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 : unagamuf_p
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 : 46
  Gene deletion: b3399 b0474 b2518 b2502 b2744 b3708 b3008 b0512 b4152 b0871 b2925 b2097 b2926 b1612 b1611 b4122 b2690 b2920 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0822 b1701 b1805 b4138 b4123 b0621 b1727 b0114 b0728 b0886 b2366 b2492 b0904 b0591 b2578 b1533 b3927 b4042 b1511 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.551857 (mmol/gDw/h)
  Minimum Production Rate : 0.041269 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 26.396620
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.614423
  EX_pi_e : 0.614863
  EX_so4_e : 0.138969
  EX_k_e : 0.107719
  EX_fe2_e : 0.008863
  EX_mg2_e : 0.004787
  EX_ca2_e : 0.002872
  EX_cl_e : 0.002872
  EX_cu2_e : 0.000391
  EX_mn2_e : 0.000381
  EX_zn2_e : 0.000188
  EX_ni2_e : 0.000178
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 47.135955
  EX_co2_e : 26.897704
  EX_h_e : 8.739172
  EX_succ_e : 1.027672
  EX_ura_e : 0.553847
  EX_alltn_e : 0.081249
  EX_trp__L_e : 0.048958
  Auxiliary production reaction : 0.041269
  DM_mththf_c : 0.000247
  DM_5drib_c : 0.000124
  DM_4crsol_c : 0.000123

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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