MetNetComp Database [1] / Minimal gene deletions Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : STM_v1_0 [2].
Target metabolite : ocdca_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (26 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: STM3646 STM1749 STM2463 STM2285 STM3526 STM0169 STM0861 STM4570 STM4326 STM2952 STM2947 STM1135 STM4183 STM0974 STM1448 STM1326 STM4062 STM4484 STM0542 STM2317 STM3179 STM1480 STM4126 STM4578 STM1124 STM2051 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.173820 (mmol/gDw/h)
  Minimum Production Rate : 0.129781 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 1.915524
  EX_pi_e : 0.154148
  EX_k_e : 0.030871
  EX_so4_e : 0.021203
  EX_mg2_e : 0.001372
  EX_fe2_e : 0.001274
  EX_ca2_e : 0.000823
  EX_cl_e : 0.000823
  EX_cobalt2_e : 0.000549
  EX_cu2_e : 0.000549
  EX_mn2_e : 0.000549
  EX_mobd_e : 0.000549
  EX_zn2_e : 0.000549

Product: (mmol/gDw/h)
  EX_h2o_e : 24.572430
  EX_co2_e : 19.780497
  EX_h_e : 1.603364
  EX_acald_e : 0.579808
  Auxiliary production reaction : 0.129781
  DM_hmfurn_c : 0.000078

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] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[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.

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Last updated: 27-Sep-2023
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