MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : lald__D_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (9 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4467 b1478 b1241 b4069 b2297 b2458 b2925 b2097 b2926 b1004 b3713 b1109 b0046 b3236 b2690 b2210 b1602 b2492 b0904 b1380 b2660 b1771 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.449427 (mmol/gDw/h)
  Minimum Production Rate : 1.920000 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.346593
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.853769
  EX_pi_e : 0.433520
  EX_so4_e : 0.113175
  EX_k_e : 0.087725
  EX_mg2_e : 0.003899
  EX_fe2_e : 0.003709
  EX_fe3_e : 0.003509
  EX_ca2_e : 0.002339
  EX_cl_e : 0.002339
  EX_cu2_e : 0.000319
  EX_mn2_e : 0.000311
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 47.133379
  EX_co2_e : 35.267019
  EX_h_e : 4.394670
  Auxiliary production reaction : 1.920928
  EX_ac_e : 0.261650
  DM_5drib_c : 0.000101
  DM_4crsol_c : 0.000100

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

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: 21-Sep-2023
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