Review GPR and confidence level

[sergarcia]

Description

Basic model curation by reviewing GPR, confidence level, and metabolic reactions.

Solution

• OR and AND annotations were corrected.
• New functions and genes were added.
• Confidence level was updated. And added in reactions in which it was missing.
• Gap filling was performed using metabolic maps and reference organisms.
• Literature references where added for several reactions
• etc.

All the changes can be seen by comparing the files.

basic_model_curation_reactions_curated.csv 
basic_model_curation_reactions_.csv

Note that the later was deleted in faac1178b05041be3dd229f691ddeabc237d7a19

In the comment below are a few examples of changes

[sergarcia]

Examples and references

Sodium addition

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.

• NA1abc
• PPA2 WHY KEEP PPA? (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3283130/)
• MMCD (PMC11248185)
• GLUCOAC (PMC11248185)

Transporters

• iron
• sulfur

Hydrogenases

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,

• Make hydrogenases membrane bound when applicable

C1 metabolism

Fluxomics and C1 metabolism: http://www.pnas.org/content/113/46/13180.full

Transporters

• Pay attention to transporters. Why are so many compounds associated to ABC and other non passive mechanisms. Are these the most active mechanisms in C. therm?
• Based on gpr, ABC transporters were also added for amino acids.
• Also, are some transporters added to provide necessary metabolites which are synthesized in vivo but the model cannot make? Possible case Nicotinate D-ribonucleotide, which none of the BiGG models imports. This was addressed by gap filling. Also it should have been a sink
• Many transporters are proton mediated, including ethanol transport. This should be diffusion mediated. Both cannot coexist (reversibly), because it would allow to import/export protons freely.

Useful references: https://www.ncbi.nlm.nih.gov/pubmed/18952792

Other:

https://www.ncbi.nlm.nih.gov/pubmed/28230109 used to annotate xylose dehydrogenase from overflow