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 : ser__D_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (84 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b4467 b1478 b3942 b1732 b1241 b4069 b3708 b2297 b2458 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b2463 b2797 b3117 b1814 b4471 b2210 b3551 b2799 b3945 b1602 b0153 b4219 b1832 b1778 b4381 b2406 b2366 b2492 b0904 b3035 b1533 b1380 b1710 b2480 b1511 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.447807 (mmol/gDw/h)
  Minimum Production Rate : 0.680781 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 35.457110
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.517055
  EX_pi_e : 0.431957
  EX_so4_e : 0.112767
  EX_k_e : 0.087409
  EX_fe2_e : 0.007192
  EX_mg2_e : 0.003885
  EX_ca2_e : 0.002331
  EX_cl_e : 0.002331
  EX_cu2_e : 0.000317
  EX_mn2_e : 0.000309
  EX_zn2_e : 0.000153
  EX_ni2_e : 0.000145
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 48.578466
  EX_co2_e : 35.605379
  EX_h_e : 6.780841
  EX_ac_e : 1.051495
  Auxiliary production reaction : 0.680781
  EX_mal__L_e : 0.466969
  EX_mththf_e : 0.000201
  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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