Table 1.
Substrate-specific proteins
| Specificity | Locus | Description in NCBI | Description in KEGG | Vs. Glucose | |
|---|---|---|---|---|---|
| Log2 (fold change) | FDR-adjusted p value | ||||
| Xylan | Clocel_0589 | Alpha-l-fucosidase | Alpha-l-fucosidase 2 | 2.67 | 2.07E−04 |
| Clocel_0590 | Xylose isomerase | Xylose isomerase | 3.35 | 1.43E−04 | |
| Clocel_0591 | Transaldolase | Transaldolase | 3.52 | 1.46E−06 | |
| Clocel_0592 | Xylulokinase | Xylulokinase | 2.85 | 7.29E−05 | |
| Clocel_1085 | Dinitrogenase iron–molybdenum cofactor biosynthesis protein | – | 2.32 | 4.24E−03 | |
| Clocel_1151 | Methyl-accepting chemotaxis sensory transducer | Methyl-accepting chemotaxis protein | 1.96 | 1.70E−02 | |
| Clocel_1430 | Glycoside hydrolase family protein | Alpha-d-xyloside xylohydrolase | 1.90 | 9.48E−03 | |
| Clocel_2573 | Hypothetical protein Clocel_2573 | Chemotaxis protein CheX | 1.60 | 3.95E−03 | |
| Clocel_2592 | Two component transcriptional regulator, AraC family | – | 3.72 | 1.49E−04 | |
| Clocel_2595 | Xylan 1,4-beta-xylosidase | Xylan 1,4-beta-xylosidase | 4.70 | 4.53E−06 | |
| Clocel_2596 | Sugar ABC transporter periplasmic protein | Ribose transport system substrate-binding protein | 4.62 | 1.06E−03 | |
| Clocel_2597 | Inner-membrane translocator | Ribose transport system permease protein | 4.01 | 7.36E−05 | |
| Clocel_2598 | ABC transporter | Ribose transport system ATP-binding protein | 4.34 | 1.89E−05 | |
| Clocel_2881 | PTS system lactose/cellobiose-specific transporter subunit IIB | PTS system, cellobiose-specific IIB component | 1.49 | 1.70E−02 | |
| Clocel_2940 | Putative phosphate transport regulator | Hypothetical protein | 1.44 | 2.45E−02 | |
| Clocel_3175 | phoH family protein | phoH-like ATPase | 1.64 | 3.84E−02 | |
| Clocel_3761 | ATP:guanido phosphotransferase | – | 1.31 | 1.37E−02 | |
| Clocel_3762 | UvrB/UvrC protein | – | 1.42 | 3.45E−02 | |
| Clocel_4277 | Aldo/keto reductase | – | 1.08 | 4.66E−02 | |
| Galactomannan | Clocel_0034 | Glycoside hydrolase family protein | Alpha-d-xyloside xylohydrolase | 1.73 | 1.04E−02 |
| Clocel_0391 | Glycosyltransferase | – | 1.83 | 1.96E−02 | |
| Clocel_0684 | Thiazole biosynthesis protein ThiH | 2-Iminoacetate synthase | 1.57 | 4.69E−03 | |
| Clocel_2225 | Cobalamin (vitamin B12) biosynthesis CbiX protein | – | 1.39 | 4.52E−02 | |
| Clocel_2259 | pfkB domain-containing protein | 2-Dehydro-3-deoxygluconokinase | 1.31 | 1.04E−02 | |
| Clocel_2697 | Sialate O-acetylesterase | Sialate O-acetylesterase | 1.69 | 1.69E−02 | |
| Clocel_2800 | Alpha-galactosidase | Alpha-galactosidase | 2.99 | 5.49E−05 | |
| Clocel_2962 | Inosine-5′-monophosphate dehydrogenase | IMP dehydrogenase | 1.31 | 1.96E−02 | |
| Clocel_3175 | phoH family protein | phoH-like ATPase | 1.98 | 1.14E−02 | |
| Clocel_3194 | Mannose-6-phosphate isomerase | Mannose-6-phosphate isomerase | 3.77 | 6.86E−05 | |
| Clocel_3196 | Glycosidase-like protein | Beta-1,4-mannooligosaccharide/beta-1,4-mannosyl-N-acetylglucosamine phosphorylase | 2.65 | 5.29E−03 | |
| Clocel_3198 | N-acylglucosamine 2-epimerase | Mannobiose 2-epimerase | 3.19 | 2.10E−03 | |
| Clocel_3200 | Binding-protein-dependent transport system inner membrane protein | Multiple sugar transport system permease protein | 4.76 | 8.61E−04 | |
| Clocel_3201 | Extracellular solute-binding protein | Raffinose/stachyose/melibiose transport system substrate-binding protein | 4.23 | 5.49E−05 | |
| Clocel_3205 | Glycoside hydrolase family 2 | Beta-mannosidase | 2.55 | 1.51E−03 | |
| Clocel_3657 | Xylan 1,4-beta-xylosidase | Xylan 1,4-beta-xylosidase/alpha-N-arabinofuranosidase | 1.79 | 4.26E−02 | |
| Clocel_3857 | ABC transporter | Multiple sugar transport system ATP-binding protein | 2.15 | 1.03E−03 | |
