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 : fad_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (85 of 92: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: STM3747 STM2421 STM1749 STM2463 STM4275 STM0598 STM4570 STM0974 STM0152 STM0150 STM3957 STM3279 STM4569 STM2338 STM2466 STM3885 STM3793 STM3802 STM2196 STM3240 STM2970 STM3243 STM3708 STM2971 STM1826 STM3334   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.212441 (mmol/gDw/h)
  Minimum Production Rate : 0.329661 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 11.564777
  EX_nh4_e : 5.308072
  EX_glc__D_e : 5.000000
  EX_pi_e : 0.847719
  EX_k_e : 0.037730
  EX_so4_e : 0.025914
  EX_mg2_e : 0.001677
  EX_fe2_e : 0.001557
  EX_cl_e : 0.001006
  EX_ca2_e : 0.001006
  EX_cu2_e : 0.000671
  EX_mn2_e : 0.000671
  EX_mobd_e : 0.000671
  EX_zn2_e : 0.000671
  EX_cobalt2_e : 0.000671

Product: (mmol/gDw/h)
  EX_h2o_e : 25.110195
  EX_co2_e : 10.352727
  EX_h_e : 5.372947
  EX_ac_e : 1.264330
  Auxiliary production reaction : 0.329661
  DM_hmfurn_c : 0.000095

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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