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 : 12dgr140_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (52 of 105: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: STM1749 STM2463 STM2285 STM3526 STM4567 STM4326 STM1511 STM1885 STM2947 STM3709 STM1620 STM0491 STM0368 STM1448 STM1326 STM4062 STM3069 STM0518 STM4184 STM4484 STM0542 STM2317 STM3179 STM1480 STM4126 STM1124 STM4467 STM2196 STM3240 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.070886 (mmol/gDw/h)
  Minimum Production Rate : 0.061846 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 9.204204
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.781169
  EX_pi_e : 0.062862
  EX_k_e : 0.012589
  EX_so4_e : 0.008647
  EX_mg2_e : 0.000560
  EX_fe2_e : 0.000520
  EX_ca2_e : 0.000336
  EX_cl_e : 0.000336
  EX_cobalt2_e : 0.000224
  EX_cu2_e : 0.000224
  EX_mn2_e : 0.000224
  EX_mobd_e : 0.000224
  EX_zn2_e : 0.000224

Product: (mmol/gDw/h)
  EX_h2o_e : 12.090350
  EX_co2_e : 10.074309
  EX_dha_e : 4.928803
  EX_h_e : 0.604486
  EX_acald_e : 0.236452
  Auxiliary production reaction : 0.061847
  EX_glyclt_e : 0.003544
  DM_hmfurn_c : 0.000032

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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