MetaboLights MTBLS1 → GO bridge coverage
Input: MetaboLights MTBLS1
Generated by coverage_probe.py — all numbers
computed live from OLS4 (ChEBI), the Rhea REST API, and the GO rhea2go mapping.
Why this probe exists
Reported metabolite ChEBI ids rarely match Rhea participants directly,
for two reasons we test as successive normalization tiers:
- Protonation — Rhea writes participants in their major protonation
state at pH 7.3 (citrate(3-),ATP(4-)); repositories report neutral
forms. We expand over ChEBIis_protonated_form_of/
is_deprotonated_form_of(the protonation family). - Structure / skeleton — a study reports a generic, non-stereospecific
compound (isoleucine) while Rhea uses the stereospecific zwitterion
(L-isoleucine zwitterion). We expand over the broader structural
relations (+ tautomer/enantiomer + generic→specificchildren), bounded
to the seed's InChIKey skeleton. This tier is stereo/charge-blind, so
it is reported separately as the more permissive fallback.
Headline
- Metabolites probed: 64 (resolved to ChEBI: 64)
- In a Rhea reaction — exact: 8/64 → +protonation: 49/64 → +structure: 58/64
- Reaching a GO MF term (rhea2go) — exact: 7 → +protonation: 48 → +structure: 57 (of 64)
- Recovered by protonation: 41; additionally by structure/skeleton: 9
Per-metabolite
Tier reached: exact < proton (protonation) < struct (skeleton) < — (miss).
| Metabolite | Seed ChEBI | q | Tier | GO MF (exact→proton→struct) | Rhea-matched form |
|---|---|---|---|---|---|
| p-aminohippuric acid | CHEBI:104011 | 0 | — | 0→0→0 | — |
| 2-hydroxybutyric acid | CHEBI:1148 | 0 | proton | 0→11→11 | 2-hydroxybutyrate (CHEBI:64552, q=-1) |
| acetoacetic acid | CHEBI:15344 | 0 | proton | 0→21→21 | acetoacetate (CHEBI:13705, q=-1) |
| acetone | CHEBI:15347 | 0 | exact | 7→7→7 | acetone (CHEBI:15347, q=0) |
| acetic acid | CHEBI:15366 | 0 | proton | 0→83→83 | acetate (CHEBI:30089, q=-1) |
| sarcosine | CHEBI:15611 | 0 | proton | 0→10→10 | sarcosine zwitterion (CHEBI:57433, q=0) |
| allantoin | CHEBI:15676 | 0 | exact | 0→0→0 | allantoin (CHEBI:15676, q=0) |
| succinic acid | CHEBI:15741 | 0 | proton | 0→92→92 | succinate(2-) (CHEBI:30031, q=-2) |
| nicotinic acid | CHEBI:15940 | 0 | proton | 0→6→6 | nicotinate (CHEBI:32544, q=-1) |
| ethanol | CHEBI:16236 | 0 | exact | 8→8→8 | ethanol (CHEBI:16236, q=0) |
| adenosine | CHEBI:16335 | 0 | exact | 9→9→9 | adenosine (CHEBI:16335, q=0) |
| alanine | CHEBI:16449 | 0 | proton | 0→11→11 | propionate (CHEBI:17272, q=-1) |
| 3-methyl-2-oxobutanoic acid | CHEBI:16530 | 0 | proton | 0→30→30 | 3-methyl-2-oxobutanoate (CHEBI:11851, q=-1) |
| methylguanidine | CHEBI:16628 | 0 | proton | 0→1→1 | methylguanidinium (CHEBI:57840, q=1) |
| uridine | CHEBI:16704 | 0 | exact | 8→8→8 | uridine (CHEBI:16704, q=0) |
| creatinine | CHEBI:16737 | 0 | exact | 2→2→2 | creatinine (CHEBI:16737, q=0) |
| 2-oxoglutarate(2-) | CHEBI:16810 | -2 | exact | 148→152→152 | 2-oxoglutarate(2-) (CHEBI:16810, q=-2) |
