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 : frdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (53 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3831 b3614 b0910 b3752 b4152 b2781 b1612 b1611 b4122 b0907 b1759 b0411 b1701 b1805 b4138 b4123 b0621 b4381 b2943 b3918 b3437 b4268 b4042 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.575727 (mmol/gDw/h)
  Minimum Production Rate : 0.101356 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.784822
  EX_o2_e : 279.887699
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.034353
  EX_pi_e : 0.758061
  EX_so4_e : 0.144980
  EX_k_e : 0.112378
  EX_mg2_e : 0.004994
  EX_ca2_e : 0.002997
  EX_cl_e : 0.002997
  EX_cu2_e : 0.000408
  EX_mn2_e : 0.000398
  EX_zn2_e : 0.000196
  EX_ni2_e : 0.000186
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990753
  EX_h2o_e : 549.060060
  EX_co2_e : 30.814163
  EX_succ_e : 0.600363
  EX_ura_e : 0.408276
  Auxiliary production reaction : 0.101356
  DM_5drib_c : 0.000130
  DM_4crsol_c : 0.000128

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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