Difference between revisions of "Part:BBa K857000"
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First, we measured the growth of E. Coli bacteria under the conditions in which the insertion of mhpF allows the production of hydrogen to glucose uptake ratio to be 4:1. This was done using the Constraint Model Based Reconstruction and Analysis (COBRA) toolbox on Matlab platform which allowed us to constrain the uptake of glucose and hydrogen release to a ratio of 4:1 on our E. Coli glucose metabolism model. Our results were performed using Flux Balance Analysis (FBA) on the Core E. Coli Model by the Systems Biology Research Group at the University of California generated from the current gene expression data on E. coli. | First, we measured the growth of E. Coli bacteria under the conditions in which the insertion of mhpF allows the production of hydrogen to glucose uptake ratio to be 4:1. This was done using the Constraint Model Based Reconstruction and Analysis (COBRA) toolbox on Matlab platform which allowed us to constrain the uptake of glucose and hydrogen release to a ratio of 4:1 on our E. Coli glucose metabolism model. Our results were performed using Flux Balance Analysis (FBA) on the Core E. Coli Model by the Systems Biology Research Group at the University of California generated from the current gene expression data on E. coli. | ||
https://2019.igem.org/wiki/images/b/bc/T--NYU_Abu_Dhabi--characterization-graph1.png | https://2019.igem.org/wiki/images/b/bc/T--NYU_Abu_Dhabi--characterization-graph1.png | ||
| + | |||
| + | Figure 1. Demonstrates the growth of E.coli when subject to the hydrogen release to glucose uptake requirement. | ||
| + | |||
Our results showed that when the MhpF gene is introduced, E. Coli growth is higher under anaerobic conditions than aerobic conditions when under stress requirement to produce a 4:1 hydrogen to glucose ratio. This was achieved by setting oxygen flux values to both unlimited and zero for aerobic and anaerobic conditions respectively, whilst measuring E. coli’s growth in rate per hour. Growth measurements were done as a quantitative measure of how E.coli performs against the gene modification added to its metabolism. | Our results showed that when the MhpF gene is introduced, E. Coli growth is higher under anaerobic conditions than aerobic conditions when under stress requirement to produce a 4:1 hydrogen to glucose ratio. This was achieved by setting oxygen flux values to both unlimited and zero for aerobic and anaerobic conditions respectively, whilst measuring E. coli’s growth in rate per hour. Growth measurements were done as a quantitative measure of how E.coli performs against the gene modification added to its metabolism. | ||
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https://2019.igem.org/wiki/images/0/0d/T--NYU_Abu_Dhabi--character-graph3.png | https://2019.igem.org/wiki/images/0/0d/T--NYU_Abu_Dhabi--character-graph3.png | ||
| − | Figure | + | Figure 2.Shift in metabolism flux network when E. coli model is subjected to hydrogen release to glucose uptake 4:1 ratio under aerobic conditions (left) and anaerobic conditions(right). |
| − | Next, we analyzed the effect of deleting the mhpF gene on the growth rate of E. Coli (in biomass/hour). The quantitative analysis shows that the growth remained the same, which indicates that the mhpF gene does not affect the growth rate of E. Coli. This served as motivation to perform more single gene deletions on the E.coli model. We analyzed the effect of creating knockouts of all the genes involved in glucose metabolism on the bacteria by examining the lethality of deleting each gene. Team UC Merced attempted to create knockouts of three genes, and below we present suggestions regarding the genes in the dark fermentation process that can be deleted without being lethal. Deletions of genes in the dark fermentation process, a form of anaerobic conversion would facilitate the conversion of organic substrate to biohydrogen. | + | Next, we analyzed the effect of deleting the mhpF gene on the growth rate of E. Coli (in biomass/hour). The quantitative analysis shows that the growth remained the same, which indicates that the mhpF gene does not affect the growth rate of E. Coli. This served as motivation to perform more single gene deletions on the E.coli model. We analyzed the effect of creating knockouts of all the genes involved in glucose metabolism on the bacteria by examining the lethality of deleting each gene. Team UC Merced attempted to create knockouts of three genes, and below we present suggestions regarding the genes in the dark fermentation process that can be deleted without being lethal. Deletions of genes in the dark fermentation process, a form of anaerobic conversion would facilitate the conversion of organic substrate to biohydrogen. (see Table 1) |
For instance our analysis from the gene deletion suggested that the deletion zwf gene( glucose-6-phosphate 1-dehydrogenase) which is principal in the pentose pathway would be lethal to the E. coli. It turns out that zwf and mphF gene is overexpressed in the dark fermentation process. Even though both are very necessary for hydrogen production, mphF deletion would not result in much difference in the flux. Further our metabolic network flux predicts that the overexpression of zwf leads to the diversion of carbon flux through the PP pathway and hence result in an increase in the efficiency of the production of H2. | For instance our analysis from the gene deletion suggested that the deletion zwf gene( glucose-6-phosphate 1-dehydrogenase) which is principal in the pentose pathway would be lethal to the E. coli. It turns out that zwf and mphF gene is overexpressed in the dark fermentation process. Even though both are very necessary for hydrogen production, mphF deletion would not result in much difference in the flux. Further our metabolic network flux predicts that the overexpression of zwf leads to the diversion of carbon flux through the PP pathway and hence result in an increase in the efficiency of the production of H2. | ||
