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 : grdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (38 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b0474 b2518 b2744 b4152 b0871 b2925 b2097 b2926 b2781 b1612 b1611 b4122 b2690 b1759 b4374 b4161 b0675 b2361 b2291 b3945 b4138 b4123 b0621 b0114 b2492 b0904 b3918 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.596415 (mmol/gDw/h)
  Minimum Production Rate : 0.116020 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.426611
  EX_o2_e : 276.611399
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.287130
  EX_pi_e : 0.807346
  EX_so4_e : 0.150189
  EX_k_e : 0.116416
  EX_mg2_e : 0.005174
  EX_cl_e : 0.003104
  EX_ca2_e : 0.003104
  EX_cu2_e : 0.000423
  EX_mn2_e : 0.000412
  EX_zn2_e : 0.000203
  EX_ni2_e : 0.000193
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990421
  EX_h2o_e : 546.789855
  EX_co2_e : 26.850270
  EX_pyr_e : 1.109958
  EX_succ_e : 0.621937
  EX_ura_e : 0.422947
  Auxiliary production reaction : 0.116020
  DM_5drib_c : 0.000134
  DM_4crsol_c : 0.000133

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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