[14] P R Rich. The molecular machinery of keilin's respiratory chain. *Biochem. Soc. Trans.*, 31(Pt 6):1095-1105, December 2003. doi: 10.1042/bst0311095.

[15] Steffen Klamt, Stefan Müller, Georg Regensburger, and Jürgen Zanghellini. A mathematical framework for yield (vs. rate) optimization in constraint-based modeling and applications in metabolic engineering. *Metab. Eng.*, 47:153-169, May 2018. doi: 10.1016/j.ymben.2018.02.001.

[16] E. Noor, A. Flamholz, W. Liebermeister, A. Bar-Even, and R. Milo. A note on the kinetics of enzyme action: a decomposition that highlights thermodynamic effects. *FEBS Lett*, 587(17):2772-7, 2013. ISSN 1873-3468 (Electronic) 0014-5793 (Linking). doi: 10.1016/j.febslet.2013.07.028.

[17] Wolfram Liebermeister and Edda Klipp. Bringing metabolic networks to life: convenience rate law and thermodynamic constraints. *Theor. Biol. Med. Model.*, 3(1):41, 2006. doi: 10.1186/1742-4682-3-41.

[18] Dan Davidi, Elad Noor, Wolfram Liebermeister, Arren Bar-Even, Avi Flamholz, Katja Tummler, Uri Barenholz, Miki Goldenfeld, Tomer Shlomi, and Ron Milo. Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro $k_{cat}$ measurements. *Proceedings of the National Academy of Sciences*, 113 (12):3401-3406, 2016. doi: 10.1073/pnas.1514240113.

[19] Avi Flamholz, Elad Noor, Arren Bar-Even, Wolfram Liebermeister, and Ron Milo. Glycolytic strategy as a tradeoff between energy yield and protein cost. *Proc. Natl. Acad. Sci. U. S. A.*, 110(24):10039-10044, June 2013. doi: 10.1073/pnas.1215283110.

[20] Elad Noor, Arren Bar-Even, Avi Flamholz, Ed Reznik, Wolfram Liebermeister, and Ron Milo. Pathway thermodynamics highlights kinetic obstacles in central metabolism. *PLoS Comput. Biol.*, 10(2):e1003483, February 2014. doi: 10.1371/journal.pcbi.1003483.

[21] Oliver Hädicke, Axel von Kamp, Timur Aydogan, and Steffen Klamt. OptMDF pathway: Identification of metabolic pathways with maximal thermodynamic driving force and its application for analyzing the endogenous CO2 fixation potential of escherichia coli. *PLoS Comput. Biol.*, 14(9):e1006492, September 2018. doi: 10.1371/journal.pcbi.1006492.

[22] Avi Flamholz, Elad Noor, Arren Bar-Even, and Ron Milo. equilibrator—the biochemical thermodynamics calculator. *Nucleic Acids Res.*, 40, January 2012. doi: 10.1093/nar/gkr874.

[23] E. Noor, A. Bar-Even, A. Flamholz, Y. Lubling, D. Davidi, and R. Milo. An integrated open framework for thermodynamics of reactions that combines accuracy and coverage. *Bioinformatics*, 28(15):2037-44, 2012. ISSN 1367-4811 (Electronic) 1367-4803 (Print) 1367-4803 (Linking). doi: 10.1093/bioinformatics/bts317.

[24] M. E. Beber, M. G. Gollub, D. Mozaffari, K. M. Shebek, A. I. Flamholz, R. Milo, and E. Noor. eQuilibrator 3.0: a database solution for thermodynamic constant estimation. *Nucleic Acids Res*, 50(D1):D603-D609, 2022. ISSN 1362-4962 (Electronic) 0305-1048 (Print) 0305-1048 (Linking). doi: 10.1093/nar/gkab1106.

[25] Elad Noor, Avi Flamholz, Arren Bar-Even, Dan Davidi, Ron Milo, and Wolfram Liebermeister. The protein cost of metabolic fluxes: Prediction from enzymatic rate laws and cost minimization. *PLoS Comput. Biol.*, 12(11): e1005167, November 2016. doi: 10.1371/journal.pcbi.1005167.