Finally, a robustness analysis was performed to verify the validity of the results by setting fixed amounts of glucose and hydrogen and measuring the growth as a function of the oxygen concentration. This analysis was performed to demonstrate the strength of our model's prediction. The linear graph predicts a linear rise in growth with an intermittent increase in glucose intake. This agrees and supports our previous data which suggested that mphF is implied in the increase in growth of E.coli when subject to the condition stipulated above. | Finally, a robustness analysis was performed to verify the validity of the results by setting fixed amounts of glucose and hydrogen and measuring the growth as a function of the oxygen concentration. This analysis was performed to demonstrate the strength of our model's prediction. The linear graph predicts a linear rise in growth with an intermittent increase in glucose intake. This agrees and supports our previous data which suggested that mphF is implied in the increase in growth of E.coli when subject to the condition stipulated above. | ||
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Finally, a robustness analysis was performed to verify the validity of the results by setting fixed amounts of glucose and hydrogen and measuring the growth as a function of the oxygen concentration. | Finally, a robustness analysis was performed to verify the validity of the results by setting fixed amounts of glucose and hydrogen and measuring the growth as a function of the oxygen concentration. | ||
| − | + | Table 1: Possible gene deletions and their measure effects on E. coli. | |
<p> </p> | <p> </p> | ||
<table> | <table> | ||
Revision as of 03:18, 22 October 2019
acetaldehyde dehydrogenase
Coding protein for acetaldehyde dehydrogenase convert acetaldehyde into acetyl-CoA.
CH3CHO + NAD+ + CoA → acetyl-CoA + NADH + H+
This part was designed by the 2012 iGEM UC Merced team and it is a gene that is involved in the E. Coli glucose metabolism pathway. Our team characterized this part by performing an in silico knockout of this gene. Using quantitative analysis, we discovered that its deletion does not affect the growth of E. Coli when under optimal conditions to produce a 4:1 hydrogen production to glucose uptake ratio. More importantly, we identified possible non-lethal gene deletions that may help maximize hydrogen production in the dark fermentation process.
First, we measured the growth of E. Coli bacteria under the conditions in which the insertion of mhpF allows the production of hydrogen to glucose uptake ratio to be 4:1. This was done using the Constraint Model Based Reconstruction and Analysis (COBRA) toolbox on Matlab platform which allowed us to constrain the uptake of glucose and hydrogen release to a ratio of 4:1 on our E. Coli glucose metabolism model. Our results were performed using Flux Balance Analysis (FBA) on the Core E. Coli Model by the Systems Biology Research Group at the University of California generated from the current gene expression data on E. coli.
Figure 1. Demonstrates the growth of E.coli when subject to the hydrogen release to glucose uptake requirement.
Our results showed that when the MhpF gene is introduced, E. Coli growth is higher under anaerobic conditions than aerobic conditions when under stress requirement to produce a 4:1 hydrogen to glucose ratio. This was achieved by setting oxygen flux values to both unlimited and zero for aerobic and anaerobic conditions respectively, whilst measuring E. coli’s growth in rate per hour. Growth measurements were done as a quantitative measure of how E.coli performs against the gene modification added to its metabolism.
Furthermore, our analysis from Flux Balance Analysis (FBA) validated team UC Merced hypothesis that removing IdhA, pfIB and adhE from E. coli fermentation pathway and replacing it with mhpF, pyruvate decarboxylase and ferredoxin oxidoreductase. This was achieved by performing in silico knockouts of IdhA, pfIB and adhE on the E. coli model and multiple gene insertions of mhpF, pyruvate decarboxylate and ferredoxin and looking at how the shift in metabolism network improve hydrogen yield under anaerobic condition.
Figure 2.Shift in metabolism flux network when E. coli model is subjected to hydrogen release to glucose uptake 4:1 ratio under aerobic conditions (left) and anaerobic conditions(right).
Next, we analyzed the effect of deleting the mhpF gene on the growth rate of E. Coli (in biomass/hour). The quantitative analysis shows that the growth remained the same, which indicates that the mhpF gene does not affect the growth rate of E. Coli. This served as motivation to perform more single gene deletions on the E.coli model. We analyzed the effect of creating knockouts of all the genes involved in glucose metabolism on the bacteria by examining the lethality of deleting each gene. Team UC Merced attempted to create knockouts of three genes, and below we present suggestions regarding the genes in the dark fermentation process that can be deleted without being lethal. Deletions of genes in the dark fermentation process, a form of anaerobic conversion would facilitate the conversion of organic substrate to biohydrogen. (see Table 1)
For instance our analysis from the gene deletion suggested that the deletion zwf gene( glucose-6-phosphate 1-dehydrogenase) which is principal in the pentose pathway would be lethal to the E. coli. It turns out that zwf and mphF gene is overexpressed in the dark fermentation process. Even though both are very necessary for hydrogen production, mphF deletion would not result in much difference in the flux. Further our metabolic network flux predicts that the overexpression of zwf leads to the diversion of carbon flux through the PP pathway and hence result in an increase in the efficiency of the production of H2.
