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 : orot5p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (110 of 112: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 53
  Gene deletion: b4467 b1855 b2242 b1478 b4382 b0474 b2518 b1241 b0351 b3831 b4384 b3708 b3752 b3926 b2779 b2781 b3617 b3844 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1638 b1759 b0937 b4161 b4015 b0411 b2799 b3945 b1602 b4138 b4123 b0621 b1297 b0529 b2835 b3029 b3028 b1380 b3918 b0494 b2660 b1695 b1206 b2285 b1009 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.470246 (mmol/gDw/h)
  Minimum Production Rate : 0.022682 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.594945
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.294210
  EX_pi_e : 0.476284
  EX_so4_e : 0.118417
  EX_k_e : 0.091789
  EX_mg2_e : 0.004079
  EX_fe2_e : 0.003881
  EX_fe3_e : 0.003672
  EX_ca2_e : 0.002448
  EX_cl_e : 0.002448
  EX_cu2_e : 0.000333
  EX_mn2_e : 0.000325
  EX_zn2_e : 0.000160
  EX_ni2_e : 0.000152
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 51.683272
  EX_co2_e : 38.169814
  EX_h_e : 5.543492
  EX_succ_e : 0.490369
  EX_ura_e : 0.085116
  Auxiliary production reaction : 0.022682
  DM_5drib_c : 0.000106
  DM_4crsol_c : 0.000105

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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