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 : 4abut_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 112: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: STM3646 STM1463 STM0620 STM2792 STM2285 STM3526 STM1290 STM4326 STM0840 STM0842 STM3709 STM1135 STM1448 STM4184 STM4484 STM0399 STM0935 STM3179 STM1480 STM4126 STM4578 STM2338 STM2466 STM1124 STM4467 STM1305 STM0733 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.081551 (mmol/gDw/h)
  Minimum Production Rate : 1.055823 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 10.454580
  EX_glc__D_e : 5.000000
  EX_nh4_e : 3.409911
  EX_pi_e : 0.072320
  EX_k_e : 0.014484
  EX_so4_e : 0.009948
  EX_mg2_e : 0.000644
  EX_fe2_e : 0.000598
  EX_ca2_e : 0.000386
  EX_cl_e : 0.000386
  EX_cobalt2_e : 0.000258
  EX_cu2_e : 0.000258
  EX_mn2_e : 0.000258
  EX_mobd_e : 0.000258
  EX_zn2_e : 0.000258

Product: (mmol/gDw/h)
  EX_h2o_e : 16.447253
  EX_co2_e : 11.687832
  EX_h_e : 5.758928
  EX_ac_e : 2.556361
  Auxiliary production reaction : 2.511212
  DM_hmfurn_c : 0.000036

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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