Experiment set1S439 for Variovorax sp. SCN45

Compare to:

M9 with calcium pantothenate 10 mg/mL and thiamine HCl 2 mg/mL

200 most important genes:

  gene name fitness t score description  
GFF5158 -5.7 -5.6 Trehalose-6-phosphate phosphatase (EC 3.1.3.12) compare
GFF6022 -5.2 -5.0 UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) compare
GFF372 -4.9 -7.4 PMID: 11481431 compare
GFF5076 -4.8 -12.1 hypothetical protein compare
GFF6878 -4.4 -11.4 hypothetical protein compare
GFF6876 -4.3 -12.3 Aminotransferase, DegT/DnrJ/EryC1/StrS family compare
GFF5324 -4.1 -2.8 Shikimate kinase I (EC 2.7.1.71) compare
GFF4626 -4.0 -7.3 dTDP-Rha:A-D-GlcNAc-diphosphoryl polyprenol, A-3-L-rhamnosyl transferase WbbL compare
GFF4625 -3.9 -6.4 Undecaprenyl-phosphate alpha-N-acetylglucosaminyl 1-phosphate transferase (EC 2.7.8.33) compare
GFF5267 -3.8 -3.6 Glucose-6-phosphate isomerase (EC 5.3.1.9) compare
GFF1756 -3.7 -2.5 hypothetical protein compare
GFF5896 -3.6 -7.8 Anthranilate synthase, aminase component (EC 4.1.3.27) compare
GFF408 -3.6 -2.4 Two-component system response regulator OmpR compare
GFF6875 -3.6 -6.9 hypothetical protein compare
GFF5261 -3.5 -9.4 Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) compare
GFF6512 -3.5 -2.4 4-hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16) @ 2-dehydro-3-deoxyphosphogluconate aldolase (EC 4.1.2.14) compare
GFF5307 -3.5 -4.2 Lipid A biosynthesis lauroyl acyltransferase (EC 2.3.1.241) compare
GFF6182 -3.5 -3.4 Chorismate mutase I (EC 5.4.99.5) / Prephenate dehydratase (EC 4.2.1.51) compare
GFF944 -3.4 -4.0 Aromatic-amino-acid aminotransferase (EC 2.6.1.57) compare
GFF3889 -3.3 -3.2 3-isopropylmalate dehydratase small subunit (EC 4.2.1.33) compare
GFF5513 -3.2 -2.2 N5-carboxyaminoimidazole ribonucleotide synthase (EC 6.3.4.18) compare
GFF2627 -3.2 -5.3 Chorismate synthase (EC 4.2.3.5) compare
GFF5325 -3.2 -2.2 3-dehydroquinate synthase (EC 4.2.3.4) compare
GFF244 -3.1 -6.2 Cys regulon transcriptional activator CysB compare
GFF2515 -2.9 -3.4 Glutamate 5-kinase (EC 2.7.2.11) / RNA-binding C-terminal domain PUA compare
GFF6042 -2.9 -4.0 Fatty acid desaturase (EC 1.14.19.1); Delta-9 fatty acid desaturase (EC 1.14.19.1) compare
GFF255 -2.9 -3.4 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (EC 2.3.1.117) compare
GFF3651 -2.9 -2.7 PTS system, IIA component compare
GFF5666 -2.9 -4.7 Prevent host death protein, Phd antitoxin compare
GFF3838 -2.9 -16.6 Phosphoenolpyruvate carboxylase (EC 4.1.1.31) compare
GFF302 -2.8 -1.9 Phosphoribosylamine--glycine ligase (EC 6.3.4.13) compare
GFF3928 -2.7 -2.6 Histone acetyltransferase HPA2 and related acetyltransferases compare
GFF3265 -2.7 -3.6 Homoserine O-acetyltransferase (EC 2.3.1.31) compare
GFF409 -2.6 -5.9 Osmolarity sensory histidine kinase EnvZ compare
GFF3600 -2.6 -1.8 Pantothenate kinase type III, CoaX-like (EC 2.7.1.33) compare
GFF3941 -2.6 -1.8 Phosphoribosylformylglycinamidine cyclo-ligase (EC 6.3.3.1) compare
