana at chromosome level and the prediction and annotation of its genes (the data are deposited at the NCBI as bioproject 170989); the profile of the gene expression of Nannochloropsis gaditana in conditions of oil accumulation compared to conditions of standard growth (no oil) (the data are deposited at the NCBI as bioproject 231651); the elaboration of an interpretative model of the metabolic fluxes that lead to oil accumulation. My analyses of the genome and transcriptome of N. gaditana were accepted for publication on Molecular Plant in 2013 (Corteggiani Carpinelli et al. 2014) (pubmed id 23966634) Moreover together with my colleagues of the Functional Genomics Unit of the University of Padova I worked at the release of a web resource of Nannochloropsis genome (www.nannochloropsis.org) and we also opened a blog (www.nannochloropsis.org/blog) to promote communication and collaboration among scientist involved in this field of investigation. Introduction to the Nannochloropsis’ metabolism discovery project Various species of microalgae had been observed to convert efficiently the solar energy into triacylglycerols, which are optimal substrates for the production of oil-based diesel fuel. Despite some promising results obtained by cultivating the microalgae in photobioreactors, none of the currently available strains appeared to

! 2!

be suitable for energetically convenient industrial production. A leap in productivity could be possibly obtained from the genetic improvement of the available oleaginous strains. In this respect, Nannochloropsis represented an attractive candidate, being a native oil producer; moreover it was later shown to be transformable with exogenous DNA, and some strains seem to be also capable of homologous recombination. When cultured in normal growth conditions with sufficient nitrogen, Nannochloropsis cells had an oil content of about 30% of their dry weight. Various culturing conditions were observed to increase the average oil content per cell, however these conditions supported only slow growth rates of the cultures and therefore the overall productivity resulted decreased. Among these conditions there was nitrogen deprivation. Overcoming the trade-off between oil accumulation and biomass production was the first possibility that had to be tested in order to improve the productivity.! Being Nannochloropis a poorly studied organism, the sequencing and annotation of the genome seemed the most rapid strategy to start delineating the metabolic pathways present in the cell and possibly involved in the accumulation of triacylglycerols. Moreover the genome sequence is a fundamental starting point for targeted genetic mutagenesis. Important information about the up-regulated and down-regulated pathways could be gained by comparing the abundance of the transcripts expressed when cells accumulated high amounts of triacylglycerol with the abundance of the transcripts expressed when cells showed only limited accumulation of triacylglycerols. Results Gene annotation We obtained the sequence of the nuclear genome as well as of the genomes of the organelles of Nannochloropsis gaditana B-31. We assembled the 28.5 Mega bases of the nuclear genome in 58 large scaffolds, 21 of which accounted for complete chromosomes and we completely assembled the circular genomes of the organelles. We identified a total of 10646 genes and we attributed an annotation to 6311 of them. The analysis of the annotated genes using the “pathway tool” software yielded the metabolic map showed in Figure 2. The analysis of the annotated genes and pathways revealed various traits, which are relevant for the genetic manipulation of Nannochloropsis with the final goal of improving its oil productivity in a production plant:

• We identified pathways leading to the synthesis of cellulose and sulphated fucans and pathways responsible for the remodelling of the cellulose. These indications casted a light on the molecular composition of the cell wall and also suggest possible targets of genetic modification. Indeed, one of the most energy consuming steps during oil extraction from Nannochloropsis is the breakage of the cell wall. Targeted genetic mutations of the genes assigned to these pathways might help weakening the cell wall and saving energy during oil extraction.

• We identified a group of genes that could be attributed to a pathway of biosynthesis of chrysolaminarines, which are very common storage sugars found in various neighbouring species of microalgae. The identification of a pathway of sugar storage is of particular interest, since its expression can be

Figure 1 Schematic representation of Nannochloropsis single cell

! 3!

studied to better understand the metabolic fluxes of carbon and energy in Nannochloropsis in different culturing conditions.

!Figure 2 Map of the metabolic pathways identified in Nannochloropsis gaditana after genome sequencing and annotation

• A comparative analysis of the genes of Nannochloropsis in relation to the genes of various other algae of the red, brown and green groups has shown that Nannochloropsis has an expanded repertoire of some of the genes involved in triacylglycerol assembly. Most interestingly we found a high number of triacylglycerol lipases, many of them belonging to a gene family which seems to be exclusive to Nannochloropsis. Triacylglycerol lipases can affect lipid metabolism in many ways through triacylglycerol degradation and lipid remodeling. Further studies will be needed to enlighten the function of these genes are their rule in Nannochloropsis metabolism.

• We found genes essential for the RNA silencing process and we also found indication that miRNA might be expressed in Nannochloropsis. These findings open interesting perspectives for the genetic manipulation of Nannochloropsis using gene knock-down techniques based on the transient expression of siRNA.

• We found genes whose orthologous are annotated as blu-light sensors. Confocal microscopy analysis revealed the presence of red eye-spots in the cells located outside of the chloroplast that could be assigned as a blu-light sensing structure. If these attributions are correct, they open the perspective that a circadian regulation of growth and metabolic activity might be present in this microalga. Such a possibility would not be in contrast with some observations collected in outdoor cultivation plants and has important implication for the exploitation of this organism in production plants.

an organicmolecule

CCA tRNAnucleotidyltransferase,mitochondrial: CCA1

Probable Xaa-ProaminopeptidaseP: AMPP

beta-D-fructose 2,6-bisphosphate

Sulfide:quinoneoxidoreductase,mitochondrial:hmt2

H2O

Aldehydedehydrogenasefamily 3 memberH1: ALDH3H1

6-phospho-D-gluconate

[+ 2 isozymes]

CTP

a single-stranded

RNA

Probable 1-acyl-sn-glycerol-3-phosphateacyltransferase:SLC1

dihydroxyacetonephosphate

4-phospho-hydroxy-L-threonine

GDH/6PGLendoplasmicbifunctionalprotein: H6PD

Fibronectin typeIII domain protein:VDG1235_3084

Probablecysteinedesulfurase:csd

[+ 2 isozymes]

AMP

3-hydroxyanthranilate

Dihydrodipicolinatereductase 1,chloroplastic: DAPB1

prephenate

D-mannose

L-isoleucyl-tRNAile

Betaine aldehydedehydrogenase2, mitochondrial:ALDH10A9

Dihydroorotatedehydrogenase(quinone),mitochondrial:Dhodh

CAAXprenylprotease 1homolog:FACE1

a phospholipidolefinic

fatty acid

Nitrate reductase[NADH], clonePBNBR1412:NIA2

[+ 5 isozymes]

Cytosinedeaminase:FCA1

S-allantoin

a phosphatidyl-N-methylethanolamine

tRNAcys

Probable enoyl-CoA hydratase,mitochondrial:echs1

o-succinylbenzoate

GDP

[+ 2 isozymes]

glutathioneredox

reactions I

[+ 4 isozymes]

Putativeperoxisomalacyl-coenzymeA oxidase1.2: ACX1.2

UQH2

(6E,8Z,11Z,14Z)-(5s)-5-

hydroperoxycosa-6,8,11,14-tetraenoate

ATPsynthasesubunita: ATP6

1-(5-phospho-D-ribosyl)

-AMP

UDP-D-glucuronate

geranyldiphosphate

UDP-D-galacturonate

succinate

apo-4’-lycopenoate

a 5-oxoprolyl-

peptide

Probablesulfite oxidase,mitochondrial:CG7280

a holo-[acp]

pyruvate

Protease4: sppA

Probable aconitate hydratase,mitochondrial: aco2

DIMBOA-glucoside

degradation

3-keto-beta-D-galactose

1-methylnicotinamide

a peptide

pyruvate


3-isopropylmalatedehydratase: IIL1

coenzyme A

(S)-nicotine

UDP-alpha-N-acetyl-D-

glucosamine

[+ 2 isozymes]

glycerol

a polycistronictRNA precursor

7-methylguanine

[+ 2 isozymes]

nitrite

Phosphoribosylformylglycinamidinecyclo-ligase: purM

pyruvate

an alcohol

Probable 1-acyl-sn-glycerol-3-phosphateacyltransferase: SLC1

Thiamine-phosphatesynthase: thiE

L-ornithine

Deoxyuridine5’-triphosphatenucleotidohydrolase:DUT

a proteindisulfide

gly

superpathwayof serine

and glycinebiosynthesis I

7,8-dihydroneopterin

triphosphate

Diphthinesynthase:dph5

a tRNAprecursor

obtusifoliol

cellulose

UncharacterizedABC transporterATP-bindingprotein/permeaseYOL075C:YOL075C/YOL074C

GTP

GlutathioneS-transferaseL3: GSTL3

an electron-transfer-relatedquinol

Fructosamine-3-kinase: FN3K

1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)

methylideneamino]imidazole-4-carboxamide

[+ 2 isozymes]

[+ 2 isozymes]

Probablemethylmalonate-semialdehydedehydrogenase[acylating],mitochondrial: mmsdh

PutativeDNAglycosylaseMb2491c:Mb2491c

dCMP

[+ 2 isozymes]

Glucokinase: glcK

beta-D-galactosyl-1,4-N-acetyl-beta-

D-glucosaminyl-[glycoprotein]

an aldehyde

all-trans-retinyl

palmitate

leukotrieneA4

camptothecinbiosynthesis

arachidonate

tRNA(guanine(37)-N1)-methyltransferase:PITG_12867

a beta-D-glucan

with a C3-substituted

glucose

Major extracellularendoglucanase:engXCA

Superoxidedismutase[Cu-Zn]: Sod

[+ 4 isozymes]

a diacylglycerol

D-fructose-6-phosphate

ITP

2-phospho-4-(cytidine 5’-diphospho)-2-C-methyl-D-erythritol

Probablepseudouridine-5’-monophosphatase:Gs1l

Glycoprotein3-alpha-L-fucosyltransferaseA: FUT11

24-methylenecycloartanol

acetoacetate

Delta-1-pyrroline-5-carboxylatesynthase:P5CS

OPC8-CoA

guanine atposition34 of a

bacterialtRNA

D-glyceraldehyde

Cholinedehydrogenase:betA

Probable NADHdehydrogenase:DDB_G0270104

cys

O-phospho-L-seryl-

tRNASec

an aldehyde

a 2,3,4-saturatedfatty acyl CoA

Trifunctional enzymesubunit alpha,mitochondrial: HADHA

Cytosolic 5’-nucleotidase3: nt5c3

molybdopterin

sulfite


CDP

5-phospho-alpha-D-ribose 1-

diphosphate

coenzyme A

Putativeuncharacterizedprotein:SCAT_4833

a 3-oxo-myristoyl-

[acp]

argininedegradationX (arginine

monooxygenasepathway)

2,3-bisphosphoglycerate-dependent phosphoglyceratemutase: gpmA

4-aminobenzoate

L-serinedegradation

a ceramide

ammonia

asp

methylmalonatesemialdehyde

Rhamnolipidsbiosynthesis 3-oxoacyl-[acyl-carrier-protein]reductase: rhlG

a reducedelectron-transfer

flavoprotein

ATP

2,3-dihydroxy-3-methylbutanoate

Amidase:SSO2122

coumarinate

a substitutedbeta-

amino acid

7,8-dihydrofolatemonoglutamate

an oxidizedazurin

glycyl-tRNAgly

a protein

a [pyruvatedehydrogenaseE2 protein] N6-(dihydrolipoyl)

lysine

Pyrroline-5-carboxylatereductase: PROC1

a cytosine34 intRNA precursor

a 1-phosphatidyl-

1D-myo-inositol 4-phosphate

Terminaluridylyltransferase7: Zcchc6

a short RNASegment

[+ 147 isozymes]

leu

(3Z)-phycoerythrobilin


flavoprotein

a triacylglycerol

a 1-acyl-sn-glycerol-3-phosphate

leukotrieneB4

a protein

2-phospho-D-glycerate

COFACTORS, PROSTHETIC GROUPS, ELECTRON CARRIERS BIOSYNTHESIS

a protein

UDP-N-acetylglucosamine-

enolpyruvate

[+ 3 isozymes]

Ribonuclease H2subunit A putative:AlNc14C123G6738

CTP

Pyridoxalbiosynthesislyase pdxS: pdxS

tRNA methylation (yeast)

an electron-transfer-related

quinone

[+ 3 isozymes]

phosphoryl-ethanolamine

Shikimatekinase: aroK

[+ 2 isozymes]

Isocitratedehydrogenase[NADP],mitochondrial:Idh2

Phytoenesynthase:crtB

ExosomecomplexcomponentRRP43:EXOSC8

pyridoxal-P

Adenylosuccinatelyase: ADSL

XLXG xyloglucanoligosaccharide

dGDP

L-histidinol-phosphate

a protein-N-terminal-

Proline

selenide

tRNA charging

(3S)-2,3-epoxy-2,3-

dihydrosqualene

a holo-[acp]

orotate

argininedependent

acidresistance

PutativeFAD-linkedsulfhydryloxidase347L:IIV6-347L

Adeninephosphoribosyltransferase: apt

cycloeucalenone

alpha-iminosuccinate

a malonyl-[acp]

[+ 25 isozymes]

Similar toChalconeIsomerase:CHI

Dihydrolipoyllysine-residue

acetyltransferasecomponentof pyruvate

dehydrogenasecomplex,

mitochondrial: Dlat

L-idonate

Xylulosekinase: Xylb

UDP-alpha-N-acetyl-D-

glucosamine

[+ 4 isozymes]

(S)-methylmalonyl-

CoA

acrylamide

5-oxoprolinase: OXP1

7-aminomethyl-7-deazaguanine

at position34 of a tRNAcontaining

GUN anticodon

cholesterol

Phosphatidylinositol-4-phosphate 5-kinase its3: its3

formaldehyde

UDP-D-glucuronate

ser

Protochlorophyllidereductase A,chloroplastic: PORA

choline

Dihydrolipoyl dehydrogenase,mitochondrial: LPD

pyruvate

ADP

Amidase:SSO2122

tRNAGlu

prephenate

a cardiolipin

Ubiquinone/menaquinonebiosynthesismethyltransferaseubiE: ubiE

menaquinol-6biosynthesis

[+ 3 isozymes]

a ubiquitinC-terminalthioester

N-terminaloctapeptide

alpha-D-galactose

Mannosyl-oligosaccharideglucosidase:MOGS

octanal

Lipidphosphatephosphatase2: LPP2

NADPH

Probableendonuclease IIIhomolog: nth-1


Ubiquitincarboxyl-terminalhydrolase15: Usp15

Phosphoribulokinase,chloroplastic: PRKA

propanoyl-CoA

NADH

nicotinamide

D-mannose6-phosphate

a 1,2-diacylglycerol

Guanylatekinase: Guk1

a 2,3,4-saturatedfatty acid

a peptide

hydrogensulfide

a polypeptide

gln

a phytoceramide

thiamindiphosphate

alpha-ribazole-5’-phosphate

an N10-formyl-tetrahydrofolate

2-acylglycerol O-acyltransferase3: MOGAT3

sn-glycerol-3-phosphate

S-formylglutathionehydrolase: ESD

Putative long-chain-fatty-acid--CoAligase: HI_0002

Probable cytosolaminopeptidase:pepA

a 3-oxo-stearoyl-

[acp]

Peroxisomalacyl-coenzymeA oxidase1: Acox1

anandamide

dADP

ADP

acetate

Glucose-6-phosphateisomerase,cytosolic 1: PGIC1

[+ 2 isozymes]

Beta-glucosidase6: BGLU6

CO2

a peptide

Prolylendopeptidase:Prep

resolution ofrecombinational

junctionformation of two

intact strands

2-oxoglutarate

a transhex-2-

enoyl-[acp]

a 3-oxo-dodecanoyl-

[acp]

Alpha-galactosidase:rafA

UDP

L-1-glycero-3-phosphocholine

a beta-Dglucoside

Ribosomal RNAlarge subunitmethyltransferaseE: rlmE

glutathione

uroporphyrinogen-III

CARBOHYDRATES BIOSYNTHESIS

1-aminocyclopropane-1-carboxylate

G/T mismatch-specificthymine DNAglycosylase:Tdg

Pyruvatekinase: pyk

UDP

nn-dimethylaniline-

n-oxide

ATP-dependentDNAhelicaserecQ: recQ

alaninebiosynthesis III

24-epi-campesterol

4-aminobutyrate

[+ 3 isozymes]

a polypeptide

Glutathione gamma-glutamylcysteinyltransferase1: PCS1

UDP-N-acetyl-D-

glucosaminebiosynthesis II

Cytochrome b6-f complex iron-sulfur subunit 1,cyanelle: petC-1

2-methylthio-N-6-

isopentyladenosine-37 tRNA

Cysteinesynthase,chloroplastic/chromoplastic:CYSK

UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase:DPAGT1

Adenosylhomocysteinase:SAHH

R’C(R)S-S(R)CR’

[+ 7 isozymes]

Di-N-acetylchitobiase:CTBS

uridine

D-glucuronate

Putative inositolmonophosphatase3: GA13929

CDP

Argininosuccinatesynthase: argG

Mannitol 2-dehydrogenase:AO090011000230

dUDP

an L-1-phosphatidylglycerol-

phosphate

a reducedflavodoxin


coenzyme A

Dephospho-CoA kinase: coaE

anacetoacetyl-

[acp]

protoheme IX

9,9’-di-cis-zeta-carotene

a peptide

a trans-2,trans-4-

dienoyl-CoA

glutamatedegradationIX (via 4-

aminobutyrate)

a secondaryalcohol

ORF:evm.model.contig03842.1

a methyljasmonate

pyridoxamine

Alcoholdehydrogenase:gbsB

Tryptophan--tRNA

ligase: trpS

Serineprotease23: Prss23

N-acetyl-L-ornithine


ethanol

3-sulfinoalanine

Sterol-4-alpha-carboxylate 3-dehydrogenase,decarboxylating:Nsdhl

a peptide

Prolyl 4-hydroxylasesubunitalpha: phyA

pseudouridine5’-phosphate

coenzyme A

9,9’-di-cis-zeta-carotene

a (3S)-3-hydroxyacyl-CoA

tetrahydrofolate

menaquinol-6


quinone

a nucleoside3’-phosphate

a protein

(2E,6E)-farnesyl

diphosphate

arachidonate

4-(2-aminophenyl)-2,4-

dioxobutanoate

Coproporphyrinogen-III oxidase: Coprox

3-phosphoinositide biosynthesis

tRNA guanosine-2’-O-methyltransferaseTRM13 homolog:CCDC76

a holo-[acp]

asn

a polypeptide

Thiaminpyrophosphokinase1: TPK1

pentachlorophenol

NADP-dependent malicenzyme, mitochondrial: Me3

a [protein]-N6-D-

fructosyl-L-lysine

uracil20in tRNA

[+ 2 isozymes]

agmatine

indole-3-glyoxylate

Urease: ure1

Kynurenine 3-monooxygenase,putative: kmo

Phosphoserinephosphatase:PSPH

[+ 7 isozymes]


Inositol-pentakisphosphate2-kinase: IPK1

Magnesium-protoporphyrin O-methyltransferase:chlM

4-pyridoxolactone

(2R)-3-sulfolactate

a malonyl-[acp]

acetate

a holo-[acp]

7,8-dihydropteroate

OPC6-3-ketoacyl-

CoA

fumarate

a (R)-3-hydroxybehenoyl-

[acp]

pyruvate

XXXG xyloglucanoligosaccharide

an all-trans-retinyl ester

Methylcrotonoyl-CoA carboxylasebeta chain,mitochondrial:Mccc2

indoleacetaldehyde

a methylatedribosomal

protein L11

a polypeptide

kynurenine

an oxidizedcytochrome c

acetaldehyde

zeaxanthin

[+ 3 isozymes]

a retinol

[+ 5 isozymes]

[+ 2 isozymes]


glutamatebiosynthesis V

tauropine

ProbablebifunctionalP-450/NADPH-P450reductase2: cypE

cob(I)alamin

butyl acetate

UDP-D-glucuronate


diphosphate

Glutathionereductase: gsr


[+ 2 isozymes]

NAD+

Glyceraldehyde-3-phosphatedehydrogenase:GPDA

(+)-neomenthol

a 1,2-diacyl-sn-

glycerol-3-phosphate


Transketolase:TKL1

Probablecystathioninegamma-synthase:SPBC15D4.09c


flavoprotein

a protein-proline

Lathosteroloxidase:SC5DL

thiamintriphosphate

2-isopropylmalatesynthase: leuA

3-sulfopyruvate

D-glyceraldehyde-3-phosphate

tRNAval

Protochlorophyllidereductase,chloroplastic: PORA

a nucleosidediphosphate

Phosphoenolpyruvatecarboxykinase [ATP]: pckA


Probablephosphoribosylformylglycinamidinesynthase, chloroplastic/mitochondrial: At1g74260

Gluconolactonase: gnl

a 1,3-beta-D-glucan

Trans-1,2-dihydrobenzene-1,2-dioldehydrogenase:Dhdh

a tRNAprecursorwith a 5’

extensionand a short3’ extension

Phosphatidatecytidylyltransferase: cdsA

alpha-D-galactose1-phosphate

2,3-dimethylmalatelyase: Dml

(S)-malate

Thiamine-phosphatesynthase:thiE

a glutaryl-[acp]

methyl ester

1-deoxy-D-xylulose 5-phosphate

ala

a poly gamma-glutamylcysteine-

glycine

3-phospho-L-serine

Glutamatesynthase2 [NADH],chloroplastic:Os05g0555600

leucinedegradation I

(S)-methylmalonate-

semialdehyde

PentafunctionalAROM polypeptide:LACBIDRAFT_233717

Alpha-ketoglutarate-dependent taurinedioxygenase: tauD

2-oxoisovaleratedehydrogenasesubunit beta,mitochondrial: bkdB

[+ 3 isozymes]

GMP

Pyridoxalkinase: PK

Alanine--tRNAligase:

ALATS

dihydrobiopterin

N1-acetylspermine

kynurenine

lys

Probable manganese-dependent inorganicpyrophosphatase:ppaC

a phospholipidcyclopropane

fatty acid

gln

Putative inositolmonophosphatase3: GA13929

preQ1

palmitate

(2R)-2-hydroxy-2-methylbutanenitrile

L-glutamate-5-phosphate

a deoxyribonucleotide

adenosinenucleotides

degradation II


Uroporphyrinogendecarboxylase: hemE

protoheme IX

prolycopene

[+ 2 isozymes]

gamma-linolenate

CTP

Pyrroline-5-carboxylatereductase:proC

7,8-diaminopelargonate


Dihydrolipoyldehydrogenase,mitochondrial: LPD

Arginase-1: Arg1

(S)-lactate

a 2-monoacylglycerol

a (mannosyl)6-(N-acetylglucosaminyl)