| creatine | CHEBI:16919 | 0 | proton | 0→5→5 | creatine zwitterion (CHEBI:57947, q=0) |
| dimethylamine | CHEBI:17170 | 0 | proton | 0→7→7 | dimethylaminium (CHEBI:58040, q=1) |
| glycolic acid | CHEBI:17497 | 0 | proton | 0→92→92 | glycolate (CHEBI:29805, q=-1) |
| N-acetyl-L-glutamic acid | CHEBI:17533 | 0 | proton | 0→133→133 | L-glutamate(1-) (CHEBI:29985, q=-1) |
| N,N-dimethylglycine | CHEBI:17724 | 0 | struct | 0→0→5 | N,N-dimethylglycine zwitterion (CHEBI:58251, q=0) |
| fumaric acid | CHEBI:18012 | 0 | proton | 0→18→18 | fumarate(2-) (CHEBI:29806, q=-2) |
| N-benzoylglycine | CHEBI:18089 | 0 | proton | 0→2→2 | N-benzoylglycinate (CHEBI:606565, q=-1) |
| N-methylnicotinate | CHEBI:18123 | 0 | exact | 1→6→6 | N-methylnicotinate (CHEBI:18123, q=0) |
| trimethylamine | CHEBI:18139 | 0 | proton | 0→6→6 | trimethylammonium (CHEBI:58389, q=1) |
| tyrosine | CHEBI:18186 | 0 | proton | 0→11→11 | propionate (CHEBI:17272, q=-1) |
| citrulline | CHEBI:18211 | 0 | struct | 0→0→7 | L-citrulline zwitterion (CHEBI:57743, q=0) |
| glutamic acid | CHEBI:18237 | 0 | struct | 0→0→132 | L-glutamate(1-) (CHEBI:29985, q=-1) |
| ornithine | CHEBI:18257 | 0 | proton | 0→5→5 | valerate (CHEBI:31011, q=-1) |
| N-carbamoyl-beta-alanine | CHEBI:18261 | 0 | proton | 0→13→13 | N-carbamoyl-beta-alaninate (CHEBI:11892, q=-1) |
| 3-hydroxybutyric acid | CHEBI:20067 | 0 | proton | 0→11→11 | 3-hydroxybutyrate (CHEBI:37054, q=-1) |
| N-acetyl-L-aspartic acid | CHEBI:21547 | 0 | proton | 0→40→40 | N-acetyl-L-aspartate(2-) (CHEBI:16953, q=-2) |
| isoleucine | CHEBI:24898 | 0 | struct | 0→0→11 | L-isoleucine zwitterion (CHEBI:58045, q=0) |
| leucine | CHEBI:25017 | 0 | struct | 0→0→13 | L-leucine zwitterion (CHEBI:57427, q=0) |
| lysine | CHEBI:25094 | 0 | proton | 0→9→9 | hexanoate (CHEBI:17120, q=-1) |
| valine | CHEBI:27266 | 0 | struct | 0→0→14 | L-valine zwitterion (CHEBI:57762, q=0) |
| 3-aminoisobutyric acid | CHEBI:27389 | 0 | proton | 0→13→13 | isobutyrate (CHEBI:48944, q=-1) |
| N-methyl-6-pyridone-3-carboxamide | CHEBI:27410 | 0 | — | 0→0→0 | — |
| histidine | CHEBI:27570 | 0 | struct | 0→0→16 | L-histidine zwitterion (CHEBI:57595, q=0) |
| 3,4-dihydroxymandelic acid | CHEBI:27637 | 0 | proton | 0→84→84 | mandelate (CHEBI:25147, q=-1) |
| N-methyl-4-pyridone-3-carboxamide | CHEBI:27838 | 0 | — | 0→0→0 | — |
| phenylalanine | CHEBI:28044 | 0 | struct | 0→0→26 | L-phenylalanine zwitterion (CHEBI:58095, q=0) |
| glutamine | CHEBI:28300 | 0 | struct | 0→0→39 | L-glutamine zwitterion (CHEBI:58359, q=0) |
| oxaloacetic acid | CHEBI:30744 | 0 | proton | 0→129→129 | oxaloacetate(2-) (CHEBI:16452, q=-2) |
| formic acid | CHEBI:30751 | 0 | proton | 0→43→43 | formate (CHEBI:15740, q=-1) |
| citric acid | CHEBI:30769 | 0 | proton | 0→8→8 | citrate(3-) (CHEBI:16947, q=-3) |
| butyric acid | CHEBI:30772 | 0 | proton | 0→11→11 | butyrate (CHEBI:17968, q=-1) |
| methylmalonic acid | CHEBI:30860 | 0 | proton | 0→8→8 | methylmalonate(2-) (CHEBI:17453, q=-2) |
