Network Biomass WormPaths

FBAFlux Balance Analysis PEAPathway Enrichment Analysis

Instructions

The biomass composition of both the bacterial diet and the worm itself are variable. If you do not want to use the dafault values and have your own compositional parameters, you can adjust the bacterial degradation and worm biomass assembly reactions in the metabolic model in the following steps:

1. Change the parameters in the tables below (click to display) when you have the necessary data (e.g., fatty acid composition).
2. Click the submit button.
3. Download the adjusted model following file links that will appear in the grey section below.

Note that energetic parameters such as maintenance costs are also adjustable and are included in the forms.

iCEL1314

Worm biomass

► | Overall composition (click to view)▼ | Overall composition (click to hide)

Overall composition (?) Percentage (w/w basis) of macromolecular and soluble components of the animal biomass.

If the total exceeds or remains below 100%, then the algorithm will normalize each value by the total, and a warning will be issued.

back to default values

	Fraction (% w/w)
Proteins
Phospholipids
Triacylglycerides
RNA
DNA
Glycans
Glycogen
Trehalose
Other
Total

► | Protein composition (click to view)▼ | Protein composition (click to hide)

Overall composition (?) Percentage (w/w basis) of different protein types used in the model. Amino acid compositions of mitochondrial and other proteins are to be indicated separately in the tables below, while collagen composition is fixed based on pertaining protein sequences.

If the total exceeds or remains below 100%, then the algorithm will normalize each value by the total, and a warning will be issued.

back to default values

	Fraction (% w/w)
Mitochondrial
Collagen
Other
Total

Amino acid composition (mitochondrial protein) (?) Percentage (mol/mol basis) of individual amino acids in mitochondrial worm protein.

If the total exceeds or remains below 100%, then the algorithm will normalize each value by the total, and a warning will be issued.

back to default values

	Fraction (% mol/mol)
Ala
Arg
Asn
Asp
Cys
Glu
Gln
Gly
His
Ile
Leu
Lys
Met
Phe
Pro
Ser
Thr
Trp
Tyr
Val
Total

Amino acid composition (other protein) (?) Percentage (mol/mol basis) of individual amino acids in worm protein other than mitochondrial and collagen protein.

If the total exceeds or remains below 100%, then the algorithm will normalize each value by the total, and a warning will be issued.

back to default values

	Fraction (% w/w)
Ala
Arg
Asn
Asp
Cys
Glu
Gln
Gly
His
Ile
Leu
Lys
Met
Phe
Pro
Ser
Thr
Trp
Tyr
Val
Total

► | Lipid composition (click to view)▼ | Lipid composition (click to hide)

Phospholipids composition (Overall) (?) Percentage (w/w basis) of different phospholipids in total. Hover help signs to see full name and formula of each entity. In the formulas "X" and "W" indicate the fatty acids. The composition of X is to be entered separately in the table below, while W is taken as 100% octadecanoate (n-C18:0) .

If the total exceeds or remains below 100%, then the algorithm will normalize each value by the total, and a warning will be issued.

back to default values

	Fraction (% w/w)
pe (?) Name: Phosphatidylethanolamine Formula : C5H12O4NPX2
pchol (?) Name: Phosphatidylcholine Formula : C8H18O4NPX2
ps (?) Name: Phosphatidylserine Formula : C6H11O6NPX2
pail (?) Name: Phosphatidylinositol Formula : C9H16O9PX2
clpn (?) Name: Cardiolipin Formula : C9H16O9P2X4
lpchol (?) Name: Lysophosphatidylcholine Formula : C8H19O5NPX
sphmyln_ce (?) Name: Sphingomyelin Formula : C24H50N2O4PX
akac2gpe (?) Name: 1-alkyl 2-acylglycerol 3-phosphoethanolamine Formula : C5H12O5NPXW
alkenac2gpe (?) Name: 1-alkenyl 2-acylglycerol 3-phosphoethanolamine plasmalogen Formula : C5H10O5NPXW
akac2gchol (?) Name: 1-alkyl 2-acylglycerol 3-phosphocholine Formula : C8H18O5NPXW
Total

Phospholipids composition (X Fatty acids) (?) Percentage (w/w basis) of fatty cids in phospholipids. Hover help signs to see full name of each entity. These fatty acids make the pool indicated by "X" in the formula of phospholipids in the above table.