2-diphosphodolichol

Probable enoyl-CoA hydratase,mitochondrial: echs1

choline

3-ketoacyl-CoA thiolase,mitochondrial:ACAA2

Di-N-acetylchitobiase:CTBS

Farnesyldiphosphatesynthase: fps

L-aminoadipate-semialdehydedehydrogenase-phosphopantetheinyltransferase: aasdhppt

leu

arg

campesterol

a chitodextrin

Putative 3-methyladenineDNAglycosylase:DSY3705

Inosine triphosphatepyrophosphatase:PITG_03601

3-demethylubiquinone-9 3-methyltransferase:ubiG

Phosphoglyceratekinase, chloroplastic: PGK

histidinal

3-hydroxyadipyl-CoA

a CDP-diacylglycerol

gln

Epoxyqueuosinereductase: queG

arg

an mRNA

4-hydroxybutyratecoenzyme Atransferase: cat2

SeMet

a carboxylate

Pyrroline-5-carboxylatereductase:PROC1

Probable branched-chain-amino-acidaminotransferase:ilvE

[+ 3 isozymes]

methylecgonine

OTHER

N-acetylglucosaminyl-phosphatidylinositolde-N-acetylase: Pigl

Glycoprotein-N-acetylgalactosamine3-beta-galactosyltransferase1: C38H2.2

beta-D-glucose 1-phosphate

acetyl-CoA

Ribosomalprotein L11methyltransferase:prmA

a peptide

N-acetyl-D-galactosamine-[glycoprotein]


diphosphate

[+ 3 isozymes]

Serine 3-dehydrogenase:sdh

pyridoxal

a trans-2-enoyl-CoA

a reduced ferredoxin

a protein-O-(N-acetyl-D-glucosaminyl)

hydroxyproline

threoninebiosynthesis

fromhomoserine

7,9,9’-cis-neurosporene

Mannan endo-1,4-beta-mannosidase1: MAN1

Probable thiolmethyltransferase2: HOL3

glutaminedegradation I

3-(4-hydroxyphenyl)

-3-hydroxy-propionyl-CoA

Fructose-1,6-bisphosphatase,chloroplastic: FBP

Glutamyl-tRNA(Gln)amidotransferasesubunit A: gatA

Beta-galactosidase:lacZ

7-methyladenine

Tripeptidyl-peptidase2: TPP2

[+ 2 isozymes]

hydrogen sulfide

asn

3-oxo-24-ethyl-cholest-5-ene

violaxanthin

NAD+

[+ 2 isozymes]

diphthamidebiosynthesis

citrate

melibiosedegradation

glutamatebiosynthesis II

AMINOACYL-TRNA CHARGING

callosebiosynthesis

Lactase-phlorizinhydrolase:Lct

phe

alpha-D-glucose 1-phosphate

coenzymeB12

glutathione

kynurenine

succinate

Mg-protoporphyrin

ala

D-mannitol


Bifunctional 3’-phosphoadenosine5’-phosphosulfatesynthase 2: PAPSS2

L-homocysteine

2-oxoglutarate

nitrite

Pyruvate kinase: pyk

2-oxoisovalerate

D-glucose

an acyl-[acp]

(R)-3-hydroxybutanoate

asp

succinyl-CoA

a D-glucosyl-N-acylsphingosine

10-formyl-tetrahydrofolate

a ceramide

adenosine

S-methyl-5-thio-alpha-D-ribose 1-phosphate

Citrate synthase,mitochondrial: cs

a triacylglycerol

Inosine-5’-monophosphatedehydrogenase:impdh

4-methyl-2-oxopentanoate

cyanatedegradation

salicylalcohol

pregnenolone

Histidinoldehydrogenase:hisD

sulfite

Probablepolyamineoxidase4: PAO4

[+ 3 isozymes]

Enoyl-[acyl-carrier-protein]reductase[NADH]1: fabI1

Glycerol-3-phosphatedehydrogenase,mitochondrial:GPD2

GlutathioneS-transferaseL3: GSTL3

Sulfite oxidase,mitochondrial:Suox

a peptide

an aldehyde


glyoxylate cycle

Nucleosidediphosphatekinase: swoH

DNA-directedRNApolymeraseII subunitrpb3: polr2c

a carboxylate

propanoyl-CoA

dopaquinone

alpha-D-galactose

Beta-1,4-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase:Mgat3

Hormone-sensitivelipase: LIPE

3-dehydroquinatesynthase: MJ1249

a peptide

a protein

[+ 2 isozymes]

oxaloacetate

glutathione

Folylpolyglutamatesynthase,mitochondrial: FPGS

histoneN6-methyl-

L-lysine

trehalose

adenosylcobalamin5’-phosphate

Phosphoserineaminotransferase: serC

fumarate

GDP

Geranylgeranyldiphosphatereductase: chlP

a transoct-2-

enoyl-[acp]

hydroxylamine

Guanosine-3’,5’-bis(diphosphate) 3’-pyrophosphohydrolase:spoT

a CDP-2,3,4-saturated-

diacylglycerol

[+ 4 isozymes]

[+ 2 isozymes]

an RNA

a purineribonucleoside

Polyribonucleotidenucleotidyltransferase: pnp


a DNAcontaininga mismatch

Anthranilatesynthase:trpE(G)

a 5,10-methylene-tetrahydrofolate

Dihydrolipoyl dehydrogenase: lpdA

a primaryalcohol

acetyl-CoA

Purple acidphosphatase7: PAP7


sepiapterin

Aspartyl/asparaginylbeta-hydroxylase:ASPH

Uridinekinase: udk


an oligosaccharide-diphosphodolichol

sulfate

pinocembrinchalcone

beta-D-glucose-6-phosphate

an ADP-sugar

ACETYL-COA BIOSYNTHESIS

Group XIIAsecretoryphospholipaseA2: PLA2G12A

L-gulono-1,4-lactone

Glucose-6-phosphateisomerase, cytosolic 1: PGIC1

12,13-dihydroxyoctadeca-

9,15-dienoate

Malate dehydrogenase,mitochondrial: MDH2

Probableribose-5-phosphateisomerase:At2g01290

a malonyl-[acp]

[+ 2 isozymes]

[+ 7 isozymes]

Dihydroxy-aciddehydratase: ilvD

a carboxylate

Glycerolkinase: glpK

pyruvate

Enolase:PGH1

5S rRNA

hydrogensulfide

Cob(I)yrinicacid a,c-diamideadenosyltransferase,mitochondrial: Mmab

a trans-delta2-enoyl-

acyl-[acp]

Phosphoribosylaminoimidazolecarboxylase: ade6

indole-3-glycolaldehyde

a glycoproteinwith the

oligosaccharidechain attachedby N-glycosyl

linkage to proteinL-asparagine

Glycerol-3-phosphate O-acyltransferase 1: SCT1

uracil17in tRNA

p-aminobenzoatebiosynthesis

Thiamine-triphosphatase:THTPA

[+ 9 isozymes]

ATP

a peptide

3-hydroxy-5-cis-tetradecenoyl-

CoA

N1-methylguanine37

in tRNA

a nongalactosylated

galactoseacceptor

myo-inositolbiosynthesis

a 5-methylcytosine49in tRNA

ChaperoneproteinClpB1:CLPB1


2,3-dihydroxy-3-methylvalerate

acetate

Triosephosphateisomerase: tpiA

Succinate-semialdehydedehydrogenase[NADP(+)]GabD: gabD

nitrite

CytochromeP450:CYP97E3

[+ 2 isozymes]

[+ 5 isozymes]

H2O

Acyl-coenzymeA thioesterase9, mitochondrial:Acot9

methionylpeptide

aminoacetaldehyde

a ubiquitin

Aspartate--tRNA ligase,cytoplasmic:

DARS

(S)-2-acetolactate

D-threo-isocitrate

Glucose-6-phosphate isomerase,cytosolic: PGIC

DIMBOA-beta-D-

glucoside

Malonyl CoA-acyl carrierprotein transacylase:CWATWH0003_3818


biotin

an alcohol

24-methylenecholesterol

(3R)-hydroxymyristoyl-[acyl-carrier-protein]dehydratase: fabZ

a proteinwith N-terminalaspartate

[+ 2 isozymes]

5-amino-1-(5-phospho-

D-ribosyl)imidazole-4-carboxylate

NUCLEOSIDESAND NUCLEOTIDES

DEGRADATION

a DNAcontainingabasic site


quinone

cys

acetaldehyde

uridine2552in 23S rRNA

Glyceraldehyde-3-phosphatedehydrogenase: GPDA

cycloeucalenol

acetate

a protein

5’-phosphoribosyl-N-formylglycineamide

L-ornithine

UQH2



L-glutaminebiosynthesis

II (tRNA-dependent)


D-galactono-1,4-lactone


[+ 6 isozymes]


[+ 4 isozymes]

3-ketoacyl-CoA thiolase,mitochondrial: ACAA2

a phosphoprotein

Ribosomal RNAsmall subunitmethyltransferaseG: rsmG

Probable 3-hydroxyisobutyratedehydrogenase,mitochondrial: hibA

a [protein]-L-tyrosine

tRNA (cytosine(34)-C(5))-methyltransferase:nsun2

Squalenesynthase:fdfT

Predictedprotein:v1g244860

isochorismate

Nicotinate-nucleotideadenylyltransferase:nadD

a (3R)-3-hydroxyacyl-

[acp]

methylglyoxal

S-sulfanyl-[acceptor]

Enolase: PGH1

chitin

Trifunctionalenzymesubunit alpha,mitochondrial:HADHA

fumarate

urea

pro

a 3-oxo-cis-delta9-

hexadecenoyl-[acp]

3-hydroxy-L-kynurenine

L-glutamyl-tRNAGlu

L-serinedehydratase: sds

L-dehydro-ascorbate

Glycine N-methyltransferase(Fragment): GNMT

Aspartate-semialdehydedehydrogenase: asd

S-adenosyl-L-methionine

Ribulose-phosphate3-epimerase:rpe

5-amino-levulinate

tRNA(Ile)-lysidinesynthase:tilS

nicotinate


tRNAdimethylallyltransferase9: IPT9

Methylenetetrahydrofolatereductase 1: MTHFR1

a [protein]-L-arginine

Thymidylatekinase: dtymk

tRNA (guanine(26)-N(2))-dimethyltransferase:Trmt1


diphthamidein eEF-2

linamarin

D-erythrose-4-phosphate

Probablegamma-butyrobetainedioxygenase:mll1440

Probable cysteinedesulfurase,mitochondrial:CG12264

D-ribose-5-phosphate

Histidinebiosynthesistrifunctionalprotein: HIS4

2-oxoglutarate

a dipetidewith

aspartate atN-terminal

methylglyoxaldegradation I

a single-stranded

RNA

UDP-alpha-N-acetyl-D-glucosamine

(1S,2R)-1-C-

(indol-3-yl)glycerol 3-phosphate

Homoserinekinase: thrB

2-oxo-3-hydroxy-4-phosphobutanoate

2-aceto-2-hydroxy-butanoate

ATP

dTDP-4-dehydro-6-deoxy-beta-L-mannose


[+ 3 isozymes]

Violaxanthinde-epoxidase,chloroplastic:VDE1

a dodecanoyl-[acp]

a trans-2,trans-4-

dienoyl-CoA

7-keto-8-aminopelargonate

UMP


[+ 3 isozymes]

S-adenosylmethionine:tRNAribosyltransferase-isomerase: queA

GTP:AMPphosphotransferase,mitochondrial: AK3

4-amino-4-deoxychorismate

Fructokinase:scrK

LL-diaminopimelateaminotransferase:dapL

dCDP

L-methionyl-tRNAfmet

a peptide

glutamatedegradation X

D-beta-hydroxybutyratedehydrogenase,mitochondrial:Bdh1


AMINO ACIDS BIOSYNTHESIS

acetyl-CoA

biotin

[+ 160 isozymes]

cys

Ornithine cyclodeaminase:PHATRDRAFT_54222

an anilide

Fumarate hydrataseclass I, aerobic: fumA

a ADP-D-ribosylacceptor

Delta-aminolevulinicaciddehydratase,chloroplastic:HEMB

AMP

2-[(2R,5Z)-(2-carboxy-4-methylthiazol-

5(2H)-ylidene]ethylphosphate

4-hydroxyphenylpyruvatedioxygenase: HPD

3-oxoacyl-[acyl-carrier-protein]synthase2: fabF

L-idonate

[+ 3 isozymes]


acetate

cadaverine

an N2-methylguanine10

in tRNA

an AP(apurinicor apyrimidinic)

site createdby glycosylic

bond cleavage

dUDP

(S)-lactate

an L-histidinein eEF-2

Dihydrolipoyldehydrogenase,

mitochondrial: LPD

diphthinein eEF-2

Histonedeacetylase1: HDAC1

Xyloseisomerase:XYLA

[+ 7 isozymes]

Amidophosphoribosyltransferase: purF

oxaloacetatea peptide

5-chloro-5-deoxy-

D-ribonate

a guanine26in tRNA

[+ 6 isozymes]

UDP-D-glucose

D-3-phosphoglyceratedehydrogenase: Phgdh


a peptide

Iduronate 2-sulfatase: Ids

beta-D-galactose

argininedegradationVI (arginase2 pathway)

formaldehydeoxidation II

(glutathione-dependent)

RibonucleaseZ: rnz

inosine



Putativeuncharacterizedprotein:PITG_05764

a long-chainacyl-CoA

gln

a trans-tetracos-2-enoyl-[acp]

Serine--tRNA ligase,cytoplasmic:serS

a dolichol

formate

prostaglandin-H2

[+ 4 isozymes]



[+ 22 isozymes]

Proteasomesubunit betatype-3: PBC1

Probable ribose-5-phosphate

isomerase: At2g01290

GMP

Pyrophosphate--fructose 6-phosphate 1-phosphotransferasesubunit beta: PFP-BETA

nicotine-delta1’5’-

iminium ion

Aminomethyltransferase:gcvT

RNase IIdegradation

substratemRNA

selenocysteine

a protein-N-ubiquityl-

lysine

tRNA (guanine-N(7)-)-methyltransferase:trmB

[+ 2 isozymes]

(+)-neomentholdehydrogenase:SDR1

a mitochondrialpreproteinincluding a

mitochondrialtargetingsequence

Glucose-6-phosphateisomerase,cytosolic 1: PGIC1

Probable enoyl-CoA hydratase,

mitochondrial: echs1

2-hydroxyphenylacetate


Phenylalanine-4-hydroxylase: pah

2-amino-3-carboxymuconate-6-semialdehydedecarboxylase: acmsd

a phenolicdonor

cholesterol

Pyridoxalkinase: PK

1,4-dihydroxy-

2-naphthoyl-CoA

adenosine 3’,5’-bisphosphate

[+ 3 isozymes]

catechol

1D-myo-inositol (3)-

monophosphateGTP

3-amino-3-deoxy-D-

fructose 6-phosphate

an alcohol

a peptide

a deoxyribonucleosidetriphosphate

Epoxidehydrolase2: EPHX2

3-mercaptopyruvate

Propionyl-CoAcarboxylasebeta chain,mitochondrial:PCCB

Glutamatedecarboxylase:GAD

acetaldehyde

D-lactatedehydrogenase:ldhA

(2R)-3-sulfolactate


2-diphosphodolichol

adenosine



Phosphoglycolatephosphatase: PGP

N2-succinyl-L-glutamate 5-semialdehyde

L-lysyl-tRNAlys

(1,4)-beta-xylan

degradation

queuosine atposition 34of a tRNAcontaining

GUNanticodon

trp

cys

Zeta-carotenedesaturase:crtQ

[+ 2 isozymes]


an all-transretinal-[cellular-retinol-

binding-protein]

TryptophanbiosynthesisproteinTRP1: TRP1

propionate

Dolicholkinase: Dolk

ethanolS-(2-

hydroxyacyl)glutathione

[+ 2 isozymes]

an L-1-phosphatidyl-

inositol

a carboxylate

valine degradation I

GDP

Phosphopantothenoylcysteinedecarboxylase: Ppcdc

an (R)-3-hydroxyoctanoyl-

[acp]

Thioredoxinreductase2: trxr2

Probable aldehydedehydrogenase:FIS1

Peptidyl-prolylcis-transisomeraseD: PPID

arg

a 1,3-beta-D-glucan

3-deoxy-D-arabino-

heptulosonate-7-phosphate

oxaloacetate

D-sedoheptulose-7-phosphate

[+ 2 isozymes]

a crotonyl-[acp]

Alpha-galactosidase:Os10g0493600

ADP

[+ 2 isozymes]

AMP

Arachidonate 5-lipoxygenase:ALOX5


Putativeenoyl-CoAhydratase/isomeraseyngF: yngF

a phosphoprotein

UTPGlutamatedecarboxylase:GAD

lys

a tetrahydrofolate-glutamate


Pyridoxamine5’-phosphateoxidase-relatedFMN-binding:Esi_0074_0067

an RNA


Ceramidesynthase4: CERS4

precorrin-1

2-dehydropantoate

D-glucuronate



[+ 2 isozymes]

delta24-25-sitosterol

Indoleamine2,3-dioxygenase1: Ido1

biotin biosynthesisfrom 7-keto-8-

aminopelargonate

Lipoyl synthase,apicoplast: lipA

an [apo BCAA dehydrogenaseE2 protein] N6-(S-[2-

methylpropanoyl]dihydrolipoyl)lysine

gln

tRNA-dihydrouridine(16/17) synthase[NAD(P)(+)]: DUS1

molybdenum cofactor biosynthesis

a calmodulinN6-methyl-

L-lysine

GLYCOLYSIS

Enoyl-[acyl-carrier-protein]reductase[NADH]FabI: fabI

Calmodulin-lysine N-methyltransferase:Camkmt

[+ 2 isozymes]

Probable 6-phosphogluconolactonase 4,chloroplastic: Os09g0529100

Indoleamine2,3-dioxygenasefamilyprotein: BNA2

cytosine

Glucokinase:glcK

4alpha-methyl-5alpha-ergosta-

8,14,24(28)-trien-3beta-ol

2,4-dienoyl-CoAreductase[NADPH]:fadH

5-dehydro-D-gluconate

ATP

Cysteinesynthase2: cys12

Protease4: sppA

Cysteinesynthase2: cys12

2-oxoisovaleratedehydrogenase subunit

alpha, mitochondrial:BCKDHA

a 3-oxo-myristoyl-

[acp]

a carboxylate


octanoate

adenosyl-cobyrinatea,c-diamide

a 2-lysophosphatidylcholinefolate transformations I

Serinehydroxymethyltransferase2: shmt2

arsenite

ppGpp

N-acetylneuraminate

Lysine--tRNA

ligase: Kars

beta-D-galactose

Dihydrodipicolinatesynthase: dapA

an (R)-3-hydroxydecanoyl-

[acp]

Hydroxymethylglutaryl-CoA lyase,mitochondrial: HMGCL


Betaine aldehydedehydrogenase2, mitochondrial:ALDH10A9 Putative 3-

mercaptopyruvatesulfurtransferase:SPCC4B3.01

a sphingomyelin

glutamatedependent

acidresistance

pyruvate

Cycloartenolsynthase: cas1

(2E,6E)-farnesal

a tRNAuridine38-40

an [L-cysteinedesulfurase]-S-sulfanyl-L-cysteine

keto-phenylpyruvate

ChalconeIsomerase:CHI

Ribonucleoside-diphosphatereductase largesubunit: RNR1

UTP--glucose-1-phosphateuridylyltransferase:Ugp2

6-hydroxymethyl-dihydropterindiphosphate

Cholinesterase:BCHE

a (R)-3-hydroxyarachidoyl-

[acp]

[+ 3 isozymes]

glt

2-phospho-4-(cytidine 5’-diphospho)-2-C-methyl-D-erythritol

[+ 6 isozymes]

succinate


diphosphate

FATTY ACID AND LIPIDS DEGRADATION

sulfiteoxidation IV

tRNA(guanine(9)-N1)-methyltransferase:trm10

4-(cytidine 5’-diphospho)-2-C-methyl-D-erythritol

trans-delta2-decenoyl-

CoA

RESPIRATION

Riboflavinsynthasealphachain: rib5

tetrahydrobiopterin

[+ 3 isozymes]

[+ 21 isozymes]

a 3’-phosphate-terminated

RNA

Transketolase:tkt-1

Cystathioninebeta-lyasePatB: patB


D-sedoheptulose-1,7-bisphosphate

Transaldolase: tal

octanoate

a phosphatidylcholine

Bifunctionaldihydrofolatereductase-thymidylatesynthase2: THY-2

Cysteinesynthase,chloroplastic/chromoplastic:CYSK

Leucoanthocyanidindioxygenase: A2

5-enolpyruvyl-shikimate-3-phosphate

[+ 128 isozymes]

a protein

5’,5’’’-P-1,P-4-tetraphosphatephosphorylase2: APA2

a holo-[acp]

lys

N1-methylguanine9

in tRNA

Pheophorbidea oxygenase,chloroplastic:PAO

Phosphoribosylformylglycinamidinecyclo-ligase: purM

NADbiosynthesis

I (fromaspartate)

beta-D-glucose

5-dehydroavenasterol

3-diphospho-1D-myo-inositol

(1,2,4,5,6)pentakisphosphate

a 2,3,4-saturated 2-lysophosphatidate


a feruloyl-polysaccharide

a cis-5-enoyl-CoA

a peptide

a dolichylbeta-D-

mannosylphosphate

Sepiapterinreductase:SPR


beta-D-glucose

dCMP

Glutamatesynthase1 [NADH],chloroplastic:GLT1

2-O-methylguanosine2251

in 23S rRNA

thiaminsalvage III

D-myo-inositol (1,3,4)-trisphosphatebiosynthesis

a palmitoleoyl-[acp]

Asparagine--tRNA

ligase: asnS

a DNA pairof adjacentpyrimidines

RiboflavinbiosynthesisproteinRibD: ribD

5-amino-6-(D-ribitylamino)

uracil


N(4)-{N-acetyl-beta-D-glucosaminyl-(1,2)-alpha-D-mannosyl-

(1,3)-[N-acetyl-beta-D-glucosaminyl-(1,2)-alpha-D-mannosyl-(1,6)]-beta-D-mannosyl-(1,4)-N-acetyl-

beta-D-glucosaminyl-(1,4)-[alpha-L-fucosyl-(1,3)]-N-acetyl-beta-D-

glucosaminyl}asparagine

2-keto-3-methyl-valerate

UTP



3-ketoacyl-CoA thiolase,mitochondrial: ACAA2

L-glutaminyl-peptide

D-xylulose-5-phosphate

[+ 2 isozymes]

ceramidebiosynthesis

dephospho-CoA

Dipeptidylpeptidase3: dpp3

a holo-[acp]

