Specific Phenotypes for Herbaspirillum seropedicae SmR1 in carbon source experiments

Condition Gene Description Fitness Cons.
2-Deoxy-D-Ribose HSERO_RS01920 50S ribosomal protein L11 methyltransferase +1.4  
2-Deoxy-D-Ribose HSERO_RS05085 sugar ABC transporter permease +10.7 Yes
2-Deoxy-D-Ribose HSERO_RS05090 sugar ABC transporter ATP-binding protein +10.4  
2-Deoxy-D-Ribose HSERO_RS05095 LacI family transcription regulator +11.0 Yes
2-Deoxy-D-Ribose HSERO_RS05100 sugar ABC transporter permease +10.8 Yes
2-Deoxy-D-Ribose HSERO_RS05105 ribokinase -3.3 Yes
2-Deoxy-D-Ribose HSERO_RS05115 aldehyde dehydrogenase -3.2 Yes
2-Deoxy-D-Ribose HSERO_RS05590 esterase +1.5  
2-Deoxy-D-Ribose HSERO_RS05820 IclR family transcriptional regulator -1.7  
2-Deoxy-D-Ribose HSERO_RS07435 formate dehydrogenase accessory protein FdhD +1.9  
2-Deoxy-D-Ribose HSERO_RS16360 DNA mismatch repair protein MutS +2.2  
2-Deoxy-D-Ribose HSERO_RS20790 cytochrome B559 subunit alpha -1.5  
2-Deoxy-D-Ribose HSERO_RS21690 PrkA family serine protein kinase +4.9  
2-Deoxy-D-Ribose HSERO_RS21695 hypothetical protein +4.8  
2-Deoxy-D-Ribose HSERO_RS21700 SpoVR family protein +5.1  
2-Deoxy-D-Ribose HSERO_RS21980 membrane protein -1.1  
2-Deoxy-D-Ribose HSERO_RS22105 glycosyl transferase +1.4  
2-Deoxyadenosine 5-monophosphate HSERO_RS00970 glucoamylase -1.2  
2-Deoxyadenosine 5-monophosphate HSERO_RS00975 alpha,alpha-trehalose-phosphate synthase -1.4  
2-Deoxyadenosine 5-monophosphate HSERO_RS02410 acriflavine resistance protein B -2.8  
2-Deoxyadenosine 5-monophosphate HSERO_RS02415 hemolysin D -3.2  
2-Deoxyadenosine 5-monophosphate HSERO_RS05085 sugar ABC transporter permease -2.0  
2-Deoxyadenosine 5-monophosphate HSERO_RS05090 sugar ABC transporter ATP-binding protein -2.5  
2-Deoxyadenosine 5-monophosphate HSERO_RS05095 LacI family transcription regulator -1.8  
2-Deoxyadenosine 5-monophosphate HSERO_RS05100 sugar ABC transporter permease -2.0  
2-Deoxyadenosine 5-monophosphate HSERO_RS05105 ribokinase -3.5  
2-Deoxyadenosine 5-monophosphate HSERO_RS05115 aldehyde dehydrogenase -4.0  
2-Deoxyadenosine 5-monophosphate HSERO_RS05120 deoxyribose-phosphate aldolase -3.7  
2-Deoxyadenosine 5-monophosphate HSERO_RS05220 porin -2.8  
2-Deoxyadenosine 5-monophosphate HSERO_RS16300 peptidase M20 -2.0  
D-Galactose HSERO_RS04225 permease -2.2  
D-Galactose HSERO_RS05155 2-dehydro-3-deoxy-6-phosphogalactonate aldolase -7.2 Yes
D-Galactose HSERO_RS05160 2-dehydro-3-deoxygalactonokinase dgoK (EC 2.7.1.58) (from data) -3.4 Yes
D-Galactose HSERO_RS22820 ArsR family transcriptional regulator +2.3  
D-Galacturonic Acid monohydrate HSERO_RS15785 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) (from data) -5.8 Yes
D-Galacturonic Acid monohydrate HSERO_RS15795 galactaro-1,5-lactonase (from data) -4.1  
D-Galacturonic Acid monohydrate HSERO_RS15800 Galactarate dehydratase (EC 4.2.1.42) (from data) -4.4 Yes
D-Galacturonic Acid monohydrate HSERO_RS15805 glucarate transporter -5.4 Yes
D-Galacturonic Acid monohydrate HSERO_RS17255 transporter +1.2  
D-Galacturonic Acid monohydrate HSERO_RS17265 glucosyltransferase MdoH +1.3  
D-Galacturonic Acid monohydrate HSERO_RS23010 D-galacturonate transporter ExuT (from data) -3.9 Yes
D-Galacturonic Acid monohydrate HSERO_RS23040 D-galacturonate dehydrogenase (EC 1.1.1.203) (from data) -3.1 Yes