[26] D. A. Beard and H. Qian. Relationship between thermodynamic driving force and one-way fluxes in reversible processes. *PLoS One*, 2(1):e144, 2007. ISSN 1932-6203 (Electronic) 1932-6203 (Linking). doi: 10.1371/journal.pone.0000144.

[27] Erez Dekel and Uri Alon. Optimality and evolutionary tuning of the expression level of a protein. *Nature*, 436 (7050):588-592, July 2005.
[28] I. Shachrai, A. Zaslaver, U. Alon, and E. Dekel. Cost of unneeded proteins in E. coli is reduced after several generations in exponential growth. *Molecular Cell*, 38:1–10, 2010. doi: 10.1016/j.molcel.2010.04.015.

[29] W Liebermeister and E Noor. The enzyme cost of given metabolic flux distributions, as a function of logarithmic metabolite levels, is convex. *arXiv: 1501.02454*, 2015. doi: 10.48550/arXiv.1501.02454.

[30] V. Hatzimanikatis, C. Li, J.A. Ionita, C.S. Henry, M.D. Jankowski, and L.J. Broadbelt. Exploring the diversity of complex metabolic networks. *Bioinformatics*, 21(8):1603–1609, 2005. doi: 10.1093/bioinformatics/bti213.

[31] Ed Reznik, Dimitris Christodoulou, Joshua E Goldford, Emma Briars, Uwe Sauer, Daniel Segrè, and Elad Noor. Genome-Scale architecture of small molecule regulatory networks and the fundamental Trade-Off between regulation and enzymatic activity. *Cell Rep.*, 20(11):2666–2677, September 2017. doi: 10.1016/j.celrep.2017.08.066.

[32] P L Rogers, K J Lee, M L Skotnicki, and D E Tribe. Ethanol production by zymomonas mobilis. In *Microbial Reactions*, pages 37–84. Springer Berlin Heidelberg, 1982.

[33] Gerrich Behrendt, Jonas Frohwitter, Maria Vlachonikolou, Steffen Klamt, and Katja Bettenbrock. Zymo-Parts: A golden gate modular cloning toolbox for heterologous gene expression in zymomonas mobilis. *ACS Synth. Biol.*, November 2022.

[34] Tobias Fuhrer, Eliane Fischer, and Uwe Sauer. Experimental identification and quantification of glucose metabolism in seven bacterial species. *J. Bacteriol.*, 187(5):1581–1590, March 2005. doi: 10.1128/JB.187.5.1581-1590.2005.

[35] Richard C Law, Glenn Nurwono, and Junyoung O Park. A parallel glycolysis supports rapid adaptation in dynamic environments. *bioRxiv*, page 2022.08.19.504590, August 2022. doi: 10.1101/2022.08.19.504590.

[36] Michael Volpers, J Nico Claassens, Elad Noor, der John van Oost, de Willem M Vos, M Servé W Kengen, and dos Vitor A P Martins Santos. Integrated in silico analysis of pathway designs for synthetic Photo-Electro-Autotrophy. *PLoS One*, 11, June 2016. doi: 10.1371/journal.pone.0157851.

[37] Hannes Löwe and Andreas Kremling. In-Depth computational analysis of natural and artificial carbon fixation pathways. *BioDesign Research*, 2021, September 2021. doi: 10.34133/2021/9898316.

[38] Tyler B Jacobson, Paul A Adamczyk, David M Stevenson, Matthew Regner, John Ralph, Jennifer L Reed, and Daniel Amador-Noguez. 2H and 13C metabolic flux analysis elucidates in vivo thermodynamics of the ED pathway in zymomonas mobilis. *Metab. Eng.*, 54:301–316, July 2019. doi: 10.1016/j.ymben.2019.05.006.

[39] Meike T Wortel, Elad Noor, Michael Ferris, Frank J Bruggeman, and Wolfram Liebermeister. Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield. *PLoS Comput. Biol.*, 14(2):e1006010, February 2018. doi: 10.1371/journal.pcbi.1006010.