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 : q8_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3708 b3008 b4152 b0871 b2925 b2097 b1238 b1612 b1611 b4122 b1779 b2797 b3117 b1814 b4471 b3946 b0825 b4138 b4123 b0621 b4381 b2406 b0114 b1539 b2492 b0904 b1533 b3927 b3821 b0516 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.604316 (mmol/gDw/h)
  Minimum Production Rate : 0.029363 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.333516
  EX_o2_e : 276.267364
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.397815
  EX_pi_e : 0.582927
  EX_so4_e : 0.152179
  EX_k_e : 0.117958
  EX_mg2_e : 0.005242
  EX_ca2_e : 0.003145
  EX_cl_e : 0.003145
  EX_cu2_e : 0.000428
  EX_mn2_e : 0.000418
  EX_zn2_e : 0.000206
  EX_ni2_e : 0.000195
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990294
  EX_h2o_e : 546.667491
  EX_co2_e : 26.590321
  EX_pyr_e : 0.967757
  EX_succ_e : 0.632535
  EX_ura_e : 0.430909
  Auxiliary production reaction : 0.029363
  EX_alltn_e : 0.002359
  DM_5drib_c : 0.000136
  DM_4crsol_c : 0.000135

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.

Last updated: 21-Sep-2023
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