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 : pa120_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 128: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: STM3646 STM1749 STM2463 STM2285 STM3526 STM4326 STM1885 STM2952 STM0840 STM0842 STM3709 STM1135 STM4183 STM0370 STM0974 STM1448 STM3069 STM4484 STM2317 STM3179 STM4569 STM1480 STM4126 STM2338 STM2466 STM1124 STM3802 STM2196 STM3240 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.239465 (mmol/gDw/h)
  Minimum Production Rate : 0.009958 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.638935
  EX_pi_e : 0.222321
  EX_k_e : 0.042529
  EX_so4_e : 0.029210
  EX_mg2_e : 0.001891
  EX_fe2_e : 0.001755
  EX_ca2_e : 0.001134
  EX_cl_e : 0.001134
  EX_cobalt2_e : 0.000756
  EX_cu2_e : 0.000756
  EX_mn2_e : 0.000756
  EX_mobd_e : 0.000756
  EX_zn2_e : 0.000756

Product: (mmol/gDw/h)
  EX_h2o_e : 25.263234
  EX_co2_e : 18.641678
  EX_h_e : 2.737719
  EX_ac_e : 0.707627
  EX_acald_e : 0.205530
  Auxiliary production reaction : 0.009958
  DM_hmfurn_c : 0.000107

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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