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 : udpLa4fn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b0474 b2518 b1241 b0351 b3831 b3752 b4152 b2781 b3617 b1612 b1611 b4122 b0907 b1779 b1759 b4161 b0411 b4138 b4123 b0621 b4381 b0529 b2492 b0904 b3918 b1912 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.422541 (mmol/gDw/h)
  Minimum Production Rate : 0.223163 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.853363
  EX_o2_e : 284.533908
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.385863
  EX_pi_e : 0.853912
  EX_so4_e : 0.106404
  EX_k_e : 0.082477
  EX_mg2_e : 0.003666
  EX_ca2_e : 0.002199
  EX_cl_e : 0.002199
  EX_cu2_e : 0.000300
  EX_mn2_e : 0.000292
  EX_zn2_e : 0.000144
  EX_ni2_e : 0.000136
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993214
  EX_h2o_e : 549.605497
  EX_co2_e : 35.172917
  EX_acald_e : 1.033918
  EX_succ_e : 0.440623
  Auxiliary production reaction : 0.223163
  EX_ura_e : 0.076481
  DM_5drib_c : 0.000095
  DM_4crsol_c : 0.000094

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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