Table 4 B. longum and MetaCyc reactions whose directionality was manually curated during B. longum model development. Reaction identifiers can be mapped to actual reactions at the MetaCyc.org website
From: How accurate is automated gap filling of metabolic models?
BioCyc Reaction ID | Metabolic Goal | Curated Direction |
|---|---|---|
METHENYLTHFCYCLOHYDRO-RXN | Glycine and one-carbon metabolism | REVERSIBLE |
HYPOXANPRIBOSYLTRAN-RXN | Histidine synthesis | PHYSIOL-R2L (PPi produced) |
IMP-DEHYDROG-RXN | Xanthine synthesis | REVERSIBLE |
RIBOKIN-RXN | Ribose synthesis | PHYSIOL-L2R (kinase activity) |
RXN-14223 | Ribose degradation | PHYSIOL-L2R |
TYROSINE-AMINOTRANSFERASE-RXN | Tyrosine synthesis | REVERSIBLE (aminotransferase activity) |
GLYC3PDEHYDROGBIOSYN-RXN | Phospholipid synthesis | PHYSIOL-R2L (avoid spontaneous |
NADH → NADPH transhydrogenation) | ||
1.1.1.8-RXN | Phospholipid synthesis | PHYSIOL-R2L (avoid spontaneous |
NADH → NADPH transhydrogenation) | ||
MALONYL-COA-ACP-TRANSACYL-RXN | Phospholipid synthesis | PHYSIOL-L2R (biosynthetic direction) |
3-OXOACYL-ACP-REDUCT-RXN | Phospholipid synthesis | PHYSIOL-R2L (avoid NADPH-generating cycle) |
RXN0-6705 | Phospholipid synthesis | PHYSIOL-R2L (avoid NADPH-generating cycle) |
PHOSPHAGLYPSYN-RXN | Phospholipid synthesis | PHYSIOL-L2R (avoid NADPH-generating cycle) |
H2PTERIDINEPYROPHOSPHOKIN-RXN | THF synthesis | PHYSIOL-L2R |
RXN-9772 | NAD synthesis | PHYSIOL-L2R |
RIBULP3EPIM-RXN | Pentose phosphate pathway | REVERSIBLE |
RIB5PISOM-RXN | Pentose phosphate pathway | REVERSIBLE |
1TRANSKETO-RXN | Pentose phosphate pathway | REVERSIBLE |
2TRANSKETO-RXN | Pentose phosphate pathway | REVERSIBLE |
TRANSALDOL-RXN | Pentose phosphate pathway | REVERSIBLE |
PHOSACETYLTRANS-RXN | Central carbon metabolism | REVERSIBLE |
RXN-12195 | Phosphorylation debugging | PHYSIOL-L2R |
RXN-12196 | Phosphorylation debugging | PHYSIOL-L2R |
XANPRIBOSYLTRAN-RXN | Phosphorylation debugging | PHYSIOL-R2L |
DCTP-PYROPHOSPHATASE-RXN | Phosphorylation debugging | PHYSIOL-L2R |
RXN-7913 | Phosphorylation debugging | PHYSIOL-L2R |
ATPASE-RXN | Phosphorylation debugging | PHYSIOL-L2R |
RXN0-5468 | Phosphorylation debugging | PHYSIOL-L2R |
ALDHDEHYDROG-RXN | Phosphorylation debugging | PHYSIOL-L2R |