Table 1 Extracted sub-graphs. EcoCyc-ids of the reactions, their corresponding enzyme annotations, their observed regulation due to a changing from aerobic to anaerobic conditions and the confidence value for this observation. Listed are the first 10 extracted sub-graphs.
id | enzymes | regulation | p-value |
|---|---|---|---|
1st extracted sub-graph (formate metabolism) | |||
FHLMULTI-RXN | formate hydrogenlyase complex | 1 | 3.8e-16 |
FORMYLTHFDEFORMYL-RXN | formyltetrahydrofolate deformylase | -1 | 0.0015 |
GTP-CYCLOHYDRO-I-RXN | GTP cyclohydrolase I | -1 | 0.00088 |
GTP-CYCLOHYDRO-II-RXN | GTP cyclohydrolase II | (1) | 0.57 |
H2NEOPTERINP3PYROPHOSPHOHYDRO-RXN | dihydroneopterin triphosphate pyrophosphohydrolase | (0) | 1 |
H2NTPEPIM-RXN | dihydroneopterin triphosphate 2'-epimerase | -1 | 1.024e-05 |
KETOBUTFORMLY-RXN | 2-ketobutyrate formate-lyase | (-1) | 0.20 |
PYRUVFORMLY-RXN | pyruvate formate-lyase | 1 | 2.2e-18 |
RXN0-1382 | formyl-CoA transferase | -1 | 0.023 |
TRANS-RXN-1 | transporter | 1 | 4.5e-20 |
2nd extracted sub-graph (formate metabolism) | |||
FHLMULTI-RXN | formate hydrogenlyase complex | 1 | 3.8e-16 |
FORMYLTHFDEFORMYL-RXN | formyltetrahydrofolate deformylase | -1 | 0.0015 |
GTP-CYCLOHYDRO-I-RXN | GTP cyclohydrolase I | -1 | 0.00088 |
GTP-CYCLOHYDRO-II-RXN | GTP cyclohydrolase II | (1) | 0.57 |
KETOBUTFORMLY-RXN | 2-ketobutyrate formate-lyase | (-1) | 0.20 |
PYRUVFORMLY-RXN | pyruvate formate-lyase | 1 | 2.2e-18 |
RXN0-443 | (0) | 1 | |
TRANS-RXN-1 | transporter | 1 | 4.5e-20 |
3rd extracted sub-graph (leucine) | |||
ABC-35-RXN | Transporters | -1 | 4.1e-09 |
BRANCHED-CHAINAMINOTRANSFERLEU-RXN | branched chain amino acid aminotransferase | 1 | 0.080 |
LEUCINE – TRNA-LIGASE-RXN | leucyl-tRNA synthetase | (1) | 0.13 |
LEUCYLTRANSFERASE-RXN | leucyl phenylalanyl-tRNA-protein transferase | 1 | 0.011 |
RXN0-261 | (0) | 1 | |
TRANS-RXN-126B | transporter | 1 | 6.2e-10 |
4th extracted sub-graph (aspartate metabolism) | |||
2-METHYLCITRATE-SYNTHASE-RXN | methylcitrate synthase | (1) | 0.32 |
ARGSUCCINSYN-RXN | argininosuccinate synthase | 1 | 0.027 |
ASNSYNA-RXN | aspartate-ammonia ligase | 1 | 0.0032 |
ASPARTASE-RXN | aspartate ammonia-lyase | 1 | 1.6e-06 |
ASPARTATE – TRNA-LIGASE-RXN | aspartyl-tRNA synthetase | (1) | 0.61 |
ASPARTATEKIN-RXN | aspartate kinase I | 1 | 0.0082 |
ASPCARBTRANS-RXN | aspartate carbamoyltransferase | (-1) | 0.16 |
