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 : cdpdhdec9eg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (38 of 49: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b4382 b0474 b2518 b3831 b4384 b4152 b2779 b2925 b2097 b2781 b0030 b1612 b1611 b4122 b0907 b0651 b2162 b2690 b1759 b4161 b3945 b4138 b4123 b0621 b2406 b0452 b2197 b3918 b1912 b1206 b0221 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.390579 (mmol/gDw/h)
  Minimum Production Rate : 0.206282 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.528094
  EX_o2_e : 278.550217
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.978461
  EX_pi_e : 0.789320
  EX_so4_e : 0.098356
  EX_k_e : 0.076238
  EX_mg2_e : 0.003388
  EX_ca2_e : 0.002033
  EX_cl_e : 0.002033
  EX_cu2_e : 0.000277
  EX_mn2_e : 0.000270
  EX_zn2_e : 0.000133
  EX_ni2_e : 0.000126

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993727
  EX_h2o_e : 545.304410
  EX_co2_e : 31.550987
  EX_ac_e : 0.714576
  EX_succ_e : 0.407293
  Auxiliary production reaction : 0.206282
  EX_ura_e : 0.070696
  DM_5drib_c : 0.000088
  DM_4crsol_c : 0.000087

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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