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 : hisp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (120 of 122: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: STM3009 STM2927 STM0051 STM1749 STM2463 STM4275 STM0661 STM3554 STM2009 STM1511 STM2282 STM0974 STM0152 STM3069 STM0150 STM4569 STM2338 STM2466 STM4452 STM2196 STM3240 STM2970 STM3243 STM3708 STM2971 STM1826 STM3334   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.301947 (mmol/gDw/h)
  Minimum Production Rate : 0.476812 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 13.716639
  EX_glc__D_e : 5.000000
  EX_nh4_e : 4.809736
  EX_pi_e : 0.744586
  EX_k_e : 0.053626
  EX_so4_e : 0.036832
  EX_mg2_e : 0.002384
  EX_fe2_e : 0.002213
  EX_ca2_e : 0.001430
  EX_cl_e : 0.001430
  EX_cobalt2_e : 0.000954
  EX_cu2_e : 0.000954
  EX_mn2_e : 0.000954
  EX_mobd_e : 0.000954
  EX_zn2_e : 0.000954

Product: (mmol/gDw/h)
  EX_h2o_e : 24.910691
  EX_co2_e : 13.601767
  EX_h_e : 4.437520
  EX_ac_e : 0.872301
  Auxiliary production reaction : 0.476812
  EX_ins_e : 0.010140
  EX_gua_e : 0.002248
  DM_hmfurn_c : 0.000135

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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