GFF2847 -2.5 -2.9 histone-like nucleoid-structuring protein H-NS compare
GFF6513 -2.4 -6.2 Phosphogluconate dehydratase (EC 4.2.1.12) compare
GFF6701 -2.3 -3.1 Regulatory protein, RpfE type compare
GFF239 -2.3 -2.7 DNA polymerase III chi subunit (EC 2.7.7.7) compare
GFF5523 -2.3 -1.5 Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) compare
GFF4748 -2.3 -2.2 Triosephosphate isomerase (EC 5.3.1.1) compare
GFF5065 -2.2 -1.5 Orotate phosphoribosyltransferase (EC 2.4.2.10) compare
GFF3888 -2.2 -6.3 3-isopropylmalate dehydrogenase (EC 1.1.1.85) compare
GFF966 -2.1 -8.5 Probable two-component transmembrane sensor histidine kinase transcription regulator protein (EC 2.7.3.-) compare
GFF1106 -2.1 -3.4 UvrD/REP helicase compare
GFF5509 -2.1 -4.0 Phosphoribosylaminoimidazole-succinocarboxamide synthase (EC 6.3.2.6) compare
GFF339 -2.1 -4.6 Exodeoxyribonuclease I (EC 3.1.11.1) compare
GFF1105 -2.0 -3.5 Helicase compare
GFF967 -2.0 -13.9 Pyruvate dehydrogenase E1 component (EC 1.2.4.1) compare
GFF3089 -2.0 -3.0 Amidophosphoribosyltransferase (EC 2.4.2.14) compare
GFF3401 -2.0 -1.7 P-hydroxylaminobenzoate lyase compare
GFF5512 -2.0 -3.0 N5-carboxyaminoimidazole ribonucleotide mutase (EC 5.4.99.18) compare
GFF6263 -2.0 -1.2 Uncharacterized protein Atu0170, clustered with phosphonate utilization compare
GFF1324 -2.0 -2.9 Phosphoribosylformylglycinamidine synthase, synthetase subunit (EC 6.3.5.3) / Phosphoribosylformylglycinamidine synthase, glutamine amidotransferase subunit (EC 6.3.5.3) compare
GFF243 -2.0 -3.7 Sirohydrochlorin cobaltochelatase CbiX(small) (EC 4.99.1.3) compare
GFF3264 -2.0 -3.6 Methionine biosynthesis protein MetW compare
GFF3890 -1.9 -4.0 3-isopropylmalate dehydratase large subunit (EC 4.2.1.33) compare
GFF968 -1.9 -3.3 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex (EC 2.3.1.12) compare
GFF168 -1.9 -6.4 MCP methyltransferase, CheR-type compare
GFF577 -1.8 -3.8 TolA protein compare
GFF624 -1.8 -1.6 hypothetical protein compare
GFF7295 -1.8 -5.8 HPr kinase/phosphorylase compare
GFF821 -1.7 -2.8 Acetoacetyl-CoA reductase (EC 1.1.1.36) compare
GFF273 -1.7 -8.2 Transcriptional regulator, Xre family compare
GFF5317 -1.7 -1.6 Frataxin homolog CyaY, facilitates Fe-S cluster assembly, interacts with IscS compare
GFF7018 -1.7 -2.0 ABC transporter, permease protein 1 (cluster 5, nickel/peptides/opines) compare
GFF4216 -1.7 -1.5 ABC transporter, permease protein (cluster 3, basic aa/glutamine/opines) compare
GFF946 -1.7 -2.7 Iron-sulfur cluster regulator IscR compare
GFF5118 -1.7 -3.4 gluconolactonase family protein compare
GFF2073 -1.7 -3.6 Holliday junction ATP-dependent DNA helicase RuvA (EC 3.6.4.12) compare
GFF6250 -1.6 -8.7 Glutamate--cysteine ligase-like protein YbdK compare
GFF5246 -1.6 -8.5 Threonine dehydratase biosynthetic (EC 4.3.1.19) compare
GFF1206 -1.6 -6.8 Sulfite reductase [NADPH] hemoprotein beta-component (EC 1.8.1.2) compare