Finally, a robustness analysis was performed to verify the validity of the results by setting fixed amounts of glucose and hydrogen and measuring the growth as a function of the oxygen concentration. This analysis was performed to demonstrate the strength of our model's prediction. The linear graph predicts a linear rise in growth with an intermittent increase in glucose intake. This agrees and supports our previous data which suggested that mphF is implied in the increase in growth of E.coli when subject to the condition stipulated above.
In sum , using metabolic modeling allow for in silico gene knockouts and metabolic analysis that unveiled non lethal gene deletions and insertion that would prove useful for the generation of biohydrogen from E.coli. Using metabolic modeling, it is easier to generate genetic changes that would optimize hydrogen production from E.coli. graph robustness
Finally, a robustness analysis was performed to verify the validity of the results by setting fixed amounts of glucose and hydrogen and measuring the growth as a function of the oxygen concentration.
Table 1: Possible gene deletions and their measure effects on E. coli.
|
LOCUS |
GENE |
PRODUCT |
FUNCTION |
NOTE |
LETHALITY |
|
b0008 |
talB |
transaldolase B |
enzyme; Central intermediary metabolism:Non-oxidative branch, pentose pathway |
not lethal |
|
|
b0118 |
acnB |
aconitate hydratase 2; aconitase B;2-methyl-cis-aconitate hydratase |
enzyme; Energy metabolism, carbon: TCA cycle |
aconitate hydrase B |
not lethal |
|
b0351 |
mhpF |
acetaldehyde-CoA dehydrogenase II, NAD-binding |
enzyme; Degradation of small molecules: Carboncompounds |
acetaldehyde dehydrogenase |
not lethal |
|
b0356 |
frmA |
alcohol dehydrogenase class III;glutathione-dependent formaldehyde dehydrogenase |
enzyme; Energy metabolism, carbon:Fermentation |
alcohol dehydrogenase class III; formaldehydedehydrogenase, glutathione-dependent |
not lethal |
|
b0451 |
amtB |
ammonium transporter |
putative transport; Central intermediarymetabolism: Pool, multipurpose conversions |
probable ammonium transporter |
not lethal |
|
b0474 |
adk |
adenylate kinase |
enzyme; Purine ribonucleotide biosynthesis |
adenylate kinase activity; pleiotropic effects onglycerol-3-phosphate acyltransferase activity |
not lethal |
|
b0485 |
glsA |
glutaminase 1 |
enzyme; l-glutamine catabolism |
putative glutaminase |
not lethal |
|
b0733 |
cydA |
cytochrome d terminal oxidase, subunit I |
enzyme; Energy metabolism, carbon: Electrontransport |
cytochrome d terminal oxidase, polypeptide subunitI |
not lethal |
|
b0734 |
cydB |
cytochrome d terminal oxidase, subunit II |
enzyme; Energy metabolism, carbon: Electrontransport |
cytochrome d terminal oxidase polypeptide subunitII |
not lethal |
|
b0755 |
gpmA |
phosphoglyceromutase 1 |
enzyme; Energy metabolism, carbon: Glycolysis |
not lethal |
|
|
b0809 |
glnQ |
glutamine transporter subunit |
transport; Transport of small molecules: Aminoacids, amines |
ATP-binding component of glutamine high-affinitytransport system |
not lethal |
|
b0810 |
glnP |
glutamine transporter subunit |
transport; Transport of small molecules: Aminoacids, amines |
glutamine high-affinity transport system; membranecomponent |
not lethal |
|
b0811 |
glnH |
glutamine transporter subunit |
transport; Transport of small molecules: Aminoacids, amines |
periplasmic glutamine-binding protein; permease |
not lethal |
|
b0875 |
aqpZ |
aquaporin Z |
transport; Transport of small molecules: Other |
transmembrane water channel; aquaporin Z |
not lethal |
|
b0902 |
pflA |
pyruvate formate-lyase 1-activating enzyme;[formate-C-acetyltransferase 1]-activating enzyme; PFLactivase |
enzyme; Energy metabolism, carbon: Anaerobicrespiration |
not lethal |
|
|
b0903 |
pflB |
formate C-acetyltransferase 1, anaerobic;pyruvate formate-lyase 1 |
enzyme; Energy metabolism, carbon: Anaerobicrespiration |
formate acetyltransferase 1 |