Tryptophansynthase:TRP-1

benzyl-HCH

a cytosine48in tRNA

3-dehydrosphinganine

N-tetradecanoylglycyl-peptide

Transketolase:TKL1

ProteinCbbY: cbbY

bicarbonate

OligopeptidaseA: prlC


cis-homoaconitate

an alcohol

5,6,7,8-tetrahydropteridine

N4-{N-acetyl-beta-D-glucosaminyl-(1,2)-alpha-D-mannosyl-

(1,3)-[N-acetyl-beta-D-glucosaminyl-(1,2)-alpha-D-mannosyl-(1,6)]-beta-D-mannosyl-(1,4)-N-acetyl-

beta-D-glucosaminyl-(1,4)-N-acetyl-beta-D-

glucosaminyl}asparagine

a fatty acid

a dietaryall-trans-

retinyl ester

superoxideradicals

degradation

leukotrieneA4

an (R)-3-hydroxybutanoyl-

[acp]


[acp]

[+ 6 isozymes]

Deoxyhypusinesynthase: Dhps

taurine

[+ 3 isozymes]

pro

Ornithinecarbamoyltransferase:argF

2,3-bisphosphoglycerate-dependentphosphoglyceratemutase: gpmA


Ornithineaminotransferase,mitochondrial: Oat

an aliphaticamine

Ketol-acidreductoisomerase,chloroplastic: AHRI

glutamatebiosynthesis IV

Phycoerythrobilin:ferredoxinoxidoreductase: pebB

histone-L-lysine

AROMATIC COMPOUNDS BIOSYNTHESIS

Argininosuccinatelyase: ASL

L-glutamyl-tRNAGln

a tRNAuridine34

a peptide

Aspartokinase 3,chloroplastic: AK3

4beta-hydroxymethyl-4alpha-methyl-5alpha-cholest-7-en-3beta-ol

cyclopropanefatty acid

(CFA)biosynthesis

1-hydroxy-2-methyl-2-(E)-butenyl 4-

diphosphate

Methylsterolmonooxygenase1: Msmo1

[+ 2 isozymes]

Serine--tRNA ligase,cytoplasmic:

serS

a reducedazurin

alpha-D-ribose-1-

phosphate

Putativeacyl-CoAsynthetaseYngI: yngI


a [TusE sulfurcarrier protein]-S-sulfanylcysteine

D-ribulose-5-phosphate

Epidermal retinoldehydrogenase2: SDR16C5

a steryl-ester

Fatty-acid amidehydrolase 1: FAAH

23S rRNA(guanosine-2’-O-)-methyltransferaseRlmB: rlmB

GDP-4-dehydro-6-deoxy-

D-mannose

trans-oct-2-enoyl-CoA

thiosulfate

succinate

an L-1-phosphatidyl-glycerol

5’,5’’’-diadenosinetriphosphate


adenosylcobinamide


L-gulonolactoneoxidase: Gulo

pppGpp

UTP

acetyl-CoA

Argininedecarboxylase:speA

Probable aconitatehydratase,mitochondrial: aco2

an N2dimethylguanine26in tRNA


2-diphosphodolichol

hypoxanthine

pyruvate

a protein

a plasmaretinol-bindingprotein

Callosesynthase7: CALS7

guanine atposition34 of a

bacterialtRNA

L-idonate 5-dehydrogenase:VIT_16s0100g00290

fumarate

vernolate

xanthine andxanthosine

salvage

Glutathione synthetase,chloroplastic: GSH2

O-acetylhomoserine(thiol)-lyase: cysD


Putativecarbonicanhydrase3: cah-3

a polysaccharide

ser

[+ 3 isozymes]


Homogentisate1,2-dioxygenase:hmgA

Phosphatidylinositol4-kinase beta1: PI4KBETA1

tRNA (uracil(54)-C(5))-methyltransferase:SPAC4G8.07c

2-oxoglutarate

OPC6-3-hydroxyacyl-

CoA

superpathwayof ammoniaassimilation

(plants)


L-ornithine

Probablemethylmalonate-semialdehydedehydrogenase[acylating],mitochondrial:mmsdh

an aldehyde

thr

OPC6-trans-2-

enoyl-CoA


Probable aconitatehydratase,mitochondrial: aco2


[+ 2 isozymes]

a [glycine-cleavage complex

H protein] N6-(dihydrolipoyl)

lysine


phosphate

a 1,2-diacyl-sn-glycerol-3-phosphate

Probable glutamineamidotransferaseDUG3: DUG3

Beta-1,4-galactosyltransferase3: B4GALT3

D-mannosedegradation

an oxidizedelectron-transfer

flavoprotein

L-homocysteine

L-homoserine

xanthosine

alpha-L-galactose-1-phosphate

a peptide

CDP

betanidinquinone

a [2-oxoglutaratedehydrogenase

E2 protein] N6-(S-succinyldihydrolipoyl)lysine

phosphatidylethanolaminebiosynthesis III

2-aminoadipate


Poly(A)polymerase:papA

[+ 3 isozymes]

Nucleosidediphosphatekinase 4,chloroplastic:NDK4

cysteinebiosynthesis

IV (fungi)


a [protein]-L-cysteine



Transketolase: TKL1

[+ 4 isozymes]

Branched-chain-amino-acid aminotransferase:37018



ethanoldegradation II

a chitodextrina 3beta-hydroxy-delta5-steroid

L-allo-threoninealdolase:ltaA

Glutamate--tRNA ligase,chloroplastic/mitochondrial:At5g64050

a 3’ half-tRNA

moleculewith a

hydroxylon its 5’ end

inosine

[+ 2 isozymes]

[+ 2 isozymes]

succinyl-CoA

campest-4-en-3beta-ol

Glycine--tRNA

ligase: glyQS

DNAn

a 1-phosphatidyl-


pyridoxal-P

a tRNAcontaining a3’ CCA end

SAL1phosphatase:SAL1

propanoyl-CoA

Catalase: CAT

Obtusifoliol14-alphademethylase:CYP51




Xaa-Prodipeptidase:PEPD

Putative gamma-glutamyltransferaseywrD: ywrD

[+ 2 isozymes]

nicotinamide

GDP-mannose 4,6-dehydratase: gmd


S-methyl-5’-thioadenosine


an organicmolecule



ubiquinone-8

a trans-delta2-

decenoyl-[acp]

a tRNA 2-thiouridine34

sulfite


thio-molybdenum

cofactor

[+ 5 isozymes]


beta-D-fructose 2,6-

bisphosphate

a phospholipid

[+ 7 isozymes]

a 3-oxo-decanoyl-

[acp]

1,3-bisphospho-D-glycerate

Probablecytochromec-type hemelyase: cchl-1

Ribulose-phosphate3-epimerase:RPE


a deacetylatedhistone

an [apo BCAAdehydrogenase E2

protein] N6-(lipoyl)lysine

4alpha-hydroxymethyl,4beta,14alpha-

dimethyl-9beta,19-cyclo-5alpha-ergost-24(241)-en-3beta-ol

Epoxidehydrolase4: Ephx4

2-oxoglutarate


succinate

Protein-L-isoaspartate(D-aspartate) O-methyltransferase:PCMT1

Malonyl CoA-acyl carrierproteintransacylase:fabD

a sugarphosphate

Phosphoribosylaminoimidazole-succinocarboxamide synthase: purC

Putative L-ascorbateperoxidase6: APX6


[+ 2 isozymes]

a 3-oxoacyl-[acp]

(R)-lactate

[+ 3 isozymes]

all-trans-zeta-

carotene

71-hydroxychlorophyllide a

Glutathione gamma-glutamylcysteinyltransferase1: PCS1

Gamma-glutamylhydrolaseA: gghA

D-glucose

[+ 2 isozymes]

NADH

DNA-directedDNA/RNApolymerasemu: Polm

a plastoquinone

formate

NADPH

[+ 3 isozymes]


L-aspartate-semialdehyde

Putative dipeptidylpeptidase IV:Esi_0282_0006

a [protein]-L-aspartate

Endo-1,3(4)-beta-glucanase1: eng1

Purine nucleosidephosphorylase1: punA


4alpha-carboxy-

stigmasta-7,24(241)

-dien-3beta-ol

ADP

Sphingolipiddelta(4)-desaturaseDES1: degs1

cob(I)yrinate a,c-

diamide

glt

L-selenocysteinyl-tRNAsec

ABCtransporterATP-bindingprotein/permeasewht-1: wht-1

Cholinesterase:BCHE

guanine46in tRNA


met


diphosphate

4-(2’-carboxyphenyl)-

4-oxobutyryl-CoA

dUTP

[+ 3 isozymes]

a holo-[acp]

a [2-oxoglutaratedehydrogenase E2 protein]

N6-(dihydrolipoyl)lysine

4-hydroxy-3-methylbut-2-enyldiphosphatereductase: ispH

Enolase: PGH1

Hydrolase, putative:RCOM_1499940



[+ 8 isozymes]

Peroxisomalacyl-coenzyme Aoxidase 1: Acox1

Protoporphyrinogenoxidase,chloroplastic: PPOX1

Glucokinase:glcK

Xanthinephosphoribosyltransferase: xpt

[+ 2 isozymes]

15-cis-phytoene

phosphatidylethanolaminebiosynthesis II

phosphate

Glutamine-dependentNAD(+)synthetase:Nadsyn1

Glucokinase: glk

Thiamine-phosphatesynthase: thiE

phosphateutilizationin cell wall

regeneration

4-hydroxybutanoyl-CoA

a protein


[+ 2 isozymes]

NADH

Phosphoethanolamine N-methyltransferase 3: NMT3

5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase: metE

UMP

[+ 2 isozymes]


Bifunctionalaspartokinase/homoserinedehydrogenase2, chloroplastic:AKHSDH2

D-glucosamine-6-phosphate


ketolysis

a nucleosidemonophosphate

Dual specificityproteinphosphatase:VH-PTP13

melibiose


an L-1-phosphatidyl-ethanolamine

a [protein]-L-lysine

formaldehyde

beta-D-glucose

[+ 2 isozymes]

an L-1-phosphatidylserine

Probable CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase:pgs1

a purine base

ProteinPYR1-3: pyr1-3

UDP-sugarpyrophosphorylase1: USP1

acetyl-CoA

tRNAarg

Phosphoserinephosphatase:PSPH

ser

S-adenosylmethioninesynthase: metK

oxaloacetate



UMP

2-iminoacetatesynthase: thiH

Galactokinase:GALK1

[+ 7 isozymes]

L(or D)-O-phosphoserine

(S)-malate

Threoninesynthase:thrc

(2E,6E)-farnesyl

diphosphate

ethanoldegradation I



a diacylglycerol

a phenoxylradical of

a phenolicdonor

a 1-phosphatidyl-

1D-myo-inositol 4,5-

bisphosphate


Guaninedeaminase:guaD

D-mannose6-phosphate

ala

a (3R)-3-hydroxyacyl-

[acp]



Cholinephosphotransferase1: Chpt1

Probable 3-hydroxyacyl-CoAdehydrogenaseB0272.3:B0272.3

a long-chainfatty acid

[Skp1-protein]-hydroxyproline N-acetylglucosaminyltransferase: gnt1

a [tRNAIle2]-cytidine34

Mannitol 1-phosphatedehydrogenase:MPDH2

Succinyl-CoA:3-ketoacid-coenzyme Atransferase 1,mitochondrial:OXCT1

oleate

[+ 2 isozymes]

L-glutamategamma-

semialdehyde


9,12-dienoate


[+ 2 isozymes]

fumarate

3-sulfopyruvate

anoligopeptide

Cysteinesynthase 2: cys12

Transketolase:tkt-1

[+ 3 isozymes]

3-phosphoshikimate 1-carboxyvinyltransferase,chloroplastic: At2g45300

Probablerhamnosebiosyntheticenzyme1: RHM1

13’-hydroxy-alpha-

tocopherol

succinate

a [protein]-L-methionine


Probable aldehydedehydrogenase: FIS1

Alcoholdehydrogenase[NADP(+)]: AKR1A1

cis-aconitate

Serinepalmitoyltransferase2: SPTLC2

Fumarate hydrataseclass II: fumC

L-allo-threonine

[+ 2 isozymes]

BifunctionalpurinebiosyntheticproteinpurD: purD

a 3-oxoacyl-[acp]

type-1transmemberane

domains

PutativeHollidayjunctionresolvase:CAB571

a plastoquinol

Phosphoserinephosphatase: PSPH

24-hydroxy-3-oxocholest-

4-en-26-oyl-CoA

[+ 16 isozymes]

succinate

GTPaseHflX: hflX

a peptide3-hydroxy-L-aspartate

7-dehydro-cholesterol

[+ 6 isozymes]

NUCLEOSIDES AND NUCLEOTIDES BIOSYNTHESIS

2-phosphoglycolate

5-chloro-4-hydroxy-2-

oxopentanoate


flavoprotein

Probable 3-hydroxyisobutyryl-CoA hydrolase3: At2g30660

a phosphorylase a

ethanol

a peptide

Probableserineracemase: srr

L-aspartyl-4-phosphate


Leucine--tRNA

ligase: leuS


L-seryl-tRNA(Sec)kinase: Pstk

a 1,3-beta-D-glucan

1-phosphatidyl-1D-myo-

inositol 3,5-bisphosphate

phosphoryl-ethanolamine

12,13-epoxyoctadeca-9,15-dienoate

Acetylornithinedeacetylase: argE



colanic acid building blocks biosynthesis

(S)-3-hydroxy-isobutyrate

PENTOSE PHOSPHATE PATHWAYS

(deoxynucleotides)(m)

PPPi

Alcoholdehydrogenase:adh

Probable glutamineamidotransferaseDUG3: DUG3

[+ 5 isozymes]

benzoyl-CoA

sirohydrochlorin

a 2-lysophosphatidylcholine

indole-3-glyoxal

D-erythro-imidazole-glycerol-

phosphate

pyruvate

phosphatidylcholinebiosynthesis I

N1-methyladenine58

in tRNA

Dihydrolipoyldehydrogenase,

mitochondrial: LPD

shikimate

1-deoxy-D-xylulose5-phosphatereductoisomerase: dxr

thr

Cobalaminsynthase:cobS

[+ 2 isozymes]



glt

a peptide

O-succinyl-L-homoserine

a protein-L-methionine-(S)-S-oxide

a proteinL-beta-

isoaspartatealpha-

methyl ester

DNA combinedwith exogenousDNA to form a

recombinationaljunction

ADP

[+ 3 isozymes]

pyruvate

choloyl-CoA

intracellularS0

NAD+

Peroxiredoxin-1: PRDX1

ala


Fe3+

cobinamide

Methylmalonatesemialdehydedehydrogenase[acylating] 1: iolA1

a protein

Aspartylaminopeptidase:DNPEP

Putativethreonine-phosphatedecarboxylase:cobD


a [pyruvatedehydrogenaseE2 protein] N6-

(lipoyl)lysine

D-glucosamine-6-phosphate

Transketolase:tkt-1

L-citrulline

beta-D-xylopyranosyl-(1->4)-beta-D-xylopyranose-oligosaccharide

acetylcholine

chenodeoxycholoyl-CoA

ProbableNAD kinase 2,chloroplastic:Os11g0191400


acyl-[acp]



an acetyl-[acp]

UDP-glucuronate4-epimerase4: GAE4

5,10-methylenetetrahydrofolate


2-methoxy-6-(all-trans-octaprenyl)

phenol


Aldose 1-epimerase:Galm

met

2-aminomuconatesemialdehyde

a trans-hexacos-2-enoyl-[acp]

4alpha-methyl-

zymosterol

L-homocysteine

Fructose-bisphosphatealdolase, chloroplastic:Os11g0171300


a (mannosyl)8-(N-acetylglucosaminyl)2

2-oxoglutarate


D-fructuronate

Phosphopantothenate--cysteine ligase: PPCS

ammoniumtransport


Peptidyl-tRNAhydrolase 2,mitochondrial:Ptrh2

7,8-dihydro-8-oxoguaninetriphosphatase:Nudt1

1D-myo-inositol1,2,3,4,5,6-

hexakisphosphate

AminopeptidaseN: pepN

Probablephosphoadenosinephosphosulfatereductase:SPAC13G7.06

Deoxycytidylatedeaminase: Dctd

a (R)-3-hydroxycerotoyl-

[acp]

phosphoribosyl-ATP

5alpha-cholesta-

7,24-dien-3beta-ol

2-C-methyl-D-

erythritol-4-phosphate

dTMP


riboflavin

[+ 4 isozymes]

(S)-3-hydroxy-isobutyryl-CoA

a reducedthioredoxin

guanine527in 16S rRNA

a 5,10-methylene-tetrahydrofolate

[+ 2 isozymes]

Cocaineesterase:cocE

C1 COMPOUNDS UTILIZATION AND ASSIMILATION

Dihydrolipoyldehydrogenase:lpdA

L-aspartateoxidase:nadB

Chitindeacetylase1: cda1

a [ThiI sulfur-carrier protein]-S-sulfanylcysteine


a 2,3,4-saturated

fattyacyl-[acp]

asp

24-methylenelophenol

Octanoyltransferase: lipB

tRNA-dihydrouridine(16/17) synthase[NAD(P)(+)]: DUS1

L-asparaginase1: ansA

an oligosaccharide

a peptide


Glucose-6-phosphateisomerase,cytosolic1: PGIC1

methanol

a protein-L-tyrosinephosphate

Uricase: UOX

apo-4’-lycopenal

PutativeserineproteaseHhoA: hhoA

[+ 5 isozymes]

a phosphoprotein

a standardalpha

amino acid

Glucose-6-phosphate1-epimerase:YMR099C

a standardalpha

amino acid

Arogenatedehydrogenase2, chloroplastic:TYRAAT2

glutathionedisulfide

Queuine tRNA-ribosyltransferase:qtrt1


[+ 2 isozymes]

Glutamatedehydrogenase2: glud2

a DNAcontaining

a purinic site

(2R)-3-sulfolactate

Cystathioninegamma-lyase: cysA

all-trans-retinol

all-trans-retinal

[+ 2 isozymes]

a trans2,cis-5-dienoyl-

CoA

UDP

[+ 2 isozymes]

glutamatebiosynthesis III

D-fructose

an alpha-D-aldose-1-

phosphate

D,L-malicsemialdehyde

shikimate-3-phosphate

Transketolase: TKL1


2-oxoisovalerate

L-glutamyl-tRNAGlu

3beta-hydroxy-

4beta-methyl-5alpha-

cholest-7-ene-4alpha-carboxylate


[+ 2 isozymes]

an oxidizedflavodoxin

[+ 3 isozymes]

urea

[+ 3 isozymes]

phosphoribulosylformimino-AICAR-P

GDP-L-fucose

coenzyme A




a 5-L-glutamyl-L-amino acid

RNase Gdegradation

substratemRNA


4-amino-2-methyl-5-diphosphomethylpyrimidine

Phytoenedehydrogenase:carB

(S)-2-amino-6-oxohexanoate

Acyl-[acyl-carrier-protein]desaturase 7,chloroplastic:FAB2

a glycerophosphodiester

asn

Trehalosephosphorylase: TP

beta-D-glucose

hemebiosynthesis from

uroporphyrinogen-III I

Probablediacylglycerolkinase 3: dgk-3


a DNAcyclobutadipyrimidine

uridine

tRNAgln

a thiol

ProteinaseK: PROK

Proteinfarnesyltransferasesubunit beta: FTB

a [protein]-L-histidine

2-[(1R,6S)-1,6-dihydroxycyclohexa-

2,4-dien-1-yl]acetyl-coA

Co2+

an aldehyde

Succinyl-CoAligase [ADP-forming]subunit alpha-1,mitochondrial:SCOA

a phenol

all-trans-retinol

selenohomocysteine



13-[O(2’)-beta-D-glucopyranosyl-beta-D-

glucopyranosyloxy]docosanoateO(6’’)-acetate

[+ 2 isozymes]

a 1,4-alpha-D-glucan

Leukotriene-B(4) omega-hydroxylase1: CYP4F2

N-terminalamino acid

glutathione

O-acetyl-L-serine

DETOXIFICATIONL-arginyl-tRNAarg


beta-D-galactose

[+ 2 isozymes]

FMN

HORMONES BIOSYNTHESIS

Pantothenatesynthetase: panC

5’,5’’’-diadenosine

tetraphosphate

Aspartateaminotransferase,mitochondrial: aatA

N-acetyl-O-acetylneuraminate

methylglyoxal

3beta-hydroxy-4beta-methyl-

5alpha-cholest-7-

ene-4alpha-carbaldehyde

stigmasterol

D-galacturonate

asn

Probablemethylisocitratelyase 1: prpB1

adenosine 5’-phosphosulfate

succinate

a 3-oxo-octanoyl-

[acp]

superpathway of acetyl-CoA biosynthesis

a protein



a 3-oxoacyl-[acp]

L-valyl-tRNAval

a 1-phosphatidyl-


bisphosphate

a relaxedDNA


[+ 14 isozymes]

phosphoribosyl-formamido-

carboxamide

an aldehyde

hypoglycin B

Delta(3,5)-Delta(2,4)-dienoyl-CoAisomerase,mitochondrial:Ech1

a 1,4-beta-D-glucan

Ferredoxin-dependentglutamatesynthase 2: gltS

a (glucosyl)2(mannosyl)9-(N-

acetylglucosaminyl)2-diphosphodolichol

N-acetylmuramoyl-L-alanyl-gamma-D-glutamyl-L-

lysyl- D-alanyl-D-alanine-diphosphoundecaprenol

GTP

2-C-methyl-D-erythritol-2,4-

cyclodiphosphate

L-dehydro-ascorbate

all-trans-retinyl

palmitate

octanoyl-CoA

Cytochromeb-c1 complexsubunit Rieske,mitochondrial:FES1

D-myo-inositol(1,3,4,5,6)-

pentakisphosphate


IMP

Peroxisomalacyl-coenzyme Aoxidase 1: Acox1

myo-inositol

5-dehydro-D-gluconate

CMP

Sialate O-acetylesterase:Siae



citrate

phytyldiphosphate

Homoaconitase,mitochondrial:LYS4

acetyl-CoA

L-phenylalanyl-tRNAphe

a protein


nitrate


ALDEHYDE DEGRADATION


[+ 3 isozymes]

UMP


thiamindiphosphate

[+ 2 isozymes]


O-acetyl-L-serine

a holo-[acp]

a protein

tRNAtrp

ala

thiamin diphosphatebiosynthesis

IV (eukaryotes)

3-hydroxyadipyl-CoA

Sulfitereductase[ferredoxin]: sir


Deoxyhypusinehydroxylase: dohh


cis-aconitate


Bifunctionalprotein

FolD: folD

(6E)-8-hydroxygeranial

DNAhelicaseII: uvrD

Proteindisulfide-isomeraseTMX3: tmx3

Arginase-1: Arg1

a [pyruvate dehydrogenaseE2 protein] N6-(lipoyl)lysine

L-threoninedehydratasebiosyntheticIlvA: ilvA

AMP

CDP-choline

NADP-dependentglyceraldehyde-3-phosphate

dehydrogenase: GPN1


Queuine tRNA-ribosyltransferase:qtrt1

glt

Proline--tRNA

ligase: proS

S-methyl-5-thio-

D-ribose

ATP

Trehalase:tre1

an organicmolecule

Glycylpeptide N-tetradecanoyltransferase2: NMT2

NADP+



geranyldiphosphatebiosynthesis

Arsenitemethyltransferase:As3mt

fructose-1,6-bisphosphate



aniline

spermidinebiosynthesis I

Alcoholdehydrogenase[NADP(+)]: Akr1a1

ProbableferuloylesteraseC: faeC

5-hydroxytryptophol

Magnesium-chelatasesubunitChlD: chlD

Ubiquitin-activatingenzymeE1 1: ptr3

(9S,10S)-10-hydroxy-9-

(phosphonooxy)octadecanoate


N1-acetylspermine

Citrate synthase,mitochondrial: cs

citrate


L-idonate 5-dehydrogenase:VIT_16s0100g00290

a tripeptidewith prolineat the third

position

Beta-1,4-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase:Mgat3

a carboxylate

glycolate


Ferredoxin-dependentglutamatesynthase2: gltS


[+ 4 isozymes]



