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_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (73 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: STM1463 STM1749 STM2463 STM2285 STM3526 STM0169 STM0861 STM4326 STM2947 STM1620 STM0369 STM3597 STM1326 STM4062 STM4408 STM1291 STM0518 STM4184 STM4484 STM0542 STM2317 STM3179 STM1480 STM4126 STM1124 STM4467 STM3802 STM2196 STM3240 STM0402 STM0608 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.273552 (mmol/gDw/h)
  Minimum Production Rate : 0.194457 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 14.958713
  EX_glc__D_e : 5.000000
  EX_nh4_e : 3.014581
  EX_pi_e : 0.242592
  EX_k_e : 0.048583
  EX_so4_e : 0.033368
  EX_mg2_e : 0.002160
  EX_fe2_e : 0.002005
  EX_ca2_e : 0.001296
  EX_cl_e : 0.001296
  EX_cu2_e : 0.000864
  EX_mn2_e : 0.000864
  EX_mobd_e : 0.000864
  EX_zn2_e : 0.000864
  EX_cobalt2_e : 0.000864

Product: (mmol/gDw/h)
  EX_h2o_e : 23.632188
  EX_co2_e : 16.090821
  EX_h_e : 2.527205
  EX_acald_e : 0.483308
  Auxiliary production reaction : 0.194457
  EX_glyclt_e : 0.013678
  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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