ASPDECARBOX-RXN | aspartate-1-decarboxylase | (1) | 0.23 |
L-ASPARTATE-OXID-RXN | L-aspartate oxidase | 1 | 0.00033 |
PEPCARBOXYKIN-RXN | phosphoenolpyruvate carboxykinase (ATP) | (1) | 0.58 |
PEROXID-RXN | thiol peroxidase | (1) | 0.20 |
PYRIDOXKIN-RXN | pyridoxal kinase 2 | (-1) | 0.045 |
PYROXALTRANSAM-RXN | pyridoxamine-oxaloacetate transaminase | (0) | 1 |
QUINOLINATE-SYNTHE-MULTI-RXN | quinolinate synthetase | 1 | 0.00051 |
RXN0-267 | thiol peroxidase 2 | -1 | 8.1e-08 |
SAICARSYN-RXN | phosphoribosylaminoimidazole- succinocarboxamide synthase | 1 | 9.0e-07 |
TRANS-RXN-106A | transporter | 1 | 0.015 |
TRANS-RXN-122A | transporter | 1 | 2.2e-06 |
5th extracted sub-graph (formate metabolism) | |||
FHLMULTI-RXN | formate hydrogenlyase complex | 1 | 3.8e-16 |
FORMYLTHFDEFORMYL-RXN | formyltetrahydrofolate deformylase | -1 | 0.0015 |
GTP-CYCLOHYDRO-I-RXN | GTP cyclohydrolase I | -1 | 0.00088 |
GTP-CYCLOHYDRO-II-RXN | GTP cyclohydrolase II | (1) | 0.57 |
H2NEOPTERINP3PYROPHOSPHOHYDRO-RXN | dihydroneopterin triphosphate pyrophosphohydrolase | (0) | 1 |
H2NTPEPIM-RXN | dihydroneopterin triphosphate 2'-epimerase | -1 | 1.0e-05 |
KETOBUTFORMLY-RXN | 2-ketobutyrate formate-lyase | (-1) | 0.2 |
PYRUVFORMLY-RXN | pyruvate formate-lyase | 1 | 2.2e-18 |
RXN0-443 | (0) | 1 | |
TRANS-RXN-1 | transporter | 1 | 4.5e-20 |
6th extracted sub-graph (formate metabolism) | |||
3.5.1.88-RXN | dihydroxyacetone kinase | -1 | 0.059 |
FORMYLTHFDEFORMYL-RXN | formyltetrahydrofolate deformylase | -1 | 0.0015 |
GARTRANSFORMYL2-RXN | GAR transformylase 2 | (-1) | 0.41 |
GTP-CYCLOHYDRO-I-RXN | GTP cyclohydrolase I | -1 | 0.00088 |
METHENYLTHFCYCLOHYDRO-RXN | methenyltetrahydrofolate cyclohydrolase | 1 | 0.0052 |
PYRUVFORMLY-RXN | pyruvate formate-lyase | 1 | 2.2e-18 |
RXN0-1382 | formyl-CoA transferase | -1 | 0.023 |
RXN0-443 | (0) | 1 | |
TRANS-RXN-1 | transporter | 1 | 4.5e-20 |
7th extracted sub-graph (lysine) | |||
DIAMINOPIMDECARB-RXN | diaminopimelate decarboxylase | -1 | 0.0012 |
GLU6PDEHYDROG-RXN | glucose 6-phosphate-1-dehydrogenase | 1 | 0.027 |
LYSDECARBOX-RXN | lysine decarboxylase 2 | (-1) | 0.14 |
LYSINE – TRNA-LIGASE-RXN | lysyl tRNA synthetase | -1 | 0.0060 |
RXN0-1961 | tRNA-Ile-lysidine synthetase | -1 | 0.015 |
RXN0-963 | fructoselysine 6-phosphate deglycase | 1 | 0.0059 |
TRANS-RXN-58 | Transporter | -1 | 0.049 |
TRANS-RXN-68 | Transporter | (0) | 0.81 |
8th extracted sub-graph (Glycolysis) | |||