Extracellularsignal-regulatedkinase 1: erkA

2-epi-5-epi-valiolone

a [methioninesynthase]-

cob(II)alamin

[+ 2 isozymes]

Homoserine O-acetyltransferase:metX

Indole-3-glycerolphosphatesynthase:trpC


CDP-diacylglycerol--inositol 3-phosphatidyltransferase1: PIS1


UDP-D-glucose

ethanoldegradation IV


[+ 2 isozymes]

[+ 7 isozymes]

L-histidyl-tRNAhis


adenine andadenosinesalvage II


Succinatedehydrogenasecytochromeb560 subunit,mitochondrial:sdhC

24-ethylidenelophenol

Sulfateadenylyltransferase:MET3

glutathione


bicarbonate


8-amino-7-oxononanoatesynthase: bioF

Amidophosphoribosyltransferase: purF

[+ 2 isozymes]

a malonyl-[acp]

Hydroxyacylglutathionehydrolase 3,mitochondrial: GLY3

an RNA

stearoyl-CoA

[+ 25 isozymes]

L-citrulline

N-carbamoylputrescine


[+ 4 isozymes]

4-guanidinobutyrate

sulfite

a peptide


17-alpha-hydroxypregnenolone


2,4-dinitrophenyl-S-glutathione

Ribulose-phosphate3-epimerase: RPE

Prolinedehydrogenase1, mitochondrial:PRODH

acetoacetate

Alpha,alpha-trehalose-phosphatesynthase[UDP-forming]5: TPS5

dTMP

histidinol

pyruvate

Isoleucine--tRNA

ligase: ileS


monophosphate

ADP-ribosepyrophosphatase:nudF

a [TusEsulfur carrier

protein]-L-cysteine

propanoyl-CoA

GDP-L-galactosephosphorylase1: VTC2

carbamoyl-phosphate

2-phenylethylamine

tRNA-specificadenosinedeaminase:tadA

CTPsynthase:

URA7

[+ 2 isozymes]

Tyrosineaminotransferase: TAT

Emopamil-bindingprotein-like: Ebpl


UQ


Molybdenumcofactorsulfurase:MOCOS

Retinoldehydrogenase14: RDH14

GDP-L-fucosesynthase: ger

a 5’-phosphooligonucleotide

phosphoenolpyruvate

a peptide

N-acetyl-L-glutamate 5-semialdehyde

a tripeptide

gamma-butyrobetaine

phosphoribosyl-ATP

lipoamide

4alpha-methyl-5alpha-ergosta-

8,24-dien-3beta-ol

a singlestranded

DNA

homogentisate

an [alpha-tubuline]-L-lysine

trehalose 6-phosphate

L-threonineO-3-

phosphate

7,8-dihydroneopterin

triphosphate

NAD-dependentmethanoldehydrogenase:mdh

a tRNA

a diacylglycerol

DNAn

ser


crotonyl-CoA


[+ 4 isozymes]


2-diphosphodolichol


Branched-chain-amino-acidaminotransferase:37018

Fe3+

N-acetyl-beta-glucosaminylamine

Ferredoxin--NADPreductase, embryoisozyme, chloroplastic:Os07g0147900

3-methyl-2-oxobutanoatehydroxymethyltransferase:panB

met

Allantoicase:allc

salicylate

HCC

A(H2)

isofucosterol



trehalosedegradationII (trehalase)

dTDP

alpha-D-galactose

Proteindisulfide-isomeraseA3: Pdia3

Putative L-ascorbateperoxidase6: APX6

[+ 2 isozymes]

NAD+


tyr

S-sulfo-L-cysteine

a palmitoyl-[acp]

Phosphopantetheineadenylyltransferase: COAD

A(H2)

a dialkylphosphate

Reducingend xylose-releasing exo-oligoxylanase:BH2105

val

a L-prolylpeptide

O-phospho-L-homoserine

Catalase:CAT


benzylalcohol

Histidinol-phosphateaminotransferase:hisC

ATP

an oxidizedflavoprotein


a cis-3-enoyl-CoA

ATP


Tyrosine--tRNAligase:YARS

a [protein]-N6-(3-O-phospho-

D-fructosyl)-L-lysine

5-hydroxyisourate


aspsuccinate

[unspecifieddegradation

products]


bicarbonate


thiamin

a cytidine4in tRNAPro

RX


[+ 26 isozymes]

XLLG xyloglucanoligosaccharide

anapocytochrome c

a flavanone

adenylo-succinate

4-hydroxy-3-methylbut-2-enyldiphosphatereductase: ispH

Phosphatidylserinesynthase 2: PTDSS2

(2E,6E)-farnesal

nicotinate

4-hydroxyphenylpyruvate

[+ 2 isozymes]

nitrite

Purine nucleosidephosphorylase 1: punA

Pyridoxine/pyridoxamine5’-phosphateoxidase: pdxH


Acyl-coenzyme Adehydrogenase:fadE

antheraxanthin

[+ 4 isozymes]

Nicotinatephosphoribosyltransferase:naprt

[+ 2 isozymes]

[+ 9 isozymes]


cysteinylglycine

2-oxoglutarate

cis-3-hexenal

tRNAcontaining 5,6-dihydrouridine

dimethylallyldiphosphate

DNAn

ADP


Lipoyl synthase,mitochondrial:PITG_14852

All-trans-retinol13,14-reductase:Retsat

a tRNAprecursor

with ashort 3’

extension

[+ 4 isozymes]

[+ 3 isozymes]

a 2,3,4-saturated L-

phosphatidate

3-methyladenine

tRNAasn

Pseudouridine-5’-phosphateglycosidase: psuG

coenzyme A

an oligosaccharide-diphosphodolichol

(3Z)-hex-3-en-1-

yl acetate


extension

a 1-phosphatidyl-


bisphosphate

[+ 2 isozymes]

GDP-L-fucosebiosynthesis

II (fromL-fucose)

[+ 3 isozymes]

5,6-dihydrouracil17

in tRNA

Dihydroorotase:pyrC

Ferredoxin-dependentglutamatesynthase2: gltS

a reducedhemoprotein

nitrite

a nucleosidetriphosphate

thromboxane A2

[+ 2 isozymes]


quinone

OPC6-CoA


2-aminoadipate


monophosphate

coenzyme A

Uracilphosphoribosyltransferase:

FUR1

ATP

L-leucyl-tRNAleu

a (1->4)-beta-D-xylan

[+ 4 isozymes]

acetate

spermidine

4’-phosphopantetheine

[+ 12 isozymes]

Enolase: PGH1

Asparaginesynthetase[glutamine-hydrolyzing]:Os06g0265000

[+ 6 isozymes]

UDP-D-galactose D-xylose

anacylcholine


a [protein]-hydroxyproline

a 2’-phospho-

[ligatedtRNA]


Mitochondrialintermediatepeptidase:MIPEP

a 5 methylcytosine34in tRNA precursor

Probableacetyl-CoAacetyltransferase,cytosolic 2:At5g47720


ChaperoneproteinClpB: clpB

an (R)-3-hydroxyhexanoyl-

[acp]

IMP


Cystathioninegamma-lyase: cysA

sulfite

Succinyl-CoA ligase [ADP-forming] subunit alpha-1, mitochondrial: SCOA

Phosphatidylinositol3-kinase catalyticsubunit type 3: Pik3c3

[+ 3 isozymes]


acyl-[acp]

3-isopropylmalatedehydratase smallsubunit 2: leuD2

xanthine

a peptide

D-ribose

fatty acid beta-oxidation III(unsaturated,odd number)

a non-methylatedribosomal

protein L11

GTPpyrophosphokinase: relA


a [methioninesynthase]-

methylcob(I)alamin

[+ 2 isozymes]

Aldehydedehydrogenasefamily 3 memberH1: ALDH3H1Malate dehydrogenase,

mitochondrial: MDH2

alpha-D-galactose

a glucuronosylatedglucuronoside

acceptor

L-glutaminyl-tRNAgln

7,9,9’-cis-neurosporene

nicotine-1’-N-oxide

Putativenicotinamide N-methyltransferase:NNT1

nicotinate D-ribonucleotide

ditrans,octacis-undecaprenylphosphate

UQH2

Putative carbonicanhydrase 3: cah-3

UDP-D-glucose

UDP-D-galactose

a tRNAcontaining 5-

methyluridine54

L-seryl-tRNAser

a 2,3,4-saturated

fattyacyl-[acp]

Kynurenine--oxoglutaratetransaminase:ccbl

ammonia

Glycerophosphodiesterphosphodiesterasedomain-containingprotein 1: GDPD1

a protein

an aryldialkyl

phosphate

[+ 2 isozymes]

[+ 2 isozymes]

a [protein]-L-methionine

1,4-Dihydroxy-2-naphthoyl-CoAsynthase:menB

Type-1 glutaminesynthetase1: glnA1

Valine--tRNA

ligase: valS

Bis(5’-nucleosyl)-tetraphosphatase,symmetrical: apaH

superoxide



N-(5’-phosphoribosyl)

-anthranilate


2-diphosphodolichol

N-acetylneuraminate

inositol pyrophosphates biosynthesis

glycolysis III(glucokinase)

urocanate

FADsynthase:flad1

Cytosolic 5’-nucleotidaseIII: NT5C3

[tRNAArg2]-adenosine34

Uridylatekinase:URA6

a protein

cyclic pyranopterinmonophosphate

UDP-D-galactosea pimelyl-

[acp]

(S)-2,3,4,5-tetrahydrodipicolinate

an organichydroperoxide

a primaryalcohol

Phytoenedehydrogenase:carB

L-prolyl-tRNApro

[+ 2 isozymes]

pyridoxal-P

6,7-dihydropteridine

5’-deoxyadenosine

Branched-chain-amino-acidaminotransferase-like protein 3,chloroplastic:At5g57850

2-carboxymethyl-3-hydroxyphenylpropionyl-CoA

Mannose-6-phosphateisomerase: PMI1

a [pyruvatedehydrogenase

E2 protein] N6-(S-acetyldihydrolipoyl)

lysine

IMP

AMP

avenastenone

antheraxanthin

catechol

a reducedcytochrome

[+ 2 isozymes]


DNApolymeraseepsilonsubunitC: DPB3


met

acetate

chorismate

carbamoyl-phosphate

Peroxiredoxin-1: PRDX1

Probableglucan1,3-beta-glucosidaseA: exgA

Methionyl-tRNAformyltransferase: fmt

(R)-lactate


[+ 6 isozymes]

tetrahydrofolate

(S)-malate


glyoxylate

a peptide

Peptidedeformylase 1B,chloroplastic:PDF1B

3-oxo-3-phenylpropionyl-

CoA

a methylatednucleobasewithin DNA

[+ 3 isozymes]

Serinehydroxymethyltransferase

2: shmt2

[+ 4 isozymes]


cholinedegradation I

carbamoyl-phosphate


lotaustralin

Choline/ethanolaminekinase: Chkb

Adenosylhomocysteinase:SAHH

Glucose-6-phosphate isomerase,cytosolic 1: PGIC1

[+ 4 isozymes]

adenine

[+ 2 isozymes]

1,5-bisdiphosphoinositol-1D-myo-inositol (2,3,4,6)

tetrakisphosphate

[+ 2 isozymes]

a [glycine-cleavage complex

H protein] N6-(lipoyl)lysine

a [ThiI sulfur-carrier

protein]-L-cysteine

coenzyme A

an (R)-3-hydroxypalmitoyl-

[acp]

D-fructose

an alcohol

L-canaline

D-myo-inositol (1,4,5)-trisphosphatebiosynthesis

[+ 3 isozymes]

an adenosine4in tRNAHis

a long-chainaldehyde

[+ 2 isozymes]



Enolase: PGH1

a peptide

N7-methylguanine527in 16S rRNA

N5-carboxyaminoimidazoleribonucleotide

3-dehydroquinate

Carbonylreductase[NADPH]1: Cbr1

a 6-(N-acetyl-D-glucosaminyl)-

1-phosphatidyl-1D-myo-inositol

NADP+

RNase Edegradation

substratemRNA

phosphopantothenatebiosynthesis I

a dihydroceramide

glyoxylate

a sphinganine(C18)

NAD+

Sialidase:TCNA

a proteinc-terminalS-farnesyl-L-cysteine


GDP


endothelin 1

tRNA (uracil(54)-C(5))-methyltransferase:trmA

Phosphoenolpyruvatecarboxylase: ppc

met

Xaa-Proaminopeptidase1: xpnpep1

5-hydroxy-2-oxo-4-ureido-2,5-dihydro-

1H imidazole-5-carboxylate

Ornithine cyclodeaminase:PHATRDRAFT_54222


in tRNA


2-trans,5-cis-tetradecadienoyl-

CoA

imidazoleacetol-

phosphate

a polypeptide


1-chloro-2,4-dinitrobenzene

[+ 4 isozymes]

Spermidine synthase1: SPDSYN1

prephenate

3-acetamidopropanal

Cysteine--tRNA ligase,cytoplasmic:

cysS

a cytidine32/guanosine34

in tRNA


a carboxylate


acetate

a carboxymethyluridine34in tRNA

Cystathioninegamma-synthase: metB


2-oxoisovalerate

alpha-D-galactose

coenzyme A3alpha,7alpha,12alpha-trihydroxy-24-oxo-5-beta-cholestanoyl CoA

hydrogencyanide

salicyl-HCH

Dihydrolipoyllysine-residueacetyltransferase componentof pyruvate dehydrogenase

complex, mitochondrial: Dlat

Phosphorylasephosphatase,putative:IMG5_051480

pro

DNA ligase (Fragment):GSTENG00019603001

choline

a 2,3,4-saturated

fattyacyl-[acp]

D-glucono-1,5-lactone

a peptide

2-trans,5-cis-tetradecadienoyl-

CoA

[+ 15 isozymes]


(S)-malate

Peptidyl-tRNAhydrolase ICT1,mitochondrial:ict1

an oleoyl-[acp]

tributyrin

beta-D-galactose

pyridoxal-P

(R)-1-amino-2-propanol

O-2-phosphate

[+ 4 isozymes]

glutamate-1-semialdehyde

chlorophyllide a

a carboxylicester



3-isopropylmalatedehydratase smallsubunit 2: leuD2

homoisocitrate

a reducedcytochrome

c550

an oxidizedhemoprotein

2-oxoglutarate

Diaminopimelatedecarboxylase: lysA

a 2’-O-methylcytidine4

in tRNAPro

acetyl-CoA

4-amino-2-methyl-5-phosphomethylpyrimidine

4-aminobutyrate

serineracemization

1,2-dibutyrin

CO2


Hydroxymethylglutaryl-CoA synthase A: hgsA

4-aminobutyrate

tetrachlorohydroquinone

molybdenumcofactor

N-acetyl-beta-D-glucosaminyl-

1,2-alpha-D-mannosyl-1,3-(N-acetyl-

beta-D-glucosaminyl-

1,2-alpha-D-mannosyl-1,6)-beta-D-mannosyl-

1,4-N-acetyl-beta-D-

glucosaminyl-R

menaquinone-7

Putativepterin-4-alpha-carbinolaminedehydratase:Plav_1388

a cytochrome c

[+ 4 isozymes]

choline

AMP

[+ 152 isozymes]

4-diphosphocytidyl-2-C-methyl-D-erythritolkinase: ispE


[+ 3 isozymes]

a ribonucleosidediphosphate

a 1-phosphatidyl-


bisphosphate

chorismate


trans-1,2-dihydrobenzene-

1,2-diol

Biotin--[acetyl-CoA-carboxylase]synthetase:birA

4-guanidinobutyramide

Coppermethylamineoxidase: maoII


Fe2+

Putativelong-chain-fatty-acid--CoA ligase:HI_0002

glt

ammonium

Thiamine-phosphatesynthase:thiE

Xyloseisomerase:XYLA

ADP

dTDP-alpha-L-

rhamnose

Glucokinase: glk

a (mannosyl)9-(N-acetylglucosaminyl)2

Di-N-acetylchitobiase: CTBS

an (3R)-3-hydroxymyristoyl-

[acp]

Uracil-regulatedprotein1: urg1

ammonia


superpathway of sulfuramino acid biosynthesis

(Saccharomycescerevisiae)


hemedegradation

a palmitoyl-[acp]


[+ 10 isozymes]

[+ 4 isozymes]

D-inositol-3-phosphateglycosyltransferase:mshA

PhospholipaseD p2: PLDP2

fatty acidactivation

menaquinol-8biosynthesis

[+ 6 isozymes]

L-seryl-tRNAsec

Triosephosphate isomerase: tpiA

anuncharged

tRNA

citrate

Topoisomerase6 subunitB: TOP6B

Imidazoleglycerolphosphatesynthase hisHF,chloroplastic:At4g26900

anandamidedegradation


NAD(P)transhydrogenase,mitochondrial: NNT

[+ 4 isozymes]

anacetylatedhistone

[+ 13 isozymes]

RNase IIsubstratewith no

poly-A tail

Cyclopropane-fatty-acyl-phospholipidsynthase: cfa

a cytosine49in tRNA

[+ 2 isozymes]

IMP


SH2 domaincontaining protein:Esi_0183_0042

L-citrulline

a plantceramide (I)

Argininebiosynthesisbifunctionalprotein ArgJ,mitochondrial:PITG_04698

a trans-2-enoyl-CoA

a D-hexose


a holo-[acp]


methylarsonate

an RNA

[+ 3 isozymes]

OPC4-3-ketoacyl-

CoA

chlorophyllide b

a triacylglycerol

oxaloacetate

Inositolpolyphosphatemultikinase: IPMK

a 3-oxo-hexanoyl-

[acp]

UDP-N-acetylmuramoyl-L-alanyl-gamma-

D-glutamyl-L-lysyl-D-alanyl-

D-alanine


acyl-[acp]

(S)-malate

Pyruvatecarboxylase,mitochondrial: PC


fructose-1-phosphate

UDP

beta-L-galactose

[+ 3 isozymes]

a RAD21cohesinsubunit

Transketolase:TKL1

thiamin phosphate

FATTY ACIDS AND LIPIDS BIOSYNTHESIS o-diquinonesbiosynthesis

(2R,3S)-2-methylisocitrate

7-dehydro-cholesterol

Fatty aciddesaturase2: fads2


L-dopachromebiosynthesis

oxygenic photosynthesis

Pyrroline-5-carboxylatereductase: proC

ATP

Methioninesynthase: mtr

PhosphatidylglycerophosphataseGEP4, mitochondrial: GEP4

a phosphorylase b

[+ 28 isozymes]

Putativefatty acidelongationprotein3: elo-3

Fattyacyl-CoAsynthetaseA: fcsA

GMP

indole-3-acetate

[+ 2 isozymes]

adenylyl-molybdopterin

NADP+

D-glucose-6-phosphate

(S)-2,3,4,5-tetrahydropiperidine-

2-carboxylate

L-ascorbate

NADH-cytochromeb5 reductase2: CYB5R2

RibonucleaseZ: rnz

succinate

5-phospho-ribosyl-

glycineamide

D-tryptophan

Arsenitemethyltransferase:As3mt

adenosylcobinamide-GDP

4alpha-hydroxymethyl-

ergosta-7,24(241)-

dien-3beta-ol

[+ 6 isozymes]

a tripeptide

cysteinylglycine

a malonyl-[acp]


(6E,8Z,11Z,14Z)-(5s)-5-

hydroperoxycosa-6,8,11,14-tetraenoate

coproporphyrinogen III

a non-glucuronosylated

glucuronosideacceptor

a trans-eicos-2-

enoyl-[acp]

[+ 2 isozymes]


L-lactaldehyde

nicotinamidemononucleotide

Probable aconitatehydratase,

mitochondrial: aco2

pseudouridinedegradation



L-methionyl-tRNAmet

1-O-(2-acetamido-2-deoxy-alpha-D-glucopyranosyl)-D-myo-inositol-

3-phosphate

a carboxy-adenylated

small subunit ofmolybdopterin

synthase

malonyl-CoA

[+ 2 isozymes]


a reducedcytochrome

c550

a sugar

Arginase-1: Arg1

porphobilinogen

D-xylulosekinase: xylB

a malonyl-[acp]


salvage pathways of pyrimidine ribonucleotides

Neuropathytargetesterase:Pnpla6


epoxyqueuosineat position 34 of atRNA containingGUN anticodon

ADPribose 1’’-phosphate

a proteinwith

incorrectdisulfidebonds

GDP-L-fucose

alpha-D-ribose-1-

phosphate

methanethiol

[+ 4 isozymes]

a 2-hydroxycarboxylate

Cysteinedioxygenase:CDO1

isochorismate

[+ 4 isozymes]

L-cystathionine

4-nitrophenylphosphatase:pho2


an eIF5Adeoxyhypusine

glutathione

phosphoadenosine-5’-phosphosulfate

Glyceraldehyde-3-phosphatedehydrogenase2: gpd3

N-acetyl-D-glucosamine-6-phosphate

Putativecarbonic

anhydrase3: cah-3

(2S)-pinocembrin

gln

a monocarboxylate


Phospho-2-dehydro-3-deoxyheptonatealdolase 1,chloroplastic:SHKA

D-lactatedehydrogenase:ldhA

dihydroxyacetone phosphate

[+ 3 isozymes]


an (R)-3-hydroxyhexanoyl-

[acp]

an oxidizedcytochrome cL

folate


a malonyl-[acp]


a [glycine-cleavagecomplex H protein] N6-

(aminomethyldihydrolipoyl)lysine

a peptide

[+ 6 isozymes]

[+ 17 isozymes]

OPC4-trans-2-

enoyl-CoA

ATP


gluconeogenesis I

Bifunctionalprotein folC: folC


an aldehyde

MitochondrialtRNA-specific2-thiouridylase1: trmu

a (R)-3-hydroxystearoyl-

[acp]

an all-transretinol-[cellular-retinol-

binding-protein]

Glycinedehydrogenase

[decarboxylating]:gcvP

4-methylphenol

oleamide

2-[3-carboxy-3-(methylammonio)

propyl]-L-histidine in eEF-2


UTP

Probable bifunctionalmethylthioribulose-1-phosphatedehydratase/enolase-phosphatase E1:Os11g0484000

a 5’-phosphopolynucleotide

[+ 4 isozymes]

