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 (29 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4467 b1478 b4269 b0493 b3588 b3003 b3011 b0474 b2518 b1241 b0871 b3844 b1004 b3713 b1109 b0046 b3236 b2799 b3945 b1602 b0153 b2975 b3603 b0584 b0755 b3612 b2492 b0904 b1380 b2660 b0514 b1517 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.496562 (mmol/gDw/h)
  Minimum Production Rate : 0.295725 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.635401
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.362830
  EX_pi_e : 0.774712
  EX_so4_e : 0.125044
  EX_k_e : 0.096925
  EX_fe2_e : 0.007975
  EX_mg2_e : 0.004308
  EX_ca2_e : 0.002585
  EX_cl_e : 0.002585
  EX_cu2_e : 0.000352
  EX_mn2_e : 0.000343
  EX_zn2_e : 0.000169
  EX_ni2_e : 0.000160
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 50.955773
  EX_co2_e : 37.842938
  EX_h_e : 4.562612
  Auxiliary production reaction : 0.295725
  DM_mththf_c : 0.000222
  DM_5drib_c : 0.000112
  DM_4crsol_c : 0.000111

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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