Experiment set3S479 for Variovorax sp. SCN45

Compare to:

Community=Kojac gum; Passage=4

200 most important genes:

  gene name fitness t score description  
GFF5512 -6.3 -4.4 N5-carboxyaminoimidazole ribonucleotide mutase (EC 5.4.99.18) compare
GFF2567 -6.0 -4.1 Molybdopterin-synthase adenylyltransferase (EC 2.7.7.80) compare
GFF5917 -5.9 -2.3 T6SS component TssB (ImpB/VipA) compare
GFF5158 -5.8 -4.0 Trehalose-6-phosphate phosphatase (EC 3.1.3.12) compare
GFF1190 -5.6 -3.4 Glycine oxidase ThiO (EC 1.4.3.19) compare
GFF5513 -5.6 -3.9 N5-carboxyaminoimidazole ribonucleotide synthase (EC 6.3.4.18) compare
GFF6383 -5.6 -1.3 FIG00440100: hypothetical protein compare
GFF2000 -5.5 -6.6 Phosphomethylpyrimidine synthase ThiC (EC 4.1.99.17) compare
GFF6250 -5.5 -3.8 Glutamate--cysteine ligase-like protein YbdK compare
GFF2128 -5.4 -3.7 Enoyl-CoA hydratase (EC 4.2.1.17) compare
GFF3957 -5.4 -2.4 Ribosome small subunit biogenesis RbfA-release protein RsgA compare
GFF902 -5.3 -3.7 Transcriptional regulator, AsnC family compare
GFF6249 -5.2 -3.6 Transporter, monovalent cation:proton antiporter-2 (CPA2) family compare
GFF936 -5.2 -3.6 Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) compare
GFF3495 -5.1 -1.9 ABC transporter, ATP-binding protein 1 (cluster 4, leucine/isoleucine/valine/benzoate) compare
GFF2818 -5.1 -12.8 Phosphoenolpyruvate synthase (EC 2.7.9.2) compare
GFF270 -5.0 -4.9 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) compare
GFF624 -5.0 -1.9 hypothetical protein compare
GFF268 -4.9 -3.4 Carboxyvinyl-carboxyphosphonate phosphorylmutase (EC 2.7.8.23) compare
GFF5509 -4.9 -3.4 Phosphoribosylaminoimidazole-succinocarboxamide synthase (EC 6.3.2.6) compare
GFF3089 -4.9 -2.6 Amidophosphoribosyltransferase (EC 2.4.2.14) compare
GFF126 -4.8 -4.5 Repressor homolog compare
GFF1324 -4.8 -3.3 Phosphoribosylformylglycinamidine synthase, synthetase subunit (EC 6.3.5.3) / Phosphoribosylformylglycinamidine synthase, glutamine amidotransferase subunit (EC 6.3.5.3) compare
GFF3264 -4.8 -3.3 Methionine biosynthesis protein MetW compare
GFF1187 -4.8 -3.3 Thiamin-phosphate pyrophosphorylase (EC 2.5.1.3) compare
GFF2573 -4.7 -3.3 Glycerol-3-phosphate dehydrogenase [NAD(P)+] (EC 1.1.1.94) compare
GFF934 -4.7 -3.3 Propionyl-CoA carboxylase carboxyl transferase subunit (EC 6.4.1.3) compare
GFF903 -4.7 -6.5 Acetolactate synthase large subunit (EC 2.2.1.6) compare
GFF273 -4.7 -3.2 Transcriptional regulator, Xre family compare
GFF374 -4.6 -3.8 Transcription elongation factor GreA compare
GFF3941 -4.5 -3.1 Phosphoribosylformylglycinamidine cyclo-ligase (EC 6.3.3.1) compare
GFF2714 -4.5 -4.2 2-ketogluconate utilization repressor PtxS compare
GFF2329 -4.5 -1.7 Phosphoglycerate mutase (EC 5.4.2.11) compare
GFF1899 -4.5 -11.2 Indolepyruvate ferredoxin oxidoreductase, alpha and beta subunits compare
GFF272 -4.5 -1.4 thioesterase superfamily protein compare
GFF6195 -4.4 -2.4 ABC transporter, ATP-binding protein (cluster 5, nickel/peptides/opines) compare
