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 : 1tdecg3p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (112 of 125: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: STM2927 STM4482 STM1749 STM2463 STM2285 STM3526 STM3091 STM3512 STM3541 STM4326 STM1511 STM2952 STM0321 STM2947 STM3709 STM3068 STM2141 STM1620 STM0370 STM4408 STM1291 STM0518 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM2332 STM3968 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 : 0.249816 (mmol/gDw/h)
  Minimum Production Rate : 0.058970 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.753004
  EX_pi_e : 0.280512
  EX_k_e : 0.044367
  EX_so4_e : 0.030473
  EX_mg2_e : 0.001972
  EX_fe2_e : 0.001831
  EX_ca2_e : 0.001183
  EX_cl_e : 0.001183
  EX_cobalt2_e : 0.000789
  EX_cu2_e : 0.000789
  EX_mn2_e : 0.000789
  EX_mobd_e : 0.000789
  EX_zn2_e : 0.000789

Product: (mmol/gDw/h)
  EX_h2o_e : 25.854624
  EX_co2_e : 18.908657
  EX_h_e : 2.130334
  EX_acald_e : 0.200167
  Auxiliary production reaction : 0.058970
  EX_glyclt_e : 0.012491
  DM_hmfurn_c : 0.000111

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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