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 : ps181_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (132 of 132: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: STM3646 STM0158 STM2927 STM1749 STM2463 STM2285 STM3526 STM0322 STM1290 STM4570 STM4326 STM1511 STM1884 STM2947 STM3709 STM0525 STM3247 STM2959 STM2492 STM1135 STM4183 STM1326 STM4062 STM4408 STM1291 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM2332 STM4467 STM2196 STM3240 STM0402 STM0608 STM2971 STM1826 STM1341 STM4559_S   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.068475 (mmol/gDw/h)
  Minimum Production Rate : 0.049484 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 9.190998
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.804078
  EX_pi_e : 0.110208
  EX_k_e : 0.012161
  EX_so4_e : 0.008353
  EX_mg2_e : 0.000541
  EX_fe2_e : 0.000502
  EX_ca2_e : 0.000324
  EX_cl_e : 0.000324
  EX_cu2_e : 0.000216
  EX_mn2_e : 0.000216
  EX_mobd_e : 0.000216
  EX_zn2_e : 0.000216
  EX_cobalt2_e : 0.000216

Product: (mmol/gDw/h)
  EX_h2o_e : 12.210346
  EX_co2_e : 10.025727
  EX_dha_e : 4.931225
  EX_h_e : 0.582209
  EX_acald_e : 0.224178
  Auxiliary production reaction : 0.049484
  EX_glyc__R_e : 0.001712
  DM_hmfurn_c : 0.000031

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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