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 : pa161_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 113: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: STM1749 STM2463 STM4108 STM2285 STM3526 STM1290 STM4570 STM4326 STM1885 STM3709 STM3529 STM1620 STM1448 STM2403 STM0518 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM3241 STM0973 STM3661 STM1124 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.208839 (mmol/gDw/h)
  Minimum Production Rate : 0.038523 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.301429
  EX_so4_e : 0.551526
  EX_pi_e : 0.223726
  EX_k_e : 0.037090
  EX_mg2_e : 0.001649
  EX_fe2_e : 0.001531
  EX_ca2_e : 0.000989
  EX_cl_e : 0.000989
  EX_cu2_e : 0.000660
  EX_mn2_e : 0.000660
  EX_mobd_e : 0.000660
  EX_zn2_e : 0.000660
  EX_cobalt2_e : 0.000660

Product: (mmol/gDw/h)
  EX_h2o_e : 26.004778
  EX_co2_e : 20.093361
  EX_h_e : 0.790747
  EX_h2s_e : 0.526052
  EX_acald_e : 0.167333
  EX_ac_e : 0.061954
  Auxiliary production reaction : 0.038523
  EX_glyclt_e : 0.010442
  EX_glyald_e : 0.000145
  DM_hmfurn_c : 0.000093

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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