| 2-oxoglutaric acid | CHEBI:30915 | 0 | proton | 0→152→152 | 2-oxoglutarate(2-) (CHEBI:16810, q=-2) |
| pyruvic acid | CHEBI:32816 | 0 | proton | 0→135→135 | pyruvate (CHEBI:15361, q=-1) |
| phloretic acid | CHEBI:32980 | 0 | proton | 0→12→12 | phloretate (CHEBI:16331, q=-1) |
| 3-methyl-2-oxovaleric acid | CHEBI:35932 | 0 | proton | 0→6→6 | 3-methyl-2-oxovalerate (CHEBI:28654, q=-1) |
| indoxyl sulfate | CHEBI:43355 | 0 | proton | 0→1→1 | indoxyl sulfate(1-) (CHEBI:144643, q=-1) |
| 2-hydroxyisobutyric acid | CHEBI:50129 | 0 | proton | 0→14→14 | 2-hydroxyisobutyrate (CHEBI:19641, q=-1) |
| 2-hydroxy-3-methylbutyric acid | CHEBI:60645 | 0 | proton | 0→4→4 | isovalerate (CHEBI:48942, q=-1) |
| 2-hydroxypentanoic acid | CHEBI:60647 | 0 | proton | 0→5→5 | valerate (CHEBI:31011, q=-1) |
| N-hexanoylglycine | CHEBI:64390 | 0 | — | 0→0→0 | — |
| N-methylnicotinamide | CHEBI:64399 | 0 | — | 0→0→0 | — |
| 3-(3-sulfooxyphenyl)propanoic acid | CHEBI:64414 | 0 | proton | 0→11→11 | propionate (CHEBI:17272, q=-1) |
| malic acid | CHEBI:6650 | 0 | proton | 0→93→93 | malate(2-) (CHEBI:15595, q=-2) |
| isocaproic acid | CHEBI:74903 | 0 | proton | 0→3→3 | isocaproate (CHEBI:74904, q=-1) |
| methyl N-acetylvalinate | CHEBI:74911 | 0 | — | 0→0→0 | — |
| 2-hydroxypropanoic acid | CHEBI:78320 | 0 | proton | 0→34→34 | lactate (CHEBI:24996, q=-1) |
Recovered by structure (skeleton) normalization
Generic / stereochemistry mismatches the protonation tier could not fix,
recovered by InChIKey-skeleton expansion:
- N,N-dimethylglycine (CHEBI:17724) → N,N-dimethylglycine zwitterion (CHEBI:58251, q=0)
- citrulline (CHEBI:18211) → L-citrulline zwitterion (CHEBI:57743, q=0)
- glutamic acid (CHEBI:18237) → L-glutamate(1-) (CHEBI:29985, q=-1)
- isoleucine (CHEBI:24898) → L-isoleucine zwitterion (CHEBI:58045, q=0)
- leucine (CHEBI:25017) → L-leucine zwitterion (CHEBI:57427, q=0)
- valine (CHEBI:27266) → L-valine zwitterion (CHEBI:57762, q=0)
- histidine (CHEBI:27570) → L-histidine zwitterion (CHEBI:57595, q=0)
- phenylalanine (CHEBI:28044) → L-phenylalanine zwitterion (CHEBI:58095, q=0)
- glutamine (CHEBI:28300) → L-glutamine zwitterion (CHEBI:58359, q=0)
Example GO molecular functions reached
- 2-hydroxybutyric acid (CHEBI:1148) → GO:0004029 aldehyde dehydrogenase (NAD+) activity; GO:0004806 triacylglycerol lipase activity; GO:0031955 short-chain fatty acid-CoA ligase activity
- acetoacetic acid (CHEBI:15344) → GO:0003858 3-hydroxybutyrate dehydrogenase activity; GO:0004029 aldehyde dehydrogenase (NAD+) activity; GO:0004334 fumarylacetoacetase activity
- acetic acid (CHEBI:15366) → GO:0000225 N-acetylglucosaminylphosphatidylinositol deacetylase activity; GO:0003847 1-alkyl-2-acetylglycerophosphocholine esterase activity; GO:0003961 O-acetylhomoserine aminocarboxypropyltransferase activity
- sarcosine (CHEBI:15611) → GO:0008115 sarcosine oxidase activity; GO:0008480 sarcosine dehydrogenase activity; GO:0016980 creatinase activity
