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 : ocdca_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: STM3646 STM1463 STM1749 STM2463 STM2285 STM3526 STM0322 STM1290 STM0169 STM0861 STM4326 STM0517 STM3709 STM3068 STM2141 STM1135 STM4183 STM0370 STM1448 STM4484 STM2317 STM3179 STM1480 STM4126 STM3802 STM2196 STM3240 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.230743 (mmol/gDw/h)
  Minimum Production Rate : 0.005346 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.542824
  EX_pi_e : 0.204629
  EX_k_e : 0.040980
  EX_so4_e : 0.028147
  EX_mg2_e : 0.001822
  EX_fe2_e : 0.001691
  EX_ca2_e : 0.001093
  EX_cl_e : 0.001093
  EX_cu2_e : 0.000729
  EX_mn2_e : 0.000729
  EX_mobd_e : 0.000729
  EX_zn2_e : 0.000729
  EX_cobalt2_e : 0.000729

Product: (mmol/gDw/h)
  EX_h2o_e : 25.331183
  EX_co2_e : 18.969980
  EX_h_e : 1.973038
  EX_acald_e : 0.992475
  EX_glyclt_e : 0.011537
  Auxiliary production reaction : 0.005346
  DM_hmfurn_c : 0.000103

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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