D-Glucose HSERO_RS19360 2-keto-3-deoxyxylonate dehydratase (EC 4.2.1.141) (from data) +1.1  
D-Glucose-6-Phosphate sodium salt HSERO_RS17870 glucokinase +1.2 Yes
D-Glucose-6-Phosphate sodium salt HSERO_RS22795 N-acetyltransferase -1.4  
D-Mannitol HSERO_RS02190 sugar ABC transporter substrate-binding protein -3.5 Yes
D-Mannitol HSERO_RS02195 sugar ABC transporter permease -3.2 Yes
D-Mannitol HSERO_RS02200 mannitol ABC transporter permease -3.3 Yes
D-Mannitol HSERO_RS02210 sugar ABC transporter ATP-binding protein -4.3 Yes
D-Mannitol HSERO_RS02220 xylulokinase -3.0 Yes
D-Mannose HSERO_RS03630 fructose transporter -4.7  
D-Mannose HSERO_RS03640 D-mannose ABC transporter, ATPase component (from data) -4.7  
D-Mannose HSERO_RS03645 D-mannose ABC transporter, permease component (from data) -3.4  
D-Mannose HSERO_RS03650 Mannose isomerase (EC 5.3.1.7) (from data) -4.8 Yes
D-Mannose HSERO_RS20790 cytochrome B559 subunit alpha -1.5  
D-Mannose HSERO_RS21415 lytic transglycosylase -2.0  
D-Mannose HSERO_RS22480 dihydroxy-acid dehydratase -3.5  
D-Ribose HSERO_RS05330 glucose dehydrogenase +2.0  
D-Ribose HSERO_RS07710 hypothetical protein +3.2  
D-Ribose HSERO_RS08610 anhydrase -2.8  
D-Ribose HSERO_RS11480 D-ribose ABC transporter, substrate-binding component RbsB (from data) -4.9 Yes
D-Ribose HSERO_RS11485 D-ribose ABC transporter, ATPase component RbsA (from data) -3.3 Yes
D-Ribose HSERO_RS11490 D-ribose ABC transporter, permease component RbsC (from data) -5.0 Yes
D-Ribose HSERO_RS11500 Ribokinase (EC 2.7.1.15) (from data) -6.0 Yes
D-Ribose HSERO_RS12295 histidine kinase -1.5  
D-Ribose HSERO_RS17135 peptide ABC transporter permease -1.3  
D-Ribose HSERO_RS17145 peptide ABC transporter substrate-binding protein -1.4  
D-Ribose HSERO_RS19355 galactarate dehydratase +2.5  
D-Ribose HSERO_RS22795 N-acetyltransferase -1.9  
D-Sorbitol HSERO_RS02190 sugar ABC transporter substrate-binding protein -3.7 Yes
D-Sorbitol HSERO_RS02195 sugar ABC transporter permease -3.2 Yes
D-Sorbitol HSERO_RS02200 mannitol ABC transporter permease -2.9 Yes
D-Sorbitol HSERO_RS02210 sugar ABC transporter ATP-binding protein -3.3 Yes
D-Sorbitol HSERO_RS02220 xylulokinase -4.0  
D-Sorbitol HSERO_RS17000 ABC transporter for D-sorbitol/xylitol, substrate-binding component (from data) -2.3  
D-Sorbitol HSERO_RS17005 ABC transporter for D-sorbitol/xylitol, permease component 1 (from data) -3.8  
D-Sorbitol HSERO_RS17015 sorbitol dehydrogenase (EC 1.1.1.14); xylitol dehydrogenase (EC 1.1.1.9) (from data) -2.5 Yes
D-Sorbitol HSERO_RS17020 ABC transporter for D-sorbitol/xylitol, ATPase component (from data) -2.7  
D-Sorbitol HSERO_RS17025 AraC family transcriptional regulator -4.6 Yes
D-Sorbitol HSERO_RS17030 xylulokinase +3.5  
D-Xylose HSERO_RS00735 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (from data) -3.1 Yes
D-Xylose HSERO_RS02600 bile acid:sodium symporter variable  
D-Xylose HSERO_RS19325 LysR family transcriptional regulator -5.6  
D-Xylose HSERO_RS19330 FAH family protein -3.1  
D-Xylose HSERO_RS19355 galactarate dehydratase -2.0  
D-Xylose HSERO_RS19360 2-keto-3-deoxyxylonate dehydratase (EC 4.2.1.141) (from data) -4.3 Yes
D-Xylose HSERO_RS19365 2-keto-3-deoxy-L-fuconate 4-dehydrogenase FucDH (from data) +1.3  
