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 : ppgpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 53
  Gene deletion: b4467 b1478 b3399 b4382 b0474 b2518 b1241 b4069 b2502 b4384 b2744 b0512 b3115 b1849 b2296 b2926 b2781 b0099 b0030 b3844 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b0937 b1982 b4139 b1623 b4015 b0261 b0411 b2799 b3945 b1602 b3654 b3714 b3664 b4064 b4464 b0529 b2492 b0904 b2954 b1298 b3029 b1380 b2660 b3662 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.430199 (mmol/gDw/h)
  Minimum Production Rate : 0.451618 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.759639
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.906128
  EX_pi_e : 2.221444
  EX_so4_e : 0.108333
  EX_k_e : 0.083972
  EX_mg2_e : 0.003732
  EX_fe2_e : 0.003550
  EX_fe3_e : 0.003359
  EX_ca2_e : 0.002239
  EX_cl_e : 0.002239
  EX_cu2_e : 0.000305
  EX_mn2_e : 0.000297
  EX_zn2_e : 0.000147
  EX_ni2_e : 0.000139
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 55.458655
  EX_co2_e : 37.322331
  EX_h_e : 5.563434
  Auxiliary production reaction : 0.451618
  EX_ac_e : 0.250456
  EX_alltn_e : 0.000481
  DM_5drib_c : 0.000289
  DM_4crsol_c : 0.000096

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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