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 : dudp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b4467 b1478 b4382 b1241 b4069 b4384 b2744 b3708 b3752 b2297 b2458 b2926 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b2797 b3117 b1814 b4471 b2210 b0261 b0411 b1701 b1805 b1602 b3915 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b1380 b2660 b1771 b3662 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.418011 (mmol/gDw/h)
  Minimum Production Rate : 0.531205 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.994025
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.578761
  EX_pi_e : 1.465625
  EX_so4_e : 0.105263
  EX_k_e : 0.081593
  EX_fe3_e : 0.006714
  EX_mg2_e : 0.003626
  EX_cl_e : 0.002176
  EX_ca2_e : 0.002176
  EX_cu2_e : 0.000296
  EX_mn2_e : 0.000289
  EX_zn2_e : 0.000143
  EX_ni2_e : 0.000135
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 49.644465
  EX_co2_e : 35.159536
  EX_h_e : 4.623999
  EX_12ppd__S_e : 0.804070
  Auxiliary production reaction : 0.531205
  EX_ac_e : 0.243360
  EX_hxan_e : 0.000468
  DM_5drib_c : 0.000280
  DM_4crsol_c : 0.000093

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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