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 : phe__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (85 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: STM3646 STM0158 STM2927 STM1749 STM2463 STM2285 STM3526 STM4326 STM1885 STM2952 STM2947 STM3709 STM3068 STM2141 STM1135 STM0141 STM2081 STM1448 STM0170 STM0317 STM0150 STM4184 STM4484 STM0568 STM2317 STM3179 STM4569 STM1480 STM4126 STM2338 STM2466 STM1937 STM3103 STM0977 STM1124 STM4467 STM3802 STM2196 STM3240 STM0007 STM2473 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.061973 (mmol/gDw/h)
  Minimum Production Rate : 0.042575 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 9.638401
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.725523
  EX_pi_e : 0.054959
  EX_k_e : 0.011006
  EX_so4_e : 0.007560
  EX_mg2_e : 0.000489
  EX_fe2_e : 0.000454
  EX_ca2_e : 0.000294
  EX_cl_e : 0.000294
  EX_cobalt2_e : 0.000196
  EX_cu2_e : 0.000196
  EX_mn2_e : 0.000196
  EX_mobd_e : 0.000196
  EX_zn2_e : 0.000196

Product: (mmol/gDw/h)
  EX_h2o_e : 12.016013
  EX_co2_e : 10.094654
  EX_dha_e : 4.923562
  EX_h_e : 0.883729
  EX_acald_e : 0.861334
  EX_ac_e : 0.315773
  Auxiliary production reaction : 0.042575
  DM_hmfurn_c : 0.000028

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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