not lethal |
|
b0904 |
focA |
formate channel |
putative transport; Degradation of smallmolecules: Carbon compounds |
probable formate transporter (formate channel 1) |
not lethal |
|
b0978 |
cbdA |
cytochrome bd-II oxidase, subunit I |
putative enzyme; Energy metabolism, carbon:Electron transport |
not lethal |
|
|
b0979 |
cbdB |
cytochrome bd-II oxidase, subunit II |
putative enzyme; Energy metabolism, carbon:Electron transport |
probable third cytochrome oxidase, subunit II |
not lethal |
|
b1101 |
ptsG |
fused glucose-specific PTS enzymes: IIBcomponent/IIC component |
transport; Transport of small molecules:Carbohydrates, organic acids, alcohols |
PTS system, glucose-specific IIBC component |
not lethal |
|
b1241 |
adhE |
fused acetaldehyde-CoAdehydrogenase/iron-dependent alcoholdehydrogenase/pyruvate-formate lyase deactivase |
enzyme; Energy metabolism, carbon:Fermentation |
CoA-linked acetaldehyde dehydrogenase andiron-dependent alcohol dehydrogenase;pyruvate-formate-lyase deactivase |
not lethal |
|
b1276 |
acnA |
aconitate hydratase 1; aconitase A |
enzyme; Energy metabolism, carbon: TCA cycle |
aconitate hydrase 1 |
not lethal |
|
b1297 |
puuA |
glutamate--putrescine ligase |
enzyme; Degradation of small molecules: Carboncompounds |
putative glutamine synthetase |
not lethal |
|
b1380 |
ldhA |
fermentative D-lactate dehydrogenase,NAD-dependent |
enzyme; Energy metabolism, carbon:Fermentation |
not lethal |
|
|
b1478 |
adhP |
ethanol-active dehydrogenase/acetaldehyde-activereductase |
enzyme; Energy metabolism, carbon: Anaerobicrespiration |
alcohol dehydrogenase |
not lethal |
|
b1479 |
maeA |
malate dehydrogenase, decarboxylating,NAD-requiring; malic enzyme |
enzyme; Central intermediary metabolism:Gluconeogenesis |
NAD-linked malate dehydrogenase (malic enzyme) |
not lethal |
|
b1524 |
glsB |
glutaminase 2 |
enzyme; l-glutamine catabolism |
putative glutaminase |
not lethal |
|
b1602 |
pntB |
pyridine nucleotide transhydrogenase, betasubunit |
enzyme; Central intermediary metabolism: Pool,multipurpose conversions |
not lethal |
|
|
b1603 |
pntA |
pyridine nucleotide transhydrogenase, alphasubunit |
enzyme; Central intermediary metabolism: Pool,multipurpose conversions |
not lethal |
|
|
b1611 |
fumC |
fumarate hydratase (fumarase C),aerobic ClassII |
enzyme; Energy metabolism, carbon: TCA cycle |
fumarase C |
not lethal |
|
b1612 |
fumA |
fumarate hydratase (fumarase A), aerobic ClassI |
enzyme; Energy metabolism, carbon: TCA cycle |
fumarase A isozyme |
not lethal |
|
b1621 |
malX |
maltose and glucose-specific PTS enzyme IIBcomponent and IIC component |
transport; Transport of small molecules:Carbohydrates, organic acids, alcohols |
PTS system, maltose and glucose-specific IIABCcomponent |
not lethal |
|
b1676 |
pykF |
pyruvate kinase I |
enzyme; Energy metabolism, carbon: Glycolysis |
pyruvate kinase I (formerly F), fructosestimulated |
not lethal |
|
b1702 |
ppsA |
phosphoenolpyruvate synthase |
enzyme; Central intermediary metabolism:Gluconeogenesis |
not lethal |
|
|
b1723 |
pfkB |
6-phosphofructokinase II |
enzyme; Energy metabolism, carbon: Glycolysis |
6-phosphofructokinase II; suppressor of pfkA |
not lethal |
|
b1773 |
ydjI |
putative aldolase |
putative enzyme; Not classified |
not lethal |
|
|
b1812 |
pabB |
aminodeoxychorismate synthase, subunit I |
enzyme; Biosynthesis of cofactors, carriers:Folic acid |
p-aminobenzoate synthetase, component I |
not lethal |
|
b1817 |
manX |
fused mannose-specific PTS enzymes: IIAcomponent/IIB component |
enzyme; Transport of small molecules:Carbohydrates, organic acids, alcohols |
PTS enzyme IIAB, mannose-specific |
not lethal |
|
b1818 |
manY |
mannose-specific enzyme IIC component of PTS |
transport; Transport of small molecules:Carbohydrates, organic acids, alcohols |
PTS enzyme IIC, mannose-specific |
not lethal |
|
b1819 |
manZ |
mannose-specific enzyme IID component of PTS |
