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 : 2p4c2me_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (112 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b4467 b2836 b2242 b0474 b2518 b1241 b0351 b2744 b1278 b2781 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1759 b4374 b4161 b0675 b2361 b2291 b4014 b2976 b1602 b4138 b4123 b0621 b1727 b0306 b3605 b2492 b0904 b3028 b1380 b3918 b2660 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.461990 (mmol/gDw/h)
  Minimum Production Rate : 0.243998 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.456491
  EX_o2_e : 284.818679
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.721448
  EX_pi_e : 1.177632
  EX_so4_e : 0.116338
  EX_k_e : 0.090177
  EX_mg2_e : 0.004008
  EX_ca2_e : 0.002405
  EX_cl_e : 0.002405
  EX_cu2_e : 0.000328
  EX_mn2_e : 0.000319
  EX_zn2_e : 0.000158
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992580
  EX_h2o_e : 550.561463
  EX_co2_e : 35.443552
  EX_succ_e : 0.481760
  Auxiliary production reaction : 0.243998
  EX_3hpp_e : 0.083622
  DM_5drib_c : 0.000104
  DM_4crsol_c : 0.000103

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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