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 : g3pg_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (100 of 110: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b4467 b2242 b2744 b3614 b0910 b2781 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1759 b3449 b4374 b0675 b2361 b2291 b4014 b2976 b4388 b4138 b4123 b0621 b2239 b0306 b3605 b2492 b0904 b2197 b3028 b3918 b0789 b1249 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.525300 (mmol/gDw/h)
  Minimum Production Rate : 0.277434 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.601395
  EX_o2_e : 282.524669
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.418223
  EX_pi_e : 0.784142
  EX_so4_e : 0.132281
  EX_k_e : 0.102535
  EX_mg2_e : 0.004557
  EX_ca2_e : 0.002734
  EX_cl_e : 0.002734
  EX_cu2_e : 0.000372
  EX_mn2_e : 0.000363
  EX_zn2_e : 0.000179
  EX_ni2_e : 0.000170
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991563
  EX_h2o_e : 549.370225
  EX_co2_e : 33.092375
  EX_succ_e : 0.547778
  EX_ura_e : 0.372515
  EX_g3pg_e : 0.277434
  EX_glyclt_e : 0.000351
  DM_5drib_c : 0.000118
  DM_4crsol_c : 0.000117

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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