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 : cdpdodecg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (53 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b1855 b2836 b4382 b4384 b2744 b3614 b0910 b4152 b2781 b1612 b1611 b4122 b1759 b4374 b0675 b4138 b4123 b0621 b2406 b2197 b3918 b0789 b1249 b1206 b0221   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.536437 (mmol/gDw/h)
  Minimum Production Rate : 0.283316 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 16.787430
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.837613
  EX_pi_e : 1.084083
  EX_so4_e : 0.135085
  EX_k_e : 0.104709
  EX_fe2_e : 0.008616
  EX_mg2_e : 0.004654
  EX_cl_e : 0.002792
  EX_ca2_e : 0.002792
  EX_cu2_e : 0.000380
  EX_mn2_e : 0.000371
  EX_zn2_e : 0.000183
  EX_ni2_e : 0.000173
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 40.083765
  EX_co2_e : 21.756601
  EX_h_e : 6.525287
  EX_succ_e : 0.559392
  Auxiliary production reaction : 0.283316
  EX_ura_e : 0.097097
  DM_5drib_c : 0.000121
  DM_4crsol_c : 0.000120

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
Contact