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 : ddca_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (84 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: STM2927 STM1749 STM2463 STM2122 STM2285 STM2009 STM3526 STM4326 STM1884 STM2947 STM3709 STM3068 STM2141 STM1620 STM0368 STM1448 STM3069 STM0518 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM2332 STM1124 STM4467 STM3802 STM2196 STM3240 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.072389 (mmol/gDw/h)
  Minimum Production Rate : 0.161916 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 9.218078
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.797732
  EX_pi_e : 0.064196
  EX_k_e : 0.012856
  EX_so4_e : 0.008830
  EX_mg2_e : 0.000572
  EX_fe2_e : 0.000531
  EX_ca2_e : 0.000343
  EX_cl_e : 0.000343
  EX_cu2_e : 0.000229
  EX_mn2_e : 0.000229
  EX_mobd_e : 0.000229
  EX_zn2_e : 0.000229
  EX_cobalt2_e : 0.000229

Product: (mmol/gDw/h)
  EX_h2o_e : 12.093974
  EX_co2_e : 10.098346
  EX_dha_e : 4.927293
  EX_h_e : 0.779218
  EX_acald_e : 0.184680
  Auxiliary production reaction : 0.161916
  EX_glyclt_e : 0.003619
  DM_hmfurn_c : 0.000032

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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