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 : dcmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 117: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3942 b1732 b1241 b0351 b4069 b4384 b1479 b3752 b2297 b2458 b3617 b2407 b3844 b3236 b2463 b1982 b2210 b3551 b4219 b1832 b1778 b4381 b2406 b0114 b0529 b2492 b0904 b1710 b2480 b1511 b3662 b1206 b0606   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.503087 (mmol/gDw/h)
  Minimum Production Rate : 1.928978 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 19.802282
  EX_nh4_e : 11.221580
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.414258
  EX_so4_e : 0.126687
  EX_k_e : 0.098199
  EX_fe2_e : 0.008080
  EX_mg2_e : 0.004364
  EX_ca2_e : 0.002619
  EX_cl_e : 0.002619
  EX_cu2_e : 0.000357
  EX_mn2_e : 0.000348
  EX_zn2_e : 0.000172
  EX_ni2_e : 0.000162
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 48.189210
  EX_co2_e : 18.422558
  EX_h_e : 12.193063
  Auxiliary production reaction : 1.928978
  EX_ac_e : 0.735559
  EX_fum_e : 0.523328
  EX_xan_e : 0.000339
  DM_mththf_c : 0.000225
  DM_5drib_c : 0.000113
  DM_4crsol_c : 0.000112

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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