MetNetComp Database [1] / Core Genes

A set of core genes for simulation-based growth-coupled production. You can also see minimal gene deletions.

Model : STM_v1_0 [2].
Target metabolite : 2dr1p_c
Core genes for growth-coupled production (at least stoichioemetrically feasible)
  #Remaining genes : 280
  Remaining genes: STM4122 STM2992 STM3795 STM3796 STM0320 STM1883 STM3190 STM4120 STM1712 STM3468 STM1067 STM2384 STM1195 STM4273 STM2378 STM1197 STM1198 STM3469 STM1824 STM0812 STM0488 STM0165 STM0203 STM0984 STM0207 STM1196 STM0483 STM2933 STM1232 STM4366 STM0730 STM2953 s0001 STM3710 STM0232 STM3379 STM3173 STM3380 STM4121 STM2366 STM4176 STM0533 STM2430 STM0534 STM2432 STM2433 STM2431 STM1557 STM0380 STM0441 STM0442 STM0440 STM4247 STM0443 STM2555 STM0980 STM4300 STM3013 STM3947 STM3862 STM0222 STM3195 STM3923 STM0202 STM4235 STM0760 STM3740 STM3904 STM3700 STM0064 STM2489 STM0087 STM2365 STM1724 STM1723 STM3206 STM1058 STM0416 STM1163 STM3295 STM3486 STM1358 STM3719 STM1752 STM4123 STM1900 STM2098 STM1290 STM2500 STM3539 STM3861 STM3877 STM3535 STM3722 STM4459 STM2649 STM3718 STM3717 STM4460 STM0002 STM1200 STM4568 STM2641 STM0998 STM3692 STM1700 STM3713 STM2071 STM3926 STM1465 STM1155 STM3536 STM4007 STM1889 STM2952 STM3314 STM1299 STM2362 STM4131 STM0113 STM1777 STM2415 STM3909 STM0988 STM3316 STM1772 STM2141 STM3880 STM1647 STM4248 STM3200 STM0248 STM2510 STM0229 STM1467 STM1194 STM0045 STM2193 STM1711 STM3359 STM0171 STM2472 STM3721 STM3716 STM4062 STM3712 STM3711 STM3723 STM3090 STM4115 STM3714 STM4114 STM3294 STM4221 STM2072 STM3069 STM2074 STM3938 STM3704 STM0183 STM0003 STM2820 STM4182 STM2073 STM3724 STM1238 STM3715 STM1945 STM0782 STM0783 STM0781 STM2077 STM2075 STM1725 STM2531 STM3903 STM0542 STM3589 STM4105 STM2511 STM4414 STM0112 STM0110 STM0111 STM0372 STM2683 STM4119 STM2669 STM1310 STM2667 STM4175 STM2078 STM2487 STM3001 STM2565 STM2076 STM4081 STM0645 STM1780 STM0978 STM0145 STM4348 STM2652 STM1727 STM1726 STM0226 STM0123 STM0228 STM3307 STM0128 STM0126 STM0129 STM4137 STM1888 STM0756 STM1426 STM0417 STM0776 STM0124 STM3720 STM0134 STM2817 STM0218 STM3937 STM1707 STM2807 STM2808 STM0535 STM3114 STM3733 STM1617 STM3063 STM0386 STM0310 STM1710 STM0125 STM2946 STM2934 STM2935 STM2483 STM4465 STM3699 STM4466 STM3477 STM3401 STM0388 STM0166 STM3624A STM0738 STM0739 STM2094 STM2096 STM2097 STM0985 STM0213 STM2082 STM2085 STM2086 STM2087 STM2083 STM1332 STM3905 STM2092 STM2091 STM2090 STM2093 STM0004 STM2089 STM2474 STM2232 STM2079 STM2838_S STM3290_S STM4188_S STM4559_S STM2499_S STM2105_S STM2549 STM2550 STM2548   (List of alternative genes)
  Computed by: AddGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.008337 (mmol/gDw/h)
  Minimum Production Rate : 0.015993 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glc__D_e : 5.000000
  EX_nh4_e : 0.145575
  EX_so4_e : 0.056086
  EX_co2_e : 0.045769
  EX_pi_e : 0.023385
  EX_o2_e : 0.009647
  EX_k_e : 0.001481
  EX_mg2_e : 0.000066
  EX_fe2_e : 0.000061
  EX_ca2_e : 0.000039
  EX_cl_e : 0.000039
  EX_cobalt2_e : 0.000026
  EX_cu2_e : 0.000026
  EX_mn2_e : 0.000026
  EX_mobd_e : 0.000026
  EX_zn2_e : 0.000026

Product: (mmol/gDw/h)
  EX_h_e : 9.827228
  EX_lac__D_e : 9.454832
  EX_h2o_e : 0.720006
  EX_pyr_e : 0.331403
  EX_h2s_e : 0.055070
  EX_4abz_e : 0.021720
  EX_acald_e : 0.021268
  Auxiliary production reaction : 0.015993
  EX_thym_e : 0.015993
  EX_ac_e : 0.004615
  EX_glyclt_e : 0.000417

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].

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: 27-Sep-2023
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