GFF2815 -4.4 -2.2 Primosomal replication protein N compare
GFF269 -4.4 -5.2 2-methylaconitate isomerase compare
GFF4724 -4.4 -4.2 Uroporphyrinogen-III methyltransferase (EC 2.1.1.107) compare
GFF2617 -4.3 -1.9 no description compare
GFF5627 -4.3 -3.0 [4Fe-4S] cluster assembly scaffold protein Mrp (=ApbC) compare
GFF271 -4.3 -5.9 2-methylcitrate synthase (EC 2.3.3.5) compare
GFF6198 -4.3 -6.5 D-malate dehydrogenase [decarboxylating] (EC 1.1.1.83) compare
GFF5246 -4.3 -5.8 Threonine dehydratase biosynthetic (EC 4.3.1.19) compare
GFF1900 -4.2 -4.5 Transcriptional regulator, LysR family compare
GFF577 -4.2 -1.8 TolA protein compare
GFF576 -4.2 -2.6 Tol biopolymer transport system, TolR protein compare
GFF5156 -4.2 -19.3 Alpha,alpha-trehalose-phosphate synthase [UDP-forming] (EC 2.4.1.15) compare
GFF1188 -4.2 -2.4 Thiazole synthase (EC 2.8.1.10) compare
GFF1683 -4.1 -0.9 3-isopropylmalate dehydratase small subunit (EC 4.2.1.33) compare
GFF302 -4.1 -2.6 Phosphoribosylamine--glycine ligase (EC 6.3.4.13) compare
GFF292 -4.1 -2.8 Tol-Pal system beta propeller repeat protein TolB compare
GFF6379 -4.1 -2.4 ABC transporter, ATP-binding protein 2 (cluster 4, leucine/isoleucine/valine/benzoate) compare
GFF5919 -4.1 -0.9 KEGG: type VI secretion system secreted protein Hcp compare
GFF1598 -4.1 -1.8 no description compare
GFF5361 -4.0 -0.9 FIG146285: Diadenosine tetraphosphate (Ap4A) hydrolase and other HIT family hydrolases compare
GFF7380 -4.0 -5.5 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) compare
GFF5813 -4.0 -1.5 Heavy metal sensor histidine kinase compare
GFF7381 -4.0 -10.0 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) compare
GFF946 -4.0 -3.8 Iron-sulfur cluster regulator IscR compare
GFF4825 -4.0 -3.7 SWIB/MDM2 domain-containing proteins compare
GFF1206 -4.0 -5.4 Sulfite reductase [NADPH] hemoprotein beta-component (EC 1.8.1.2) compare
GFF5203 -4.0 -1.2 hypothetical protein compare
GFF4557 -3.9 -2.7 Dihydroorotase (EC 3.5.2.3) compare
GFF143 -3.9 -1.5 Dethiobiotin synthase BioD (EC 6.3.3.3) compare
GFF1256 -3.9 -0.9 Probable NADH dehydrogenase/NAD(P)H nitroreductase compare
GFF2562 -3.9 -0.9 UPF0391 membrane protein RGE_28580 compare
GFF6028 -3.9 -8.0 2-polyprenylphenol hydroxylase and related flavodoxin oxidoreductases / CDP-6-deoxy-delta-3,4-glucoseen reductase-like compare
GFF6704 -3.9 -1.9 no description compare
GFF6512 -3.9 -1.7 4-hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16) @ 2-dehydro-3-deoxyphosphogluconate aldolase (EC 4.1.2.14) compare
GFF3425 -3.9 -2.1 no description compare
GFF2987 -3.9 -4.6 CBS domain protein compare
GFF2367 -3.9 -2.4 Transcriptional regulator, LysR family compare
GFF7377 -3.8 -4.5 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) compare
GFF4216 -3.7 -0.8 ABC transporter, permease protein (cluster 3, basic aa/glutamine/opines) compare
GFF1773 -3.7 -11.4 D-amino acid dehydrogenase (EC 1.4.99.6) compare