transport; Transport of small molecules:Carbohydrates, organic acids, alcohols |
PTS enzyme IID, mannose-specific |
not lethal |
|
b1849 |
purT |
phosphoribosylglycinamide formyltransferase 2 |
enzyme; Purine ribonucleotide biosynthesis |
not lethal |
|
|
b1854 |
pykA |
pyruvate kinase II |
enzyme; Energy metabolism, carbon: Glycolysis |
pyruvate kinase II, glucose stimulated |
not lethal |
|
b2097 |
fbaB |
fructose-bisphosphate aldolase class I |
not lethal |
||
|
b2133 |
dld |
D-lactate dehydrogenase, FAD-binding, NADHindependent |
enzyme; Energy metabolism, carbon: Aerobicrespiration |
D-lactate dehydrogenase, FAD protein, NADHindependent |
not lethal |
|
b2296 |
ackA |
acetate kinase A and propionate kinase 2 |
enzyme; Energy metabolism, carbon: Electrontransport |
acetate kinase |
not lethal |
|
b2297 |
pta |
phosphate acetyltransferase |
enzyme; Degradation of small molecules: Carboncompounds |
phosphotransacetylase |
not lethal |
|
b2417 |
crr |
glucose-specific enzyme IIA component of PTS |
enzyme; Transport of small molecules:Carbohydrates, organic acids, alcohols |
PTS system, glucose-specific IIA component |
not lethal |
|
b2458 |
eutD |
phosphate acetyltransferase |
putative enzyme; Degradation of smallmolecules: Amines |
ethanolamine utilization; homolog of Salmonellaacetyl/butyryl P transferase |
not lethal |
|
b2463 |
maeB |
malic enzyme: putativeoxidoreductase/phosphotransacetylase |
putative enzyme; Not classified |
putative multimodular enzyme |
not lethal |
|
b2464 |
talA |
transaldolase A |
enzyme; Central intermediary metabolism:Non-oxidative branch, pentose pathway |
not lethal |
|
|
b2465 |
tktB |
transketolase 2, thiamine triphosphate-binding |
enzyme; Central intermediary metabolism:Non-oxidative branch, pentose pathway |
transketolase 2 isozyme |
not lethal |
|
b2492 |
focB |
putative formate transporter |
putative transport; Transport of smallmolecules: Carbohydrates, organic acids, alcohols |
probable formate transporter (formate channel 2) |
not lethal |
|
b2579 |
grcA |
autonomous glycyl radical cofactor |
putative enzyme; Energy metabolism, carbon:Anaerobic respiration |
putative formate acetyltransferase |
not lethal |
|
b2587 |
kgtP |
alpha-ketoglutarate transporter |
transport; Transport of small molecules:Carbohydrates, organic acids, alcohols |
alpha-ketoglutarate permease |
not lethal |
|
b2914 |
rpiA |
ribose 5-phosphate isomerase, constitutive |
enzyme; Central intermediary metabolism:Non-oxidative branch, pentose pathway |
ribosephosphate isomerase, constitutive |
not lethal |
|
b2925 |
fbaA |
fructose-bisphosphate aldolase, class II |
enzyme; Energy metabolism, carbon: Glycolysis |
not lethal |
|
|
b2935 |
tktA |
transketolase 1, thiamine triphosphate-binding |
enzyme; Central intermediary metabolism:Non-oxidative branch, pentose pathway |
transketolase 1 isozyme |
not lethal |
|
b2975 |
glcA |
glycolate transporter |
putative transport; Not classified |
putative permease |
not lethal |
|
b2976 |
glcB |
malate synthase G |
enzyme; Central intermediary metabolism:Glyoxylate bypass |
not lethal |
|
|
b2987 |
pitB |
phosphate transporter |
transport; Transport of small molecules:Anions |
low-affinity phosphate transport |
not lethal |
|
b3114 |
tdcE |
pyruvate formate-lyase 4/2-ketobutyrateformate-lyase |
putative enzyme; Energy metabolism, carbon:Anaerobic respiration |
probable formate acetyltransferase 3 |
not lethal |
|
b3115 |
tdcD |
propionate kinase/acetate kinase C, anaerobic |
putative enzyme; Not classified |
propionate kinase/acetate kinase II, anaerobic |
not lethal |
|
b3212 |
gltB |
glutamate synthase, large subunit |
enzyme; Central intermediary metabolism: Pool,multipurpose conversions |
not lethal |
|
|
b3213 |
gltD |
glutamate synthase, 4Fe-4S protein, smallsubunit |
enzyme; Central intermediary metabolism: Pool,multipurpose conversions |
glutamate synthase, small subunit |
not lethal |
|
b3386 |
rpe |
D-ribulose-5-phosphate 3-epimerase |
