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 (26 of 128: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM4108 STM2285 STM3526 STM0322 STM1290 STM4326 STM1511 STM1884 STM3529 STM1620 STM4408 STM1291 STM0518 STM4184 STM4484 STM2317 STM3179 STM4569 STM1480 STM4126 STM2338 STM2466 STM0402 STM0608 STM1341   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.256146 (mmol/gDw/h)
  Minimum Production Rate : 0.036226 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.822759
  EX_pi_e : 0.263382
  EX_k_e : 0.045491
  EX_so4_e : 0.031245
  EX_mg2_e : 0.002022
  EX_fe2_e : 0.001877
  EX_ca2_e : 0.001213
  EX_cl_e : 0.001213
  EX_cobalt2_e : 0.000809
  EX_cu2_e : 0.000809
  EX_mn2_e : 0.000809
  EX_mobd_e : 0.000809
  EX_zn2_e : 0.000809

Product: (mmol/gDw/h)
  EX_h2o_e : 25.937695
  EX_co2_e : 18.803746
  EX_h_e : 2.326123
  EX_ac_e : 0.141810
  Auxiliary production reaction : 0.036226
  EX_glyclt_e : 0.012807
  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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