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 (48 of 98: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b2436 b4382 b0474 b2518 b3831 b4384 b1278 b3752 b4152 b2925 b2097 b2781 b1612 b1611 b4122 b2690 b1759 b4161 b0411 b3945 b4138 b4123 b0621 b2913 b0529 b3918 b0418 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.713115 (mmol/gDw/h)
  Minimum Production Rate : 0.007490 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.915019
  EX_o2_e : 274.870258
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.698012
  EX_pi_e : 0.687875
  EX_so4_e : 0.179577
  EX_k_e : 0.139195
  EX_mg2_e : 0.006186
  EX_ca2_e : 0.003712
  EX_cl_e : 0.003712
  EX_cu2_e : 0.000506
  EX_mn2_e : 0.000493
  EX_zn2_e : 0.000243
  EX_ni2_e : 0.000230
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_fe3_e : 999.981057
  EX_h2o_e : 547.547916
  EX_co2_e : 25.378934
  EX_succ_e : 0.743631
  EX_ura_e : 0.483234
  DM_5drib_c : 0.015459
  Auxiliary production reaction : 0.007490
  DM_4crsol_c : 0.000159

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