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 : ddca_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (13 of 113: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: STM2927 STM1749 STM2463 STM2285 STM2009 STM3526 STM4326 STM1511 STM1885 STM2952 STM0321 STM2947 STM3709 STM1620 STM2081 STM0370 STM1326 STM4062 STM4408 STM1291 STM4184 STM4484 STM2317 STM3179 STM1480 STM4126 STM4578 STM2338 STM2466 STM3248 STM0519 STM4467 STM2196 STM3240 STM0007 STM2473 STM0402 STM0608 STM2971 STM1826 STM1341   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.066347 (mmol/gDw/h)
  Minimum Production Rate : 0.160254 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 9.111789
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.776720
  EX_pi_e : 0.058836
  EX_k_e : 0.011783
  EX_so4_e : 0.008093
  EX_mg2_e : 0.000524
  EX_fe2_e : 0.000486
  EX_ca2_e : 0.000314
  EX_cl_e : 0.000314
  EX_cobalt2_e : 0.000210
  EX_cu2_e : 0.000210
  EX_mn2_e : 0.000210
  EX_mobd_e : 0.000210
  EX_zn2_e : 0.000210

Product: (mmol/gDw/h)
  EX_h2o_e : 12.057569
  EX_co2_e : 10.000635
  EX_dha_e : 4.918170
  EX_h_e : 0.771606
  EX_acald_e : 0.169264
  Auxiliary production reaction : 0.160254
  EX_tyr__L_e : 0.045578
  EX_glyclt_e : 0.003317
  DM_hmfurn_c : 0.000030

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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