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 : mnl1p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b3553 b1478 b3399 b4382 b1241 b0351 b4384 b2744 b0871 b2779 b2925 b2097 b0160 b3844 b1004 b3713 b1109 b0046 b3236 b2690 b2210 b1033 b2361 b2291 b4015 b2799 b3945 b1602 b2913 b3915 b0529 b2492 b0904 b3927 b1380 b1517 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.376892 (mmol/gDw/h)
  Minimum Production Rate : 0.040947 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.287538
  EX_o2_e : 280.351601
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.071674
  EX_pi_e : 0.404499
  EX_so4_e : 0.094909
  EX_k_e : 0.073567
  EX_mg2_e : 0.003270
  EX_ca2_e : 0.001962
  EX_cl_e : 0.001962
  EX_cu2_e : 0.000267
  EX_mn2_e : 0.000260
  EX_zn2_e : 0.000129
  EX_ni2_e : 0.000122

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993947
  EX_h2o_e : 543.750497
  EX_co2_e : 28.556198
  EX_pyr_e : 5.242103
  Auxiliary production reaction : 0.040947
  EX_ade_e : 0.000254
  DM_mththf_c : 0.000169
  DM_5drib_c : 0.000085
  DM_4crsol_c : 0.000084

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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