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 : pa120_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (33 of 128: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: STM2927 STM2122 STM4108 STM2285 STM3526 STM4326 STM3709 STM3529 STM1620 STM3542 STM4485 STM1448 STM3069 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM3248 STM0519 STM2332 STM1124 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.256723 (mmol/gDw/h)
  Minimum Production Rate : 0.039134 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.829122
  EX_pi_e : 0.266802
  EX_k_e : 0.045594
  EX_so4_e : 0.031316
  EX_mg2_e : 0.002027
  EX_fe2_e : 0.001882
  EX_ca2_e : 0.001216
  EX_cl_e : 0.001216
  EX_cobalt2_e : 0.000811
  EX_cu2_e : 0.000811
  EX_mn2_e : 0.000811
  EX_mobd_e : 0.000811
  EX_zn2_e : 0.000811

Product: (mmol/gDw/h)
  EX_h2o_e : 25.989801
  EX_co2_e : 18.834115
  EX_h_e : 2.265396
  EX_ac_e : 0.076160
  Auxiliary production reaction : 0.039134
  EX_glyclt_e : 0.012836
  EX_glyald_e : 0.000178
  DM_hmfurn_c : 0.000114

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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