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 : hxan_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (76 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3500 b3553 b4382 b0474 b2518 b1241 b0351 b4384 b0871 b2781 b0099 b0160 b2235 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b1033 b1623 b0261 b3945 b1602 b0153 b1727 b0529 b2492 b0904 b2954 b0591 b1380 b2660 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.505919 (mmol/gDw/h)
  Minimum Production Rate : 0.019600 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 38.104848
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.543987
  EX_pi_e : 0.488013
  EX_so4_e : 0.127401
  EX_k_e : 0.098752
  EX_fe2_e : 0.008126
  EX_mg2_e : 0.004389
  EX_ca2_e : 0.002633
  EX_cl_e : 0.002633
  EX_cu2_e : 0.000359
  EX_mn2_e : 0.000350
  EX_zn2_e : 0.000173
  EX_ni2_e : 0.000163
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 52.674371
  EX_co2_e : 39.134638
  EX_h_e : 4.728690
  EX_hxan_e : 0.019600
  EX_ade_e : 0.000340
  DM_5drib_c : 0.000114
  DM_4crsol_c : 0.000113

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.

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Last updated: 21-Sep-2023
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