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 : udpLa4o_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (78 of 83: 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 b0907 b0651 b2162 b1759 b2210 b1033 b1415 b4138 b4123 b0621 b4381 b2406 b0529 b2197 b3825 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 : 0.529614 (mmol/gDw/h)
  Minimum Production Rate : 0.279713 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.828679
  EX_o2_e : 281.599221
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.470931
  EX_pi_e : 1.070294
  EX_so4_e : 0.133367
  EX_k_e : 0.103377
  EX_mg2_e : 0.004594
  EX_cl_e : 0.002757
  EX_ca2_e : 0.002757
  EX_cu2_e : 0.000375
  EX_mn2_e : 0.000366
  EX_zn2_e : 0.000181
  EX_ni2_e : 0.000171
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991494
  EX_h2o_e : 549.562171
  EX_co2_e : 31.752079
  EX_succ_e : 0.552277
  Auxiliary production reaction : 0.279713
  EX_ura_e : 0.095862
  EX_dxylnt_e : 0.000236
  DM_5drib_c : 0.000119
  DM_4crsol_c : 0.000118

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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