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 : utp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 64
  Gene deletion: b4467 b2242 b3399 b0474 b2518 b1241 b0351 b4069 b2502 b2744 b3708 b2297 b2458 b2781 b1612 b1611 b4122 b1779 b1759 b3962 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b4374 b4161 b0675 b2361 b2291 b1415 b1014 b0822 b3709 b4138 b4123 b0621 b2913 b3161 b0112 b0452 b2868 b4265 b0114 b2366 b2492 b0904 b3035 b1533 b3028 b1380 b3918 b1912 b0325 b0508 b1473 b4266 b1518 b1206 b0221 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.291430 (mmol/gDw/h)
  Minimum Production Rate : 0.774342 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.568919
  EX_o2_e : 284.049787
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.983734
  EX_pi_e : 2.604142
  EX_so4_e : 0.073388
  EX_k_e : 0.056885
  EX_mg2_e : 0.002528
  EX_ca2_e : 0.001517
  EX_cl_e : 0.001517
  EX_cu2_e : 0.000207
  EX_mn2_e : 0.000201
  EX_zn2_e : 0.000099
  EX_ni2_e : 0.000094

Product: (mmol/gDw/h)
  EX_fe3_e : 999.995319
  EX_h2o_e : 552.220063
  EX_co2_e : 31.752698
  EX_succ_e : 1.176753
  EX_ac_e : 1.107294
  Auxiliary production reaction : 0.774342
  EX_ade_e : 0.436426
  EX_ura_e : 0.052750
  EX_dxylnt_e : 0.000195
  DM_mththf_c : 0.000131
  DM_5drib_c : 0.000066
  DM_4crsol_c : 0.000065

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.

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Last updated: 21-Sep-2023
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