- succinic acid (CHEBI:15741) → GO:0000104 succinate dehydrogenase activity; GO:0000908 taurine dioxygenase activity; GO:0003962 cystathionine gamma-synthase activity
- nicotinic acid (CHEBI:15940) → GO:0004516 nicotinate phosphoribosyltransferase activity; GO:0008936 nicotinamidase activity; GO:0008938 nicotinate N-methyltransferase activity
- alanine (CHEBI:16449) → GO:0004029 aldehyde dehydrogenase (NAD+) activity; GO:0004031 aldehyde oxidase activity; GO:0004040 amidase activity
- 3-methyl-2-oxobutanoic acid (CHEBI:16530) → GO:0001716 L-amino-acid oxidase activity; GO:0003852 2-isopropylmalate synthase activity; GO:0003863 branched-chain 2-oxo acid dehydrogenase activity
- methylguanidine (CHEBI:16628) → GO:0050098 methylguanidinase activity
- creatine (CHEBI:16919) → GO:0004111 creatine kinase activity; GO:0016980 creatinase activity; GO:0030731 guanidinoacetate N-methyltransferase activity
- dimethylamine (CHEBI:17170) → GO:0016403 dimethylargininase activity; GO:0043791 dimethylamine methyltransferase activity; GO:0043834 trimethylamine methyltransferase activity
- glycolic acid (CHEBI:17497) → GO:0000225 N-acetylglucosaminylphosphatidylinositol deacetylase activity; GO:0003847 1-alkyl-2-acetylglycerophosphocholine esterase activity; GO:0003961 O-acetylhomoserine aminocarboxypropyltransferase activity
- N-acetyl-L-glutamic acid (CHEBI:17533) → GO:0000107 imidazoleglycerol-phosphate synthase activity; GO:0000514 3-sulfino-L-alanine: proton, glutamate antiporter activity; GO:0000515 aspartate:glutamate, proton antiporter activity
- N,N-dimethylglycine (CHEBI:17724) → GO:0047150 betaine-homocysteine S-methyltransferase activity; GO:0047865 dimethylglycine dehydrogenase activity; GO:0047866 dimethylglycine oxidase activity
- fumaric acid (CHEBI:18012) → GO:0000104 succinate dehydrogenase activity; GO:0004018 N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity; GO:0004056 argininosuccinate lyase activity
- N-benzoylglycine (CHEBI:18089) → GO:0047962 glycine N-benzoyltransferase activity; GO:0047980 hippurate hydrolase activity
- trimethylamine (CHEBI:18139) → GO:0033795 betaine reductase activity; GO:0034899 trimethylamine monooxygenase activity; GO:0043834 trimethylamine methyltransferase activity
- tyrosine (CHEBI:18186) → GO:0004029 aldehyde dehydrogenase (NAD+) activity; GO:0004031 aldehyde oxidase activity; GO:0004040 amidase activity
- citrulline (CHEBI:18211) → GO:0004055 argininosuccinate synthase activity; GO:0004517 nitric-oxide synthase activity; GO:0004585 ornithine carbamoyltransferase activity
- glutamic acid (CHEBI:18237) → GO:0000107 imidazoleglycerol-phosphate synthase activity; GO:0000514 3-sulfino-L-alanine: proton, glutamate antiporter activity; GO:0000515 aspartate:glutamate, proton antiporter activity
- ornithine (CHEBI:18257) → GO:0031955 short-chain fatty acid-CoA ligase activity; GO:0033721 aldehyde dehydrogenase (NADP+) activity; GO:0050168 pentanamidase activity
