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 : ps181_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 132: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: STM1749 STM2463 STM2285 STM3526 STM0169 STM0861 STM4570 STM4326 STM1511 STM2952 STM0840 STM0842 STM2947 STM3709 STM1570 STM1620 STM4036 STM1448 STM0518 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM0977 STM1124 STM2051   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.227513 (mmol/gDw/h)
  Minimum Production Rate : 0.011235 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.600116
  EX_pi_e : 0.212998
  EX_k_e : 0.040406
  EX_so4_e : 0.027752
  EX_mg2_e : 0.001796
  EX_fe2_e : 0.001667
  EX_ca2_e : 0.001078
  EX_cl_e : 0.001078
  EX_cobalt2_e : 0.000718
  EX_cu2_e : 0.000718
  EX_mn2_e : 0.000718
  EX_mobd_e : 0.000718
  EX_zn2_e : 0.000718

Product: (mmol/gDw/h)
  EX_h2o_e : 25.399166
  EX_co2_e : 18.977959
  EX_h_e : 2.089297
  EX_acald_e : 0.591672
  EX_val__L_e : 0.081661
  EX_ac_e : 0.067494
  EX_glyclt_e : 0.011376
  Auxiliary production reaction : 0.011235
  DM_hmfurn_c : 0.000101

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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