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 : 2omph_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (53 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b1478 b4382 b1241 b0351 b4069 b4384 b0512 b2297 b2458 b2925 b2097 b3617 b0030 b2407 b3236 b1779 b2690 b1982 b2210 b0675 b0411 b0822 b2406 b0114 b0529 b2492 b0904 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.509444 (mmol/gDw/h)
  Minimum Production Rate : 0.052647 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.405025
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.281128
  EX_pi_e : 0.491413
  EX_so4_e : 0.128288
  EX_k_e : 0.099440
  EX_fe2_e : 0.008182
  EX_mg2_e : 0.004419
  EX_ca2_e : 0.002652
  EX_cl_e : 0.002652
  EX_cu2_e : 0.000361
  EX_mn2_e : 0.000352
  EX_zn2_e : 0.000174
  EX_ni2_e : 0.000165
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 48.338819
  EX_co2_e : 26.087890
  EX_h_e : 9.918447
  EX_ac_e : 1.458297
  EX_gsn_e : 0.713443
  EX_alltn_e : 0.052990
  DM_mththf_c : 0.052875
  Auxiliary production reaction : 0.052647
  DM_5drib_c : 0.000115
  DM_4crsol_c : 0.000114

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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