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 : pe140_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 110: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: STM1463 STM1749 STM2463 STM2285 STM3526 STM0322 STM4567 STM4326 STM1511 STM1884 STM2947 STM3709 STM3068 STM2141 STM1620 STM0974 STM1448 STM0772 STM4585 STM3704 STM4184 STM4484 STM0542 STM2317 STM3179 STM1480 STM4126 STM4578 STM2338 STM2466 STM3248 STM0519 STM4467 STM2196 STM3240 STM2041 STM3708 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.061018 (mmol/gDw/h)
  Minimum Production Rate : 0.055296 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 9.504456
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.729991
  EX_pi_e : 0.109407
  EX_k_e : 0.010837
  EX_so4_e : 0.007443
  EX_mg2_e : 0.000482
  EX_fe2_e : 0.000447
  EX_ca2_e : 0.000289
  EX_cl_e : 0.000289
  EX_cu2_e : 0.000193
  EX_mn2_e : 0.000193
  EX_mobd_e : 0.000193
  EX_zn2_e : 0.000193
  EX_cobalt2_e : 0.000193

Product: (mmol/gDw/h)
  EX_h2o_e : 12.213796
  EX_co2_e : 10.361213
  EX_dha_e : 4.938714
  EX_h_e : 0.467311
  EX_acald_e : 0.314582
  Auxiliary production reaction : 0.055296
  EX_glyclt_e : 0.003051
  EX_ade_e : 0.000454
  DM_hmfurn_c : 0.000027

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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