| Clocel_4053 | LPXTG-motif cell wall anchor domain-containing protein | Sialate O-acetylesterase | 2.28 | 3.79E−02 | |
| Clocel_4087 | Aldose 1-epimerase | Aldose 1-epimerase | 1.45 | 2.68E−02 | |
| Clocel_4088 | Galactose-1-phosphate uridylyltransferase | UDP-glucose–hexose-1-phosphate uridylyltransferase | 3.38 | 1.83E−04 | |
| Clocel_4089 | UDP-glucose 4-epimerase | UDP-glucose 4-epimerase | 2.09 | 1.82E−03 | |
| Clocel_4277 | Aldo/keto reductase | – | 1.08 | 4.26E−02 | |
| Pectin | Clocel_0048 | Transcriptional regulator, AbrB family | Transcriptional pleiotropic regulator of transition state genes | 1.91 | 2.50E−03 |
| Clocel_0322 | tatD family hydrolase | tatD DNase family protein | 1.74 | 8.66E−03 | |
| Clocel_0513 | Extracellular solute-binding protein | Raffinose/stachyose/melibiose transport system substrate-binding protein | 2.12 | 2.50E−03 | |
| Clocel_0519 | Glycogen/starch/alpha-glucan phosphorylase | Starch phosphorylase | 1.88 | 1.37E−02 | |
| Clocel_1243 | Extracellular solute-binding protein | Multiple sugar transport system substrate-binding protein | 2.53 | 9.20E−05 | |
| Clocel_1892 | Acetate kinase | Acetate kinase | 1.31 | 6.43E−03 | |
| Clocel_2210 | Nicotinate-nucleotide–dimethyl-benzimidazole phosphoribosyltransferase | Nicotinate-nucleotide–dimethyl-benzimidazole phosphoribosyltransferase | 1.08 | 1.47E−02 | |
| Clocel_2214 | ATP:corrinoid adenosyltransferase BtuR/CobO/CobP |
Coblalamin adenosyltransferase | 1.37 | 4.25E−02 | |
| Clocel_2222 | Precorrin-3B C(17)-methyltransferase | Precorrin-3B C17-methyltransferase | 1.70 | 6.63E−03 | |
| Clocel_2225 | Cobalamin (vitamin B12) biosynthesis CbiX protein | – | 1.95 | 4.32E−03 | |
| Clocel_2227 | Precorrin-4 C(11)-methyltransferase | Precorrin-4/cobalt-precorrin-4 C11-methyltransferase | 2.11 | 7.92E−03 | |
| Clocel_2250 | Altronate dehydratase | Altronate hydrolase | 4.07 | 1.02E−05 | |
| Clocel_2251 | Mannitol dehydrogenase domain-containing protein | Tagaturonate reductase | 4.50 | 4.39E−06 | |
| Clocel_2253 | Crp family transcriptional regulator | – | 2.37 | 2.50E−03 | |
| Clocel_2254 | Glycoside hydrolase family protein | – | 4.36 | 4.39E−06 | |
| Clocel_2255 | Major facilitator superfamily protein | Oligogalacturonide transporter | 4.33 | 4.02E−05 | |
| Clocel_2256 | Glycosyl hydrolase family protein | Unsaturated rhamnogalacturonyl hydrolase | 4.19 | 1.49E−05 | |
| Clocel_2259 | pfkB domain-containing protein | 2-Dehydro-3-deoxygluconokinase | 3.75 | 1.49E−06 | |
| Clocel_2262 | Short-chain dehydrogenase/reductase SDR | Gluconate 5-dehydrogenase | 3.21 | 2.11E−02 | |
| Clocel_2263 | 4-Deoxy-l-threo-5-hexosulose-uronate ketol-isomerase | 4-Deoxy-l-threo-5-hexosulose-uronate ketol-isomerase | 3.15 | 4.92E−03 | |
| Clocel_2403 | Glucosamine/fructose-6-phosphate aminotransferase | Glucosamine–fructose-6-phosphate aminotransferase (isomerizing) | 1.45 | 4.57E−03 | |
| Clocel_2737 | Small GTP-binding protein | – | 1.10 | 2.98E−02 | |
| Clocel_3380 | LPXTG-motif cell wall anchor domain-containing protein | – | 4.03 | 1.27E−04 | |
| Clocel_3909 | Quorum-sensing autoinducer 2 (AI-2), LuxS | S-ribosylhomocysteine lyase | 1.19 | 2.34E−02 | |
| Clocel_4088 | Galactose-1-phosphate uridylyltransferase | UDP-glucose–hexose-1-phosphate uridylyltransferase | 1.62 | 1.73E−02 | |
| Clocel_4277 | Aldo/keto reductase | – | 1.31 | 8.08E−03 | |
To standardize data, obtained data were normalized with the median for all identified quantitative data. P values were adjusted with the Benjamini–Hochberg method to avoid the problem of multiple testing. For thresholds, we adopted an FDR-adjusted p value of <0.05 and fold change of protein ratio >2.0, compared to glucose.