GFF3854 -3.7 -1.8 FIG01269488: protein, clustered with ribosomal protein L32p compare
GFF4626 -3.7 -2.6 dTDP-Rha:A-D-GlcNAc-diphosphoryl polyprenol, A-3-L-rhamnosyl transferase WbbL compare
GFF4625 -3.7 -2.6 Undecaprenyl-phosphate alpha-N-acetylglucosaminyl 1-phosphate transferase (EC 2.7.8.33) compare
GFF4469 -3.7 -2.0 Cell division protein FtsA compare
GFF4328 -3.7 -2.9 hypothetical protein compare
GFF3166 -3.6 -1.2 Transcriptional regulator, IclR family compare
GFF2307 -3.6 -10.1 Heme O synthase, protoheme IX farnesyltransferase, COX10-CtaB compare
GFF3838 -3.6 -14.4 Phosphoenolpyruvate carboxylase (EC 4.1.1.31) compare
GFF575 -3.6 -2.5 Tol-Pal system protein TolQ compare
GFF4447 -3.5 -2.4 2-keto-3-deoxy-D-arabino-heptulosonate-7-phosphat e synthase I alpha (EC 2.5.1.54) compare
GFF6194 -3.5 -3.1 ABC transporter, ATP-binding protein (cluster 5, nickel/peptides/opines) compare
GFF7059 -3.5 -1.1 Zinc uptake regulation protein Zur compare
GFF3660 -3.5 -12.0 integral membrane sensor signal transduction histidine kinase compare
GFF1047 -3.5 -10.3 hypothetical protein compare
GFF2572 -3.5 -13.6 Protein-export protein SecB (maintains pre-export unfolded state) compare
GFF5831 -3.4 -2.2 Ketosteroid isomerase-related protein compare
GFF371 -3.4 -1.7 RNA-binding protein YhbY compare
GFF5666 -3.4 -2.4 Prevent host death protein, Phd antitoxin compare
GFF3250 -3.4 -1.3 Barstar, ribonuclease (Barnase) inhibitor compare
GFF6570 -3.4 -1.5 hypothetical protein compare
GFF7379 -3.4 -7.8 Branched-chain acyl-CoA dehydrogenase (EC 1.3.99.12) compare
GFF313 -3.3 -1.8 FIG027190: Putative transmembrane protein compare
GFF4107 -3.3 -1.0 ABC transporter, permease protein (cluster 3, basic aa/glutamine/opines) compare
GFF168 -3.3 -5.8 MCP methyltransferase, CheR-type compare
GFF859 -3.2 -2.2 Lactoylglutathione lyase (EC 4.4.1.5) compare
GFF1356 -3.2 -2.0 Putative manganese efflux pump MntP compare
GFF7231 -3.2 -1.2 no description compare
GFF84 -3.2 -1.5 Oxidoreductase, short-chain dehydrogenase/reductase family compare
GFF6190 -3.2 -6.6 3-hydroxyisobutyrate dehydrogenase family protein compare
GFF2227 -3.2 -2.7 Tricarboxylate transport protein TctC compare
GFF1741 -3.2 -3.7 UPF0324 inner membrane protein YeiH compare
GFF3600 -3.2 -2.2 Pantothenate kinase type III, CoaX-like (EC 2.7.1.33) compare
GFF244 -3.2 -2.2 Cys regulon transcriptional activator CysB compare
GFF6127 -3.1 -11.2 Phenylpropionate dioxygenase and related ring-hydroxylating dioxygenases, large terminal subunit compare
GFF7255 -3.1 -1.2 BUG/TctC family periplasmic protein compare
GFF6328 -3.1 -0.7 LPS-assembly lipoprotein LptE compare
GFF443 -3.1 -1.4 Cobalamin biosynthesis protein BluB @ 5,6-dimethylbenzimidazole synthase, flavin destructase family compare
GFF1167 -3.1 -13.1 Predicted Lactate-responsive regulator, IclR family compare
GFF6015 -3.1 -1.6 Transcriptional regulator PA0877, LysR family compare
GFF2273 -3.1 -3.0 Transcriptional regulator, AcrR family compare
GFF3335 -3.1 -2.4 no description compare