Deoxyribonucleic acid from herring sperm HSERO_RS04830 alcohol dehydrogenase -1.1  
Deoxyribonucleic acid from herring sperm HSERO_RS09465 aldehyde dehydrogenase -1.2  
Deoxyribonucleic acid from herring sperm HSERO_RS09475 Fis family transcriptional regulator -1.1  
Glycerol HSERO_RS04870 glycerol ABC transporter, substrate-binding component (from data) -2.3 Yes
Glycerol HSERO_RS04875 glycerol kinase -3.6 Yes
Glycerol HSERO_RS19100 FAD-binding protein -1.6  
L-Arabinose HSERO_RS00725 LysR family transcriptional regulator -2.5  
L-Arabinose HSERO_RS05205 L-arabonate dehydratase (EC 4.2.1.25) (from data) -3.1 Yes
L-Arabinose HSERO_RS05210 L-arabinose 1-dehydrogenase (EC 1.1.1.46) (from data) -4.1 Yes
L-Arabinose HSERO_RS05225 L-arabinolactonase (EC 3.1.1.15) (from data) -3.7 Yes
L-Arabinose HSERO_RS06870 L-2-keto-3-deoxyarabonate dehydratase (EC 4.2.1.43) (from data) -3.9 Yes
L-Arabinose HSERO_RS06875 LysR family transcriptional regulator -4.0 Yes
L-Asparagine HSERO_RS05895 Patatin +1.3  
L-Asparagine HSERO_RS19240 arginine ABC transporter ATP-binding protein variable  
L-Fucose HSERO_RS01735 ATPase AAA -2.4 Yes
L-Fucose HSERO_RS05235 L-fuconate dehydratase (EC 4.2.1.68) (from data) variable Yes
L-Fucose HSERO_RS05250 ABC transporter for L-fucose, ATPase component (from data) -2.2  
L-Fucose HSERO_RS05255 ABC transporter for L-fucose, permease component (from data) -1.8  
L-Fucose HSERO_RS05260 ABC transporter for L-fucose, substrate-binding component (from data) variable  
L-Fucose HSERO_RS06350 3-oxoacyl-ACP reductase variable  
L-Fucose HSERO_RS06870 L-2-keto-3-deoxyarabonate dehydratase (EC 4.2.1.43) (from data) variable  
L-Fucose HSERO_RS06875 LysR family transcriptional regulator variable  
L-Fucose HSERO_RS09360 lysine transporter LysE variable  
L-Fucose HSERO_RS10840 cyanophycin synthetase variable  
L-Fucose HSERO_RS16610 transcriptional regulator +1.3  
L-Fucose HSERO_RS16705 dihydroxy-acid dehydratase variable  
L-Fucose HSERO_RS19325 LysR family transcriptional regulator variable  
L-Fucose HSERO_RS19330 FAH family protein variable  
L-Fucose HSERO_RS19340 amino acid ABC transporter permease +2.8  
L-Fucose HSERO_RS19345 amino acid ABC transporter ATP-binding protein variable  
L-Fucose HSERO_RS19350 amino acid ABC transporter variable  
L-Fucose HSERO_RS22795 N-acetyltransferase variable  
L-Glutamine HSERO_RS11610 NADH dehydrogenase -1.5  
L-Malic acid disodium salt monohydrate HSERO_RS03275 regulatory protein RecX -1.5  
L-Malic acid disodium salt monohydrate HSERO_RS05850 exodeoxyribonuclease VII large subunit -1.5  
L-Malic acid disodium salt monohydrate HSERO_RS05920 endonuclease -2.7  
L-Proline HSERO_RS00865 AsnC family transcriptional regulator -5.8 Yes
L-Proline HSERO_RS00870 L-proline ABC transporter, substrate-binding component (from data) -6.2  
L-Proline HSERO_RS00875 hypothetical protein -3.1  
L-Proline HSERO_RS00880 ornithine cyclodeaminase -1.9  
L-Proline HSERO_RS00905 L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (from data) -5.4 Yes
L-Proline HSERO_RS01975 4-hydroxybenzoate synthetase -1.5  
L-Rhamnose monohydrate HSERO_RS22200 Rhamnulokinase (EC 2.7.1.5) (from data) -6.3 Yes
L-Rhamnose monohydrate HSERO_RS22210 branched-chain amino acid ABC transporter permease -5.4 Yes
