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 : sbt6p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (46 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4467 b1478 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b0871 b2925 b2097 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b2690 b3616 b3589 b2210 b0261 b2799 b3945 b1602 b0153 b4381 b0584 b2492 b0904 b1380 b2660 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.397969 (mmol/gDw/h)
  Minimum Production Rate : 0.397232 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.376591
  EX_o2_e : 282.636654
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.298035
  EX_pi_e : 0.781115
  EX_so4_e : 0.100217
  EX_k_e : 0.077681
  EX_mg2_e : 0.003452
  EX_ca2_e : 0.002071
  EX_cl_e : 0.002071
  EX_cu2_e : 0.000282
  EX_mn2_e : 0.000275
  EX_zn2_e : 0.000136
  EX_ni2_e : 0.000129

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993608
  EX_h2o_e : 542.543094
  EX_co2_e : 32.037020
  EX_glyclt_e : 3.960316
  EX_acald_e : 0.662072
  Auxiliary production reaction : 0.397232
  DM_5drib_c : 0.000090
  DM_4crsol_c : 0.000089

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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