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 : 2odecg3p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: STM3646 STM0158 STM1749 STM2463 STM2122 STM2285 STM3526 STM1290 STM4570 STM4326 STM1299 STM2947 STM1135 STM3597 STM1326 STM4062 STM4408 STM1291 STM4184 STM4484 STM0542 STM2317 STM3179 STM1480 STM4126 STM1124 STM0402 STM0608 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.271388 (mmol/gDw/h)
  Minimum Production Rate : 0.039390 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 17.215655
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.990735
  EX_pi_e : 0.280064
  EX_k_e : 0.048199
  EX_so4_e : 0.033104
  EX_mg2_e : 0.002143
  EX_fe2_e : 0.001989
  EX_cl_e : 0.001286
  EX_ca2_e : 0.001286
  EX_cobalt2_e : 0.000857
  EX_cu2_e : 0.000857
  EX_mn2_e : 0.000857
  EX_mobd_e : 0.000857
  EX_zn2_e : 0.000857

Product: (mmol/gDw/h)
  EX_h2o_e : 25.236918
  EX_co2_e : 17.715815
  EX_h_e : 2.261336
  EX_acald_e : 0.479485
  Auxiliary production reaction : 0.039390
  DM_hmfurn_c : 0.000121

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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