6-PHOSPHO-BETA-GLUCOSIDASE-RXN | phenylacetate-CoA ligase | 1 | 2.9e-06 |
AMYLOMALT-RXN | amylomaltase | (-1) | 0.34 |
GALACTURIDYLYLTRANS-RXN | UDP-glucose-hexose-1-phosphate uridylyltransferase | -1 | 1.1e-06 |
GLUCDEHYDROG-RXN | glucose dehydrogenase (pyrroloquinoline-quinone) | -1 | 5.3e-05 |
GLUCOKIN-RXN | glucokinase | 1 | 1.4e-07 |
GLUCOSE-1-PHOSPHAT-RXN | glucose-1-phosphatase | (0) | 0.78 |
MALTACETYLTRAN-RXN | maltose acetyltransferase | (-1) | 0.43 |
MALTDEG-RXN | maltose degrading enzyme | (-1) | 0.34 |
MALTODEG-RXN | maltose degrading enzyme 2 | (-1) | 0.34 |
MALTODEXGLUCOSID-RXN | maltodextrin glucosidase | (1) | 0.26 |
PGLUCISOM-RXN | phosphoglucose isomerase | 1 | 3.3e-07 |
RXN0-2543 | flavorubredoxin reductase | (-1) | 0.13 |
TRE6PHYDRO-RXN | trehalose-6-phosphate hydrolase | (-1) | 0.097 |
TREHALOSE6PSYN-RXN | trehalose-6-phosphate synthase | (0) | 0.87 |
9th extracted sub-graph (Glycolysis/NAD biosynthesis) | |||
QUINOLINATE-SYNTHA-RXN | quinolinate synthetase A | 1 | 0.0016 |
QUINOLINATE-SYNTHE-MULTI-RXN | quinolinate synthetase | 1 | 0.00051 |
RHAMNULPALDOL-RXN | rhamnulose-1-phosphate aldolase | (-1) | 0.25 |
RXN0-313 | fructose 6-phosphate aldolase 1 | (-1) | 0.51 |
TAGAALDOL-RXN | tagatose-16-bisphosphate aldolase 1 | (1) | 0.60 |
TRIOSEPISOMERIZATION-RXN | triose phosphate isomerase | 1 | 1.9e-12 |
10th extracted sub-graph (aspartate metabolism) | |||
2-METHYLCITRATE-SYNTHASE-RXN | methylcitrate synthase | (1) | 0.32 |
ARGSUCCINSYN-RXN | argininosuccinate synthase | 1 | 0.027 |
ASNSYNA-RXN | aspartate-ammonia ligase | 1 | 0.0032 |
ASPARTASE-RXN | aspartate ammonia-lyase | 1 | 1.6e-06 |
ASPARTATE – TRNA-LIGASE-RXN | aspartyl-tRNA synthetase | (1) | 0.61 |
ASPARTATEKIN-RXN | aspartate kinase I | 1 | 0.0082 |
ASPCARBTRANS-RXN | aspartate carbamoyltransferase | (-1) | 0.16 |
ASPDECARBOX-RXN | aspartate-1-decarboxylase | (1) | 0.23 |
L-ASPARTATE-OXID-RXN | L-aspartate oxidase | 1 | 0.00033 |
PEPCARBOXYKIN-RXN | phosphoenolpyruvate carboxykinase (ATP) | (1) | 0.57 |
PEROXID-RXN | thiol peroxidase | (1) | 0.20 |
PYRIDOXKIN-RXN | pyridoxal kinase 2 | -1 | 0.045 |
PYROXALTRANSAM-RXN | pyridoxamine-oxaloacetate transaminase | (0) | 1 |
QUINOLINATE-SYNTHE-MULTI-RXN | quinolinate synthetase | 1 | 0.00051 |
RXN0-267 | thiol peroxidase 2 | -1 | 8.1e-08 |
SAICARSYN-RXN | phosphoribosylaminoimidazole- succinocarboxamide synthase | 1 | 9.0e-07 |
TRANS-RXN-122A | transporter | 1 | 2.2e-06 |