If the total exceeds or remains below 100%, then the algorithm will normalize each value by the total, and a warning will be issued.

back to default values

	Fraction (% w/w)
tdcoa (?) Name: Tetradecanoyl-CoA (n-C14:0CoA)
pmtcoa (?) Name: Palmitoyl-CoA (n-C16:0CoA)
stcoa (?) Name: Stearoyl-CoA (n-C18:0CoA)
fa16p1n7coa (?) Name: Palmitoleyl-coA
odecoa (?) Name: Octadecenoyl-CoA (n-C18:1CoA)
vacccoa (?) Name: Vaccenyl coenzyme A
lnlccoa (?) Name: linoleic coenzyme A
dlnlcgcoa (?) Name: dihomo-gamma-linolenyl coenzyme A
arachdcoa (?) Name: C20:4-CoA
eicostetcoa (?) Name: eicosatetranoyl coenzyme A
tmndnccoa (?) Name: timnodonyl coenzyme A
fa15p0isocoa (?) Name: Fatty acyl (C15:iso) coa
fa17p0isocoa (?) Name: Fatty acyl (C17:iso) coa
fa17c9coa (?) Name: cis-9,10-methylenehexadecanoyl coa
fa19c11coa (?) Name: cis-11,12-methyleneoctadecanoyl coa
lgnccoa (?) Name: lignocericyl coenzyme A
Total

TAG composition (Y Fatty acids) (?) Percentage (w/w basis) of fatty cids as triacylglycerides (TAG). Hover help signs to see full name of each entity. These fatty acids make the pool indicated by "Y" in the formula of TAG, which is C3H5Y3.

If the total exceeds or remains below 100%, then the algorithm will normalize each value by the total, and a warning will be issued.

back to default values

	Fraction (% w/w)
tdcoa (?) Name: Tetradecanoyl-CoA (n-C14:0CoA)
pmtcoa (?) Name: Palmitoyl-CoA (n-C16:0CoA)
stcoa (?) Name: Stearoyl-CoA (n-C18:0CoA)
fa16p1n7coa (?) Name: Palmitoleyl-coA
odecoa (?) Name: Octadecenoyl-CoA (n-C18:1CoA)
vacccoa (?) Name: Vaccenyl coenzyme A
lnlccoa (?) Name: linoleic coenzyme A
dlnlcgcoa (?) Name: dihomo-gamma-linolenyl coenzyme A
arachdcoa (?) Name: C20:4-CoA
eicostetcoa (?) Name: eicosatetranoyl coenzyme A
tmndnccoa (?) Name: timnodonyl coenzyme A
fa15p0isocoa (?) Name: Fatty acyl (C15:iso) coa
fa17p0isocoa (?) Name: Fatty acyl (C17:iso) coa
fa17c9coa (?) Name: cis-9,10-methylenehexadecanoyl coa
fa19c11coa (?) Name: cis-11,12-methyleneoctadecanoyl coa
lgnccoa (?) Name: lignocericyl coenzyme A
Total

► | Nucleic acid composition (click to view)▼ | Nucleic acid composition (click to hide)

DNA composition (?) Percentage (mol/mol basis) of nucleotides in DNA.

back to default values

	Fraction (% mol/mol)
Adenine
Guanine
Cytosine
Thymine
Total

RNA composition (?) Percentage (mol/mol basis) of nucleotides in RNA.

back to default values

	Fraction (% mol/mol)
Adenine
Guanine
Cytosine
Thymine
Total

► | Other (click to view)▼ | Other (click to hide)

Glycan composition (?) Percentage (w/w basis) of different types of glycans in total glycans. Only chitin and N-linked glycans are included in the current model. Click metabolite abbreviations to reach the metabolite page for details.

If the total exceeds or remains below 100%, then the algorithm will normalize each value by the total, and a warning will be issued.

back to default values

	Fraction (% w/w)
chitin
m4masn
nm2masn
fn2m2masn
nm3masn
m3masn
m2masn
fm2masn
Total

Growth associated maintenance cost (?) ATP requirement (mmol/gDW/h, with gDW indicating dry worm biomass in grams) for maintenance during growth, in excess of polymerization costs for biomass assembly.

back to default values

	Cost (mmol/gDW/h)
ATP

Bacterial biomass

► | Overall composition (click to view)▼ | Overall composition (click to hide)

Overall composition (?) Percentage (w/w basis) of macromolecular and soluble components of the bacterial biomass.