enzyme; Central intermediary metabolism:Non-oxidative branch, pentose pathway |
not lethal |
|
|
b3403 |
pck |
phosphoenolpyruvate carboxykinase [ATP] |
enzyme; Central intermediary metabolism:Gluconeogenesis |
not lethal |
|
|
b3493 |
pitA |
phosphate transporter, low-affinity; telluriteimporter |
transport; Transport of small molecules:Anions |
low-affinity phosphate transport |
not lethal |
|
b3528 |
dctA |
C4-dicarboxylic acid, orotate and citratetransporter |
transport; Transport of small molecules:Carbohydrates, organic acids, alcohols |
uptake of C4-dicarboxylic acids |
not lethal |
|
b3603 |
lldP |
L-lactate permease |
transport; Transport of small molecules:Carbohydrates, organic acids, alcohols |
not lethal |
|
|
b3612 |
gpmM |
phosphoglycero mutase III, cofactor-independent |
putative enzyme; Not classified |
putative 2,3-bisphosphoglycerate-independentphosphoglycerate mutase |
not lethal |
|
b3739 |
atpI |
ATP synthase, membrane-bound accessory factor |
enzyme; ATP-proton motive forceinterconversion |
membrane-bound ATP synthase, dispensable protein,affects expression of atpB |
not lethal |
|
b3870 |
glnA |
glutamine synthetase |
enzyme; Amino acid biosynthesis: Glutamine |
not lethal |
|
|
b3916 |
pfkA |
6-phosphofructokinase I |
enzyme; Energy metabolism, carbon: Glycolysis |
not lethal |
|
|
b3925 |
glpX |
fructose 1,6-bisphosphatase II |
phenotype; Not classified |
not required for growth on glycerol |
not lethal |
|
b3951 |
pflD |
putative glycine radical domain-containingpyruvate formate-lyase |
enzyme; Energy metabolism, carbon: Anaerobicrespiration |
formate acetyltransferase 2 |
not lethal |
|
b3952 |
pflC |
putative [formate-C-acetyltransferase2]-activating enzyme; pyruvate formate-lyase 1-activatingenzyme |
putative enzyme; Energy metabolism, carbon:Anaerobic respiration |
probable pyruvate formate lyase activating enzyme2 |
not lethal |
|
b3962 |
sthA |
pyridine nucleotide transhydrogenase, soluble |
putative enzyme; Not classified |
not lethal |
|
|
b4014 |
aceB |
malate synthase A |
enzyme; Central intermediary metabolism:Glyoxylate bypass |
not lethal |
|
|
b4015 |
aceA |
isocitrate lyase |
enzyme; Central intermediary metabolism:Glyoxylate bypass |
not lethal |
|
|
b4077 |
gltP |
glutamate/aspartate:proton symporter |
transport; Transport of small molecules: Aminoacids, amines |
glutamate-aspartate symport protein |
not lethal |
|
b4090 |
rpiB |
ribose 5-phosphate isomerase B/allose6-phosphate isomerase |
enzyme; Central intermediary metabolism:Non-oxidative branch, pentose pathway |
ribose 5-phosphate isomerase B |
not lethal |
|
b4122 |
fumB |
anaerobic class I fumarate hydratase (fumaraseB) |
enzyme; Energy metabolism, carbon: TCA cycle |
fumarase Bisozyme |
not lethal |
|
b4151 |
frdD |
fumarate reductase (anaerobic), membrane anchorsubunit |
enzyme; Energy metabolism, carbon: Anaerobicrespiration |
fumarate reductase, anaerobic, membrane anchorpolypeptide |
not lethal |
|
b4152 |
frdC |
fumarate reductase (anaerobic), membrane anchorsubunit |
enzyme; Energy metabolism, carbon: Anaerobicrespiration |
fumarate reductase, anaerobic, membrane anchorpolypeptide |
not lethal |
|
b4153 |
frdB |
fumarate reductase (anaerobic), Fe-S subunit |
enzyme; Energy metabolism, carbon: Anaerobicrespiration |
fumarate reductase, anaerobic, iron-sulfur proteinsubunit |
not lethal |
|
b4154 |
frdA |
anaerobic fumarate reductase catalytic andNAD/flavoprotein subunit |
enzyme; Energy metabolism, carbon: Anaerobicrespiration |
fumarate reductase, anaerobic, flavoproteinsubunit |
not lethal |
|
b4232 |
fbp |
fructose-1,6-bisphosphatase I |
enzyme; Central intermediary metabolism:Gluconeogenesis |
not lethal |
|
|
b4301 |
sgcE |
putative epimerase |
putative enzyme; Not classified |
not lethal |
|
|
b4395 |
ytjC |
phosphatase |
enzyme; Not classified |
phosphoglyceromutase 2 |
not lethal |
|
b0114 |
aceE |
pyruvate dehydrogenase, decarboxylase componentE1, thiamine triphosphate-binding |
