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 : pg120_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b2836 b4382 b0474 b2518 b3831 b4384 b4152 b2781 b0030 b1612 b1611 b4122 b0651 b2162 b1759 b4161 b4138 b4123 b0621 b2406 b3915 b2197 b3918 b4042 b1695 b1206 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.590789 (mmol/gDw/h)
  Minimum Production Rate : 0.311536 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.802622
  EX_o2_e : 268.503314
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.218380
  EX_pi_e : 0.881415
  EX_so4_e : 0.148772
  EX_k_e : 0.115318
  EX_mg2_e : 0.005125
  EX_ca2_e : 0.003075
  EX_cl_e : 0.003075
  EX_cu2_e : 0.000419
  EX_mn2_e : 0.000408
  EX_zn2_e : 0.000201
  EX_ni2_e : 0.000191
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990511
  EX_h2o_e : 541.189091
  EX_co2_e : 22.258814
  EX_succ_e : 0.616070
  EX_ura_e : 0.418957
  Auxiliary production reaction : 0.311536
  EX_hxa_e : 0.000971
  DM_5drib_c : 0.000133
  DM_4crsol_c : 0.000132

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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