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 : ps160_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (45 of 119: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: STM3646 STM2285 STM3526 STM1290 STM4567 STM4326 STM0321 STM3709 STM3068 STM0525 STM2141 STM3247 STM2959 STM2492 STM1135 STM3542 STM4485 STM4183 STM0370 STM1448 STM4484 STM2317 STM3179 STM1480 STM4126 STM2338 STM2466 STM3708   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.232486 (mmol/gDw/h)
  Minimum Production Rate : 0.044204 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 2.606233
  EX_pi_e : 0.250378
  EX_k_e : 0.041290
  EX_so4_e : 0.028359
  EX_mg2_e : 0.001835
  EX_fe2_e : 0.001704
  EX_ca2_e : 0.001101
  EX_cl_e : 0.001101
  EX_cobalt2_e : 0.000734
  EX_cu2_e : 0.000734
  EX_mn2_e : 0.000734
  EX_mobd_e : 0.000734
  EX_zn2_e : 0.000734

Product: (mmol/gDw/h)
  EX_h2o_e : 25.638277
  EX_co2_e : 19.052212
  EX_h_e : 2.105454
  EX_ac_e : 0.128712
  Auxiliary production reaction : 0.044204
  EX_glyc__R_e : 0.005812
  DM_hmfurn_c : 0.000104

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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