enzyme; Energy metabolism, carbon: Pyruvatedehydrogenase |
pyruvate dehydrogenase (decarboxylase component) |
lethal |
|
b0115 |
aceF |
pyruvate dehydrogenase,dihydrolipoyltransacetylase component E2 |
enzyme; Energy metabolism, carbon: Pyruvatedehydrogenase |
pyruvate dehydrogenase (dihydrolipoyltransacetylasecomponent) |
lethal |
|
b0116 |
lpd |
dihydrolipoyl dehydrogenase; E3 component ofpyruvate and 2-oxoglutarate dehydrogenases complexes;glycine cleavage system L protein; dihydrolipoamidedehydrogenase |
enzyme; Energy metabolism, carbon: Pyruvatedehydrogenase |
lipoamide dehydrogenase (NADH); component of2-oxodehydrogenase and pyruvate complexes; L-protein ofglycine cleavage complex |
lethal |
|
b0720 |
gltA |
citrate synthase |
enzyme; Energy metabolism, carbon: TCA cycle |
lethal |
|
|
b0721 |
sdhC |
succinate dehydrogenase, membrane subunit, bindscytochrome b556 |
enzyme; Energy metabolism, carbon: TCA cycle |
succinate dehydrogenase, cytochrome b556 |
lethal |
|
b0722 |
sdhD |
succinate dehydrogenase, membrane subunit, bindscytochrome b556 |
enzyme; Energy metabolism, carbon: TCA cycle |
succinate dehydrogenase, hydrophobic subunit |
lethal |
|
b0723 |
sdhA |
succinate dehydrogenase, flavoprotein subunit |
enzyme; Energy metabolism, carbon: TCA cycle |
lethal |
|
|
b0724 |
sdhB |
succinate dehydrogenase, FeS subunit |
enzyme; Energy metabolism, carbon: TCA cycle |
succinate dehydrogenase, iron sulfur protein |
lethal |
|
b0726 |
sucA |
2-oxoglutarate decarboxylase, thiaminetriphosphate-binding |
enzyme; Energy metabolism, carbon: TCA cycle |
2-oxoglutarate dehydrogenase (decarboxylasecomponent) |
lethal |
|
b0727 |
sucB |
dihydrolipoyltranssuccinase |
enzyme; Energy metabolism, carbon: TCA cycle |
2-oxoglutarate dehydrogenase(dihydrolipoyltranssuccinase E2 component) |
lethal |
|
b0728 |
sucC |
succinyl-CoA synthetase, beta subunit |
enzyme; Energy metabolism, carbon: TCA cycle |
lethal |
|
|
b0729 |
sucD |
succinyl-CoA synthetase, NAD(P)-binding, alphasubunit |
enzyme; Energy metabolism, carbon: TCA cycle |
succinyl-CoA synthetase, alpha subunit |
lethal |
|
b0767 |
pgl |
6-phosphogluconolactonase |
orf; Not classified |
putative isomerase |
lethal |
|
b1136 |
icd |
isocitrate dehydrogenase; e14 prophageattachment site; tellurite reductase |
enzyme; Energy metabolism, carbon: TCA cycle;Phage or Prophage Related |
isocitrate dehydrogenase, specific for NADP+ |
lethal |
|
b1761 |
gdhA |
glutamate dehydrogenase, NADP-specific |
enzyme; Amino acid biosynthesis: Glutamate |
NADP-specific glutamate dehydrogenase |
lethal |
|
b1779 |
gapA |
glyceraldehyde-3-phosphate dehydrogenase A |
enzyme; Energy metabolism, carbon: Glycolysis |
lethal |
|
|
b1852 |
zwf |
glucose-6-phosphate 1-dehydrogenase |
enzyme; Energy metabolism, carbon: Oxidativebranch, pentose pathway |
lethal |
|
|
b2029 |
gnd |
6-phosphogluconate dehydrogenase,decarboxylating |
enzyme; Energy metabolism, carbon: Oxidativebranch, pentose pathway |
lethal |
|
|
b2276 |
nuoN |
NADH:ubiquinone oxidoreductase, membrane subunitN |
enzyme; Energy metabolism, carbon: Aerobicrespiration |
NADH dehydrogenase I chain N |
lethal |
|
b2277 |
nuoM |
NADH:ubiquinone oxidoreductase, membrane subunitM |
enzyme; Energy metabolism, carbon: Aerobicrespiration |
NADH dehydrogenase I chain M |
lethal |
|
b2278 |
nuoL |
NADH:ubiquinone oxidoreductase, membrane subunitL |
enzyme; Energy metabolism, carbon: Aerobicrespiration |
NADH dehydrogenase I chain L |
lethal |
|
b2279 |
nuoK |
NADH:ubiquinone oxidoreductase, membrane subunitK |
enzyme; Energy metabolism, carbon: Aerobicrespiration |
NADH dehydrogenase I chain K |
lethal |
|
b2280 |
nuoJ |
NADH:ubiquinone oxidoreductase, membrane subunitJ |
enzyme; Energy metabolism, carbon: Aerobicrespiration |
NADH dehydrogenase I chain J |
lethal |
|
b2281 |
nuoI |
NADH:ubiquinone oxidoreductase, chain I |
enzyme; Energy metabolism, carbon: Aerobicrespiration |
