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 : dtdp4addg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (85 of 107: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b0474 b2518 b3831 b3752 b4152 b2925 b2097 b2926 b2781 b1850 b1612 b1611 b4122 b1759 b1200 b4161 b4138 b4123 b0621 b4381 b2406 b0529 b3821 b3918 b0789 b1249 b1511 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.606638 (mmol/gDw/h)
  Minimum Production Rate : 0.018719 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.026394
  EX_o2_e : 277.217734
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.229639
  EX_pi_e : 0.622604
  EX_so4_e : 0.152764
  EX_k_e : 0.118412
  EX_mg2_e : 0.005263
  EX_ca2_e : 0.003158
  EX_cl_e : 0.003158
  EX_cu2_e : 0.000430
  EX_mn2_e : 0.000419
  EX_zn2_e : 0.000207
  EX_ni2_e : 0.000196
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.889699
  EX_h2o_e : 548.056971
  EX_co2_e : 28.410838
  EX_succ_e : 0.632598
  EX_ura_e : 0.109803
  EX_pheme_e : 0.100558
  Auxiliary production reaction : 0.018719
  DM_mththf_c : 0.000272
  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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