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 : dutp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 47
  Gene deletion: b3553 b1478 b3399 b4382 b1241 b4069 b4384 b2744 b2297 b2458 b2779 b0160 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b2937 b3908 b1656 b4139 b1033 b3665 b0675 b2361 b2291 b0261 b2799 b3945 b1602 b0153 b3654 b3714 b3664 b0509 b3125 b0529 b2492 b0904 b2954 b0591 b1380 b2660 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.406652 (mmol/gDw/h)
  Minimum Production Rate : 0.855162 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 35.125400
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.102135
  EX_pi_e : 2.957747
  EX_so4_e : 0.102403
  EX_k_e : 0.079376
  EX_mg2_e : 0.003528
  EX_fe2_e : 0.003356
  EX_fe3_e : 0.003175
  EX_ca2_e : 0.002117
  EX_cl_e : 0.002117
  EX_cu2_e : 0.000288
  EX_mn2_e : 0.000281
  EX_zn2_e : 0.000139
  EX_ni2_e : 0.000131
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 53.572272
  EX_co2_e : 35.138835
  EX_h_e : 3.976406
  Auxiliary production reaction : 0.855162
  EX_ac_e : 0.236747
  DM_5drib_c : 0.000091
  DM_4crsol_c : 0.000091

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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