[+ 2 isozymes]

succinatesemialdehyde

episterone


HistoneacetyltransferaseGCN5: GCN5

Endo-1,4-beta-xylanaseB: xynB

a glucosyl-(mannosyl)9-(N-

acetylglucosaminyl)2-diphosphodolichol

superpathway of glyoxylatecycle and fatty acid degradation

a phenolsulfate


Histidineammonia-lyase: hutH

peptidylproline(omega = 0)

Glucose-6-phosphateisomerase,cytosolic: PGIC

succinate

leu

(6E)-8-oxogeranial



5-(methylthio)-2,3-

dioxopentylphosphate

Undecaprenylpyrophosphatesynthase: uppS

all-trans-retinol

coenzyme A

[+ 5 isozymes]

hydrogenselenide

[+ 3 isozymes]

a tRNAcontaining

GUNanticodon

withquenosine atposition 34

6-hydroxymethyl-dihydropterindiphosphate

guanosine

hydrogenperoxide

2,3,5,6-tetracholorphenol

[+ 6 isozymes]

Aldehydeoxidase1: AAO1

FMN

IMP

an N-substitutedamino acid

Ketol-acidreductoisomerase,chloroplastic: AHRI

D-4’-phosphopantothenate

L-aspartyl-tRNAasp

Pantothenatekinase 2: At4g32180

(1S,2R)-1-C-

(indol-3-yl)glycerol 3-phosphate

N-acetyl-L-glutamate

Chitinasedomain-containingprotein1: Chid1

a reducedflavoprotein


Gluconokinase:gntK

[+ 3 isozymes]

BifunctionalpurinebiosynthesisproteinPURH: ATIC

a stearoyl-[acp]


extensionand a long

3’ trailer

H2O

L-carnitine

linoleate

a mannanoligosaccharide

D-gluconate

1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)

methylideneamino]imidazole-4-carboxamide

pro

Glycolipid 2-alpha-mannosyltransferase:KRE2

N-carbamoyl-L-aspartate

tRNA (cytosine(34)-C(5))-methyltransferase:nsun2

[+ 2 isozymes]

6,7-dimethyl-8-(1-D-ribityl)

lumazine

asp

glt

lactosedegradation III

D-galactonate

6-phosphofructokinase3: PFK3

Alpha-glucosidaseyihQ: yihQ

sucrose

Ornithinecarbamoyltransferase:

argF

Serine/threonine-proteinphosphatase2A activator:Ppp2r4

D-isomer specific2-hydroxyaciddehydrogenaseNAD-bindingprotein:Snas_3082

thiocyanate


[+ 2 isozymes]

3,22-dioxochol-4-en-24-oyl-CoA


pyridoxamine5’-phosphate

[+ 2 isozymes]

Tryptophan--tRNA ligase,cytoplasmic:

Wars



inositol

orotidine-5’-phosphate

DNA ligase (Fragment):GSTENG00019603001


a 1-phosphatidyl-1D-myo-inositol

4,5-bisphosphate


5-hydroxyindoleacetaldehyde

D-threo-isocitrate

S-adenosyl-L-methionine cycle II

4-nitrophenol

[+ 2 isozymes]

imidazoleacetol-

phosphate

2,3-bisphosphoglycerate-dependent phosphoglyceratemutase: gpmA


inositol



a carboxylate

UDP-D-galacturonatebiosynthesis I(from UDP-D-glucuronate)


a carboxylate

glutamatedegradation I

an aldehyde

an aldehyde

tyrosinebiosynthesis I

acetaldehyde

7-aminomethyl-7-deazaguanine

at position34 of a tRNA

containingGUN anticodon

demethylmenaquinone-7

a biotinylated[BCCP

monomer]

beta-D-glucose



Hemeoxygenase1: HMOX1

cis-coumarinicacid-beta-

D-glucoside


Flavin-containingmonooxygenaseFMO GS-OX3:FMOGS-OX3

NADP-dependent malicenzyme, chloroplastic: MOD1

acetyl-CoA

all-trans-phytoene

Homoserine O-acetyltransferase:metX

a proteinc-terminals-farnesyl-l-cysteine

methyl ester

Probable serineacetyltransferase2: SAT2

pro

Kynurenine 3-monooxygenase:BNA4

glt

S-adenosyl-L-methioninamine

DIMBOA

Xylosyltransferase1 (Fragment): Xylt1

Arginine--tRNA

ligase: argS

a protein

Formate--tetrahydrofolateligase: THFS

cardiolipinbiosynthesis I

Probablemethionine--tRNA ligase:

Os06g0508700

coenzyme A

Ornithinedecarboxylase:ODC1

aminocarboxymuconatesemialdehyde

pyridoxal

AMP

a 3-oxo-decanoyl-

[acp]

Orotatephosphoribosyltransferase: pyrE

asp


a [protein]-N4-(N-acetyl-D-

glucosaminyl)-L-asparagine

1-(o-carboxyphenylamino)

-1’-deoxyribulose-5’-phosphate

L-homocysteine

Probable 2-aminoethanethioldioxygenase: ado-1

UDP-glucose 4-epimerase: galE

adenine andadenosinesalvage VI

dUTP

Sepiapterinreductase:SPR

L-ornithine



[+ 2 isozymes]

9,15,9’-tri-cis-zeta-carotene

gamma-glutamyl cycle

DNAprimaselargesubunit:Prim2

Farnesylcysteinelyase: FLCY

[+ 2 isozymes]

2-oxoglutarate

a nonrhamnosylated

rhamnosylacceptor



a protein-L-methionine-(R)-S-oxide

Transketolase:tkt-1


succinate


urate

Probable aconitate hydratase,mitochondrial: aco2


beta-D-glucose

Transketolase:TKL1

1-phosphatidylinositol-3-phosphate 5-kinase: PIKFYVE

trehalose

met



Tyrosinase:melC2

Protochlorophyllidereductase A,chloroplastic: PORA

a farnesylatedprotein


a peptide

Pyridoxamine5’-phosphateoxidase-relatedFMN-binding:Esi_0074_0067

RibonucleaseZ: rnz

S-adenosyl-L-homocysteine


inositol

Trans-1,2-dihydrobenzene-1,2-dioldehydrogenase:dhdh

Leukotriene-B(4) omega-hydroxylase1: CYP4F2

[+ 2 isozymes]


a chitodextrin


[acp]

[Pyruvatedehydrogenase[lipoamide]]kinase,mitochondrial:SPAC644.11c

a UDP-sugar

dihydroxyacetone

Serinehydroxymethyltransferase2: shmt2


[procollagen]trans 4-hyroxy-

L-proline

4alpha-hydroxy-tetrahydrobiopterin

D-threo-isocitrate

1-(o-carboxyphenylamino)

-1’-deoxyribulose-5’-phosphate

keto-phenylpyruvate

beta-D-xylopyranose

an alpha-D-galactoside

a doublestranded

DNA

Phosphoglyceratekinase,chloroplastic: PGK

beta-D-glucose

ATP

Alpha-ketoglutarate-dependent taurinedioxygenase: tauD

indoleacetaldehyde

pyruvate

UDP

[+ 2 isozymes]

ATP synthase subunitbeta, mitochondrial: ATP2

a 2’-O-methylcytidine4

in tRNAGly(GCC)

[+ 6 isozymes]

an alcohol

ethanol

thiocyanate

an RNA

di-trans,poly-cis-

undecaprenylphosphate

biosynthesis

Argininedecarboxylase:speA

[+ 3 isozymes]

Solublecalcium-activatednucleotidase1: Cant1

glycerol

phosphatidylglycerolbiosynthesis II(non-plastidic)



a DNAwith uracil

met

Fructose-bisphosphate aldolase,chloroplastic: Os11g0171300


N6-acetyl-L-lysine

Phosphomannomutase:PMM

a holo-[acp]

methylsalicylate

CathepsinE: Ctse

a guanine26in tRNA

pro

Chitinasedomain-containingprotein1: Chid1


[+ 6 isozymes]


a proteinwith correct

disulfidebonds

[+ 2 isozymes]


an [apo BCAAdehydrogenaseE2 protein] N6-(dihydrolipoyl)

lysine

a protein N-phospho-L-histidine


a 1-phosphatidyl-


bisphosphate

[+ 3 isozymes]

CDP-ethanolamine

nicotinamide

Enolase:PGH1

RNA 3’-terminalphosphatecyclase:RTCD1

hydroxymethylbilane

Pyrroline-5-carboxylatereductase:proC

[+ 3 isozymes]

UDP-N-acetylmuramoyl-L-alanyl-gamma-

D-glutamyl-L-lysyl-D-alanine



methylarsonite

a cis-delta3-decenoyl-

[acp]


N-ethylsuccinimide5-aminopentanal

Threonine--tRNA

ligase: thrS

4-(N-acetyl-beta-D-

glucosaminyl)-beta-D-

mannosyl-[glycoprotein]

alpha-D-galactosyl-

(1,3)-beta-D-galactosyl-(1,4)

-N-acetyl-D-glucosaminyl-[glycoprotein]

pyruvate

ser


9-enoate

4-acetamidobutanoate

S-allantoin

[+ 7 isozymes]

sphingosine

[+ 3 isozymes]

CO2



Ferredoxin--NADP reductase,embryo isozyme,chloroplastic:Os07g0147900

protoporphyrin IX

PeptidemethioninesulfoxidereductaseA3: MSRA3

biliverdin-IX-alpha

a dicarboxylate

Ethanolamine-phosphatecytidylyltransferase:pctA

2-aminomalonate-semialdehyde

S-(2E,6E)-farnesyl-

L-cysteine



phosphoribulosylformimino-AICAR-P

2-dehydro-3-deoxy-6-phosphogalactonatealdolase: dgoA

his

acetyl-CoA

[+ 2 isozymes]


[+ 3 isozymes]

6,7-dimethyl-8-ribityllumazinesynthase:MGG_04626

epoxyqueuosineat position 34 of atRNA containingGUN anticodon

2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylatesynthase: menD

[procollagen]-L-proline

A

a deoxyribonucleosidediphosphate

(R)-lactate

a cytidine4 intRNAGly(GCC)

coenzyme A

L-lactaldehyde



beta-D-glucose

4beta-hydroxymethyl-4alpha-methyl-5alpha-cholest-7-en-3beta-ol


2-oxobutanoate


[+ 3 isozymes]

ubiquinol-8

squalene

Putative fumaratereductase:SPAC17A2.05

Sulfide:quinoneoxidoreductase,mitochondrial:sqrdl

betanidin

[+ 27 isozymes]

Probable 2-oxoglutaratedehydrogenase E1

component DHKTD1homolog, mitochondrial: odhA

(S)-3-hydroxyhexanoyl-

CoA


a (3S)-3-hydroxyacyl-CoA

methylacrylyl-CoA

[+ 2 isozymes]

a RNA-DNA hybrid

S-adenosylmethioninedecarboxylaseproenzyme: amd1

Probableglutamine-

-tRNAligase: glnS

Glucose-6-phosphate 1-dehydrogenase,cytoplasmicisoform 1: ACG9

4-acetamidobutanal

[+ 2 isozymes]

(S)-2,3,4,5-tetrahydrodipicolinate

Probablecysteinedesulfurase,mitochondrial:CG12264

Alcoholdehydrogenase[NADP(+)]: Akr1a1

a nitrile


carbamate

3-oxoadipyl-CoA


Alpha-L-rhamnosidase:Mahau_1189

a 5-methylcytosine48in tRNA

Tyrosinase:melC2

Dihydrodipicolinatereductase 1,chloroplastic: DAPB1

Guanosine-3’,5’-bis(diphosphate) 3’-pyrophosphohydrolase:spoT


cholest-5-en-3-one

citrulline biosynthesis

a 3-oxo-hexanoyl-

[acp]

a cis-delta7-tetradecenoyl-

[acp]

a (R)-3-hydroxybehenoyl-

[acp]

Polyribonucleotidenucleotidyltransferase: pnp

N-acetyl-L-glutamate 5-semialdehyde

a standardalpha

amino acid

RibonucleaseZ: rnz

purine nucleotides denovo biosynthesis II

3beta-hydroxy-4beta-methyl-

5alpha-cholest-7-

ene-4alpha-carbaldehyde

O2

[+ 2 isozymes]

Dihydrolipoyl dehydrogenase,mitochondrial: LPD

TCA CYCLE

[+ 12 isozymes]

Probable UDP-glucose 6-dehydrogenase1: UGD1

[+ 2 isozymes]

Soluble pyridinenucleotidetranshydrogenase:sthA

AMP

DNAn

a ferricytochromeb5

5’,5’’’-diadenosine

tetraphosphate

nitrate

cys

a protein

methanol

Phosphatidatecytidylyltransferase:cdsA


an [alpha-tubulin]-

N6-acetyl-L-lysine


nicotinateadenine

dinucleotide


cys

N2-succinylglutamate

a malonyl-[acp]

gly

tRNApro

tRNAmet

5,6-dihydrouracil20

in tRNA


a (R)-3-hydroxydodecanoyl-

[acp]

(E)-2-benzylidenesuccinyl-

CoA

Glucose-6-phosphateisomerase, cytosolic: PGIC

an alkylatedDNA

an octanoylatedprotein

lipoyl-domain

sitosterol


a polypeptide

1,2-benzoquinone

betainealdehyde

4alpha-formyl,4beta,14alpha-

dimethyl-9beta,19-cyclo-5alpha-ergost-24(241)-en-3beta-ol

glutathione

L-cystathionine

phycoerythrobilinbiosynthesis

pyruvate

arg

pro

tRNA(guanine(10)-N2)-methyltransferasehomolog: trmt11

guanine9in tRNA


Enolase:PGH1

L-aspartateoxidase:nadB

protoheme IX

cyanate

an aldehyde

hypoglycin A


Methioninesynthasereductase:MTRR

ornithinedegradation

I (prolinebiosynthesis)

a long-chainalcohol

a [tRNAIle2]-2-lysidine34

Solublecalcium-activatednucleotidase1: Cant1

wound-induced

proteolysis I

a malonyl-[acp]


zeaxanthin

ALCOHOLS DEGRADATION

[+ 126 isozymes]


[+ 2 isozymes]Nucleosidediphosphatekinase: swoH

[+ 2 isozymes]

FlavoproteinMonooxygenase:Esi_0008_0229

a triacylglycerol


Formamidopyrimidine-DNA glycosylase: mutM

tetrahydrofolate


NADH

triacylglyceroldegradation

ala

Adenosinekinase1: ADK1

glt

tRNA(guanine(37)-N1)-methyltransferase:PITG_12867

thiosulfate

ABCtransporter

ATP-bindingprotein/

permeasewht-1: wht-1

Protoheme IXfarnesyltransferase,mitochondrial: COX10

(L) or (D)-serine

Alanineaminotransferase2, mitochondrial:ALAAT2

phosphoryl-choline

Histidinol-phosphateaminotransferase:HIS5

a peptide

Uridinekinase: udk

3-demethylubiquinol-8

[+ 2 isozymes]

2-[3-carboxy-3-(dimethylammonio)

propyl]-L-histidine in eEF-2

a polypeptide

a polypeptide

carbamoyl-phosphate

[+ 3 isozymes]

a ferrocytochromeb5

a peptide



beta-L-fucose 1-

phosphate

Acetylesterase: aes


Ribosomal RNAsmall subunitmethyltransferaseG: rsmG

[+ 5 isozymes]

aminoimidazolecarboxamide

ribonucleotide


Sterol 3-beta-glucosyltransferase:ATG26

an N-acetylglucosaminyl-diphosphodolichol

guanine

asp

Isopentenyl-diphosphateDelta-isomerase: idi1

Lysosomalalpha-mannosidase:manA

beta-D-glucose

(2-trans-6-trans)-

farnesoate

L-homoserine

loganin

3,5-bisdiphosphoinositol-1D-myo-inositol (2,3,4,6)

tetrakisphosphate

myo-inositol

ADP ribose1’’,2’’-cyclicphosphate

[+ 2 isozymes]

aminoimidazolecarboxamide

ribonucleotide

1-deoxy-L-glycero-tetrulose 4-phosphate




GTP

15,16-dihydrobiliverdin:ferredoxinoxidoreductase: pebA



a peptide


[+ 2 isozymes]


a dolichylphosphate

an eIF5A-hypusine

[+ 2 isozymes]

acetate

Probable cardiolipinsynthase 1: crls-1

pelargonidin


choline

tyr

(S)-1-pyrroline-5-carboxylate

an aldehyde

Probable cysteinedesulfurase: csd

a (R)-3-hydroxylignoceroyl-

[acp]

Omega-amidaseNIT2: nit2

N-(5’-phosphoribosyl)

-anthranilate

Molybdenumcofactorbiosynthesisprotein1: mocs1



Phenylalanine--tRNA ligase

alpha subunit:FARSA

RNaseIII mRNA

processingsubstrate

a [pyruvate dehydrogenase E2protein] N6-(dihydrolipoyl)lysine

a 1,2-diacyl-sn-


[+ 2 isozymes]

Putativeagmatinedeiminase:aguA


[+ 3 isozymes]

5-oxoproline


L-glutamategamma-

semialdehyde

cis-aconitate

D-hexose 6-phosphate

tRNAleu

an acyl-[acp]

Adenosylmethionine-8-amino-7-oxononanoateaminotransferase: bioA

methanoloxidation to

formaldehyde II

a plastoquinol


Putative 6-carboxy-5,6,7,8-tetrahydropterinsynthase: queD

prephytoenediphosphate

benzylacetate

palmitate

cobalt-sirohydrochlorin


[+ 2 isozymes]


3-isopropylmalatedehydrogenase:leuB

camptothecin

an acylphosphate

beta-D-galactosyl-


glucosamine

Predicted protein:MICPUN_62507

dUMP



Tyrosineaminotransferase: TAT



[+ 2 isozymes]

Probable 1-acyl-sn-glycerol-3-phosphateacyltransferase:SLC1

acetoacetate

Putativeuncharacterizedprotein:PB2503_10024


Dihydrofolatereductase:Rmar_0341

chlorophyllide a

[+ 2 isozymes]

RibonucleaseZ: rnz

an N2dimethylguanine26in tRNA

cys

Protochlorophyllidereductase,chloroplastic: PORA

3-dehydroshikimate

NAD(P)Hdehydrogenase[quinone] 1: NQO1

Hydroxylaminereductase: hcp

beta-D-mannosyl-

[glycoprotein]

Dihydrolipoyldehydrogenase: lpdA

Probable enoyl-CoA hydratase,mitochondrial: echs1

adenine

pro


Serine--tRNAligase: serS

Monoglyceridelipase: Mgll

tyr

cocaine

sulfite oxidationI (sulfite

oxidoreductase)

[+ 27 isozymes]


(6E)-8-oxogeraniol

S-(-)-ureidoglycolate

mannitol-1-phosphate


alpha-tocopherol

Guanylatekinase: Guk1

a plastoquinol

FAD linkedoxidase domain-containing protein:Esi_0523_0007

[+ 2 isozymes]

(+)-neomentholdehydrogenase:SDR1

Inositol-3-phosphatesynthase: ino1

lactose

formaldehyde


CARBOHYDRATES DEGRADATION


Arogenatedehydrogenase2, chloroplastic:TYRAAT2

[+ 2 isozymes]

AMINES AND POLYAMINES DEGRADATION

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


Ribokinase:rbsK

urate

indole-3-glycolate

a lipoyl-carrierprotein

5-phosphoribosyl-N-formylglycineamidine

a holo-[acp]

5,6-dihydrouracil16

in tRNA

a thiopurineS-methylether

sitosterol

CTP

methioninedegradation I (tohomocysteine)


2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate

chitosan


Glutaminyl-peptidecyclotransferase:QCT

RibonucleaseZ: rnz

[+ 2 isozymes]



a protein

Pyruvatekinase: pyk

2,5-diamino-6-(5-phospho-D-ribosylamino)

pyrimidin-4(3H)-one

4-hydroxyphenylpyruvatebiosynthesis

xanthine

Cytochrome b6-fcomplex subunit 4: petD


Phosphotriesterase-related protein:v1g177083

a glutathione-toxin

conjugate

a 3-oxo-pimelyl-[acp]methyl ester

a 5-(2-methoxy-2-oxoethyl)

uridine34 in tRNA

beta-D-xylopyranose

6-phosphofructokinase3: PFK3

Probable Dol-P-Man:Man(7)GlcNAc(2)-PP-Dol alpha-1,6-mannosyltransferase:CG8412

homogentisate

chorismate

UQ

1-deoxy-D-xylulose 5-phosphate


Glucose-6-phosphate isomerase,cytosolic: PGIC

Thioredoxinreductase 2,mitochondrial:Txnrd2

an (R)-3-hydroxyoctanoyl-

[acp]

Nitrilasehomolog1: NIT1

adenosinenucleotides de

novo biosynthesis

Argininosuccinatesynthase: argG

AMP

3-dehydroquinate


O-ureidohomoserine

3-dehydroquinate

a dolichylphosphate

GDP-alpha-D-mannose

isopentenyldiphosphate

oxaloacetate

R’C(R)SH

spermidine

tetrahydrofolate


trehalose

an aldehyde

3-[(3aS,4S,5R,7aS)-5-hydroxy-7a-methyl-1-oxo-octahydro-1H-inden-4-yl]-3-

oxopropanoyl-CoA

a 3-oxo-palmitoyl-

[acp]



[lipoamide acyltransferase] N6-(S-[2-methylbutanoyl]dihydrolipoyl)

lysine


[+ 2 isozymes]

pro

tRNAlys

2,4-dienoyl-CoAreductase[NADPH]:fadH

Ribulosebisphosphatecarboxylaselarge chain: rbcL

precorrin-1

NAD+

CO2fixation intooxaloacetate(anapleurotic)

4alpha-formyl-

ergosta-7,24(241)

-dien-3beta-ol

a 2-lyso-phosphatidyl-ethanolamine


2-diphosphodolicholGlucosamine--fructose-6-phosphateaminotransferase[isomerizing]: glmS

Coproporphyrinogen-III oxidase,chloroplastic: CPX

a phenol

bigendothelin


UDP

alpha-L-galactose-1-phosphate

a mannan

Indoleamine2,3-dioxygenase1: Ido1

leucocyanidin

OPC8-3-hydroxyacyl-

CoA


a reduced plastocyanin

tRNAasn

Trehalosephosphorylase: TP


an alcohol

Flavin-containingmonooxygenaseFMO GS-OX3:FMOGS-OX3

Glucokinase: glk

[+ 2 isozymes]

Folic acidsynthesisproteinfol1: fol1

N-acetyl-alpha-D-glucosamine1-phosphate

[+ 11 isozymes]


[+ 2 isozymes]

a peptide

2-oxoisovaleratedehydrogenase

subunit beta,mitochondrial: bkdB

1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase,chloroplastic: HIS6

a tRNApseudouridine38-40


Fructose-1,6-bisphosphatase,

chloroplastic: FBP


acetate

sulfite

L-sulfolactatedehydrogenase:comC

Cysteine--tRNA

ligase: cysS

[+ 3 isozymes]

