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 : ncam_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (114 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4467 b2242 b4269 b0493 b3588 b3003 b3011 b0474 b2518 b3831 b0910 b3752 b0871 b2297 b2458 b2779 b2925 b2097 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b2690 b2210 b1415 b3945 b4388 b4138 b4123 b0621 b3028 b1380 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.379569 (mmol/gDw/h)
  Minimum Production Rate : 0.200468 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.792122
  EX_o2_e : 282.180216
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.637660
  EX_pi_e : 0.366135
  EX_so4_e : 0.095583
  EX_k_e : 0.074089
  EX_mg2_e : 0.003293
  EX_ca2_e : 0.001976
  EX_cl_e : 0.001976
  EX_cu2_e : 0.000269
  EX_mn2_e : 0.000262
  EX_zn2_e : 0.000129
  EX_ni2_e : 0.000123

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993904
  EX_h2o_e : 544.552894
  EX_co2_e : 32.590427
  EX_ac_e : 4.383927
  EX_succ_e : 0.395812
  Auxiliary production reaction : 0.200468
  EX_ura_e : 0.068703
  EX_dxylnt_e : 0.000254
  DM_5drib_c : 0.000085
  DM_4crsol_c : 0.000085

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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