NADH dehydrogenase I chain I |
lethal |
|
b2282 |
nuoH |
NADH:ubiquinone oxidoreductase, membrane subunitH |
enzyme; Energy metabolism, carbon: Aerobicrespiration |
NADH dehydrogenase I chain H |
lethal |
|
b2283 |
nuoG |
NADH:ubiquinone oxidoreductase, chain G |
enzyme; Energy metabolism, carbon: Aerobicrespiration |
NADH dehydrogenase I chain G |
lethal |
|
b2284 |
nuoF |
NADH:ubiquinone oxidoreductase, chain F |
enzyme; Energy metabolism, carbon: Aerobicrespiration |
NADH dehydrogenase I chain F |
lethal |
|
b2285 |
nuoE |
NADH:ubiquinone oxidoreductase, chain E |
enzyme; Energy metabolism, carbon: Aerobicrespiration |
NADH dehydrogenase I chain E |
lethal |
|
b2286 |
nuoC |
NADH:ubiquinone oxidoreductase, fused CDsubunit |
enzyme; Energy metabolism, carbon: Aerobicrespiration |
NADH dehydrogenase I chain C, D |
lethal |
|
b2287 |
nuoB |
NADH:ubiquinone oxidoreductase, chain B |
enzyme; Energy metabolism, carbon: Aerobicrespiration |
NADH dehydrogenase I chain B |
lethal |
|
b2288 |
nuoA |
NADH:ubiquinone oxidoreductase, membrane subunitA |
enzyme; Energy metabolism, carbon: Aerobicrespiration |
NADH dehydrogenase I chain A |
lethal |
|
b2415 |
ptsH |
phosphohistidinoprotein-hexosephosphotransferase component of PTS system (Hpr) |
enzyme; Transport of small molecules:Carbohydrates, organic acids, alcohols |
PTS system protein HPr |
lethal |
|
b2416 |
ptsI |
PEP-protein phosphotransferase of PTS system(enzyme I) |
enzyme; Transport of small molecules:Carbohydrates, organic acids, alcohols |
PEP-protein phosphotransferase system enzyme I |
lethal |
|
b2779 |
eno |
enolase |
enzyme; Energy metabolism, carbon: Glycolysis |
lethal |
|
|
b2926 |
pgk |
phosphoglycerate kinase |
enzyme; Energy metabolism, carbon: Glycolysis |
lethal |
|
|
b3236 |
mdh |
malate dehydrogenase, NAD(P)-binding |
enzyme; Energy metabolism, carbon: TCA cycle |
malate dehydrogenase |
lethal |
|
b3731 |
atpC |
F1 sector of membrane-bound ATP synthase,epsilon subunit |
enzyme; ATP-proton motive forceinterconversion |
membrane-bound ATP synthase, F1 sector,epsilon-subunit |
lethal |
|
b3732 |
atpD |
F1 sector of membrane-bound ATP synthase, betasubunit |
enzyme; ATP-proton motive forceinterconversion |
membrane-bound ATP synthase, F1 sector,beta-subunit |
lethal |
|
b3733 |
atpG |
F1 sector of membrane-bound ATP synthase, gammasubunit |
enzyme; ATP-proton motive forceinterconversion |
membrane-bound ATP synthase, F1 sector,gamma-subunit |
lethal |
|
b3734 |
atpA |
F1 sector of membrane-bound ATP synthase, alphasubunit |
enzyme; ATP-proton motive forceinterconversion |
membrane-bound ATP synthase, F1 sector,alpha-subunit |
lethal |
|
b3735 |
atpH |
F1 sector of membrane-bound ATP synthase, deltasubunit |
enzyme; ATP-proton motive forceinterconversion |
membrane-bound ATP synthase, F1 sector,delta-subunit |
lethal |
|
b3736 |
atpF |
F0 sector of membrane-bound ATP synthase,subunit b |
enzyme; ATP-proton motive forceinterconversion |
membrane-bound ATP synthase, F0 sector, subunit b |
lethal |
|
b3737 |
atpE |
F0 sector of membrane-bound ATP synthase,subunit c |
enzyme; ATP-proton motive forceinterconversion |
membrane-bound ATP synthase, F0 sector, subunit c |
lethal |
|
b3738 |
atpB |
F0 sector of membrane-bound ATP synthase,subunit a |
enzyme; ATP-proton motive forceinterconversion |
membrane-bound ATP synthase, F0 sector, subunit a |
lethal |
|
b3919 |
tpiA |
triosephosphate isomerase |
enzyme; Energy metabolism, carbon: Glycolysis |
lethal |
|
|
b3956 |
ppc |
phosphoenolpyruvate carboxylase |
enzyme; Energy metabolism, carbon:Fermentation |
lethal |
|
|
b4025 |
pgi |
glucosephosphate isomerase |
enzyme; Energy metabolism, carbon: Glycolysis |
lethal |
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21INCOMPATIBLE WITH RFC[21]Illegal XhoI site found at 349
- 23COMPATIBLE WITH RFC[23]
- 25INCOMPATIBLE WITH RFC[25]Illegal AgeI site found at 765
- 1000COMPATIBLE WITH RFC[1000]