GFF5919 -1.5 -1.1 KEGG: type VI secretion system secreted protein Hcp compare
GFF2730 -1.5 -3.1 DNA topoisomerase IV subunit A (EC 5.99.1.3) compare
GFF15 -1.5 -1.8 no description compare
GFF6360 -1.4 -1.5 FIG00432660: hypothetical protein compare
GFF4482 -1.4 -3.9 Transcriptional regulator MraZ compare
GFF2574 -1.4 -7.0 Quinolinate phosphoribosyltransferase [decarboxylating] (EC 2.4.2.19) compare
GFF2575 -1.4 -9.0 Quinolinate synthetase (EC 2.5.1.72) compare
GFF1205 -1.4 -5.3 Oxidoreductase probably involved in sulfite reduction compare
GFF5627 -1.3 -4.8 [4Fe-4S] cluster assembly scaffold protein Mrp (=ApbC) compare
GFF4724 -1.3 -4.9 Uroporphyrinogen-III methyltransferase (EC 2.1.1.107) compare
GFF2815 -1.3 -2.5 Primosomal replication protein N compare
GFF6334 -1.3 -1.7 no description compare
GFF270 -1.3 -9.7 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) compare
GFF1047 -1.2 -7.4 hypothetical protein compare
GFF2422 -1.2 -2.8 Polysaccharide deacetylase compare
GFF4790 -1.2 -4.8 Nudix-related transcriptional regulator NrtR compare
GFF7380 -1.2 -6.6 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) compare
GFF2128 -1.2 -5.0 Enoyl-CoA hydratase (EC 4.2.1.17) compare
GFF5266 -1.2 -7.5 Transaldolase (EC 2.2.1.2) compare
GFF4447 -1.2 -5.6 2-keto-3-deoxy-D-arabino-heptulosonate-7-phosphat e synthase I alpha (EC 2.5.1.54) compare
GFF4250 -1.2 -3.6 Transcriptional regulator, AcrR family compare
GFF2027 -1.2 -7.1 2-hydroxychromene-2-carboxylate isomerase family protein compare
GFF5333 -1.2 -1.9 Glutamate synthase [NADPH] small chain (EC 1.4.1.13) compare
GFF291 -1.2 -6.0 Tol-Pal system peptidoglycan-associated lipoprotein PAL compare
GFF1594 -1.2 -3.3 Antitoxin DinJ (binds YafQ toxin) compare
GFF5156 -1.2 -9.6 Alpha,alpha-trehalose-phosphate synthase [UDP-forming] (EC 2.4.1.15) compare
GFF2734 -1.2 -5.5 DNA topoisomerase IV subunit B (EC 5.99.1.3) compare
GFF2273 -1.2 -3.9 Transcriptional regulator, AcrR family compare
GFF4309 -1.1 -2.5 Branched-chain amino acid ABC transporter, ATP-binding protein LivF (TC 3.A.1.4.1) compare
GFF5057 -1.1 -9.2 Peptidoglycan D,D-transpeptidase MrdA (EC 3.4.16.4) compare
GFF5941 -1.1 -1.3 hypothetical protein compare
GFF1474 -1.1 -2.0 Transcriptional regulator, LysR family compare
GFF5049 -1.1 -1.2 NAD-dependent protein deacetylase of SIR2 family compare
GFF2659 -1.1 -1.4 Electron transfer flavoprotein, alpha subunit compare
GFF487 -1.1 -6.2 ATP-dependent protease La (EC 3.4.21.53) Type I compare
GFF269 -1.1 -4.1 2-methylaconitate isomerase compare
GFF6246 -1.1 -4.2 Ribulose-phosphate 3-epimerase (EC 5.1.3.1) compare
GFF5688 -1.1 -2.4 Transcriptional regulator, LysR family compare
GFF3152 -1.1 -2.8 hypothetical protein compare
GFF2123 -1.1 -1.4 Copper metallochaperone PCu(A)C, inserts Cu(I) into cytochrome oxidase subunit II compare
GFF4091 -1.1 -1.5 Glutamate/aspartate ABC transporter, ATP-binding protein GltL (TC 3.A.1.3.4) compare
GFF6839 -1.1 -1.8 hypothetical protein compare
