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 : pyr_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (13 of 99: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 15
  Gene deletion: STM0620 STM2792 STM1749 STM2463 STM0737 STM2654 STM1756 STM3680 STM4184 STM2317 STM0935 STM2338 STM2466 STM0007 STM2473   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.110535 (mmol/gDw/h)
  Minimum Production Rate : 0.351969 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_glc__D_e : 5.000000
  EX_o2_e : 4.466036
  EX_nh4_e : 1.218107
  EX_pi_e : 0.098025
  EX_k_e : 0.019631
  EX_so4_e : 0.013483
  EX_mg2_e : 0.000873
  EX_fe2_e : 0.000810
  EX_cl_e : 0.000524
  EX_ca2_e : 0.000524
  EX_cobalt2_e : 0.000349
  EX_cu2_e : 0.000349
  EX_mn2_e : 0.000349
  EX_mobd_e : 0.000349
  EX_zn2_e : 0.000349

Product: (mmol/gDw/h)
  EX_h2o_e : 11.716207
  EX_h_e : 9.376139
  EX_pyr_e : 8.377873
  EX_co2_e : 0.291081
  EX_acald_e : 0.088567
  EX_ac_e : 0.061196
  DM_hmfurn_c : 0.000049

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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