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 : 3mop_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (1 of 65: See next) for growth-coupled production (at least stoichioemetrically feasible)
Gene deletion size : 5
Gene deletion: CLJU_RS11895 CLJU_RS07210 CLJU_RS03475 CLJU_RS08715 CLJU_RS18530 (List of alternative genes)
Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
Growth Rate : 0.213765 (mmol/gDw/h)
Minimum Production Rate : 0.068217 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
EX_fru_e : 5.000000
EX_nh4_e : 1.622074
EX_pi_e : 0.247678
EX_k_e : 0.040867
EX_so4_e : 0.040366
EX_fe2_e : 0.002955
EX_mg2_e : 0.001816
EX_ca2_e : 0.001090
EX_cl_e : 0.001090
EX_fol_e : 0.000191
EX_cu2_e : 0.000148
EX_mn2_e : 0.000145
EX_ribflv_e : 0.000095
EX_zn2_e : 0.000071
EX_ni2_e : 0.000068
EX_cobalt2_e : 0.000053
EX_thm_e : 0.000048

Product: (mmol/gDw/h)
EX_co2_e : 7.854856
EX_etoh_e : 6.219278
EX_h2o_e : 5.801669
EX_h_e : 1.250423
Auxiliary production reaction : 0.068217
DM_succ_c : 0.027031
DM_mththf_c : 0.000477

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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