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_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 113: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: STM3646 STM1749 STM2463 STM4108 STM2285 STM3526 STM0169 STM0861 STM4326 STM3709 STM1135 STM4183 STM0491 STM1448 STM1326 STM4062 STM3069 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM3248 STM0519 STM1124   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.245141 (mmol/gDw/h)
  Minimum Production Rate : 0.001532 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.701486
  EX_pi_e : 0.218929
  EX_k_e : 0.043537
  EX_so4_e : 0.029903
  EX_mg2_e : 0.001935
  EX_fe2_e : 0.001797
  EX_ca2_e : 0.001161
  EX_cl_e : 0.001161
  EX_cobalt2_e : 0.000774
  EX_cu2_e : 0.000774
  EX_mn2_e : 0.000774
  EX_mobd_e : 0.000774
  EX_zn2_e : 0.000774

Product: (mmol/gDw/h)
  EX_h2o_e : 25.200108
  EX_co2_e : 19.064337
  EX_h_e : 2.163192
  EX_etoh_e : 0.625411
  EX_ac_e : 0.072724
  EX_glyclt_e : 0.012257
  Auxiliary production reaction : 0.001532
  DM_hmfurn_c : 0.000109

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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