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 : 1odec11eg3p_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (122 of 133: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: STM3646 STM1463 STM1749 STM2463 STM4108 STM2285 STM3526 STM4326 STM1511 STM1885 STM1299 STM2947 STM3068 STM2141 STM1135 STM0141 STM0974 STM4408 STM1291 STM3069 STM4184 STM4484 STM0542 STM2317 STM3179 STM4569 STM1480 STM4126 STM3218 STM1124 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 : 0.052285 (mmol/gDw/h)
  Minimum Production Rate : 0.114800 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 9.383304
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.576179
  EX_pi_e : 0.161166
  EX_k_e : 0.009286
  EX_so4_e : 0.006378
  EX_mg2_e : 0.000413
  EX_fe3_e : 0.000383
  EX_ca2_e : 0.000248
  EX_cl_e : 0.000248
  EX_cobalt2_e : 0.000165
  EX_cu2_e : 0.000165
  EX_mn2_e : 0.000165
  EX_mobd_e : 0.000165
  EX_zn2_e : 0.000165

Product: (mmol/gDw/h)
  EX_h2o_e : 12.045628
  EX_co2_e : 10.374835
  EX_dha_e : 4.947486
  EX_h_e : 0.443713
  EX_acald_e : 0.174404
  Auxiliary production reaction : 0.114800
  EX_hxa_e : 0.000084
  EX_glyald_e : 0.000036
  DM_hmfurn_c : 0.000023

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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