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 : 1odec11eg3p_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (4 of 133: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM3646 STM2285 STM3526 STM4326 STM1511 STM1299 STM0840 STM0842 STM0517 STM2947 STM1135 STM4183 STM0370 STM0772 STM4585 STM3704 STM4484 STM2317 STM3179 STM1480 STM4126 STM4578 STM2338 STM2466 STM1124   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.293310 (mmol/gDw/h)
  Minimum Production Rate : 0.001323 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 3.232317
  EX_pi_e : 0.261437
  EX_k_e : 0.052092
  EX_so4_e : 0.035779
  EX_mg2_e : 0.002316
  EX_fe2_e : 0.002150
  EX_ca2_e : 0.001389
  EX_cl_e : 0.001389
  EX_cobalt2_e : 0.000926
  EX_cu2_e : 0.000926
  EX_mn2_e : 0.000926
  EX_mobd_e : 0.000926
  EX_zn2_e : 0.000926

Product: (mmol/gDw/h)
  EX_h2o_e : 26.511550
  EX_co2_e : 18.422842
  EX_h_e : 2.588251
  EX_ac_e : 0.087014
  EX_glyclt_e : 0.014666
  Auxiliary production reaction : 0.001323
  DM_hmfurn_c : 0.000131

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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