L-Rhamnose monohydrate HSERO_RS22215 branched-chain amino acid ABC transporter permease -4.4 Yes
L-Rhamnose monohydrate HSERO_RS22220 D-ribose transporter ATP-binding protein -3.5 Yes
L-Rhamnose monohydrate HSERO_RS22225 ABC transporter substrate-binding protein -4.8 Yes
L-Rhamnose monohydrate HSERO_RS22230 DeoR faimly transcriptional regulator -6.6 Yes
L-Rhamnose monohydrate HSERO_RS22235 rhamnulose-1-phosphate aldolase (EC 4.1.2.19) / lactaldehyde dehydrogenase (EC 1.2.1.22) (from data) -6.1 Yes
L-Rhamnose monohydrate HSERO_RS22240 L-rhamnose isomerase (EC 5.3.1.14) (from data) -5.1 Yes
L-Rhamnose monohydrate HSERO_RS22795 N-acetyltransferase variable  
L-mannose HSERO_RS03620 LysR family transcriptional regulator +1.5  
L-mannose HSERO_RS03630 fructose transporter -5.3  
L-mannose HSERO_RS03640 D-mannose ABC transporter, ATPase component (from data) -4.4  
L-mannose HSERO_RS03650 Mannose isomerase (EC 5.3.1.7) (from data) -5.6  
L-mannose HSERO_RS06185 response regulator protein +1.0  
L-mannose HSERO_RS16925 chemotaxis protein CheR +1.3  
L-mannose HSERO_RS22480 dihydroxy-acid dehydratase -3.8  
L-mannose HSERO_RS22750 sugar ABC transporter ATP-binding protein -1.2  
Phenylacetic acid HSERO_RS06705 MFS transporter -1.5  
Phenylacetic acid HSERO_RS08100 nicotinate phosphoribosyltransferase -1.7  
Phenylacetic acid HSERO_RS08185 sulfate transporter subunit -1.1  
Phenylacetic acid HSERO_RS08575 glyoxalase -1.1  
Phenylacetic acid HSERO_RS10515 membrane protein +4.1  
Phenylacetic acid HSERO_RS10520 hypothetical protein +4.2  
Phenylacetic acid HSERO_RS10525 fusaric acid resistance protein +4.0  
Phenylacetic acid HSERO_RS10530 RND transporter +4.2  
Phenylacetic acid HSERO_RS10535 LysR family transcriptional regulator -4.5  
Phenylacetic acid HSERO_RS11305 membrane protein -1.6  
Phenylacetic acid HSERO_RS15990 MarR family transcriptional regulator -1.7  
Phenylacetic acid HSERO_RS16340 transcriptional regulator -1.7  
Phenylacetic acid HSERO_RS20590 fused 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase and oxepin-CoA hydrolase (EC 3.3.2.12; EC 1.2.1.91) (from data) -4.2 Yes
Phenylacetic acid HSERO_RS20595 branched-chain amino acid ABC transporter substrate-binding protein -1.8  
Phenylacetic acid HSERO_RS20635 aldehyde dehydrogenase -3.9 Yes
Phenylacetic acid HSERO_RS20640 enoyl-CoA hydratase -4.9 Yes
Phenylacetic acid HSERO_RS20645 3-hydroxyacyl-CoA dehydrogenase -4.7 Yes
Phenylacetic acid HSERO_RS20650 phenylacetic acid degradation protein -2.5 Yes
Phenylacetic acid HSERO_RS20655 phenylacetate-CoA ligase -5.0 Yes
Phenylacetic acid HSERO_RS20660 bifunctional thiolase PaaJ: 3-oxo-5,6-dehydrosuberyl-CoA thiolase (EC 2.3.1.223); 3-oxoadipyl-CoA thiolase (EC 2.3.1.174) (from data) -4.9  
Phenylacetic acid HSERO_RS20665 2,3-dehydroadipyl-CoA hydratase -4.7 Yes
Sodium D,L-Lactate HSERO_RS02355 phosphoglucomutase variable  
Sodium D,L-Lactate HSERO_RS06975 penicillin-binding protein 1A variable  
Sodium D,L-Lactate HSERO_RS09950 chain-length determining protein -1.6  
Sodium D,L-Lactate HSERO_RS09995 N-acetylglucosaminyldiphospho-UDP N-acetyl-beta-D-mannosaminyltransferase variable  
Sodium D,L-Lactate HSERO_RS10560 membrane protein variable  
Sodium D,L-Lactate HSERO_RS16735 alcohol dehydrogenase -1.8  
Sodium D,L-Lactate HSERO_RS16740 GMC family oxidoreductase variable  