L-threonyl-tRNAthr

beta-D-galactosyl-1,3-

N-acetyl-D-galactosaminyl-[glycoprotein]

a tRNA containing N6-dimethylallyladenosine

[+ 3 isozymes]

trp

leucopelargonidin

indole-3-acetate

[protein] N6-(dihydrolipoyl)

lysine

bilirubin

beta-D-glucose

3-methylguanine

a peptide

L-canavanine

INORGANIC NUTRIENTS METABOLISM

a malonyl-[acp]



[+ 3 isozymes]

Probablephosphoglucomutase,cytoplasmic2: At1g70730

glycinebetaine

Acetate--CoAligase ACS,chloroplastic/glyoxysomal:ACS


n-butanol

an alcohol

PHOTOSYNTHESIS


Alpha-tubulin N-acetyltransferase:PITG_13069

an oxidizedthioredoxin

indole-3-acetonitrile

Group XIIAsecretoryphospholipaseA2: PLA2G12A

anthranilate


a sialyloligosaccharide

PyruvatedehydrogenaseE1 componentsubunit beta: pdhB

a 3-oxo-delta5-steroid

4-methyl-5-(2-phosphonooxyethyl)

thiazole



D-tagaturonate

glt

guanine andguanosinesalvage I

formyl-L-methionylpeptide


Nitratereductase[NADH]1: NIA1

glt

an mRNA

chitotriose

Citrate synthase, mitochondrial: cs

CathepsinZ: CTSZ

nicotinamideriboside

Transaldolase: tal

a ubiquitin

Delta(7)-sterol-C5(6)-desaturase1: STE1


a 1-phosphatidyl-


guanine37in tRNA

1-deoxy-L-glycero-

tetrulose 4-phosphate


thiamin diphosphate

a 1,4-beta-D-glucan

his



O-phosphoseryl-tRNA(Sec)seleniumtransferase:SEPSECS

NADP+

crinosterol

glt


L-homoserine

cholinebiosynthesis III

dihydrobiopterin

linoleate

acetyl-CoA

[+ 2 isozymes]

L-homocysteine

a 3-oxo-dodecanoyl-

[acp]

Glutamatesynthase2 [NADH],chloroplastic:Os05g0555600

benzoate

2-oxoisovaleratedehydrogenase subunitalpha, mitochondrial:BCKDHA

nitrite

all-trans-13,14-dihydroretinol


indole-3-ethanol

a peptide

acyl-CoAhydrolysis

Chitinase domain-containing protein 1: Chid1

trans-4-hydroxy-L-proline

2-(3-carboxy-3-aminopropyl)

-L-histidinein eEF-2

glt

[+ 2 isozymes]

a 2’-O-methylcytidine32/2-O-methylguanosine34

in tRNA

Solublecalcium-

activatednucleotidase

1: Cant1


divinylchlorophyllide a

glycine betainebiosynthesis

I (Gram-negativebacteria)

5-amino-6-(5-phospho-D-ribosylamino)

uracil

NADH



[+ 2 isozymes]

CO2

Probabledipeptidase:pipD

Pyrroline-5-carboxylatereductase:PROC1

[+ 6 isozymes]

4-methyl-2-oxopentanoate

Transketolase:tkt-1

3’-ketolactose

glyceroldegradation I


DNAn

a fatty acid

a peptide

Dihydrolipoyldehydrogenase:lpdA

a holo-[acp]

ubiquinol-8


a glutamate

cardiolipinbiosynthesis II

a primaryalcohol

glutathioneredox

reactions II

Putativeuncharacterizedprotein:CAOG_03223


alpha-L-rhamnose

Probable tRNA-dihydrouridinesynthase 2: dus2

22-hydroxy-3-oxochol-

4-en-24-oyl-CoA

D-ribulose-1,5-bisphosphate


Inosine triphosphatepyrophosphatase:At4g13720

a hexanoyl-[acp]

NAD(P)transhydrogenase,mitochondrial: NNT

pyridoxal 5’-phosphate

biosynthesis II

succinate

[+ 6 isozymes]

pyruvate

Phosphoglyceratekinase,

chloroplastic: PGK


Bifunctionalaspartokinase/homoserinedehydrogenase2, chloroplastic:AKHSDH2

Ribosomalprotein L11methyltransferase:prmA



a beta-D glucan

Serine--tRNA

ligase: serS

a (R)-3-hydroxy-cis-vaccenoyl-

[acp]

Medium-chain-fatty-acid--CoAligase: alkK

fumarate

uracil16in tRNA

Phosphatidylinositol4-kinase beta1: PI4KBETA1

a nucleobasewithin DNA

[+ 3 isozymes]


hypoxanthine

nitrate

formate

glycyl-peptide

Phospholipid:diacylglycerolacyltransferase 1: PDAT1

arg


[+ 3 isozymes]


Arginase-1: Arg1

uracil

pyruvate

[+ 3 isozymes]

Hydroxylaminereductase: hcp

6-pyruvoyltetrahydropterin


dihydroxyacetone phosphate


a [protein]-L-beta-

isoaspartate

a protein


myo-inositol


GTP

L-galactono-1,4-lactone


inositol 3,4,5-trisphosphate

a DNA

pyruvate

Adenylosuccinatesynthetase:PITG_16736

glutathionedisulfide

N1-acetylspermidine

Kynureninase:kynu


[+ 4 isozymes]



[+ 3 isozymes]

a supercoiledduplex DNA

tRNAasp

a long-chainaldehyde


[+ 3 isozymes]

UDP


coenzyme A

guanine

thr


4-aminobenzoate



a monocarboxylic-acid-amide

all-transneurosporene

5-hydroxyisouratehydrolase: hiuH

2-aminoadipate

Lactoylglutathionelyase, putative:RCOM_0911940


an organichydroperoxide

thymine

RhomboidproteasegluP: gluP

lathosterol

Alcoholdehydrogenaseclass-3: ADHIII

D-gluconate

Poly(A)polymerasegamma:Papolg

methionine biosynthesis II

[+ 2 isozymes]

Glc2Man9GlcNAc2

Dihydrolipoyllysine-residue succinyltransferase

component of 2-oxoglutaratedehydrogenase complex,

mitochondrial (Fragment): dlst

dolichyl-diphosphooligosaccharide

biosynthesis

Transketolase: tkt-1

Branched-chain-amino-acidaminotransferase: ilvE

GDP

RNase Eprocessing

productmRNA

(3Z)-hex-3-en-ol

Phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase 2: Inppl1

phospholipases

L-allo-threoninealdolase:ltaA

Bifunctionalglutamate/

proline--tRNAligase: EPRS

an (N-acetylglucosaminyl)

2-diphosphodolichol

a 1,4-alpha-D-glucan


Probableuroporphyrinogen-IIIC-methyltransferase:SPCC1739.06c

3-aminopropanal


guanine

beta-D-glucuronosyl-(1->3)-beta-

D-galactosyl-(1->3)-beta-

D-galactosyl-(1->4)-beta-D-xylosyl-

[core protein]

(S)-3-hydroxybutanoyl-

CoA


riboflavin

Nucleosidediphosphate

kinase 4,chloroplastic:

NDK4

(S)-3-hydroxy-3-methylglutaryl-

CoA

a holo-[acp]

24-methyldesmosterol

an (3R)-3-hydroxymyristoyl-

[acp]

3-oxoacyl-[acyl-carrier-protein]reductaseFabG: fabG


a histone

GDP-mannose4,6 dehydratase2: gmd-2


Ribonucleoside-diphosphatereductase smallchain: rnr-2

[+ 2 isozymes]

2-oxoglutaratemyo-inositol

a relaxedDNA

Enoyl-CoA deltaisomerase 2,mitochondrial:Eci2

triacylglycerolbiosynthesis

naringeninchalcone

Mg-protoporphyrin

a 3-oxo-octanoyl-

[acp]

succinate

13-sophorosyloxydocosanoate6’,6’’-diacetate

a cis-vaccen-2-enoyl-[acp]

2-oxoglutarate


D-fructose

RibonucleaseZ: rnz

O-ureidohomoserine

L-asparaginyl-tRNAasn

a thiopurine

alpha-D-glucose

SECONDARY METABOLITES DEGRADATION

indole-3-acetate

(2E,6E)-farnesyl

diphosphate

cellobiose

acidification andchitin degradation (incarnivorous plants)


demethylmenaquinol-8


[+ 2 isozymes]

cleaved type-1transmemberane

domains


Glycerolkinase: glpK

succinate

citrullinedegradation

[+ 6 isozymes]

hypusinebiosynthesis

Purple acidphosphatase 21: PAP21


a 2’,3’-cyclic-phosphate-terminated

RNA

pregn-5-ene-3,20-

dione

3-hydroxy-L-kynurenine

(2S)-naringenin

L-citrulline

a calmodulinL-lysine

[tRNAArg2]-inosine34

dCTPpyrophosphatase1: DCTPP1

ser


a ketone

2,5-diamino-6-(5-phospho-D-ribosylamino)

pyrimidin-4(3H)-one

Mannose-6-phosphateisomerase:PMI1

3-methylcrotonyl-CoA

Insulin-degradingenzyme: Ide

ala

tetrahydrofolatesalvage from 5,10-

methenyltetrahydrofolate

Aspartate--tRNA ligase,cytoplasmic:

DARS

6-hydroxymethyl-7,8-dihydropterin

myo-inositol

Glucose-6-phosphate isomerase,cytosolic 1: PGIC1

acetaldehyde

[+ 2 isozymes]

oleoyl-CoA

glycinebetaine

oxaloacetate


a damagedDNA

pyrimidine

[+ 126 isozymes]

[+ 2 isozymes]

Methylthioribosekinase: MTK

thiamin diphosphatebiosynthesis III

(Staphylococcus)

L-ornithine3-[(3aS,4S,7aS)

-7a-methyl-1,5-dioxo-octahydro-

1H-inden-4-yl]propanoyl-

CoA


in tRNA

Putative 3,4-dihydroxy-2-butanonekinase:DHBK




N1-acetylspermidineL-galactonate

UDP

IAAbiosynthesis V

ethylnitronate

a polypeptide

tRNAthr

UDP

2-isopropylmaleate

branched-chain alpha-ketoacid dehydrogenase complex

[+ 4 isozymes]

L-cystathionine


DNAligase: ligA


cys


strictosamide

a phosphoprotein

Protease4: sppA


xanthine

folate polyglutamylation

L-ornithine

Tauropinedehydrogenase:tadh

Fatty aciddesaturase2: fads2


an RNA

dGTP

urea

Enolase: PGH1

pyruvate

4alpha-methyl-5alpha-

cholesta-7,24-dien-3beta-ol

ferulate

NAD+



Enoyl-CoA deltaisomerase 2,mitochondrial:Eci2

L-ornithine

[+ 2 isozymes]

a peptide

L-gulonate

a peptide

a monoamideof a

dicarboxylate

Heme oxygenase1: HMOX1

dihydrobiopterin

gln

histidinol

Electron transferflavoprotein-ubiquinoneoxidoreductase,mitochondrial:ETFDH

glutamatebiosynthesis I

AMINES AND POLYAMINES BIOSYNTHESIS

ATP phosphoribosyltransferase:HIS1

a uridine44in tRNAser

[+ 11 isozymes]

tryptamine

tRNA(Ile)-lysidinesynthase:tilS

5-dehydroepisterol

[+ 2 isozymes]

pro

S-ribosyl-L-homocysteine


a [2-oxoglutaratedehydrogenase E2

protein] N6-(lipoyl)lysine

UDP-sugarpyrophosphorylase1: USP1

6-phosphofructo-2-kinase 1: PFK26

mannitol-1-phosphate

pro

pteroate

[+ 3 isozymes]

tRNAgly


a tRNA

a peptide

Molybdopterinsynthase catalyticsubunit: MOCS2

a cytosine34in tRNAprecursor

[+ 6 isozymes]

adenylo-succinate


FK-506


[+ 2 isozymes]

3-oxo-3-phenylpropionyl-

CoANAD+

[Skp1-protein]-hydroxyproline N-acetylglucosaminyltransferase: gnt1

Adenylatekinase: adk

a phosphatemonoester

[+ 2 isozymes]

ATP

(3S)-malyl-CoAthioesterase:mcl2

allantoate

Probableserine/threonine-proteinkinasepkwA: pkwA

[+ 2 isozymes]

benzylalcohol

n-butanoate

GMP

MethyltransferaseFkbM family:Tpen_1716

Fumarate hydratase class II: fumC

Dihydropteridinereductase: qdpr

IMP

beta-D-fructofuranose


all-trans-retinol


RNase IIIprocessing

productmRNA

acetonecyanohydrin

[+ 3 isozymes]

5,10-methenyltetrahydrofolate

L-aspartyl-tRNAasn



benzoyl-CoA

plant sterolbiosynthesis

a [biotin-carboxyl-

carrierprotein

monomer]

AMP

Arogenatedehydrogenase 2,chloroplastic: TYRAAT2

pimeloyl-CoA

a trans-docos-2-

enoyl-[acp]

arg

Fumarate hydrataseclass I, aerobic: fumA



diphosphate

Phospholipid:diacylglycerolacyltransferase 1: PDAT1

N-acetyl-beta-D-glucosaminyl-

1,2-alpha-D-mannosyl-1,3-(N-acetyl-

beta-D-glucosaminyl-

1,2-alpha-D-mannosyl-

1,6)-(N-acetyl-beta-D-glucosaminyl-1,4)-beta-D-mannosyl-


glucosaminyl-R

Topoisomerase6 subunitB: TOP6B

Anthranilatephosphoribosyltransferase: trpD

2-(2-carboxy-4-methylthiazol-5-

yl)ethyl phosphate



[+ 2 isozymes]

a 3’ phosphooligonucleotide

Phosphoenolpyruvatecarboxylase: ppc

[+ 129 isozymes]

a peptidewith prolinein the thirdposition


isovaleryl-CoA

3-hydroxyisobutyryl-CoA hydrolase 1: CHY1


(2S)-2-isopropyl-3-oxosuccinate

N,N’-diacetylchitobiose

a 2-oxocarboxylate

a carboxylate

ATP

octanoyl-CoA

[+ 2 isozymes]


N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-

2,6-diaminopimelyl-D-alanyl-D-alanine-

diphosphoundecaprenol

Lipase:Esi_0000_0546

[+ 7 isozymes]

sphingomyelinmetabolism

an RNA

6-phosphofructokinase 3: PFK3

[+ 2 isozymes]

RNaseE mRNA

processingsubstrate

a lipoylatedprotein

lipoyl-domain

ammonia

O-acetyl-L-homoserine

Probable cardiolipinsynthase 1: crls-1

D-xylulose

sulfatetetrahydrobiopterin

an aceticester

a cardiolipin

Kynureninase:kynu

a ribonucleosidetriphosphate

Mannitol 1-phosphatedehydrogenase:MPDH2

tRNA (guanine-N(7)-)-methyltransferaseB: mettl1-B


(2E,6E)-farnesal

a protein

ADP


zymostenol


Squalenemonooxygenase:Sqle

a 1,3-beta-D-glucan

protoheme IX

phenylacetaldehyde

L-tyrosyl-tRNAtyr

alpha-ribazole-5’-phosphate

methanol

thioredoxinpathway

Fructose-bisphosphate aldolase,chloroplastic: Os11g0171300

a butyryl-[acp]

Maleylacetatereductase1: macA

an apo-[acp]

a plastoquinone

N-substitutedaminoacyl-

tRNA


Probablemethylmalonate-semialdehydedehydrogenase[acylating],mitochondrial:mmsdh

ethanolamine

[+ 3 isozymes]

L-glutamategamma-

semialdehyde

L-ornithine

NADH

formate

UDP-N-acetylmuramate

a 3-oxo-cis-delta5-

dodecenoyl-[acp]

EndonucleaseV: ENDOV

5,10-methenyltetrahydrofolate

71-hydroxychlorophyllide a

alpha-linolenate

NADH kinase:NADK3

UDP


Formate--tetrahydrofolate

ligase: THFS



(S)-2,3,4,5-tetrahydropiperidine-

2-carboxylate



a ADP-D-ribosylacceptor

(-)-menthone

a holo-[acp]

Pheophorbidea oxygenase,chloroplastic:PAO

carbonicacid

ATP

FAD

Fructose-2,6-bisphosphatase:FBP26

adenosine

[+ 3 isozymes]

(2E,6E)-farnesyl

diphosphate

Dol-P-Glc:Glc(2)Man(9)GlcNAc(2)-PP-Dol alpha-1,2-glucosyltransferase:ALG10

ile



phosphate

putrescine

[+ 4 isozymes]

a phosphorylase b

Argininebiosynthesisbifunctionalprotein ArgJ,mitochondrial:PITG_04698

Peptidyl-tRNAhydrolase 2,mitochondrial:PTRH2

canavaninosuccinate


ADP-sugarpyrophosphatase:NUDT5

protoheme IX

[+ 5 isozymes]

beta-D-xylopyranosyl-(1->4)-beta-D-xylopyranosyl-(1->4)-beta-D-xylopyranose-oligosaccharide

cappedmRNA

with capI structure


gly

Malate synthase,glyoxysomal: acuE


15-cis-phytoene

L-ascorbate

allantoindegradation to

ureidoglycolate I(urea producing)

Malate synthase,glyoxysomal: acuE


glt

xanthosine

Dihydrolipoyldehydrogenase,mitochondrial: LPD

Calcium/calmodulin-dependentproteinkinase typeII: unc-43


formate

Probable alpha-mannosidase IMNS4: MNS4

ADP-ribose

HCC

superpathway of leucine, valine,and isoleucine biosynthesis

a carboxylate

Indoleamine2,3-dioxygenasefamilyprotein: BNA2


molybdenumcofactor

a peptide

Thromboxane-A synthase:Tbxas1

monovinylprotochlorophyllide a


Phosphoacetylglucosaminemutase: PGM3

Glucose-6-phosphateisomerase,cytosolic:PGIC

a transdodec-2-

enoyl-[acp]

UMP

L-fucose


a dolichylbeta-D-glucosyl

phosphate




[+ 2 isozymes]

an RNA

CO2

a 3-oxo-cis-vaccenoyl-

[acp]

Queuine tRNA-ribosyltransferase: tgt

Nicotinatephosphoribosyltransferase:naprt

a guanine10in tRNA

arg

a sulfuracceptor

a (R)-3-hydroxy-cis-vaccenoyl-

[acp]

pyridoxamine5’-phosphate

di-trans,octa-cis-

undecaprenyldiphosphate

Nardilysin:Nrd1

nitrite

leukotriene-C4

Transketolase: tkt-1

Nicotinate-nucleotide--dimethylbenzimidazolephosphoribosyltransferase: cobT

cysteamine

acetaldehyde

a single-stranded

RNA

methylindole-

3-acetate

a 2,3,4-saturated

fattyacyl CoA

UncharacterizedDAPA-like lyaseCaur_1967:Caur_1967

a biotinylated[BCCP dimer]

lipoatebiosynthesis

andincorporation I

ProbableAMPdeaminase:AMPD

dTDP-4-dehydro-6-deoxy-alpha-D-glucose

oleate

3-mercaptopyruvatesulfurtransferase:sseA

[+ 3 isozymes]

Nitrilasehomolog1: NIT1

Cycloartenolsynthase: CAS


a DNAcontainingpyrimidine

dimer



all-trans-retinol

Rubisco shunt

a transhexadecenoyl-

[acp]


a 5’-(N7-methylguanosine5’-triphospho)

-mRNA

a single-stranded

RNA

(2E,6E)-farnesyl

diphosphate

[+ 3 isozymes]

a single-stranded

RNA

cyanidin

Tubulin--tyrosineligase-likeprotein12: TTLL12

[+ 2 isozymes]

gln

alpha-tubulin


protoporphyrinogen IXL-gamma-

glutamylcysteine

(S)-lactate

L,L-diaminopimelate


phosphoenolpyruvate

glutathione

Phosphoserineaminotransferase:serC

GDP-L-galactose

taurine

ATP-citratesynthase: ACLY

H+


shuttle

a ribonucleosidemonophosphate


CMP

Predicted protein(Fragment):MICPUCDRAFT_6886

dCTP

phosphateacquisition

Poly [ADP-ribose]polymerase16: Parp16

Transketolase:TKL1

IMP

alpha-D-glucose


acetyl-CoA

S-adenosyl-L-methionine cycle I

3-phosphoinositidedegradation

nitrate

acetate

GDP


L-fucosekinase: FUK

a peptide


DNAendonucleaseRBBP8:RBBP8


Isovaleryl-CoAdehydrogenase,mitochondrial: Ivd

chitin

5-methylthioribulose-1-phosphate

Protein-S-isoprenylcysteine O-methyltransferase:ICMT


ProbableRNAhelicaseSDE3:SDE3

phytochelatinsbiosynthesis


inositol 3,4,5-trisphosphate

Imidazoleglycerol-phosphatedehydratase: HIS3

a [protein]-L-asparagine

episterol

RNase IIpoly-A

substratemRNA

Selenide,waterdikinase:selD

a primaryalcohol

a stearoyl-[acp]


uracil

OPC4-3-hydroxyacyl-

CoA

betainealdehyde

a peptide

O-phospho-L-homoserine

a 2,3,4-saturated

fattyacyl CoA

2-C-methyl-D-erythritol 2,4-cyclodiphosphatesynthase,chloroplastic: ISPF

(2R,3S)-2,3-dimethylmalate

RibonucleaseZ: rnz

N-acetyl-L-glutamate


methanol

[+ 3 isozymes]

Asparagine--tRNA

ligase: asnS

AROMATIC COMPOUNDSDEGRADATION

4-maleyl-acetoacetate

DNAn

a jasmonicacid

a reducedcytochrome cL

15,16-dihydrobiliverdin

[+ 3 isozymes]

propanoyl-CoA

a guanine10in tRNA

(deoxynucleotides)(m)

N-ethylmaleimidereductase: nemA

[+ 2 isozymes]


[+ 126 isozymes]


Riboflavinkinase: Rfk

(Dimethylallyl)adenosine tRNAmethylthiotransferaseMiaB: miaB

5’-deoxyadenosine

[+ 2 isozymes]


fatty acid beta-oxidation II (core pathway)

trans-delta2,cis-delta4-

decadienoyl-CoA

uracil

Riboflavinbiosynthesisprotein ribBA,chloroplastic:RIBBA

pyruvate

AMP

a holo-[acp]


5-methyl-tetrahydrofolate


3-sulfopyruvate

a (R)-3-hydroxydodecanoyl-

[acp]

N-terminaldipeptide

Putativeuncharacterized protein:CHLNCDRAFT_137846

shikimate

[+ 2 isozymes]

