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 : lipa_cold_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (112 of 128: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: STM2927 STM1749 STM2463 STM2285 STM3526 STM0322 STM1290 STM4326 STM1511 STM1884 STM2947 STM3709 STM1620 STM0369 STM3597 STM1326 STM4062 STM2403 STM4408 STM1291 STM0518 STM4184 STM4484 STM2317 STM3179 STM4569 STM1480 STM4126 STM2338 STM2466 STM3661 STM1933 STM3063 STM4467 STM2196 STM3240 STM0402 STM0608 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.021957 (mmol/gDw/h)
  Minimum Production Rate : 0.025294 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 9.274904
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.292573
  EX_pi_e : 0.070080
  EX_k_e : 0.003900
  EX_so4_e : 0.002678
  EX_mg2_e : 0.000173
  EX_fe2_e : 0.000161
  EX_ca2_e : 0.000104
  EX_cl_e : 0.000104
  EX_cobalt2_e : 0.000069
  EX_cu2_e : 0.000069
  EX_mn2_e : 0.000069
  EX_mobd_e : 0.000069
  EX_zn2_e : 0.000069

Product: (mmol/gDw/h)
  EX_h2o_e : 11.173406
  EX_co2_e : 10.163236
  EX_dha_e : 4.893600
  EX_h_e : 0.903904
  EX_ac_e : 0.615451
  EX_acald_e : 0.094440
  Auxiliary production reaction : 0.025304
  EX_glyclt_e : 0.001098

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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