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 : ocdca_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (33 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: STM3646 STM1749 STM2463 STM2285 STM3526 STM3091 STM4326 STM1511 STM1884 STM0321 STM2947 STM3068 STM2141 STM1135 STM0491 STM0368 STM4408 STM1291 STM4184 STM4484 STM2317 STM3179 STM4569 STM1480 STM4126 STM2338 STM2466 STM4467 STM2196 STM3240 STM0402 STM0608 STM3708 STM2971 STM1826 STM1341   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.175280 (mmol/gDw/h)
  Minimum Production Rate : 0.020623 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 8.490775
  EX_glc__D_e : 5.000000
  EX_nh4_e : 1.931612
  EX_pi_e : 0.155443
  EX_k_e : 0.031130
  EX_so4_e : 0.021381
  EX_mg2_e : 0.001384
  EX_fe2_e : 0.001285
  EX_ca2_e : 0.000830
  EX_cl_e : 0.000830
  EX_cobalt2_e : 0.000554
  EX_cu2_e : 0.000554
  EX_mn2_e : 0.000554
  EX_mobd_e : 0.000554
  EX_zn2_e : 0.000554

Product: (mmol/gDw/h)
  EX_h2o_e : 13.663476
  EX_co2_e : 8.831298
  EX_dha_e : 4.374273
  EX_h_e : 1.506582
  EX_acald_e : 0.447180
  Auxiliary production reaction : 0.020623
  DM_hmfurn_c : 0.000078

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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