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 : pgp180_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 130: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: STM3646 STM1463 STM1749 STM2463 STM2285 STM3526 STM4326 STM2952 STM0840 STM0842 STM0517 STM2947 STM3709 STM1135 STM4183 STM0369 STM1448 STM4484 STM2317 STM3179 STM1480 STM4126 STM4578 STM2338 STM2466 STM1124 STM4467 STM3802 STM2196 STM3240 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.286316 (mmol/gDw/h)
  Minimum Production Rate : 0.003372 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 16.956483
  EX_glc__D_e : 5.000000
  EX_nh4_e : 3.155239
  EX_pi_e : 0.260655
  EX_k_e : 0.050850
  EX_so4_e : 0.034925
  EX_mg2_e : 0.002260
  EX_fe2_e : 0.002098
  EX_ca2_e : 0.001356
  EX_cl_e : 0.001356
  EX_cobalt2_e : 0.000904
  EX_cu2_e : 0.000904
  EX_mn2_e : 0.000904
  EX_mobd_e : 0.000904
  EX_zn2_e : 0.000904

Product: (mmol/gDw/h)
  EX_h2o_e : 25.196738
  EX_co2_e : 17.293382
  EX_h_e : 2.438221
  EX_acald_e : 0.730458
  EX_glyclt_e : 0.014316
  Auxiliary production reaction : 0.003372
  DM_hmfurn_c : 0.000128

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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