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 : ttdcea_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (89 of 110: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: STM3646 STM1749 STM2463 STM2285 STM3526 STM3091 STM4326 STM1511 STM2952 STM2947 STM3709 STM1135 STM3542 STM4485 STM0491 STM0368 STM1326 STM4062 STM4408 STM1291 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM4578 STM2338 STM2466 STM1933 STM1124 STM3063 STM4467 STM2196 STM3240 STM0402 STM0608 STM2971 STM1826 STM1341   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.068837 (mmol/gDw/h)
  Minimum Production Rate : 0.170979 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 12.318078
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.917248
  EX_pi_e : 0.219705
  EX_k_e : 0.012225
  EX_so4_e : 0.008397
  EX_mg2_e : 0.000543
  EX_fe2_e : 0.000503
  EX_ca2_e : 0.000326
  EX_cl_e : 0.000326
  EX_cobalt2_e : 0.000217
  EX_cu2_e : 0.000217
  EX_mn2_e : 0.000217
  EX_mobd_e : 0.000217
  EX_zn2_e : 0.000217

Product: (mmol/gDw/h)
  EX_h2o_e : 19.124599
  EX_co2_e : 15.865966
  EX_h_e : 1.071871
  EX_acald_e : 0.175618
  Auxiliary production reaction : 0.170979
  EX_lipa_e : 0.079330
  DM_hmfurn_c : 0.000031

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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