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 : uamr_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (36 of 39: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b4467 b2836 b2242 b0474 b2518 b2744 b1278 b2781 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b1759 b2210 b4374 b4161 b0675 b4138 b4123 b0621 b4381 b2406 b0306 b3605 b2492 b0904 b2197 b3028 b3918 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.536095 (mmol/gDw/h)
  Minimum Production Rate : 0.283093 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.187118
  EX_o2_e : 279.413018
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.833219
  EX_pi_e : 1.083307
  EX_so4_e : 0.135000
  EX_k_e : 0.104642
  EX_mg2_e : 0.004651
  EX_ca2_e : 0.002790
  EX_cl_e : 0.002790
  EX_cu2_e : 0.000380
  EX_mn2_e : 0.000370
  EX_zn2_e : 0.000183
  EX_ni2_e : 0.000173
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991390
  EX_h2o_e : 548.303466
  EX_co2_e : 29.709434
  EX_succ_e : 0.559036
  Auxiliary production reaction : 0.283093
  EX_ura_e : 0.097078
  DM_5drib_c : 0.000121
  DM_4crsol_c : 0.000120

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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