Sodium D,L-Lactate HSERO_RS16745 gluconate 2-dehydrogenase variable  
Sodium D,L-Lactate HSERO_RS16750 DeoR family transcriptional regulator -1.1  
Sodium D,L-Lactate HSERO_RS19095 glycolate oxidase -5.4 Yes
Sodium D,L-Lactate HSERO_RS19100 FAD-binding protein -5.2 Yes
Sodium D,L-Lactate HSERO_RS19105 FAD-binding protein -3.2 Yes
Sodium D,L-Lactate HSERO_RS21110 dTDP-glucose 4,6-dehydratase variable  
Sodium D,L-Lactate HSERO_RS23885 XRE family transcriptional regulator variable  
Sodium D-Lactate HSERO_RS06025 histidine kinase -1.5  
Sodium D-Lactate HSERO_RS06975 penicillin-binding protein 1A -1.0  
Sodium D-Lactate HSERO_RS09950 chain-length determining protein -1.3  
Sodium D-Lactate HSERO_RS09995 N-acetylglucosaminyldiphospho-UDP N-acetyl-beta-D-mannosaminyltransferase -1.7  
Sodium D-Lactate HSERO_RS10000 mannose-1-phosphate guanylyltransferase -1.8  
Sodium D-Lactate HSERO_RS19095 glycolate oxidase -4.7 Yes
Sodium D-Lactate HSERO_RS19100 FAD-binding protein -4.7 Yes
Sodium D-Lactate HSERO_RS19105 FAD-binding protein -4.3 Yes
Sodium L-Lactate HSERO_RS16550 NAD(P)H quinone oxidoreductase -1.1  
Sodium pyruvate HSERO_RS07015 isocitrate dehydrogenase -1.3  
Xylitol HSERO_RS05335 ribulokinase +1.6  
Xylitol HSERO_RS11220 hypothetical protein +1.3  
Xylitol HSERO_RS17000 ABC transporter for D-sorbitol/xylitol, substrate-binding component (from data) -2.0 Yes
Xylitol HSERO_RS17010 ABC transporter for D-sorbitol/xylitol, permease component 2 (from data) -2.5 Yes
Xylitol HSERO_RS17015 sorbitol dehydrogenase (EC 1.1.1.14); xylitol dehydrogenase (EC 1.1.1.9) (from data) -1.8 Yes
Xylitol HSERO_RS17020 ABC transporter for D-sorbitol/xylitol, ATPase component (from data) -4.1 Yes
Xylitol HSERO_RS17025 AraC family transcriptional regulator -5.1 Yes
Xylitol HSERO_RS17030 xylulokinase +5.9 Yes
Xylitol HSERO_RS22235 rhamnulose-1-phosphate aldolase (EC 4.1.2.19) / lactaldehyde dehydrogenase (EC 1.2.1.22) (from data) +3.8  
a-Ketoglutaric acid disodium salt hydrate HSERO_RS06975 penicillin-binding protein 1A -2.0  
a-Ketoglutaric acid disodium salt hydrate HSERO_RS16810 Fis family transcriptional regulator -2.5 Yes
a-Ketoglutaric acid disodium salt hydrate HSERO_RS16815 C4-dicarboxylate ABC transporter -2.6 Yes
a-Ketoglutaric acid disodium salt hydrate HSERO_RS16820 2-oxoglutarate:H+ symporter (from data) -2.9 Yes
m-Inositol HSERO_RS05460 LacI family transcription regulator -3.7  
m-Inositol HSERO_RS06135 malonic semialdehyde reductase -2.6  
m-Inositol HSERO_RS12095 Myo-inositol 2-dehydrogenase (EC 1.1.1.18) (from data) -5.4 Yes
m-Inositol HSERO_RS12110 sugar ABC transporter substrate-binding protein -6.7 Yes
m-Inositol HSERO_RS12115 ATPase -5.7 Yes
m-Inositol HSERO_RS12120 ABC transporter ATP-binding protein -6.4 Yes
m-Inositol HSERO_RS12125 5-dehydro-2-deoxygluconokinase (EC 2.7.1.92); possible 5-dehydro-2-deoxyphosphogluconate aldolase DUF2090 (EC 4.1.2.29) (from data) -5.0 Yes
m-Inositol HSERO_RS12130 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase IolD (EC 3.7.1.22) (from data) -4.9 Yes
m-Inositol HSERO_RS12135 Myo-inosose-2 dehydratase (EC 4.2.1.44) (from data) -8.5 Yes
m-Inositol HSERO_RS14845 stationary phase survival protein SurE -3.1  
m-Inositol HSERO_RS23235 GntR family transcriptional regulator -1.1 Yes