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 (64 of 90: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3399 b4069 b2502 b2744 b3708 b3008 b2297 b2458 b2688 b2797 b3117 b1814 b4471 b3449 b1623 b3665 b4374 b0675 b2361 b2291 b2406 b3654 b3714 b3664 b0114 b2366 b2492 b0904 b2578 b1533 b3927 b0494 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.726470 (mmol/gDw/h)
  Minimum Production Rate : 0.399649 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.616249
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.907391
  EX_pi_e : 0.700757
  EX_so4_e : 0.182940
  EX_k_e : 0.141802
  EX_fe2_e : 0.011668
  EX_mg2_e : 0.006302
  EX_ca2_e : 0.003781
  EX_cl_e : 0.003781
  EX_cu2_e : 0.000515
  EX_mn2_e : 0.000502
  EX_zn2_e : 0.000248
  EX_ni2_e : 0.000235
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 48.727961
  EX_co2_e : 25.104099
  EX_h_e : 9.159614
  EX_ac_e : 0.422941
  Auxiliary production reaction : 0.399649
  EX_enter_e : 0.021110
  DM_mththf_c : 0.000325
  DM_5drib_c : 0.000163
  DM_4crsol_c : 0.000162

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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