GFF6441 -3.0 -1.7 hypothetical protein compare
GFF156 -3.0 -3.9 Glycosyl transferase, group 2 family compare
GFF2543 -3.0 -9.6 Uncharacterized membrane protein Bcep18194_A6058 compare
GFF6168 -3.0 -0.9 Na(+) H(+) antiporter subunit G compare
GFF3067 -3.0 -3.9 Nitrogen regulation protein NtrB (EC 2.7.13.3) compare
GFF291 -3.0 -4.1 Tol-Pal system peptidoglycan-associated lipoprotein PAL compare
GFF431 -3.0 -1.6 Esterase/lipase compare
GFF5317 -3.0 -0.9 Frataxin homolog CyaY, facilitates Fe-S cluster assembly, interacts with IscS compare
GFF3204 -3.0 -2.3 no description compare
GFF2847 -3.0 -1.5 histone-like nucleoid-structuring protein H-NS compare
GFF290 -3.0 -8.3 Cell division coordinator CpoB compare
GFF213 -3.0 -2.0 tmRNA-binding protein SmpB compare
GFF2843 -3.0 -2.0 Murein hydrolase activator NlpD compare
GFF2481 -3.0 -0.9 Urease accessory protein UreF compare
GFF5065 -2.9 -1.9 Orotate phosphoribosyltransferase (EC 2.4.2.10) compare
GFF982 -2.9 -14.1 Cell division protein ZapE compare
GFF7245 -2.9 -0.9 universal stress protein, UspA family compare
GFF5267 -2.9 -2.0 Glucose-6-phosphate isomerase (EC 5.3.1.9) compare
GFF944 -2.9 -1.7 Aromatic-amino-acid aminotransferase (EC 2.6.1.57) compare
GFF4454 -2.9 -4.4 Exoribonuclease II (EC 3.1.13.1) compare
GFF2949 -2.9 -1.1 no description compare
GFF3406 -2.8 -11.4 Benzoyl-CoA oxygenase component A compare
GFF6246 -2.8 -2.0 Ribulose-phosphate 3-epimerase (EC 5.1.3.1) compare
GFF2804 -2.8 -1.9 Membrane protein compare
GFF4611 -2.8 -5.4 Predicted transcriptional regulator for fatty acid degradation FadP, TetR family compare
GFF3928 -2.8 -2.6 Histone acetyltransferase HPA2 and related acetyltransferases compare
GFF5739 -2.8 -0.9 Flagellar biosynthesis protein FliQ compare
GFF3451 -2.8 -0.9 no description compare
GFF4640 -2.8 -16.3 hypothetical protein compare
GFF966 -2.8 -7.5 Probable two-component transmembrane sensor histidine kinase transcription regulator protein (EC 2.7.3.-) compare
GFF4803 -2.8 -3.3 N-acetylmuramoyl-L-alanine amidase (EC 3.5.1.28) compare
GFF7043 -2.7 -1.9 Putative transmembrane protein compare
GFF6221 -2.7 -0.9 T6SS associated component TagF (ImpM) compare
GFF3377 -2.7 -0.6 Enoyl-CoA hydratase (EC 4.2.1.17) @ Enoyl-CoA hydratase EchA5 (EC 4.2.1.17) compare
GFF2422 -2.7 -3.0 Polysaccharide deacetylase compare
GFF4748 -2.7 -1.2 Triosephosphate isomerase (EC 5.3.1.1) compare
GFF4215 -2.7 -1.4 L-amino acid ABC transporter (Glu/Asp/His/...), permease protein 1 AapQ compare
GFF3265 -2.7 -1.6 Homoserine O-acetyltransferase (EC 2.3.1.31) compare
GFF6151 -2.6 -7.1 Transcriptional regulator, LysR family compare
GFF5411 -2.6 -13.2 CAMP phosphodiesterases class-II:Metallo-beta-lactamase superfamily compare
GFF7266 -2.6 -1.1 L-threo-3-hydroxyaspartate ammonia-lyase (EC 4.3.1.16) compare
GFF408 -2.6 -1.2 Two-component system response regulator OmpR compare
GFF5332 -2.6 -18.7 Glutamate synthase [NADPH] large chain (EC 1.4.1.13) compare
