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 : pan4p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (73 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b2242 b3553 b3831 b3614 b0910 b2781 b0030 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b0651 b2162 b1759 b2210 b1033 b2440 b4138 b4123 b0621 b4381 b2406 b0452 b0306 b3605 b2197 b3028 b3918 b1912 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.532525 (mmol/gDw/h)
  Minimum Production Rate : 0.280851 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.231892
  EX_o2_e : 280.043810
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.067541
  EX_pi_e : 0.794529
  EX_so4_e : 0.414952
  EX_k_e : 0.103945
  EX_mg2_e : 0.004620
  EX_cl_e : 0.002772
  EX_ca2_e : 0.002772
  EX_cu2_e : 0.000378
  EX_mn2_e : 0.000368
  EX_zn2_e : 0.000182
  EX_ni2_e : 0.000172
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991447
  EX_h2o_e : 549.225368
  EX_co2_e : 31.321136
  EX_succ_e : 0.555313
  EX_ura_e : 0.377283
  Auxiliary production reaction : 0.280851
  EX_for_e : 0.001306
  DM_5drib_c : 0.000120
  DM_4crsol_c : 0.000119
  EX_etha_e : 0.000043

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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