Closed sergarcia closed 6 years ago
Upon investigation of the genome annotation, sodium was added to the model. And several membrane bound, sodium translocating metabolic enzymes have been added as well.
Done, genes were added where applicable These are part of the ech knockout: see plasmids and strain construction in : https://biotechnologyforbiofuels.biomedcentral.com/track/pdf/10.1186/s13068-015-0204-4?site=biotechnologyforbiofuels.biomedcentral.com
CLO1313_RS02885 | Clo1313_0564 | hypE | hydrogenase expression/formation protein HypE |
---|---|---|---|
CLO1313_RS02890 | Clo1313_0565 | hydrogenase formation protein HypD | |
CLO1313_RS02895 | Clo1313_0566 | hypC | HypC/HybG/HupF family hydrogenase formation chaperone |
CLO1313_RS02900 | Clo1313_0567 | hypF | carbamoyltransferase HypF |
CLO1313_RS02905 | Clo1313_0568 | hypB | hydrogenase accessory protein HypB |
CLO1313_RS02910 | Clo1313_0569 | hypA | hydrogenase maturation nickel metallochaperone HypA |
http://www.uniprot.org/uniprot/P30131 Also,
Fluxomics and C1 metabolism: http://www.pnas.org/content/113/46/13180.full
Useful references: https://www.ncbi.nlm.nih.gov/pubmed/18952792
https://www.ncbi.nlm.nih.gov/pubmed/28230109 used to annotate xylose dehydrogenase from overflow
Description
Basic model curation by reviewing GPR, confidence level, and metabolic reactions.
Solution
All the changes can be seen by comparing the files.
Note that the later was deleted in faac1178b05041be3dd229f691ddeabc237d7a19
In the comment below are a few examples of changes