- N-carbamoyl-beta-alanine (CHEBI:18261) → GO:0003837 beta-ureidopropionase activity; GO:0004029 aldehyde dehydrogenase (NAD+) activity; GO:0004031 aldehyde oxidase activity
- 3-hydroxybutyric acid (CHEBI:20067) → GO:0004029 aldehyde dehydrogenase (NAD+) activity; GO:0004806 triacylglycerol lipase activity; GO:0031955 short-chain fatty acid-CoA ligase activity
- N-acetyl-L-aspartic acid (CHEBI:21547) → GO:0000515 aspartate:glutamate, proton antiporter activity; GO:0001716 L-amino-acid oxidase activity; GO:0003948 N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity
- isoleucine (CHEBI:24898) → GO:0001716 L-amino-acid oxidase activity; GO:0003884 D-amino-acid oxidase activity; GO:0004046 aminoacylase activity
- leucine (CHEBI:25017) → GO:0001716 L-amino-acid oxidase activity; GO:0003884 D-amino-acid oxidase activity; GO:0004046 aminoacylase activity
- lysine (CHEBI:25094) → GO:0004031 aldehyde oxidase activity; GO:0008970 glycerophospholipid phospholipase A1 activity; GO:0017040 N-acylsphingosine amidohydrolase activity
- valine (CHEBI:27266) → GO:0001716 L-amino-acid oxidase activity; GO:0003884 D-amino-acid oxidase activity; GO:0004046 aminoacylase activity
- 3-aminoisobutyric acid (CHEBI:27389) → GO:0004029 aldehyde dehydrogenase (NAD+) activity; GO:0004031 aldehyde oxidase activity; GO:0004040 amidase activity
- histidine (CHEBI:27570) → GO:0001716 L-amino-acid oxidase activity; GO:0003884 D-amino-acid oxidase activity; GO:0004029 aldehyde dehydrogenase (NAD+) activity
- 3,4-dihydroxymandelic acid (CHEBI:27637) → GO:0000225 N-acetylglucosaminylphosphatidylinositol deacetylase activity; GO:0003847 1-alkyl-2-acetylglycerophosphocholine esterase activity; GO:0003961 O-acetylhomoserine aminocarboxypropyltransferase activity
- phenylalanine (CHEBI:28044) → GO:0003884 D-amino-acid oxidase activity; GO:0004046 aminoacylase activity; GO:0004505 phenylalanine 4-monooxygenase activity
- glutamine (CHEBI:28300) → GO:0000107 imidazoleglycerol-phosphate synthase activity; GO:0001716 L-amino-acid oxidase activity; GO:0002948 archaeosine synthase activity
- oxaloacetic acid (CHEBI:30744) → GO:0000104 succinate dehydrogenase activity; GO:0000908 taurine dioxygenase activity; GO:0001716 L-amino-acid oxidase activity
- formic acid (CHEBI:30751) → GO:0003934 GTP cyclohydrolase I activity; GO:0003935 GTP cyclohydrolase II activity; GO:0004061 arylformamidase activity
- citric acid (CHEBI:30769) → GO:0003878 ATP citrate synthase activity; GO:0003994 aconitate hydratase activity; GO:0008814 citrate CoA-transferase activity
- butyric acid (CHEBI:30772) → GO:0004029 aldehyde dehydrogenase (NAD+) activity; GO:0004806 triacylglycerol lipase activity; GO:0031955 short-chain fatty acid-CoA ligase activity
- methylmalonic acid (CHEBI:30860) → GO:0004029 aldehyde dehydrogenase (NAD+) activity; GO:0016289 acyl-CoA hydrolase activity; GO:0033722 malonate-semialdehyde dehydrogenase activity
