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 : ddca_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (2 of 113: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: STM1749 STM2463 STM2285 STM3526 STM0169 STM4567 STM0861 STM4326 STM1511 STM2947 STM3709 STM1620 STM0491 STM3597 STM1326 STM4062 STM4408 STM1291 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM3248 STM0519 STM3241 STM0973 STM1124 STM4467 STM2196 STM3240 STM0402 STM0608 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.272744 (mmol/gDw/h)
  Minimum Production Rate : 0.155486 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 15.121011
  EX_glc__D_e : 5.000000
  EX_nh4_e : 3.005675
  EX_pi_e : 0.241876
  EX_k_e : 0.048439
  EX_so4_e : 0.033270
  EX_mg2_e : 0.002153
  EX_fe2_e : 0.001999
  EX_ca2_e : 0.001292
  EX_cl_e : 0.001292
  EX_cobalt2_e : 0.000861
  EX_cu2_e : 0.000861
  EX_mn2_e : 0.000861
  EX_mobd_e : 0.000861
  EX_zn2_e : 0.000861

Product: (mmol/gDw/h)
  EX_h2o_e : 23.683854
  EX_co2_e : 16.164768
  EX_h_e : 2.481342
  EX_acald_e : 0.695833
  Auxiliary production reaction : 0.155486
  EX_glyclt_e : 0.013637
  DM_hmfurn_c : 0.000122

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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