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_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (108 of 130: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: STM3646 STM1463 STM1749 STM2463 STM2285 STM3526 STM0322 STM4326 STM1884 STM0840 STM0842 STM2947 STM1135 STM0370 STM3597 STM2403 STM4408 STM1291 STM0772 STM4585 STM3704 STM4184 STM4484 STM0542 STM2317 STM3179 STM1480 STM4126 STM4578 STM2338 STM2466 STM3661 STM4467 STM0402 STM0608 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.195101 (mmol/gDw/h)
  Minimum Production Rate : 0.015335 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.150042
  EX_pi_e : 0.188356
  EX_k_e : 0.034650
  EX_so4_e : 0.023799
  EX_mg2_e : 0.001540
  EX_fe2_e : 0.001430
  EX_ca2_e : 0.000924
  EX_cl_e : 0.000924
  EX_cobalt2_e : 0.000616
  EX_cu2_e : 0.000616
  EX_mn2_e : 0.000616
  EX_mobd_e : 0.000616
  EX_zn2_e : 0.000616

Product: (mmol/gDw/h)
  EX_h2o_e : 24.659885
  EX_co2_e : 19.250605
  EX_h_e : 1.762008
  EX_acald_e : 1.286138
  EX_ac_e : 0.108014
  Auxiliary production reaction : 0.015335
  DM_hmfurn_c : 0.000087

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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