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 : ctp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (78 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 73
  Gene deletion: b2242 b3553 b3399 b4269 b0493 b3588 b0586 b3003 b3011 b0474 b2518 b1241 b0351 b3831 b2502 b3073 b2744 b1278 b3708 b3008 b0871 b2926 b2781 b0030 b1612 b1611 b4122 b0651 b2162 b1759 b3962 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b1033 b4161 b0675 b2361 b1415 b1014 b3945 b1907 b4138 b4123 b0621 b2913 b4381 b2406 b0112 b2868 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b3028 b3821 b1380 b3918 b0325 b1473 b1511 b4266 b2842 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.361736 (mmol/gDw/h)
  Minimum Production Rate : 0.191050 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 996.027537
  EX_o2_e : 284.625617
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.044602
  EX_pi_e : 0.922079
  EX_so4_e : 0.524884
  EX_k_e : 0.070608
  EX_mg2_e : 0.003138
  EX_ca2_e : 0.001883
  EX_cl_e : 0.001883
  EX_cu2_e : 0.000256
  EX_mn2_e : 0.000250
  EX_zn2_e : 0.000123
  EX_ni2_e : 0.000117

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994189
  EX_h2o_e : 549.804041
  EX_co2_e : 36.591144
  EX_acald_e : 1.055905
  EX_met__L_e : 0.433791
  EX_succ_e : 0.377215
  Auxiliary production reaction : 0.191049
  EX_thym_e : 0.065475
  DM_5drib_c : 0.060315
  DM_4crsol_c : 0.060315
  EX_dxylnt_e : 0.000242
  EX_mththf_e : 0.000162

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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