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 : dhnpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (82 of 90: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 47
  Gene deletion: b4467 b3399 b0238 b0125 b4069 b2502 b2744 b2297 b2458 b2779 b1004 b3713 b1109 b0046 b3236 b1638 b0477 b4139 b0675 b2361 b2799 b3945 b1602 b4381 b2406 b3915 b3654 b2868 b3714 b3664 b1727 b4064 b4464 b0114 b0529 b2492 b0904 b2954 b3927 b3825 b3029 b1380 b2660 b3662 b1518 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.477809 (mmol/gDw/h)
  Minimum Production Rate : 0.123257 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.982981
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.826587
  EX_pi_e : 0.460897
  EX_so4_e : 0.120322
  EX_k_e : 0.093265
  EX_fe3_e : 0.007674
  EX_mg2_e : 0.004145
  EX_ca2_e : 0.002487
  EX_cl_e : 0.002487
  EX_cu2_e : 0.000339
  EX_mn2_e : 0.000330
  EX_zn2_e : 0.000163
  EX_ni2_e : 0.000154
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.617765
  EX_co2_e : 38.658904
  EX_h_e : 5.342439
  EX_ac_e : 0.278174
  Auxiliary production reaction : 0.123257
  EX_xan_e : 0.012502
  EX_mththf_e : 0.000214
  DM_5drib_c : 0.000108
  DM_4crsol_c : 0.000107

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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