- 2-oxoglutaric acid (CHEBI:30915) → GO:0000908 taurine dioxygenase activity; GO:0003973 (S)-2-hydroxy-acid oxidase activity; GO:0003992 N2-acetyl-L-ornithine:2-oxoglutarate 5-transaminase activity
- pyruvic acid (CHEBI:32816) → GO:0000286 L-alanine dehydrogenase (NAD+) activity; GO:0001716 L-amino-acid oxidase activity; GO:0003941 L-serine ammonia-lyase activity
- phloretic acid (CHEBI:32980) → GO:0004029 aldehyde dehydrogenase (NAD+) activity; GO:0004031 aldehyde oxidase activity; GO:0004040 amidase activity
- 3-methyl-2-oxovaleric acid (CHEBI:35932) → GO:0031955 short-chain fatty acid-CoA ligase activity; GO:0033721 aldehyde dehydrogenase (NADP+) activity; GO:0050168 pentanamidase activity
- indoxyl sulfate (CHEBI:43355) → GO:0050507 indoxyl-UDPG glucosyltransferase activity
- 2-hydroxyisobutyric acid (CHEBI:50129) → GO:0004029 aldehyde dehydrogenase (NAD+) activity; GO:0004031 aldehyde oxidase activity; GO:0004040 amidase activity
- 2-hydroxy-3-methylbutyric acid (CHEBI:60645) → GO:0004029 aldehyde dehydrogenase (NAD+) activity; GO:0031955 short-chain fatty acid-CoA ligase activity; GO:0033721 aldehyde dehydrogenase (NADP+) activity
- 2-hydroxypentanoic acid (CHEBI:60647) → GO:0031955 short-chain fatty acid-CoA ligase activity; GO:0033721 aldehyde dehydrogenase (NADP+) activity; GO:0050168 pentanamidase activity
- 3-(3-sulfooxyphenyl)propanoic acid (CHEBI:64414) → GO:0004029 aldehyde dehydrogenase (NAD+) activity; GO:0004031 aldehyde oxidase activity; GO:0004040 amidase activity
- malic acid (CHEBI:6650) → GO:0000104 succinate dehydrogenase activity; GO:0000908 taurine dioxygenase activity; GO:0003962 cystathionine gamma-synthase activity
- isocaproic acid (CHEBI:74903) → GO:0031955 short-chain fatty acid-CoA ligase activity; GO:0043712 (R)-2-hydroxy-4-methylpentanoate CoA-transferase activity; GO:0141126 short-chain fatty acyl-CoA hydrolase activity
- 2-hydroxypropanoic acid (CHEBI:78320) → GO:0004029 aldehyde dehydrogenase (NAD+) activity; GO:0004031 aldehyde oxidase activity; GO:0004040 amidase activity
Residual misses (after both normalization tiers)
Resolved to ChEBI but matched no Rhea reaction even after protonation and
skeleton normalization — typically derivatives Rhea represents only in a
conjugated/acylated form, or compounds genuinely absent from Rhea.
- p-aminohippuric acid (CHEBI:104011, family size 2)
- N-methyl-6-pyridone-3-carboxamide (CHEBI:27410, family size 1)
- N-methyl-4-pyridone-3-carboxamide (CHEBI:27838, family size 1)
- N-hexanoylglycine (CHEBI:64390, family size 2)
- N-methylnicotinamide (CHEBI:64399, family size 1)
- methyl N-acetylvalinate (CHEBI:74911, family size 1)
Method / reproducibility
- ChEBI access + protonation traversal:
chebi.py(OLS4). - Rhea network + rhea2go:
rhea.py(Rhea REST, GO external2go). - Caches under
.cache/(gitignored); delete to force a fresh pull. - This is a coverage probe (does the bridge connect?), not yet a
statistical enrichment; GO-BP lift + ORA are the next step (see the
project page).