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 : ins_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (36 of 37: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b4382 b3942 b1732 b0474 b2518 b4384 b2744 b3708 b3008 b1479 b0871 b2925 b2097 b0030 b2407 b3236 b1779 b2690 b2463 b2797 b3117 b1814 b4471 b2210 b3665 b3551 b0411 b3945 b4219 b1832 b1778 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b3821 b1710 b2480 b1511 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.356073 (mmol/gDw/h)
  Minimum Production Rate : 0.081943 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.076666
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.174530
  EX_pi_e : 0.343470
  EX_so4_e : 0.089666
  EX_k_e : 0.069503
  EX_mg2_e : 0.003089
  EX_fe2_e : 0.002939
  EX_fe3_e : 0.002780
  EX_ca2_e : 0.001853
  EX_cl_e : 0.001853
  EX_cu2_e : 0.000252
  EX_mn2_e : 0.000246
  EX_zn2_e : 0.000121
  EX_ni2_e : 0.000115

Product: (mmol/gDw/h)
  EX_h2o_e : 43.822935
  EX_co2_e : 27.663950
  EX_h_e : 9.539134
  EX_pyr_e : 5.028176
  EX_fum_e : 0.453733
  Auxiliary production reaction : 0.081943
  EX_ade_e : 0.000240
  EX_mththf_e : 0.000160
  DM_5drib_c : 0.000080
  DM_4crsol_c : 0.000079

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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