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 : malcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 53
  Gene deletion: b4467 b1478 b4382 b1241 b0351 b4069 b4384 b3708 b2297 b2458 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b2797 b3117 b1814 b4471 b0261 b0411 b2799 b3945 b1602 b3709 b2406 b3161 b0112 b3915 b0452 b2975 b3603 b0509 b3125 b1539 b2492 b0904 b1533 b1380 b0508 b1473 b1600 b2660 b4141 b1798 b0606 b2285 b1009 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.378302 (mmol/gDw/h)
  Minimum Production Rate : 0.064523 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.469519
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.046431
  EX_pi_e : 0.558474
  EX_so4_e : 0.159785
  EX_k_e : 0.073842
  EX_fe3_e : 0.006077
  EX_mg2_e : 0.003282
  EX_ca2_e : 0.001969
  EX_cl_e : 0.001969
  EX_cu2_e : 0.000268
  EX_mn2_e : 0.000261
  EX_zn2_e : 0.000129
  EX_ni2_e : 0.000122

Product: (mmol/gDw/h)
  EX_h2o_e : 51.634929
  EX_co2_e : 34.772895
  EX_h_e : 7.815884
  EX_ac_e : 1.566578
  EX_gsn_e : 0.501492
  Auxiliary production reaction : 0.064520
  EX_hxan_e : 0.000423
  DM_5drib_c : 0.000254
  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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