GFF7195 -1.1 -1.8 Oligopeptide transport system permease protein OppB (TC 3.A.1.5.1) compare
GFF575 -1.1 -6.1 Tol-Pal system protein TolQ compare
GFF2398 -1.1 -2.3 Uncharacterized MFS-type transporter compare
GFF4146 -1.1 -3.3 N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38) compare
GFF4788 -1.1 -1.7 Uncharacterized protein COG3236 compare
GFF6465 -1.1 -1.5 hypothetical protein compare
GFF6087 -1.0 -5.5 Transcriptional regulator, AcrR family compare
GFF4530 -1.0 -6.2 MBL-fold metallo-hydrolase superfamily compare
GFF5914 -1.0 -1.6 hypothetical protein compare
GFF6036 -1.0 -4.6 DNA translocase FtsK compare
GFF2240 -1.0 -1.5 hypothetical protein compare
GFF2090 -1.0 -2.6 Holliday junction ATP-dependent DNA helicase RuvB (EC 3.6.4.12) compare
GFF292 -1.0 -7.7 Tol-Pal system beta propeller repeat protein TolB compare
GFF7255 -1.0 -0.9 BUG/TctC family periplasmic protein compare
GFF694 -1.0 -1.5 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase (EC 3.7.1.-) compare
GFF4954 -1.0 -0.9 no description compare
GFF6997 -1.0 -1.1 Flagellar basal-body rod protein FlgC compare
GFF2249 -1.0 -2.1 no description compare
GFF4106 -1.0 -0.8 ABC transporter, ATP-binding protein (cluster 3, basic aa/glutamine/opines) compare
GFF2164 -1.0 -5.2 Transcriptional regulator, IclR family compare
GFF268 -1.0 -4.4 Carboxyvinyl-carboxyphosphonate phosphorylmutase (EC 2.7.8.23) compare
GFF2668 -0.9 -2.4 hypothetical protein compare
GFF143 -0.9 -1.1 Dethiobiotin synthase BioD (EC 6.3.3.3) compare
GFF1672 -0.9 -3.3 BUG/TctC family periplasmic protein compare
GFF5097 -0.9 -1.9 5-carboxymethyl-2-hydroxymuconate delta-isomerase (EC 5.3.3.10) compare
GFF4209 -0.9 -3.4 no description compare
GFF4071 -0.9 -1.9 Butyryl-CoA dehydrogenase (EC 1.3.99.2) compare
GFF3050 -0.9 -1.4 Lactam utilization protein LamB compare
GFF5411 -0.9 -6.3 CAMP phosphodiesterases class-II:Metallo-beta-lactamase superfamily compare
GFF5188 -0.9 -1.3 no description compare
GFF4069 -0.9 -1.8 DNA-binding heavy metal response regulator compare
GFF2302 -0.9 -5.5 Cytochrome c oxidase polypeptide III (EC 1.9.3.1) compare
GFF1060 -0.9 -1.9 Hydroxymethylpyrimidine ABC transporter, transmembrane component compare
GFF6638 -0.9 -5.1 no description compare
GFF5922 -0.9 -2.1 T6SS forkhead associated domain protein ImpI/VasC compare
GFF6742 -0.9 -1.9 NAD(P)H-flavin oxidoreductase compare
GFF6249 -0.9 -4.6 Transporter, monovalent cation:proton antiporter-2 (CPA2) family compare
GFF2563 -0.9 -5.7 Two-component system sensor histidine kinase compare
GFF6168 -0.9 -1.2 Na(+) H(+) antiporter subunit G compare
GFF1869 -0.9 -1.5 no description compare
GFF2300 -0.9 -5.0 Cytochrome oxidase biogenesis protein Cox11-CtaG, copper delivery to Cox1 compare
GFF2645 -0.9 -2.1 Acyl dehydratase compare
GFF6868 -0.8 -3.7 SAM-dependent methyltransferase compare
GFF7210 -0.8 -2.2 Hydroxymethylpyrimidine ABC transporter, transmembrane component compare
