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 : udpLa4n_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (84 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b2242 b3553 b4382 b0474 b2518 b3831 b4384 b3752 b2781 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b1759 b2210 b1033 b2440 b4161 b4388 b4138 b4123 b0621 b2406 b0529 b0306 b3605 b2197 b3028 b3918 b1912 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.528246 (mmol/gDw/h)
  Minimum Production Rate : 0.278637 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.844854
  EX_o2_e : 281.538556
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.732148
  EX_pi_e : 1.066823
  EX_so4_e : 0.133023
  EX_k_e : 0.103110
  EX_mg2_e : 0.004583
  EX_ca2_e : 0.002750
  EX_cl_e : 0.002750
  EX_cu2_e : 0.000375
  EX_mn2_e : 0.000365
  EX_zn2_e : 0.000180
  EX_ni2_e : 0.000171
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991516
  EX_h2o_e : 549.591721
  EX_co2_e : 31.831163
  EX_succ_e : 0.550850
  Auxiliary production reaction : 0.278637
  EX_ura_e : 0.095614
  DM_5drib_c : 0.000119
  DM_4crsol_c : 0.000118

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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