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 : 2p4c2me_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (94 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3916 b4382 b0474 b2518 b3831 b4384 b1278 b3752 b4152 b2779 b2781 b1850 b1612 b1611 b4122 b1759 b0477 b4161 b4138 b4123 b0621 b2406 b0452 b0114 b1723 b3918 b1206 b0221 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.634105 (mmol/gDw/h)
  Minimum Production Rate : 0.334899 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.497307
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.082524
  EX_pi_e : 1.616359
  EX_so4_e : 0.159680
  EX_k_e : 0.123773
  EX_fe2_e : 0.010184
  EX_mg2_e : 0.005501
  EX_ca2_e : 0.003301
  EX_cl_e : 0.003301
  EX_cu2_e : 0.000450
  EX_mn2_e : 0.000438
  EX_zn2_e : 0.000216
  EX_ni2_e : 0.000205
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 47.509327
  EX_co2_e : 26.180268
  EX_h_e : 7.713335
  EX_succ_e : 0.661239
  Auxiliary production reaction : 0.334899
  EX_ura_e : 0.114775
  DM_5drib_c : 0.000143
  DM_4crsol_c : 0.000141

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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