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Table 3 Inconsistent gene essentiality predictions identified in refinement steps 2 and 3 and corresponding corrections and interpretations

From: Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data

CORRECTION    56 NO CORRECTION    68
BIOMASS    10 Validated explanation    6
biomass precursor not essential 9 experimental error 1
   ACIAD0076 (rmlB) D step 2      ACIAD0108 (lldD) D step 3  
   ACIAD0078 (rmlD) D step 2   known gap in the understanding of pathway 4
   ACIAD0079 (rmlA) D step 2      ACIAD0856 (bioA) E step 2  
   ACIAD0080 (rmlC) D step 2      ACIAD0857 (bioF) E step 2  
   ACIAD0086 (epsM) D step 2      ACIAD0859 (bioD) E step 2  
   ACIAD0099 (galU) D step 2      ACIAD2045 (bioB) E step 2  
   ACIAD0101 (pgi) D step 2   unmodeled auxotrophy 1
   ACIAD0104 (manB) D step 2      ACIAD3523 (metE) E step 2  
   ACIAD2429 (cyoE) D step 2   Hypothetical explanation 32
missing essential biomass precursor 1    ACIAD0178 (atpI) E step 2  
   ACIAD1374 (ispU) E step 2      ACIAD0180 (atpB) E step 2  
GPR 34    ACIAD0182 (atpE) E step 2  
activity simultaneously requiring all genes 3    ACIAD0183 (atpF) E step 2  
   ACIAD0661 (hisG) E step 2      ACIAD0184 (atpH) E step 2  
   ACIAD1257 (hisZ) E step 2      ACIAD0185 (atpA) E step 2  
   ACIAD3103 (ilvH) E step 2      ACIAD0186 (atpG) E step 2  
gene associated to another essential reaction 1    ACIAD0187 (atpD) E step 2  
   ACIAD2606 E step 2      ACIAD0188 (atpC) E step 2  
isozyme not functional 22    ACIAD0556 (ndk) D step 2  
   ACIAD0151 (guaA) E step 2      ACIAD0650 (argJ) E step 2  
   ACIAD0249 (ribC) E step 2      ACIAD1150 (pyrC) E step 2  
   ACIAD0871 (fabG) E step 2      ACIAD1346 (sodB) E step 2  
   ACIAD1069 (lysS) E step 2      ACIAD1358 (rpiA) E step 2  
   ACIAD1255 (epd) E step 2      ACIAD2282 (sahH) D step 2  
   ACIAD1323 (purF) E step 2      ACIAD2314 (metZ) E step 2  
   ACIAD1375 (cdsA) E step 2      ACIAD2458 (glnA) E step 2  
   ACIAD1736 (accC) E step 2      ACIAD2842 (pckG) E step 2  
   ACIAD1737 (accB) E step 2      ACIAD2847 (folD) E step 2  
   ACIAD1925 (fda) E step 2      ACIAD3155 (mdh) E step 2  
   ACIAD2227 (dctA) E step 2      ACIAD3349 (gltD) E step 2  
   ACIAD2565 (gap) E step 2      ACIAD3350 (gltB) E step 2  
   ACIAD2666 E step 2      ACIAD3470 (msuE) E step 2  
   ACIAD2907 (prs) E step 2      ACIAD3506 (aceF) E step 2  
   ACIAD3062 (folK) E step 2      ACIAD0101 (pgi) E step 3  
   ACIAD3249 (ribA) E step 2      ACIAD0546 E step 3  
   ACIAD3365 (murE) E step 2      ACIAD0556 (ndk) D step 3  
   ACIAD3371 (gltX) E step 2      ACIAD1021 D step 3  
   ACIAD1710 (pcaC) E step 3      ACIAD1707 (pcaB) E step 3  
   ACIAD2018 (ald1) E step 3      ACIAD1711 (pcaH) E step 3  
   ACIAD2088 (aspQ) E step 3      ACIAD1712 (pcaG) E step 3  
   ACIAD2983 (gcd) E step 3      ACIAD1744 (aspA) E step 3  
presence of an alternate enzyme 6 No precise interpretation 30
   ACIAD1231 (argD) D step 2      ACIAD0072 (ugd) E step 2  
   ACIAD1642 (uppP) D step 2      ACIAD0173 (rhtB) E step 2  
   ACIAD2968 (ispA) D step 2      ACIAD0382 (ubiB) D step 2  
   ACIAD1020 (acoL) D step 3      ACIAD0505 (purU1) E step 2  
   ACIAD1715 (quiX) D step 3      ACIAD1482 (kdsD) D step 2  
   ACIAD2984 D step 3      ACIAD1483 (kdsC) D step 2  
spontaneously occurring reaction 1    ACIAD2283 (metF) D step 2  
   ACIAD2819 D step 3      ACIAD2290 (cydA) E step 2  
wrong complex subunit 1    ACIAD2525 E step 2  
   ACIAD0799 D step 2      ACIAD2667 (pdxB) D step 2  
NETWORK 12    ACIAD2788 E step 2  
false alternate pathway in the model 7    ACIAD2880 (sdhA) D step 2  
   ACIAD0239 (ppa) E step 2      ACIAD2911 (panD) D step 2  
   ACIAD0547 (proA) E step 2      ACIAD3503 (guaB) E step 2  
   ACIAD1105 (adk) E step 2      ACIAD3510 (lpxC) D step 2  
   ACIAD1920 (glnS) E step 2      ACIAD0086 (epsM) E step 3  
   ACIAD2560 (proB) E step 2      ACIAD0335 (fadB) E step 3  
   ACIAD3032 (proC) E step 2      ACIAD0382 (ubiB) D step 3  
   ACIAD0901 (dut) E step 2      ACIAD0922 E step 3  
missing alternate pathway in the model 5    ACIAD2070 (metI) E step 3  
   ACIAD0106 (lldP) D step 2      ACIAD2282 (sahH) D step 3  
   ACIAD0451 (katA) D step 2      ACIAD2283 (metF) D step 3  
   ACIAD0930 (glpK) D step 2      ACIAD2667 (pdxB) D step 3  
   ACIAD1045 (metH) D step 2      ACIAD2755 E step 3  
   ACIAD0106 (lldP) D step 3      ACIAD2875 (sucB) E step 3  
        ACIAD2876 (sucA) E step 3  
        ACIAD2880 (sdhA) D step 3  
        ACIAD2911 (panD) E step 3  
        ACIAD3071 (cysM) E step 3  
        ACIAD3549 (gshA) E step 3  
  1. Inconsistencies identified during the refinement steps using mutant library essentialities (step 2) and mutant growth phenotypes on 8 media (step 3). Inconsistencies leading to corrections (left column) are listed according to the model component that was corrected: GPR, NETWORK, and BIOMASS. Inconsistencies with no correction (right column) are listed according to the level of interpretation that could be drawn. Numbers provide the count of inconsistencies pertaining to each correction or interpretation category. For each inconsistency, E or D indicates the experimental phenotype of the mutant: E: gene is essential (on at least one medium for step 3), D gene is dispensable (on all media for step 3).