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 : pyr_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (98 of 99: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: STM0758 STM4061 STM0620 STM3747 STM3952 STM2792 STM1749 STM2463 STM0737 STM2654 STM4340 STM3680 STM1522 STM1477 STM3614 STM3869 STM1771 STM0866 STM0086 STM3457 STM2200 STM0974 STM2403 STM0785 STM0832 STM4184 STM1480 STM1806 STM0039 STM2338 STM2466 STM0977 STM3661 STM4301 STM3599 STM4325 STM0627 STM3959   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.014810 (mmol/gDw/h)
  Minimum Production Rate : 0.017438 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.163203
  EX_o2_e : 0.035533
  EX_pi_e : 0.013131
  EX_k_e : 0.002630
  EX_so4_e : 0.001806
  EX_mg2_e : 0.000117
  EX_fe2_e : 0.000109
  EX_ca2_e : 0.000070
  EX_cl_e : 0.000070
  EX_cobalt2_e : 0.000047
  EX_cu2_e : 0.000047
  EX_mn2_e : 0.000047
  EX_mobd_e : 0.000047
  EX_zn2_e : 0.000047

Product: (mmol/gDw/h)
  EX_h_e : 9.922071
  EX_lac__D_e : 9.742939
  EX_h2o_e : 0.471345
  EX_pyr_e : 0.049107
  EX_acald_e : 0.014057
  EX_co2_e : 0.013927
  EX_ac_e : 0.004393
  EX_succ_e : 0.000040

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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