MetNetComp

MetNetComp Database / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iHN637 [2].
Target metabolite : h2_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (9 of 12: See next) for growth-coupled production (at least stoichioemetrically feasible)
Gene deletion size : 5
Gene deletion: CLJU_RS12245 CLJU_RS09865 CLJU_RS09915 CLJU_RS01155 CLJU_RS02910 (List of alternative genes)
Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
Growth Rate : 0.220002 (mmol/gDw/h)
Minimum Production Rate : 1.423929 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
EX_fru_e : 5.000000
EX_nh4_e : 1.669401
EX_pi_e : 0.254905
EX_k_e : 0.042060
EX_so4_e : 0.041544
EX_fe2_e : 0.003041
EX_mg2_e : 0.001869
EX_ca2_e : 0.001122
EX_cl_e : 0.001122
EX_fol_e : 0.000196
EX_cu2_e : 0.000153
EX_mn2_e : 0.000149
EX_ribflv_e : 0.000098
EX_zn2_e : 0.000073
EX_ni2_e : 0.000070
EX_cobalt2_e : 0.000055
EX_thm_e : 0.000049

Product: (mmol/gDw/h)
EX_h_e : 10.269894
EX_ac_e : 9.053194
EX_h2o_e : 5.118566
EX_co2_e : 2.325057
EX_h2_e : 1.423929
DM_succ_c : 0.027820
DM_mththf_c : 0.000491

Visualization
1. Download JSON file.
2. Go to Escher site [3].

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Orth, J. D., Fleming, R. M., Palsson, B. Ø. (2010). Reconstruction and use of microbial metabolic networks: the core Escherichia coli metabolic model as an educational guide. EcoSal plus, 4(1).
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

Last updated: 27-Sep-2023
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