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 : pa181_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 124: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: STM3646 STM2285 STM3526 STM4326 STM1511 STM0321 STM0840 STM0842 STM3247 STM1135 STM3542 STM4485 STM4183 STM0368 STM1448 STM0772 STM4585 STM3704 STM4484 STM2317 STM3179 STM4569 STM1480 STM4126 STM2338 STM2466 STM0977   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.255001 (mmol/gDw/h)
  Minimum Production Rate : 0.025826 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.810146
  EX_pi_e : 0.251967
  EX_k_e : 0.045288
  EX_so4_e : 0.031106
  EX_mg2_e : 0.002013
  EX_fe2_e : 0.001869
  EX_ca2_e : 0.001208
  EX_cl_e : 0.001208
  EX_cobalt2_e : 0.000805
  EX_cu2_e : 0.000805
  EX_mn2_e : 0.000805
  EX_mobd_e : 0.000805
  EX_zn2_e : 0.000805

Product: (mmol/gDw/h)
  EX_h2o_e : 25.960451
  EX_co2_e : 18.827203
  EX_h_e : 2.309354
  EX_ac_e : 0.141177
  Auxiliary production reaction : 0.025826
  EX_glyc__R_e : 0.006375
  DM_hmfurn_c : 0.000114

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.

Last updated: 27-Sep-2023
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