GFF7044 -0.8 -1.7 Inner membrane protein YedI compare
GFF497 -0.8 -4.1 Phytoene synthase (EC 2.5.1.32) compare
GFF3403 -0.8 -4.1 Benzoate catabolism regulator with shikimate kinase domain compare
GFF2104 -0.8 -1.4 3-hydroxyacyl-CoA dehydrogenase [isoleucine degradation] (EC 1.1.1.35) compare
GFF4490 -0.8 -3.2 Site-specific tyrosine recombinase XerC compare
GFF4967 -0.8 -0.9 Glutathione S-transferase family protein compare
GFF3255 -0.8 -3.8 16S rRNA (uracil(1498)-N(3))-methyltransferase (EC 2.1.1.193) compare
GFF5983 -0.8 -1.0 Transcriptional regulator, LysR family compare
GFF371 -0.8 -1.4 RNA-binding protein YhbY compare
GFF210 -0.8 -2.9 Putative transmembrane protein compare
GFF3239 -0.8 -1.9 no description compare
GFF6209 -0.8 -3.0 ABC transporter, ATP-binding protein (cluster 3, basic aa/glutamine/opines) compare
GFF633 -0.8 -1.5 Urea ABC transporter, ATPase protein UrtD compare
GFF6591 -0.8 -3.5 Transcriptional regulator, GntR family compare
GFF2111 -0.8 -1.7 Permease of the drug/metabolite transporter (DMT) superfamily compare
GFF2139 -0.8 -1.0 Ribose ABC transporter, ATP-binding protein RbsA (TC 3.A.1.2.1) compare
GFF1602 -0.8 -1.1 Branched-chain amino acid transport ATP-binding protein LivF (TC 3.A.1.4.1) compare
GFF4640 -0.8 -6.3 hypothetical protein compare
GFF2356 -0.8 -5.2 RNase adapter protein RapZ compare
GFF2142 -0.8 -0.9 Glutathione S-transferase (EC 2.5.1.18) compare
GFF3402 -0.8 -2.3 no description compare
GFF7100 -0.8 -2.3 similar to protocatechuate 4,5-dioxygenase beta chain compare
GFF2971 -0.8 -1.4 Transcriptional regulator, LysR family compare
GFF3406 -0.8 -5.0 Benzoyl-CoA oxygenase component A compare
GFF2307 -0.7 -4.1 Heme O synthase, protoheme IX farnesyltransferase, COX10-CtaB compare
GFF1204 -0.7 -3.6 Phosphoadenylyl-sulfate reductase [thioredoxin] (EC 1.8.4.8) compare
GFF3177 -0.7 -1.1 hypothetical protein compare
GFF576 -0.7 -2.1 Tol biopolymer transport system, TolR protein compare
GFF1782 -0.7 -2.8 integral membrane sensor signal transduction histidine kinase compare
GFF3434 -0.7 -3.0 Organic hydroperoxide resistance protein compare
GFF4287 -0.7 -1.7 Acyl-CoA dehydrogenase compare
GFF570 -0.7 -1.3 3,4-dihydroxy-2-butanone 4-phosphate synthase (EC 4.1.99.12) / GTP cyclohydrolase II (EC 3.5.4.25) compare
GFF808 -0.7 -6.0 Polyhydroxyalkanoic acid synthase compare
GFF1075 -0.7 -1.9 no description compare
GFF7178 -0.7 -1.0 Glucose-1-phosphate thymidylyltransferase (EC 2.7.7.24) compare
GFF5601 -0.7 -1.7 Predicted hydrolase of the alpha/beta-hydrolase fold compare
GFF4438 -0.7 -3.3 Sugar kinases, ribokinase family compare
GFF6290 -0.7 -6.0 RNA polymerase sigma-54 factor RpoN compare
GFF2547 -0.7 -2.0 Type I antifreeze protein compare
GFF6429 -0.7 -1.7 Pyruvate:Oxaloacetate transcarboxylase domain protein compare


Specific Phenotypes

None in this experiment

For Variovorax sp. SCN45 in vitamin experiments

For vitamin calcium pantothenate across organisms