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 : ins_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (102 of 109: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b3553 b4382 b3942 b1732 b0474 b2518 b4069 b4384 b3752 b2297 b2458 b2779 b2407 b3844 b1004 b3713 b1109 b0046 b2463 b2210 b1033 b3551 b2799 b3945 b1602 b4219 b1832 b1778 b3915 b1727 b0114 b0529 b2492 b0904 b3927 b1380 b1710 b2480 b1518 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.415228 (mmol/gDw/h)
  Minimum Production Rate : 0.191872 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 35.514389
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.253034
  EX_pi_e : 0.400532
  EX_so4_e : 0.104563
  EX_k_e : 0.081050
  EX_fe3_e : 0.006669
  EX_mg2_e : 0.003602
  EX_ca2_e : 0.002161
  EX_cl_e : 0.002161
  EX_cu2_e : 0.000294
  EX_mn2_e : 0.000287
  EX_zn2_e : 0.000142
  EX_ni2_e : 0.000134
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 48.804709
  EX_co2_e : 34.378288
  EX_h_e : 7.919285
  EX_mal__L_e : 1.543494
  EX_ac_e : 0.241740
  EX_ins_e : 0.191872
  EX_hxan_e : 0.000279
  EX_mththf_e : 0.000186
  DM_5drib_c : 0.000093
  DM_4crsol_c : 0.000093

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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