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 : air_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (82 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b0474 b2518 b1241 b0351 b4384 b3708 b3008 b0871 b2297 b2458 b3617 b0030 b2407 b3962 b1982 b4139 b2797 b3117 b1814 b4471 b4267 b0675 b0261 b0822 b2799 b4381 b2406 b2943 b0114 b0886 b0529 b1539 b2492 b0904 b2578 b1533 b3927 b3821 b3437 b4268 b2413 b0508 b4266 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.530683 (mmol/gDw/h)
  Minimum Production Rate : 0.182716 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.566015
  EX_o2_e : 285.802673
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.280072
  EX_pi_e : 0.694616
  EX_so4_e : 0.133637
  EX_k_e : 0.103586
  EX_mg2_e : 0.004604
  EX_ca2_e : 0.002762
  EX_cl_e : 0.002762
  EX_cu2_e : 0.000376
  EX_mn2_e : 0.000367
  EX_zn2_e : 0.000181
  EX_ni2_e : 0.000171
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991477
  EX_h2o_e : 552.043611
  EX_co2_e : 36.753804
  Auxiliary production reaction : 0.182716
  DM_oxam_c : 0.000594
  DM_5drib_c : 0.000356
  DM_4crsol_c : 0.000118

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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