GFF6385 -2.6 -1.9 Mll4878 protein compare
GFF1332 -2.6 -3.6 no description compare
GFF4950 -2.6 -2.3 ABC transporter, permease protein (cluster 2, ribose/xylose/arabinose/galactose) compare
GFF4490 -2.6 -4.3 Site-specific tyrosine recombinase XerC compare
GFF6322 -2.6 -9.6 Glutathione synthetase (EC 6.3.2.3) compare
GFF89 -2.6 -1.0 hypothetical protein compare
GFF4018 -2.6 -1.8 Arsenate reductase (EC 1.20.4.4) thioredoxin-coupled, LMWP family compare
GFF487 -2.6 -8.3 ATP-dependent protease La (EC 3.4.21.53) Type I compare
GFF7393 -2.6 -1.9 Mobile element protein compare
GFF1865 -2.5 -2.5 Transcriptional regulator, AraC family compare
GFF2627 -2.5 -1.7 Chorismate synthase (EC 4.2.3.5) compare
GFF7076 -2.5 -1.7 no description compare
GFF4145 -2.5 -0.8 transcriptional regulators-like protein compare
GFF2192 -2.5 -3.3 FIG00932626: hypothetical protein compare
GFF3960 -2.5 -7.4 3'-to-5' oligoribonuclease (orn) compare
GFF2179 -2.5 -1.7 hypothetical protein compare
GFF5491 -2.5 -2.9 Peptide deformylase (EC 3.5.1.88) compare
GFF409 -2.5 -1.7 Osmolarity sensory histidine kinase EnvZ compare
GFF177 -2.5 -1.3 Glutamine ABC transporter, ATP-binding protein GlnQ compare
GFF5324 -2.5 -1.2 Shikimate kinase I (EC 2.7.1.71) compare
GFF1451 -2.5 -3.1 FIG00456379: hypothetical protein compare
GFF6998 -2.4 -1.2 Flagellar basal-body rod protein FlgB compare
GFF5097 -2.4 -1.7 5-carboxymethyl-2-hydroxymuconate delta-isomerase (EC 5.3.3.10) compare
GFF2189 -2.4 -2.7 Protocatechuate 3,4-dioxygenase alpha chain (EC 1.13.11.3) compare
GFF5390 -2.4 -6.0 RecA protein compare
GFF3320 -2.4 -1.1 3-oxoacyl-[acyl-carrier-protein] synthase, KASII (EC 2.3.1.179) compare
GFF6870 -2.4 -10.4 FIG00904791: hypothetical protein compare
GFF808 -2.4 -12.4 Polyhydroxyalkanoic acid synthase compare
GFF4766 -2.4 -0.7 identified by similarity to GB:AAK22812.1; match to protein family HMM PF06676 compare
GFF3755 -2.4 -4.5 Transcriptional regulator, GntR family compare
GFF1113 -2.4 -1.7 ABC transporter, ATP-binding protein (cluster 1, maltose/g3p/polyamine/iron); ABC transporter, ATP-binding protein (cluster 10, nitrate/sulfonate/bicarbonate) compare
GFF2870 -2.4 -10.4 Nicotinate phosphoribosyltransferase (EC 6.3.4.21) compare
GFF1756 -2.3 -1.0 hypothetical protein compare
GFF2523 -2.3 -1.3 Peptide chain release factor N(5)-glutamine methyltransferase (EC 2.1.1.297) compare
GFF3547 -2.3 -2.4 no description compare
GFF5742 -2.3 -2.3 Flagellar motor switch protein FliN compare
GFF1644 -2.3 -1.0 hypothetical protein compare
GFF1322 -2.3 -11.8 [Protein-PII] uridylyltransferase (EC 2.7.7.59) / [Protein-PII]-UMP uridylyl-removing enzyme compare
GFF2844 -2.3 -5.4 Protein-L-isoaspartate O-methyltransferase (EC 2.1.1.77) compare
GFF17 -2.3 -4.0 hypothetical protein compare


Specific Phenotypes

For 8 genes in this experiment

For complex community Community=Kojac gum; Passage=4 in Variovorax sp. SCN45

For complex community Community=Kojac gum; Passage=4 across organisms