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 : hemeO_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 98: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4467 b1478 b4382 b1241 b0351 b4069 b4384 b2297 b2458 b2926 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b0937 b1982 b0261 b0411 b2799 b3945 b1602 b0507 b2913 b2975 b3603 b0529 b2492 b0904 b1380 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.257410 (mmol/gDw/h)
  Minimum Production Rate : 0.126550 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 32.380044
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.779530
  EX_pi_e : 0.248300
  EX_fe2_e : 0.130684
  EX_so4_e : 0.064821
  EX_k_e : 0.050245
  EX_mg2_e : 0.002233
  EX_ca2_e : 0.001340
  EX_cl_e : 0.001340
  EX_cu2_e : 0.000183
  EX_mn2_e : 0.000178
  EX_zn2_e : 0.000088
  EX_ni2_e : 0.000083

Product: (mmol/gDw/h)
  EX_h2o_e : 50.016016
  EX_co2_e : 31.954939
  EX_h_e : 8.460726
  EX_ac_e : 1.589817
  EX_xtsn_e : 0.556595
  EX_ade_e : 0.253388
  DM_5drib_c : 0.253273
  Auxiliary production reaction : 0.126550
  DM_4crsol_c : 0.000057

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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