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 : dcamp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (77 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b4382 b3942 b1732 b4069 b4384 b3708 b1479 b3752 b0871 b3115 b1849 b2296 b2779 b2925 b2097 b2407 b3236 b2690 b2463 b1982 b2797 b3117 b1814 b4471 b2210 b3551 b1701 b1805 b3945 b2913 b4219 b1832 b1778 b2406 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b1710 b2480 b3662 b1517 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.344084 (mmol/gDw/h)
  Minimum Production Rate : 0.145958 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 989.883730
  EX_o2_e : 279.901771
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.446791
  EX_pi_e : 0.477863
  EX_so4_e : 0.086647
  EX_k_e : 0.067163
  EX_mg2_e : 0.002985
  EX_cl_e : 0.001791
  EX_ca2_e : 0.001791
  EX_cu2_e : 0.000244
  EX_mn2_e : 0.000238
  EX_zn2_e : 0.000117
  EX_ni2_e : 0.000111

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994474
  EX_h2o_e : 543.612797
  EX_co2_e : 27.262781
  EX_pyr_e : 4.715755
  EX_mal__L_e : 0.505229
  EX_ac_e : 0.200321
  Auxiliary production reaction : 0.145958
  EX_xan_e : 0.000232
  DM_mththf_c : 0.000154
  DM_5drib_c : 0.000077
  DM_4crsol_c : 0.000077

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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