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 : pa180_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 103: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: STM2927 STM1749 STM2463 STM2285 STM3526 STM0322 STM4326 STM1511 STM2947 STM3068 STM2141 STM1620 STM3542 STM4485 STM0370 STM4408 STM1291 STM3069 STM0518 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM2332 STM2196 STM3240 STM0402 STM0608 STM2971 STM1826 STM1341   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.221127 (mmol/gDw/h)
  Minimum Production Rate : 0.053879 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.436847
  EX_pi_e : 0.249979
  EX_k_e : 0.039272
  EX_so4_e : 0.026973
  EX_mg2_e : 0.001746
  EX_fe2_e : 0.001621
  EX_cl_e : 0.001047
  EX_ca2_e : 0.001047
  EX_cobalt2_e : 0.000698
  EX_cu2_e : 0.000698
  EX_mn2_e : 0.000698
  EX_mobd_e : 0.000698
  EX_zn2_e : 0.000698

Product: (mmol/gDw/h)
  EX_h2o_e : 25.526696
  EX_co2_e : 19.322848
  EX_h_e : 1.885685
  Auxiliary production reaction : 0.053879
  EX_glyclt_e : 0.011056
  DM_hmfurn_c : 0.000099

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.

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Last updated: 27-Sep-2023
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