Prolineiminopeptidase: pip

a quinol

tRNA (cytosine(49)-C(5))-methyltransferase:PYRAB06230

met

sulfate

Leucoanthocyanidindioxygenase: A2

Transaldolase: tal

oxaloacetate

a peptide

an alcohol

Acyl-coenzymeA thioesterase9, mitochondrial:Acot9

[+ 9 isozymes]

Hydroxyacylglutathionehydrolase 3,mitochondrial: GLY3

Methylenetetrahydrofolatedehydrogenase [NAD(+)]: thfA

hydroxylamine

NADphosphorylation anddephosphorylation

8-amino-7-oxononanoatesynthase: bioF

[+ 127 isozymes]

[+ 25 isozymes]

acetyl-CoA

[+ 2 isozymes]


[+ 3 isozymes]

a ketone

pyruvate

all-trans-retinol

Putativeuncharacterized protein:PHYSODRAFT_347522

hypotaurine

RibonucleaseZ: rnz

Choline-phosphatecytidylyltransferase B: Pcyt1b

tRNAala

a carboxylate

(R)-pantoate

3-[(3aS,4S,5R,7aS)-5-hydroxy-7a-methyl-

1-oxo-octahydro-1H-inden-4-yl]-3-

hydroxypropanoyl-CoA

an eIF5Alysine

Queuine tRNA-ribosyltransferase: tgt

Propionyl-CoAcarboxylasealpha chain,mitochondrial:PCCA

Trehalase:TREH

a proteinwith

oxidizeddisulfidebonds

Probable1-deoxy-D-xylulose-5-phosphatesynthase,chloroplastic:CLA1

lathosterol

4-(2’-carboxyphenyl)-

4-oxobutyryl-CoA

CDP-diacylglycerol--inositol 3-phosphatidyltransferase1: PIS1

2-epi-5-epi-valiolonesynthase:acbC


Fatty-acid amidehydrolase 1: FAAH

beta-D-glucose

aerobic respiration (cytochrome c)

NADP+

Nitronatemonooxygenase:PA1024

a protein-gamma-

glutamate

an oleoyl-[acp]

1-acyl-sn-glycerol-3-phosphateacyltransferase1, chloroplastic:LPAT1

[+ 4 isozymes]

6,7-dimethyl-8-(1-D-ribityl)

lumazine

5-androstene-3,17-dione

UDP

Carbamoyl-phosphatesynthase[ammonia],mitochondrial:Cps1

pentose phosphatepathway (partial)

Magnesium-chelatasesubunitH: bchH

[+ 22 isozymes]

a peptideL-glutamategamma-

semialdehyde

Choline-phosphatecytidylyltransferaseB: Pcyt1b

4,4-dimethyl-5alpha-

cholest-7-en-3beta-ol

[+ 7 isozymes]

[+ 3 isozymes]


Diacylglycerol O-acyltransferase2: DGAT2

[+ 2 isozymes]

[+ 4 isozymes]



phosphoenolpyruvate

Glutathionesynthetase: gshB

a reducedcytochrome c

tRNAarg

[+ 3 isozymes]

Glyceraldehyde-3-phosphatedehydrogenase 2: gpd3

[+ 2 isozymes]

nicotinate

ATP

a standardalpha

amino acid

Homogentisate1,2-dioxygenase:hmgA

a C-terminalamino acid

phe

an RNA


AMINO ACIDS DEGRADATION

XMP


S-methyl-5’-thioadenosine

CCA tRNAnucleotidyltransferase,mitochondrial: CCA1

argininedegradationVII (arginase3 pathway)

a 2,3,4-saturated L-

phosphatidate


PRPPbiosynthesis I

CDP

acetoacetyl-CoA

Arginase-1: Arg1

[+ 6 isozymes]


Uncharacterizedprotein Mb2253c:Mb2253c

S-formylglutathione

(3Z)-hex-3-en-ol

a beta-lactam

prolinebiosynthesis I

Purine nucleosidephosphorylase 1: punA

[+ 8 isozymes]

OPC4-CoA

[+ 3 isozymes]

a lysophospholipid

anthranilate


Bifunctionaldihydrofolatereductase-thymidylatesynthase2: THY-2

XXLG xyloglucanoligosaccharide

a nucleosidetriphosphate

alpha-D-mannose

Gluconolactonase: gnl

Ananain:AN1

Probableuroporphyrinogen-IIIC-methyltransferase:SPCC1739.06c


DNAn

glycolysis I

Dihydrolipoyldehydrogenase: lpdA

a 2’-O-methyluridine44

in tRNAser

a cellodextrin


quinolinate


N-formylkynurenine


protoporphyrin IX


ADP-ribosepyrophosphatase:nudF

L-methionine-(S)-S-oxide

Bifunctionalprotein folC: folC



extensionand a long3’ trailer

Glycine--tRNA ligase 1,mitochondrial:

GLYRS-1

3’(2’),5’-bisphosphatenucleotidaseCysQ: cysQ

L-quinate

beta-D-galactose

tRNA-specificadenosinedeaminase2: adat2

a singlestranded

DNA

D-gluconatedegradation

[+ 2 isozymes]

2-oxoglutarate

a peptide

Adipocyteplasma membrane-associatedprotein: APMAP

4alpha-hydroxymethyl-

stigmasta-7,24(241)-

dien-3beta-ol

Biotinsynthase: bioB


RibonucleaseZ: rnz

Pyruvate dehydrogenase E1component subunit beta: pdhB

Molybdenumcofactorsulfurase:ABA3

(S)-3-hydroxybutanoyl-

CoA

(S)-malate

phosphoenolpyruvate

nitrate

trehalose 6-phosphate

A

2-iminoacetate

alpha-iminosuccinate

mitochondrialintermediate

protein

Probable NADHdehydrogenase:DDB_G0270104

AMP

selenophosphate

coproporphyrinogen I

Zeaxanthinepoxidase,chloroplastic:ZEP

[+ 5 isozymes]

cys

glt

a proteinc-terminalS-farnesyl-L-cysteine

a 6-(N-acetyl-D-glucosaminyl)-


Fructose-1,6-bisphosphatase,chloroplastic: FBP

anacetylatedhistone

[+ 2 isozymes]

a 3-oxo-cis-vaccenoyl-

[acp]

Probablecytochromec-type hemelyase: cchl


adenosine 5’-phosphoselenate

[+ 2 isozymes]

tRNAGlu

a sphinganine(C18)

Branched-chain-amino-acidaminotransferase:ilvE

shikimate

asp


glucose and glucose-1-phosphate degradation

Protein-L-isoaspartate(D-aspartate) O-methyltransferase:PCMT1

a 2,3,4-saturated

fattyacyl-[acp]

Phosphatidylinositol N-acetylglucosaminyltransferasesubunit Q: PIGQ

Formate--tetrahydrofolateligase: THFS

1-hydroxy-2-methyl-2-(E)-butenyl 4-

diphosphate



S-lactoyl-glutathione


[+ 6 isozymes]


Stearoyl-CoAdesaturase5: SCD5

Reducingend xylose-releasing exo-oligoxylanase:BH2105

DNA-directedDNA/RNApolymerasemu: Polm

dUMP

GDP-L-fucose

a carboxylate

Fructose-bisphosphatealdolase, chloroplastic:

Os11g0171300

antheraxanthin

Fatty-acidamidehydrolase1: FAAH

Group XIIAsecretory

phospholipaseA2: PLA2G12A


glutaminedegradation II

choline

D-serine

thiamin diphosphate

Alpha-(1,3)-fucosyltransferase:FUT4

[+ 2 isozymes]

Pyrophosphate--fructose 6-phosphate1-phosphotransferasesubunit beta: PFP-BETA

dGDP

(S)-3-hydroxy-3-methylglutaryl-

CoA

[+ 2 isozymes]



2-diphosphodolichol

indole-3-acetate

3-dehydroquinatebiosynthesis I

anunsulfurated

sulfur acceptor

3-acetamidopropanal

tyr

Puromycin-sensitiveaminopeptidase:Npepps


meso-diaminopimelate

a monoacylglycerol

Phosphoglyceratekinase, chloroplastic: PGK


detyrosinatedalpha-tubulin

a 3-oxo-palmitoyl-

[acp]


Enolase: PGH1

a carboxylate

(S)-dihydroorotate

a (R)-3-hydroxystearoyl-

[acp]

taurinedegradation IV

Isovaleryl-CoAdehydrogenase,mitochondrial: Ivd

sphingosylphosphorylcholine

Putative peroxisomalacyl-coenzyme Aoxidase 1.2: ACX1.2

Acetylesterase: aes

Protoporphyrinogenoxidase: hemY

gln

an oxidizedcytochrome

tRNA(guanine(10)-N2)-methyltransferasehomolog: trmt11


[+ 8 isozymes]

a holo-[acp]

a peptide

Glucokinase:glcK

putrescine


adenosylcobalaminsalvage from

cobalamin

Uracil-DNAglycosylase:ung

a ceramide

N-formyl-D-kynurenine

selenocysteinebiosynthesis

II (archaea andeukaryotes)


geranyldiphosphate

2-oxoglutarate

3-oxohexanoyl-CoA

Kinesin-like proteinKIFC3:KIFC3

a phosphorylase a

Probable 3-hydroxyacyl-CoAdehydrogenaseB0272.3:B0272.3

Sphingomyelinsynthase-related protein1: SAMD8

uroporphyrinogen-I

Homoserinedehydrogenase:hom


1-palmitoylglycerol3-phosphate

a [pyruvate dehydrogenaseE2 protein] N6-(S-

acetyldihydrolipoyl)lysine

superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle

aminoacetone


isobutyryl-CoA

seedgermination

proteinturnover

tetrachlorohydroquinone

ethylacetate

Methenyltetrahydrofolatesynthase domain-containing protein: mthfsd

Glutamyl-tRNAreductase:hemA

[+ 3 isozymes]

canavaninosuccinate

brassicasterol

7,8-dihydrofolatemonoglutamate

AmmoniumtransporterNrgA: nrgA


Galactokinase:GALK1


tRNA-dihydrouridine(47)synthase[NAD(P)(+)]: dus3

Adenylyltransferaseand sulfurtransferaseMOCS3 1: GA24966

adenosine

Threoninesynthase:THR4

L-alanyl-tRNAala


Probable guaninedeaminase:SPCC1672.03c

UQ

[+ 3 isozymes]



a ferrocytochromeb5

a 1-phosphatidyl-


an O-glucosylsterol

5’-phosphoribosyl-4-(N-succinocarboxamide)

-5-aminoimidazole

a proteinwith

reducedsulfidegroups

[+ 3 isozymes]

precorrin-2

anthranilate

a peptide


SECONDARY METABOLITES BIOSYNTHESIS

Acetate--CoAligase ACS,chloroplastic/glyoxysomal: ACS


glt


ADP

a carboxylate

ATP-citrate synthase: ACLY

Dihydropteridinereductase: qdpr

demethylmenaquinol-6

Transketolase:TKL1

Glutamyl-tRNA(Gln)amidotransferasesubunit A: gatA

glt

3-phosphoshikimate 1-carboxyvinyltransferase,chloroplastic: At2g45300

ammonia

Separin:cut1

L-serinedehydratase:sds

bicarbonate

UDP-D-glucose

3-methylglutaconyl-CoA

Probable chorismatemutase: SPAC16E8.04c

Serinepalmitoyltransferase1: Sptlc1

(6E)-8-oxogeranial

NADH-quinoneoxidoreductasesubunit C: nuoC

O2

a peptide

Cyanatehydratase:

CYN

Pentachlorophenol 4-monooxygenase: pcpB

Trifunctionalpurinebiosyntheticproteinadenosine-3: Gart

a (1->4)-beta-D-xylan

oligosaccharide

Putativenicotinamide N-methyltransferase:NNT1

tetrahydrofolate

a quinone

cys

OPC8-3-ketoacyl-

CoA

tRNA-dihydrouridinesynthase A: dusA

2,3-dihydroxy-2,3-dihydrobenzoate


CDP-choline

arg

Phosphoserinephosphatase: PSPH

5-amino-1-(5-

phospho-D-ribosyl)imidazole

cacodylate

Histone-lysine N-methyltransferaseATXR2: ATXR2

[+ 4 isozymes]

a ribonucleosidediphosphate

thiamin phosphate

Methylmalonyl-CoA mutase,mitochondrial:MUT

Kynurenine--oxoglutaratetransaminase:ccbl

NADPH

uracil47in tRNA

(S)-2,3-dihydrodipicolinate


a peptide


butanal

phosphate

alpha-D-glucose


N-terminaldipeptide



[+ 2 isozymes]

biliverdin-IX-alpha


NADPH


[+ 2 isozymes]

thiamin

(9S,10S)-9,10-dihydroxyoctadecanoate

R-4’-phosphopantothenoyl-L-cysteine

a malonyl-[acp]

his

Pyrophosphate--fructose 6-phosphate 1-phosphotransferasesubunit beta: PFP-BETA

DNApolymeraseepsilonsubunitC: DPB3



pyrimidine ribonucleotides de novo biosynthesis

Dihydrolipoyldehydrogenase:

lpdA

1-deoxy-D-xylulose5-phosphatereductoisomerase: dxr

prolinedegradation

a processedmitochondrial

protein


Trifunctional enzymesubunit alpha,

mitochondrial: HADHA

[+ 22 isozymes]

5,6-dimethylbenzimidazole

Cyanatehydratase:CYN

cys


Ferredoxin-dependentglutamatesynthase 2: gltS

Maleylacetatereductase1: macA

31-O-desmethylFK-

506

[+ 2 isozymes]

COFACTORS,PROSTHETIC GROUPS,ELECTRON CARRIERS

DEGRADATION

(R)-methylmalonyl-

CoA

a monoacylglycerol




4-nitrophenylphosphate


L-canaline

L-canavanine

glt

Transketolase:TKL1


tRNA-dihydrouridine(20)synthase [NAD(P)+]-like: Dus2l

5-hydroxy-3-[(3aS,4S,5R,7aS)-7a-methyl-1,5-

dioxo-octahydro-1H-inden-4-

yl]propanoyl-CoA

BifunctionalpurinebiosynthesisproteinPURH: ATIC

a standardalpha

amino acid

OPC8-trans-2-

enoyl-CoA

a malonyl-[acp]

N,N-dimethylaniline

a trans-2-enoyl-CoA

xylose degradation IV

[+ 3 isozymes]

met


a beta-D glucan

UDP-glucuronate4-epimerase4: GAE4

Choline kinase alpha: Chka tyr

tRNAser

a DNAcontaining aapyrimidinic

site

L-homoserine

pregn-5-ene-3,20-

dione-17-ol

D-threo-isocitrate

Dolichyl-phosphate beta-glucosyltransferase:ALG5

1-deoxy-1-imino-D-

erythrose 4-phosphate

dipalmitoylphosphatidate

val

PPPi

acetyl-CoA


a mannosyl-(N-acetylglucosaminyl)

2-diphosphodolichol

a ribonucleoside

GDP-mannose 3,5-epimerase:At5g28840

tRNAile

GDP-alpha-D-mannose

Enolase: PGH1

a peptide

Deoxycytidylatedeaminase: Dctd


D-erythro-imidazole-glycerol-

phosphate

Isocitrate lyase: ACU-7


choline

Isocitrate lyase: ACU-7

Mitochondrial-processingpeptidasesubunitalpha: MPP


Imm downregulated3: Esi_0015_0185

PhosphatidatephosphataseLPIN2: Lpin2

acetoacetyl-CoA

divinylprotochlorophyllide a

guanosine2251in 23S rRNA

Adenylosuccinatesynthetase:PITG_16736

a trans-2-enoyl-CoA

dATP

8-oxo-dGMP

acetateconversionto acetyl-

CoA

sarcosine


ADP

a primaryamine


GMP

4-fumaryl-acetoacetate

Octanoyltransferase: lipB

a diphospho-1D-myo-inositol

tetrakisphosphate


NADH

shikimate-3-phosphate


Probable UDP-N-acetylglucosaminepyrophosphorylase:At2g35020

[+ 2 isozymes]

an octanoyl-[acp]

n-butanol

raffinose

UncharacterizedoxidoreductaseykwC: ykwC

ser

GDP

Putativeglucose-6-phosphate1-epimerase:yeaD

XMP

4alpha-carboxy-4beta,14alpha-

dimethyl-9beta,19-

cyclo-5alpha-ergost-24(241)

-en-3beta-ol

trphistidinal



a 1-phosphatidyl-


UDP-N-acetylmuramoyl-

L-alanyl-D-glutamyl-

meso-2,6-diaminopimelyl-D-alanyl-D-alanine

2-oxoisovaleratedehydrogenase subunit

alpha, mitochondrial:BCKDHA

Orotatephosphoribosyltransferase: pyrE

tyr

D-4’-phosphopantothenate

a galactosylatedgalactoseacceptor

ser

ADP-ribose

hydroxymethylbilane

glycine cleavage complex

[+ 2 isozymes]

tRNAsplicing

L-cysteinyl-tRNAcys

Probable 3-hydroxyisobutyratedehydrogenase,mitochondrial: hibA

succinate



butanoyl-CoA

Histidine--tRNA ligase,cytoplasmic:

hars

ala

[+ 6 isozymes]

beta-D-glucose




a ceramide

Putativeglucosamine-6-phosphatedeaminase-like proteinBT_0258:BT_0258

Cycloeucalenolcycloisomerase:CPI1

Prolinedehydrogenase1, mitochondrial:PRODH


trehalose

dehydroepiandrosterone

[+ 2 isozymes]

Fe2+

glycerol

presqualenediphosphate

[+ 3 isozymes]

GDP-L-galactose

dTDP-alpha-D-glucose

a [protein]-L-cysteine

3-dehydroshikimate

a polypeptide

succinate

tRNAtyr

matureprotein


L-ornithine

Proteinfarnesyltransferasesubunit beta: FTB

CMP

beta-alanine

Diaminopimelatedecarboxylase: lysA



AlkylatedDNA repairprotein alkBhomolog8: ALKBH8

[+ 6 isozymes]

a trans-2-enoyl-CoA

Acyl-[acyl-carrier-protein]desaturase 7,chloroplastic:FAB2


CTP

(S)-methylmalonyl-

CoA

D-arabinono-1,4-lactone

Putativepterin-4-alpha-carbinolaminedehydratase:CT0342

acetate

all-trans-geranyl-geranyl

diphosphate



diphosphate

5-amino-6-(D-ribitylamino)

uracil

S-hydroxymethylglutathione

dethiobiotin


N-acetylmuramoyl-L-alanyl-gamma-D-

glutamyl-L-lysyl- D-alanyl-diphosphoundecaprenol



urea cycle

H2O

Retrovirus-related Polpolyproteinfromtransposon297: pol

met

a myristoyl-[acp]AMP




queuine


Putativeacyl-CoAsynthetaseYngI: yngI

a holo-[acp]

gly

1-acyl-sn-glycerol-3-phosphateacyltransferase1, chloroplastic:LPAT1

acrylate

Bis(5’-adenosyl)-triphosphatase:fhit


12,15-dienoate

acetate

an aldehyde

[+ 2 isozymes]

UDP

glycinebetaine

[+ 4 isozymes]

a trans3,cis-5-dienoyl-

CoA

heme o

[+ 4 isozymes]

NAD+

OTHER BIOSYNTHESIS


ATP

Dual specificityproteinphosphatase:VH-PTP13

XMP

betainealdehyde L-lactaldehyde

N-acetylglutamyl-phosphate


tRNAhis

[+ 3 isozymes]

dCDP

pyruvate

Non-lysosomalglucosylceramidase:GBA2

Cyclopropane-fatty-acyl-phospholipidsynthase: cfa

Adenosinedeaminase: add


Putative peroxisomalacyl-coenzyme A

oxidase 1.2: ACX1.2

GMPreductase2: Gmpr2

S-sulfanyl-[acceptor]



2-ketoglutaratedehydrogenase complex





L-tryptophanyl-tRNAtrp


thiamin


GTP

betanidindegradation

cyanate




L-arginyl-tRNAarg


acetaldehyde

CO2

Fatty aciddesaturasefamily protein:Bm1_38160

liquiritigenin


Transketolase:tkt-1

Dihydroxy-aciddehydratase:ilvD

a chalcone

campest-4-en-3-one

Fatty aciddesaturasefamily protein:Bm1_38160

pseudouridine

Folic acidsynthesisproteinfol1: fol1





Putativeuncharacterized protein:PHYSODRAFT_347522

Fatty-acidamidehydrolase1: FAAH

pyridoxine-5’-phosphate

Cholinephosphotransferase1: Chpt1

3,5-tetradecadienoyl-

CoA

Glutamatecarboxypeptidase2: FOLH1

a single-stranded

RNA

3-(4-hydroxyphenyl)

-3-oxo-propionyl-CoA

N7-methylguanine46

in tRNA

agmatine

uratedegradationto allantoin

Proline--tRNAligase:proRS

L-aspartate-semialdehyde

GTPcyclohydrolase1: SPAC17A5.13

menaquinol-8

adenine



[+ 2 isozymes]

Porphobilinogendeaminase,chloroplastic: HEMC

PROTEIN DEGRADATION

gly

thio-molybdenum

cofactorbiosynthesis

[+ 7 isozymes]

2-succinylbenzoate--CoA ligase: menE

FeruloylesteraseB: ESTA

D-myo-inositol(1,3,4,5)-

tetrakisphosphate

nitrate

a 3’-terminalunsaturated

sugar

a peptide

prolycopene


flavoprotein

PhospholipaseD p2: PLDP2

a malonyl-[acp]

Endothelin-convertingenzyme2: ECE2

his

asparaginebiosynthesis I

isoliquiritigenin

PutativeuncharacterizedproteinB618R: B618R

N-methylethanolaminephosphate

Glycerol-3-phosphate O-acyltransferase1: SCT1

Arginyl-tRNA--proteintransferase1: ATE1

PPPi

Lysophospholipase2: plb2

dehydro-D-arabinono-1,4-lactone

Prolyl 4-hydroxylasesubunitalpha: phyA



(2R,3S)-3-isopropylmalate


[+ 2 isozymes]

an acyl-[acp]

Alcoholdehydrogenase: adh

a peptide

a phosphatemonoester

N-6-isopentyl

adenosine-37 tRNA

acetate

PutativeuncharacterizedproteinB618R: B618R

CO2

[+ 2 isozymes]

ATP

[+ 4 isozymes]


dCTP

palmitoyl-CoA

a small subunit ofmolybdopterin

synthase

Triacylglycerollipase:At4g13550

ile

asparaginedegradation I

Ribulose-phosphate3-epimerase: rpe

N-acetyl-beta-D-

glucosamine

Probableisoleucine--

tRNA ligase,cytoplasmic:

ileS

[+ 2 isozymes]

[+ 2 isozymes]

tRNA-specific2-thiouridylasemnmA: mnmA

keto-phenylpyruvate

4-hydroxybutyrate



UDP-D-galactose


Acetate--CoAligase ACS,chloroplastic/glyoxysomal: ACS

a transhexadecenoyl-

[acp]

a cytosine40 intRNA precursor

Adenosylmethionine-8-amino-7-oxononanoateaminotransferase: bioA

[+ 4 isozymes]


