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 : fpram_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 50
  Gene deletion: b3500 b3553 b3399 b4382 b0474 b2518 b4069 b4384 b2744 b0871 b2297 b2458 b2925 b2097 b2781 b0099 b0160 b2235 b1004 b3713 b1109 b0046 b3236 b2883 b1779 b2690 b1033 b1623 b3665 b0411 b2799 b3945 b1602 b3654 b3714 b3664 b1727 b0114 b0529 b2492 b0904 b2954 b3927 b1380 b2660 b3662 b1517 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.348928 (mmol/gDw/h)
  Minimum Production Rate : 0.242205 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.913066
  EX_o2_e : 279.860368
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.495007
  EX_pi_e : 0.578783
  EX_so4_e : 0.087867
  EX_k_e : 0.068108
  EX_mg2_e : 0.003027
  EX_ca2_e : 0.001816
  EX_cl_e : 0.001816
  EX_cu2_e : 0.000247
  EX_mn2_e : 0.000241
  EX_zn2_e : 0.000119
  EX_ni2_e : 0.000113

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994396
  EX_h2o_e : 543.622678
  EX_co2_e : 27.770338
  EX_pyr_e : 5.187690
  Auxiliary production reaction : 0.242205
  EX_ac_e : 0.203141
  DM_mththf_c : 0.000156
  DM_5drib_c : 0.000079
  DM_4crsol_c : 0.000078

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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