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 : gtp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (104 of 104: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: STM3747 STM2421 STM1749 STM2463 STM4275 STM4567 STM4570 STM1511 STM2952 STM2458 STM0974 STM0152 STM0150 STM2338 STM2466 STM2422 STM3968 STM3885 STM3793 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 : 0.308281 (mmol/gDw/h)
  Minimum Production Rate : 0.239191 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 14.250779
  EX_glc__D_e : 5.000000
  EX_nh4_e : 4.593249
  EX_pi_e : 0.990964
  EX_k_e : 0.054751
  EX_so4_e : 0.037605
  EX_mg2_e : 0.002434
  EX_fe2_e : 0.002259
  EX_cl_e : 0.001460
  EX_ca2_e : 0.001460
  EX_cu2_e : 0.000974
  EX_mn2_e : 0.000974
  EX_mobd_e : 0.000974
  EX_zn2_e : 0.000974
  EX_cobalt2_e : 0.000974

Product: (mmol/gDw/h)
  EX_h2o_e : 25.296140
  EX_co2_e : 13.448693
  EX_h_e : 4.448200
  EX_ac_e : 1.117141
  Auxiliary production reaction : 0.239191
  DM_hmfurn_c : 0.000137

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.

Last updated: 27-Sep-2023
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