5,6-dihydrouracil47

in tRNA

secologanin


Retinoldehydrogenase11: RDH11

asp


a sterol

pyruvate


CARBOXYLATES DEGRADATION

4-hydroxyphenylpyruvatedioxygenase: HPD

GMP


L-glutamate-5-phosphate


alpha-D-mannose1-phosphate

a [protein]-L-aspartate

thiaminphosphate


coenzyme A

(2E,6E)-farnesol

an alcohol

sulfideoxidationI (sulfide-quinone

reductase)

HX

Protease4: sppA

Phosphoribulokinase,chloroplastic: PRKA

dTTP

phosphoenolpyruvate

guanosine

NADPH:adrenodoxinoxidoreductase,mitochondrial: fdxr


Allantoicase:allc


an alpha L-rhamnoside




phosphoryl-choline


2-O-methyluridine2552

in 23S rRNA

ATP phosphoribosyltransferase:HIS1

Proteindisulfide-isomeraseA3: Pdia3

a 3-oxoacyl-CoA

[+ 7 isozymes]



diphosphate

formate

a negativelysupercoiled

DNA

D-ribulose-1,5-bisphosphate

ureadegradation II

a proteinS-farnesyl-L-cysteine

4alpha-carboxy-ergosta-

7,24(241)-dien-

3beta-ol


Amidase:SSO2122

Pyrophosphate--fructose 6-phosphate1-phosphotransferasesubunit beta: PFP-BETA

a trans-docos-2-

enoyl-[acp]

a 1-phosphatidyl-


Glycerophosphodiesterphosphodiesterasedomain-containingprotein 1: GDPD1

2-oxoglutarate

dolichyldiphosphate

a holo-[acp]

porphobilinogen

6-carboxy-5,6,7,8-tetrahydropterin


cytidine

Cytochromec oxidasesubunit 1: ctaD

an aldehyde

a single-stranded

RNA


[+ 3 isozymes]


an alpha-D-mannoside

L-glutamategamma-

semialdehyde

a ferricytochromeb5

phosphoenolpyruvate

[+ 6 isozymes]

an octanoyl-[acp]

5-phospho-beta-D-ribosyl-amine



glycine betainebiosynthesis

II (Gram-positivebacteria)

[+ 2 isozymes]

Ribose-phosphatepyrophosphokinase4: PRS4

ammonium

indoleacetaldehyde

a thiocarboxylatedsmall subunit ofmolybdopterin

synthase

tRNA-splicingendonucleasesubunitSen34: Tsen34

Ferrochelatase:hemH

Acetylornithineaminotransferase:argD

CarboxypeptidaseY: CPY1


a holo-[acp]

alpha-N-acetyl-D-

glucosaminyl-(1->4)-beta-D-glucuronosyl-(1->3)-beta-D-galactosyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-xylosyl-

[core protein]


Nicotinate-nucleotidepyrophosphorylase[carboxylating](Fragment): qprt

Purple acidphosphatase 21: PAP21

[+ 6 isozymes]

NADPH

cotinine

a peptide


Fructose-bisphosphatealdolase, chloroplastic:

Os11g0171300

[+ 2 isozymes]

avenasterol

Arginine--tRNA

ligase: argS



an [apo BCAAdehydrogenaseE2 protein] N6-

(dihydrolipoyl)lysine

[+ 3 isozymes]

Fructose-bisphosphatealdolase,chloroplastic:Os11g0171300

val

a 3-oxoacyl-CoA

6-phospho-D-glucono-1,5-lactone

a fatty acid

leucodopachrome

glt

ethanol


leukotriene-D4


citrate

L-ornithine


[+ 6 isozymes]

Adenylyltransferaseand sulfurtransferaseMOCS3 1: GA24966

Uracilphosphoribosyltransferase: upp

Probable beta-1,3-galactosyltransferase16: B3GALT16

O2

Dolichyl-diphosphooligosaccharide--protein glycosyltransferasesubunit 2: ost2

ammonia


a 1-phosphatidyl-


dTDP


Enolase: PGH1

[+ 2 isozymes]

Mg2+

Glutathioneperoxidase1: GPX1

Cocaineesterase:cocE

acetyl-CoA

Dihydrolipoyldehydrogenase:

lpdA

[+ 4 isozymes]


3-ketoacyl-CoA thiolaseB, peroxisomal:Acaa1b

putrescine

a malonyl-[acp]

L-homoserine

Transketolase:tkt-1

3-oxoacyl-[acyl-carrier-protein]reductaseFabG: fabG

fumarate

7-dehydrocholesterolreductase: DWF5

Uroporphyrinogen-III synthase,chloroplastic: UROS

3-isopropylmalatedehydratase: IIL1

beta-D-glucose

O-acetyl-L-serine Leukotriene

A-4 hydrolasehomolog: lkhA

8-oxo-dGTP


Probable GTPpyrophosphokinase: relA

[+ 2 isozymes]

a negativelysupercoiled

DNA

a tRNAuridine54




Pyridoxine/pyridoxamine5’-phosphateoxidase: pdxH


glt

beta-D-galactose

Pentachlorophenol 4-monooxygenase: pcpB

4alpha-formyl-

stigmasta-7,24(241)

-dien-3beta-ol


an (R)-3-hydroxypalmitoyl-

[acp]

adenine58in tRNA

anuncharged

tRNA

UDP

AMP

Frataxin,mitochondrial:fxn

strictosidine

[+ 4 isozymes]

[+ 3 isozymes]

4-hydroxysphinganine

[+ 8 isozymes]

an all-trans-retinol-

(plasma-retinol-

binding-protein)

a trans-delta2-

decenoyl-[acp]


a trans-octadec-2-enoyl-[acp]

Glycerophosphoryldiesterphosphodiesterase:glpQ

[+ 3 isozymes]

Probable ribose-5-phosphate

isomerase: At2g01290

Putative oxidoreductaseGLYR1: GLYR1

(S)-2,3-dihydrodipicolinate

Glutaminesynthetaseleaf isozyme,chloroplastic: GS2

(S)-2-amino-6-oxohexanoate

L-cystathionine

Fructokinase:scrK

3-(all-trans-octaprenyl)benzene-1,2-diol

NAD+

hydrogensulfide

acetyl-CoA

3-dehydroshikimate


ethanolamine

dihydrolipoamide


a 5’ half-tRNA

moleculewith a

2’,3’ cyclicphosphate

on its 3’ end

propanoyl-CoA

thiosulfatedisproportionation

III (rhodanese)

a tRNA

9S rRNA

L-arginino-succinate

L-dopachrome

[+ 6 isozymes]

Proteinkinase C:Pkc98E

Acylphosphatase-2: Acyp2

N-formyl-L-methionyl-tRNAfmet

trans, trans-farnesyl

diphosphatebiosynthesis

[+ 3 isozymes]


(S)-3-amino-2-methylpropanoate


a 2’-O-methyladenosine4

in tRNAHis

selenate

2-dehydro-3-deoxy-D-galactonate-6-phosphate

3,24-dioxocholest-4-en-26-oyl-CoA

a transtetradec-2-enoyl-[acp]

acetoacetyl-CoA

zymosterol

Fumarylacetoacetase: Fah

2-aminoadipate

Putative long-chain-fatty-acid--CoAligase: HI_0002

dUMP

(2S)-2-isopropylmalate

homoserinebiosynthesis

a decanoyl-[acp]

a trans-2-enoyl-CoA

a protein

6-(alpha-D-glucosaminyl)-


crotonyl-CoA

a phosphoprotein

[+ 2 isozymes]


glt

glt

[+ 2 isozymes]

L-glutaminyl-tRNAgln

3-demethylubiquinone-9 3-methyltransferase:ubiG

UMP

Enolase:PGH1

ProbableRNA 3’-terminalphosphatecyclase-likeprotein: rcl1

trp

prolinebiosynthesis II(from arginine)

L-homocysteine

Ribulose bisphosphatecarboxylase

large chain: rbcL


2-oxoglutarate

Transaldolase: tal


cysteinebiosynthesis I

Sirohydrochlorincobaltochelatase:cbiX


NADP-specificglutamatedehydrogenase:gdh

Phosphatidylinositol-4-phosphate 5-kinase its3: its3


[+ 13 isozymes]

(R)-pantothenate


3-phospho-hydroxypyruvate

3-dehydroquinate

(S)-methylmalonate-semialdehyde

Probableadenylyltransferase/sulfurtransferaseMoeZ: moeZ

putrescinebiosynthesis III

phosphoenolpyruvate

anoligopeptide



coenzyme Abiosynthesis

Lipoamideacyltransferasecomponent ofbranched-chainalpha-keto aciddehydrogenasecomplex,mitochondrial: Dbt

5-carboxyamino-1-(5-phospho-

D-ribosyl)imidazole

beta-D-glucose an acetic

ester

N-ethylmaleimide

a polypeptide

a dipeptidewith prolineat carboxyterminal

a nonglucosylated

glucoseacceptor


magnesium-protoporphyrin

IX 13-monomethyl ester


guanine

L-quinate

cys

a carboxylated-biotinylated

[BCCP dimer]

cycloartenol


a (5-L-glutamyl)-L-peptide


Glc3Man9GlcNAc2

beta-D-glucose

3alpha,7alpha-dihydroxy-24-

oxo-5beta-cholestanoyl CoA

a 5’ phosphodinucleotide

[+ 2 isozymes]

Sulfateadenylyltransferase:MET3

nicotinamidemononucleotide

6,7-dimethyl-8-ribityllumazinesynthase(Precursor): ribH

acetate(S)-lactate

tRNAphe

UDP

acetyl-CoA

ATP

NAD+

peptidylproline(omega = 180)

an acyl-CoA

Probable aconitatehydratase,

mitochondrial: aco2


Inositoloxygenase:Miox

acyl carrierprotein

metabolism

[+ 11 isozymes]

a sugar-1-phosphate


all-trans-geranyl-geranyl

diphosphate

a sterol

Long-chain-alcoholoxidaseFAO1: FAO1

Glycerol-3-phosphatedehydrogenase[NAD(P)+]: gpsA


succinate

NgaditanaCyc: Nannochloropsis gaditana Cellular OverviewAuthors: Elisa Corteggiani Carpinelli, University of PaduaAndrea Telatin, University of PaduaNicola Vitulo, University of Padua

This diagram was automatically generated by SRI International Pathway Tools version 16.0, authors S. Paley and P.D. Karp.

! 4!

Triacylglycerol accumulation in nitrogen scarcity

Upon treating Nannochloropsis cells with a substance that stains specifically the neutral lipids (Nile Red) we can observe that in nitrogen deprivation (-Nitrate) they accumulate big lipid droplets (yellow signal) usually not present in the cells grown in the presence of nitrogen (+Nitrate). Comparison of the abundance of the transcripts in the cultures with sufficient nitrogen and poor lipid accumulation and in the cultures with scarce nitrogen and high lipid accumulation, offered the possibility to delineate the activation and the tuning down of various metabolic pathways and to hypothesize the balancing of the fluxes responsible for the accumulation of triacylglycerols inside the lipid droplets in nitrogen deprivation.

The analysis of the gene expression revealed that Nannochloropsis activated various mechanisms of nitrogen assimilation and redistribution in nitrogen scarcity and survived thanks to a partial reorganisation of its cellular metabolism. Various genes whose function is related to controlled protein degradation were induced in nitrogen stress, together with genes coding for proteins involved in the formation of cytosolic sequestering vesicles, which are used for degradation and recycling of cellular components. The up-regulation of these degradative processes made aminoacids available for biosynthetic processes without the need of nitrogen input (which is normally needed for the synthesis of new aminoacids). In addition various degradative processes that release ammonium were also found over-expressed. The GS/GOGAT pathway (L-glutamine + 2-oxoglutarate + NADPH + H+ ←→ 2 L-glutamate + NADP+) was activated in the nitrogen-deprived cells. The enzymes of this pathway are: glutamine synthetase (GS), which has a high affinity for NH3 and catalyzes the incorporation of ammonia into glutamine; glutamate synthases and glutamine amidotransferase, which are able to transfer one amino group from glutamine to 2-oxoglutarate and release, as a result, two molecules of glutamic acid. The glutamic acid produced through this pathway is an available substrate for further incorporation of intracellular ammonia and represents also a source of amine groups for cellular biosynthetic processes. I therefore hypothesize that this glutamine–glutamate shuffle might act as a central intermediary of amine groups’ exchange between degradative and biosynthetic pathways.

!!

Figure! 4! Schematic! representation! of! the! reorganization! of! the! cellular! metabolism! in!Nannochloropsis!in!nitrogen!scarcity!as!deduced!from!RNA<Seq!data.!From!(Corteggiani!Carpinelli!et!al.!2014)

Figure!3!Confocal!microscopy!images!of!Nannochloropsis!cells.!In!red!the!chlorophyll,!in!yellow!the!lipid!droplets.!From!11Corteggiani!Carpinelli!et!al!2014

! 5!

The genes predicted to function in the biosynthetic processes were still actively expressed at high levels for at least for 2-3 days after nitrogen deprivation with the exception of those responsible for protein biosynthesis of the organelles, which were instead severely tuned down even during early nitrogen deprivation. In response to nitrogen deprivation, the cells reorganized their metabolism by degrading selectively unnecessary molecules and synthesizing new ones to allow survival even in the deficiency of a fundamental nutrient and the first activities that were tuned down were those that take place in the organelles. !The transcriptomic data showed that the genes involved in fatty acid and triacylglycerol biosynthesis were always abundant in the cells (both when nitrogen was available and when it was deficient) and that their expression was not correlated with the amount of oil accumulated in the cells. Also the expression of the genes involved in lipid degradation did not seem to change significantly. The general conclusion suggested by the experimental evidence was that Nannochloropsis constitutively synthesized lipids and that the metabolic reorganization that followed nitrogen deprivation increased the flux of substrates through the lipid biosynthetic pathways, which were in turn capable to sustain the increased metabolic flux. Based on the available data I proposed a model of the metabolic response of Nannochloropsis to nitrogen deficiency that could justify an overproduction of fatty acids and as a consequence an accumulation of oil.

!Figure 5 Potential Model of the flux trough the fatty acid synthesis pathways in nitrogen sufficient and nitrogen deficient culturing conditions based on transcriptomic data. P, plastid; M, mitochondrion; L, lipid droplet.

Simionato et al. showed that despite the decrease of photosynthetic yield, photosynthesis is the only energy supply of the cells in nitrogen starvation. One of the most evident effects of nitrogen starvation that we noticed was the deescalation of the organelles. The model therefore states that the energy came into the system through the photosynthetic activity of the chloroplasts in both nitrogen sufficient and nitrogen depleted cultures, and produced glucose. After degradation of the glucose by glycolysis (the genes of this pathway were expressed at similar levels in both the two culturing conditions) the Acetyl-CoA and the reduced NAD(P)H were mainly reoxidised through the Krebs cycle and the mitochondrial respiration in nitrogen sufficient cultures. Only a small fraction of the Acetyl-CoA and of the reduced NAD(P)H entered the fatty acid biosynthetic pathway in this condition. During nitrogen starvation, due to the severe down-regulation of the mitochondrial genes, the reoxidation of the Acetyl-CoA and of the reduced NAD(P)H became less efficient and more substrates were available to enter the fatty acid biosynthetic pathway,

! 6!

leading to the accumulation of oil into the lipid droplets. This interpretative model was tested experimentally using various inhibitors of the mitochondrial respiratory chain in nitrogen sufficient cultures and measuring the average amount of intracellular lipids of the growing cells. The results were encouraging but not conclusive because of the scarce uptake of the inhibitors by Nannochloropsis cells. According to this model the mitochondrial complex I subunits would be interesting targets for genetic modification aimed at increasing the lipid productivity of the cultures. !A web resource of Nannochloropsis to support research While the production of data has become faster and cheaper, the necessity to fully analyze, organize and share them has become more pressing. I was deeply persuaded that the community of biochemists, biotechnologists and physiologist that worked with Nannochloropsis would have gained a lot of utility from the full access to

the sequences of the genes and chromosomes, as well as to the metabolic and functional annotation and to the gene expression analysis in a format that could be accessible to anyone without the need of specific informatics skills. Thanks to the great resources of the bioinformatics group of the Functional Genomic Research Unit it was possible to developed a comprehensive bioinformatic platform for information retrieval and data analysis, which is available online at www.nannochloropsis.org. The platform integrates several resources: a quick search engine that, upon the input of a gene ID or function, returns the complete characterization of the gene, its sequence, and its genomic context; a

query system that allows the user to obtain all the available information concerning a gene or a group of genes that correspond to the criteria used for the research (e.g. level of expression or enzymatic function); a genome browser displaying the annotation and the level of expression of each gene in different experiments; a blast search engine; a database of the metabolic pathways elaborate using the pathway tools framework and a scientific blog.

Three months after the platform was made available on the web, it had more than 1000 unique visitors per month and the number of pageviews has been steadily growing since then.

My personal view of this scientific experience The Nannochloropsis project has represented the most complete and autonomous research experience of my early carrier as research scientist. It has allowed me to cultivate my scientific interest for metabolic biochemistry, it was the first scientific project that I had the possibility to conceive and it has been a nice teamwork experience thanks to many excellent colleagues and students. All the work was characterized by a lively curiosity, a motivational commitment and a lot of creativity.

Figure!6!Screenshot!of!the!home!page!of!the!Nannochloropsis!web!platform!

! 7!

!Metagenomics One of the first applications of the next generation sequencing technologies to sparkle my interest was metagenomics. Throughout immeasurable time, microorganisms have evolved and accumulated remarkable physiological and functional heterogeneity, and now constitute the major reserve for genetic diversity on earth. Cultivation-independent assessment of microbial genomes offers a major resource for observing the pallet of the different metabolic strategies; furthermore, this material is a major asset in the search for new enzymes for various industrial processes. Currently, there is a global political drive to promote industrial biotechnology as a central feature of the sustainable economic future of modern industrialized societies. This requires the development of novel enzymes, processes, products and applications. Metagenomics might represent an important resource for finding new molecules with diverse functions.

During my Post-Doc at CRIBI in the group of Genomics, while collaborating on various projects of the group (including the realization of a metabolic pathways database of Vitis vinifera) I was given the possibility to design and realize a metagenomic experiment together with my colleague Andrea Telatin. The experiment had to fulfill the task of testing the performances of the Ion Proton sequencer on amplicons, whole metagenomes and ribosomal RNA fragments. We identified an interesting ecosystem, the Canale Scaricatore in Padova. This river crosses for a short trait an industrial area and collects various pollutants. We collected various water samples from the polluted area and we set up an innovative protocol to extract both total DNA and RNA at the same time in order to allow a more significant comparison of the sequencing data. I also prepared the sequencing libraries and we worked together on the analysis of the sequencing data testing various available software tools. The sequences produced by this first run of Ion Proton resulted too short and too few to support significant conclusions. Nevertheless we noticed the presence of various bacteria capable to degrade toluene and benzene derivatives and we focused our attention on the search of their genomic sequences in order to gain some information about possible enzymes of interest.

Despite the poor biological conclusions that we were able to reach using the available data, this scientific experience was of great interest for the two of us. Indeed we were very happy to try ourselves at this new task and to earn some technical instruments useful for metagenomic analysis, which we both hope to use again in the future.

! 8!

Photosynthesis I carried out the research project for my Second Level Degree in the research unit of Photosynthesis of Professor James Barber at Imperial College in London. During my stay in the laboratory I focused my efforts in the purification of functional Photosystem II (PSII) complexes from various cultures of Synechocystis PCC 6803 in which the PSII was present in relatively small amounts (i.e. from cultures grown in iron depletion and from strains with mutations effecting PSII subunits). The result of my efforts was the successful purification of functional and relatively pure PSII complexes from the iron-depleted cultures and from the mutant cultures of Synechocystis. The analysis of the particles of PSII obtained from the iron depleted cultures revealed that the Photosystem II did not undergo structural or functional changes upon iron deprivation differently from PSI, which in iron scarcity was surrounded by an extra antenna giving rise to a PSI-antenna supercomplex. According to the evidence that we produced the absence of iron was affecting only the amount of Photosystem but not its structural or functional characteristics. It is during this experience in the laboratory of James Barber that I acquired much of my knowledge about photosynthesis and the lot of my abilities as scientist. The beginning of my interest for renewable energies and for artificial photosynthesis also dates back to that period and to the interesting discussions with the scientists with whom I came in touch. During the first two years of my PhD training a continued working on photosynthesis, this time in the laboratory of Professor Giorgio Giacometti at University of Padova. My work in Padova was mainly focused on the regulative aspects of the photosynthetic process and I was involved in various projects of the group. The most of my research was concentrated on the study of peroxidase activities in the thylakoid lumen. !!!!!

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Teaching During my PhD and Post-Doc I had an intense activity as Teaching Assistant in molecular biology, biochemistry and genomics and I was also given the responsibility of tutoring some Undergraduate Students during their Graduation Projects. Despite teaching in Academia is not strictly a research experience I found it relevant to include a short paragraph about this activity in my report. My research interests indeed have both shaped and been shaped by my experiences as teacher, especially in the design of the laboratory activities. The activity as teacher has been often the occasion for me for great experimentations, both for the scientific topics that I chose to examine and for the abilities that I had the chance to test and improve. When I organized my first laboratory class of metabolic biochemistry I decided to include a simple experience about photosynthesis, which I was very confident to carry out with enthusiasm and competence, and a second experience about the measuring of the ATP production of isolated mitochondria, which I had never done before but I had been willing to observe for a long time. Choosing the topics for the tutorials and exercises of metabolic biochemistry I allowed myself to study something about diets and human metabolism during one academic year and about the industrial applications of various strains of bacteria during another. I once agreed to organize a laboratory experience of metagenomics for the students of the course of genomics in order to enjoy also myself for the first time working on a project in this interesting field. To my delight both the students and me were able to learn a lot from that laboratory experience. Working in the didactic laboratories gave me the opportunity to collaborate with many different colleagues and to have various roles. Being responsible of conceiving and organizing in various occasions the didactic laboratories was a good training for learning how to manage a project and how to coordinate the work of a group of people. Teaching was a great opportunity to improve my communication skills and was also the occasion for testing various instruments. It is during my laboratory classes indeed that I decided to exploit the potential of web pages and blogs for science communication for the first time. In Figure 7 I show the screenshot of a blog that I’ve used for a few years with the students of metabolic biochemistry and that other teachers often visit. I have recently tested the video-tutorials as useful tools to integrate the lectures and I am still studying and practising to improve my capability of producing good quality videos as well as useful illustrations. !

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Figure 7 Screenshot of my blog about metabolic biochemistry, used by students and by other teachers

Elisa Corteggiani Carpinellielisacorteggiani.com/wp-content/uploads/2014/05/CVElisaCCResRepMay2014.pdfYFP by affinity chromatography; spectroscopic and electrophoretic analysis of

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