If the total exceeds or remains below 100%, then the algorithm will normalize each value by the total, and a warning will be issued.

back to default values

	Fraction (% w/w)
Proteins
Phospholipids
RNA
DNA
Peptidoglycan
LPS (?) Lipopolysaccharide
Glycogen
Soluble
Other
Total

► | Protein composition (click to view)▼ | Protein composition (click to hide)

Amino acid composition (?) Percentage (mol/mol basis) of individual amino acids in bacterial protein.

If the total exceeds or remains below 100%, then the algorithm will normalize each value by the total, and a warning will be issued.

back to default values

	Fraction (% mol/mol)
Ala
Arg
Asn
Asp
Cys
Glu
Gln
Gly
His
Ile
Leu
Lys
Met
Phe
Pro
Ser
Thr
Trp
Tyr
Val
Total

► | Lipid composition (click to view)▼ | Lipid composition (click to hide)

Phospholipids composition (Overall) (?) Percentage (w/w basis) of different bacterial phospholipids in total. Hover help signs to see full name and formula of each entity. In the formulas "R" indicates the fatty acids. The composition of R is to be entered separately in the table below.

If the total exceeds or remains below 100%, then the algorithm will normalize each value by the total, and a warning will be issued.

back to default values

	Fraction (% w/w)
pe (?) Name: Phosphatidylethanolamine (bacteria) Formula : C7H12NO8PR2
ps (?) Name: Phosphatidylserine (bacteria) Formula : C8H11NO10PR2
pg (?) Name: Phosphatidylglycerol (bacteria) Formula : C8H12O10PR2
clpn (?) Name: Cardiolipin (bacteria) Formula : C13H16O17P2R4
Total

Phospholipids composition (Fatty acids) (?) Percentage (w/w basis) of fatty acids in bacterial phospholipids. Hover help signs to see full name of each entity.

If the total exceeds or remains below 100%, then the algorithm will normalize each value by the total, and a warning will be issued.

back to default values

	Fraction (% w/w)
hdca (?) Name: Hexadecanoate (n-C16:0)
fa16p1n7 (?) Name: Palmitoleic acid
ttdca (?) Name: tetradecanoate (n-C14:0)
fa17c9 (?) Name: cis-9,10-methylenehexadecanoic acid
fa19c11 (?) Name: cis-11,12-methyleneoctadecanoic acid
vacc (?) Name: Vaccenic acid
Total

► | Nucleic acid composition (click to view)▼ | Nucleic acid composition (click to hide)

DNA composition (?) Percentage (mol/mol basis) of nucleotides in DNA.

back to default values

	Fraction (% mol/mol)
Adenine
Guanine
Cytosine
Thymine
Total

RNA composition (?) Percentage (mol/mol basis) of nucleotides in RNA.

back to default values

	Fraction (% mol/mol)
Adenine
Guanine
Cytosine
Thymine
Total

► | Other (click to view)▼ | Other (click to hide)

Soluble components (?) Percentage (w/w basis) of soluble components in total bacterial biomass.

The total is supposed to be less than the total soluble content mentioned in overall bacterial biomass composition. If this is not the case, values will be normalized to achieve a sum that equals the total soluble content, and a warning will be issued.

back to default values

	Fraction (% w/w)
pydx
pydxn
pydam
cbl1
adocbl
fe2
acser
thm
thmpp
ribflv
fmn
fad
mobd
acorn
pnto-R
fol
q8
tma
pheme
selcys
Total

Digestion cost (?) ATP requirement (mmol/gDW/h, with gDW indicating dry bacterial biomass in grams) for the degradation of bacterial biomass.

back to default values

	Cost (mmol/gDW/h)
ATP

The information and tools provided in this website are to be used for academic purposes only. Potential users of the flux analysis tools (FBA button in the vertical menu) are asked to show proof of working at an academic institution during the creation of their accounts. These mathematical tools are powered by the commercial software Gurobi.