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 : mnl1p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (34 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b2836 b3553 b1478 b1241 b0351 b0871 b2297 b2458 b2925 b2097 b2926 b1004 b3713 b1109 b0046 b3236 b2690 b2210 b1033 b2799 b3945 b1602 b2913 b2223 b4381 b3915 b4064 b4464 b0529 b2492 b0904 b1380 b0606 b2285 b1009 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.361752 (mmol/gDw/h)
  Minimum Production Rate : 0.095408 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.292814
  EX_o2_e : 280.314521
  EX_glc__D_e : 10.000000
  EX_nh4_e : 3.906888
  EX_pi_e : 0.444356
  EX_so4_e : 0.091096
  EX_k_e : 0.070611
  EX_mg2_e : 0.003138
  EX_ca2_e : 0.001883
  EX_cl_e : 0.001883
  EX_cu2_e : 0.000256
  EX_mn2_e : 0.000250
  EX_zn2_e : 0.000123
  EX_ni2_e : 0.000117

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994190
  EX_h2o_e : 543.374348
  EX_co2_e : 28.446934
  EX_pyr_e : 5.377457
  Auxiliary production reaction : 0.095408
  DM_5drib_c : 0.000081
  DM_4crsol_c : 0.000081

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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