MetNetComp Database [1] / Core Genes

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

Model : iNJ661 [2].
Target metabolite : ctp_c
Core genes for growth-coupled production (at least stoichioemetrically feasible)
  #Remaining genes : 373
  Remaining genes: Rv2281 Rv0545c Rv1559 Rv2051c Rv1201c Rv2746c Rv3464 Rv1822 Rv3396c Rv3468c Rv3784 Rv2156c Rv3266c Rv3465 Rv3068c Rv0489 Rv2397c Rv2398c Rv2399c Rv2400c Rv1739c Rv0951 Rv3317 Rv1437 Rv0946c Rv3318 Rv2996c Rv0728c Rv3010c Rv3303c Rv2496c Rv2241 Rv3316 Rv0112 Rv1511 Rv3696c Rv0234c Rv2392 Rv0391 Rv0500 Rv2834c Rv1079 Rv2833c Rv2539c Rv2832c Rv2552c Rv3859c Rv2335 Rv1338 Rv0858c Rv1602 Rv1202 Rv0808 Rv2386c Rv1286 Rv1692 Rv1285 Rv2958c Rv2962c Rv1493 Rv2465c Rv1492 Rv1408 Rv0570 Rv0855 Rv1981c Rv1878 Rv3051c Rv0046c Rv2701c Rv3048c Rv2220 Rv1236 Rv2860c Rv2222c Rv1237 Rv1416 Rv1389 Rv2124c Rv1392 Rv1093 Rv0070c Rv1512 Rv3582c Rv3777 Rv3581c Rv3436c Rv1617 Rv0956 Rv0389 Rv0649 Rv0408 Rv0436c Rv2243 Rv1436 Rv0505c Rv3042c Rv0884c Rv2381c Rv0993 Rv0437c Rv2383c Rv3227 Rv2380c Rv2382c Rv2379c Rv0619 Rv1017c Rv2378c Rv2384 Rv3757c Rv0618 Rv3756c Rv2611c Rv3758c Rv0620 Rv3255c Rv3808c Rv1603 Rv3264c Rv0788 Rv0803 Rv3455c Rv2934 Rv2932 Rv2210c Rv2982c Rv2249c Rv2935 Rv0564c Rv2883c Rv1849 Rv2933 Rv1848 Rv3302c Rv2931 Rv2928 Rv1551 Rv2122c Rv0780 Rv1606 Rv0334 Rv2157c Rv0809 Rv0772 Rv2152c Rv2155c Rv2610c Rv2153c Rv2163c Rv2158c Rv3838c Rv2957 Rv3754 Rv3809c Rv2455c Rv2702 Rv0501 Rv0536 Rv2945c Rv3634c Rv2941 Rv1248c Rv0974c Rv2501c Rv2136c Rv0382c Rv2502c Rv0482 Rv1653 Rv3818 Rv1018c Rv2321c Rv3628 Rv1315 Rv2322c Rv1612 Rv1613 Rv1385 Rv2503c Rv1373 Rv3308 Rv0295c Rv2504c Rv2200c Rv1656 Rv3265c Rv3490 Rv3372 Rv2194 Rv0253 Rv2006 Rv2196 Rv2195 Rv2391 Rv3913 Rv1699 Rv1438 Rv1163 Rv1162 Rv2764c Rv2754c Rv1161 Rv0374c Rv0375c Rv1449c Rv2498c Rv2075c Rv2949c Rv2445c Rv2540c Rv1885c Rv2612c Rv1011 Rv2329c Rv1383 Rv2317 Rv2316 Rv0156 Rv0155 Rv1031 Rv1311 Rv1029 Rv1305 Rv1304 Rv1307 Rv3150 Rv3001c Rv1309 Rv1306 Rv1310 Rv3710 Rv3147 Rv1308 Rv2988c Rv2121c Rv2987c Rv3156 Rv0337c Rv3158 Rv3149 Rv2995c Rv3565 Rv3153 Rv3709c Rv0082 Rv3393 Rv3157 Rv1380 Rv3148 Rv3152 Rv1843c Rv3145 Rv3154 Rv3155 Rv3410c Rv3411c Rv2246 Rv0957 Rv2201 Rv1611 Rv1601 Rv1483 Rv3708c Rv2245 Rv1605 Rv0098 Rv1001 Rv3800c Rv1915 Rv0644c Rv0645c Rv0642c Rv0503c Rv2859c Rv0470c Rv1609 Rv2192c Rv3624c Rv2231c Rv1023 Rv1600 Rv3293 Rv3772 Rv2682c Rv3379c Rv1294 Rv2870c Rv3423c Rv2981c Rv3276c Rv1599 Rv3398c Rv3248c Rv2538c Rv1652 Rv2537c Rv2483c Rv3588c Rv2182c Rv3273 Rv3792 Rv3793 Rv1381 Rv3795 Rv2139 Rv3794 Rv0357c Rv0777 Rv2763c Rv2753c Rv2394 Rv2773c Rv1555 Rv0189c Rv1553 Rv1086 Rv1554 Rv1552 Rv1349 Rv2899c Rv2178c Rv1099c Rv3790 Rv0363c Rv2940c Rv2881c Rv1662 Rv1663 Rv2726c Rv2524c Rv1293 Rv2947c Rv1350 Rv1484 Rv0533c Rv1323 Rv0859 Rv1623c Rv0468 Rv3801c Rv1622c Rv1621c Rv2590 Rv1185c Rv3826 Rv3340 Rv0848 Rv1529 Rv1336 Rv2334 Rv1319c Rv1451 Rv1320c Rv0733 Rv3043c Rv0255c Rv2193 Rv0013 Rv3313c Rv1655 Rv3509c Rv3003c Rv3470c Rv3002c Rv1820 Rv0409 Rv1654 Rv1302 Rv3280 Rv0904c Rv3281 Rv3815c   (List of alternative genes)
  Computed by: AddGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.011138 (mmol/gDw/h)
  Minimum Production Rate : 0.009696 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_glyc_e : 1.000000
  EX_glu__L_e : 1.000000
  EX_o2_e : 0.963074
  EX_h_e : 0.706719
  EX_cit_e : 0.279581
  EX_h2o_e : 0.116301
  EX_pi_e : 0.041428
  EX_so4_e : 0.000718
  EX_fe3_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2co3_e : 2.222687
  EX_ppa_e : 0.938735
  EX_ala__L_e : 0.469162
  EX_asp__L_e : 0.208429
  EX_val__L_e : 0.171004
  EX_ile__L_e : 0.037221
  EX_tyr__L_e : 0.012295
  Auxiliary production reaction : 0.009695
  EX_ppdima_e : 0.006754

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
Contact