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 : pa120_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 128: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: STM3646 STM2927 STM2285 STM3526 STM0169 STM0861 STM4326 STM1511 STM0321 STM2947 STM3709 STM1135 STM0370 STM1448 STM1326 STM4062 STM3069 STM4184 STM4484 STM2317 STM2501 STM3179 STM1480 STM4126 STM2332 STM2196 STM3240 STM3708 STM2971 STM1826 STM4559_S   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.220936 (mmol/gDw/h)
  Minimum Production Rate : 0.080378 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.434742
  EX_pi_e : 0.276309
  EX_k_e : 0.039238
  EX_so4_e : 0.026950
  EX_mg2_e : 0.001744
  EX_fe2_e : 0.001619
  EX_ca2_e : 0.001047
  EX_cl_e : 0.001047
  EX_cu2_e : 0.000698
  EX_mn2_e : 0.000698
  EX_mobd_e : 0.000698
  EX_zn2_e : 0.000698
  EX_cobalt2_e : 0.000698

Product: (mmol/gDw/h)
  EX_h2o_e : 25.534984
  EX_co2_e : 19.283404
  EX_h_e : 1.873010
  Auxiliary production reaction : 0.080378
  DM_hmfurn_c : 0.000099

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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