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 : pa140_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (24 of 43: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: STM3646 STM1463 STM4482 STM1749 STM2463 STM2285 STM3526 STM3512 STM3541 STM4326 STM1511 STM2952 STM2947 STM3709 STM3068 STM2141 STM1135 STM0368 STM3597 STM4408 STM1291 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM0977 STM1124 STM0402 STM0608   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.191337 (mmol/gDw/h)
  Minimum Production Rate : 0.067371 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.108561
  EX_pi_e : 0.237054
  EX_k_e : 0.033981
  EX_so4_e : 0.023340
  EX_mg2_e : 0.001511
  EX_fe2_e : 0.001402
  EX_ca2_e : 0.000906
  EX_cl_e : 0.000906
  EX_cobalt2_e : 0.000604
  EX_cu2_e : 0.000604
  EX_mn2_e : 0.000604
  EX_mobd_e : 0.000604
  EX_zn2_e : 0.000604

Product: (mmol/gDw/h)
  EX_h2o_e : 24.943346
  EX_co2_e : 19.533762
  EX_h_e : 1.622084
  EX_acald_e : 0.488145
  Auxiliary production reaction : 0.067371
  DM_hmfurn_c : 0.000085

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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