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 : pnto__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (78 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 53
  Gene deletion: b4467 b3399 b4269 b3942 b1732 b0493 b3588 b3003 b3011 b4384 b2744 b3708 b3008 b3752 b2930 b4232 b3697 b3925 b0871 b1004 b3713 b1109 b0046 b2883 b2690 b1982 b2797 b3117 b1814 b4471 b2210 b1623 b0411 b3945 b1602 b4381 b2406 b0452 b1727 b0114 b2366 b2492 b0904 b1533 b3927 b1380 b2413 b4141 b1798 b1518 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.426008 (mmol/gDw/h)
  Minimum Production Rate : 0.260676 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.191761
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.907252
  EX_pi_e : 0.410930
  EX_so4_e : 0.107278
  EX_k_e : 0.083154
  EX_mg2_e : 0.003696
  EX_fe2_e : 0.003518
  EX_fe3_e : 0.003326
  EX_ca2_e : 0.002217
  EX_cl_e : 0.002217
  EX_cu2_e : 0.000302
  EX_mn2_e : 0.000294
  EX_zn2_e : 0.000145
  EX_ni2_e : 0.000138
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 44.161336
  EX_co2_e : 28.378510
  EX_h_e : 8.395289
  EX_pyr_e : 3.910558
  Auxiliary production reaction : 0.260670
  EX_hxan_e : 0.011434
  DM_mththf_c : 0.000191
  DM_5drib_c : 0.000096
  DM_4crsol_c : 0.000095

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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