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 : clpn160_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (11 of 113: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: STM1463 STM1749 STM2463 STM2285 STM3526 STM0322 STM0169 STM0861 STM4326 STM1511 STM2947 STM3709 STM3068 STM2141 STM1620 STM3597 STM4408 STM1291 STM3069 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM3248 STM0519 STM3241 STM0973 STM2041 STM0402 STM0608   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.189266 (mmol/gDw/h)
  Minimum Production Rate : 0.037437 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.085738
  EX_pi_e : 0.242719
  EX_k_e : 0.033614
  EX_so4_e : 0.023087
  EX_mg2_e : 0.001494
  EX_fe2_e : 0.001387
  EX_cl_e : 0.000897
  EX_ca2_e : 0.000897
  EX_cu2_e : 0.000598
  EX_mn2_e : 0.000598
  EX_mobd_e : 0.000598
  EX_zn2_e : 0.000598
  EX_cobalt2_e : 0.000598

Product: (mmol/gDw/h)
  EX_h2o_e : 25.028514
  EX_co2_e : 19.623586
  EX_h_e : 1.539117
  EX_acald_e : 0.151651
  Auxiliary production reaction : 0.037437
  EX_glyclt_e : 0.009463
  DM_hmfurn_c : 0.000084

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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