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 : dtdprmn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (69 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b3831 b1278 b3614 b0910 b3752 b4152 b2925 b2097 b2781 b1850 b3617 b1612 b1611 b4122 b1759 b1200 b4138 b4123 b0621 b4381 b2406 b3825 b3918 b0494 b1518 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.588689 (mmol/gDw/h)
  Minimum Production Rate : 0.310913 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 998.765038
  EX_o2_e : 271.563016
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.192726
  EX_so4_e : 2.960480
  EX_pi_e : 1.189679
  EX_k_e : 0.114908
  EX_mg2_e : 0.005107
  EX_cl_e : 0.003064
  EX_ca2_e : 0.003064
  EX_cu2_e : 0.000417
  EX_mn2_e : 0.000407
  EX_zn2_e : 0.000201
  EX_ni2_e : 0.000190
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990545
  EX_h2o_e : 547.465146
  EX_co2_e : 27.979354
  EX_h2s_e : 2.812236
  EX_succ_e : 0.613880
  Auxiliary production reaction : 0.310913
  EX_ura_e : 0.106554
  DM_mththf_c : 0.000264
  DM_5drib_c : 0.000132
  DM_4crsol_c : 0.000131

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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