Table 3. List of enzymes without a homolog in the NR and Swiss-Prot databases and the results of SVM functional family assignment.
| Enzyme (EC number) [Swiss-Prot accession number] | Database containing no homolog | SVM assigned functional family (probability of correct prediction) | Assignment status |
|---|---|---|---|
| Thiocyanate hydrolase beta subunit (EC 3.5.5.8) [O66186]. | NR | EC 3.5 Hydrolase of non-peptide carbon–nitrogen bonds (98.9%) | + |
| EC 2.6 Transferases of nitrogenous groups (62.2%) | |||
| Potential cysteine protease avirulence protein avrPpiC2 (EC 3.4.22.-) [Q9F3T4]. | NR | EC 4.2 Carbon–oxygen lyase (93.6%) | − |
| EC 2.3 Acyltransferase (83.9%) | |||
| EC 4.1 Carbon–carbon lyase (71.3%) | |||
| Outer membrane (58.6%) | |||
| Extracellular phospholipase (EC 3.1.1.5) [P82476] | NR | EC 3.1 Hydrolase of ester bonds (98.7%) | + |
| Cytochrome c oxidase polypeptide IV, mitochondrial precursor (EC 1.9.3.1) [P30815]. | NR | EC 1.9 Oxidoreductase of a heme group of donors (99.0%) | + |
| Cytochrome c oxidase polypeptide VI (EC 1.9.3.1) [P26310]. | NR | EC 1.9 Oxidoreductase of a heme group of donors (98.4%) | + |
| Transmembrane (98.3%) | |||
| EC 3.1 Hydrolase of ester bonds (62.2%) | |||
| Alginate lyase precursor (EC4.2.2.3) [P39049]. | NR | Transmembrane (65.4%) | − |
| Outer membrane (58.6%) | |||
| EC 2.1 Transferase of one-carbon groups (58.6%) | |||
| DNA α-glucosyltransferase (EC 2.4.1.26) [P04519] | NR | EC 2.4 Glycosyltransferase (80.4%); | + |
| EC 2.7 Transferase of phosphorus-containing groups (68.5%) | |||
| Endonuclease CviAII (EC 3.1.21.4 [P31117] | NR | EC 3.1 Hydrolase of ester bonds (99.0%) | + |
| Type II restriction enzyme CviJI (EC 3.1.21.4) [P52283] | NR | EC 3.1 Hydrolase of ester bonds (99.0%); | + |
| rRNA-binding proteins (98.8%); | |||
| EC 3.4 Peptidase (68.5%) | |||
| DNA-directed RNA polymerase, subunit 10 homolog (EC 2.7.7.6) [P42488] | NR | EC 2.7 Transferase of phosphorus-containing groups (99.0%) | + |
| 7 transmembrane receptor metabotropic glutamate family (58.6%) | |||
| Endonuclease IV (EC 3.1.21.-) [P39250] | NR | No function predicted | − |
| Beta-agarase precursor (EC3.2.1.81) [P13734]. | NR | EC 4.1 Carbon–carbon lyase (96.7%) | − |
| EC 2.4 Glycosyltransferase (71.3%) | |||
| Phenylacetaldoxime dehydratase (EC 4.2.1.-) [P82604]. | Swiss-Prot | Transmembrane (98.2%) | − |
| EC 3.4 Peptidase (96.4%) | |||
| EC 3.3 Hydrolase of ether bonds (80.4%) | |||
| EC 2.7 Transferase of phosphorus-containing groups (73.8%) | |||
| ATP synthase H chain, mitochondrial precursor (EC3.6.3.14) [Q12349]. | Swiss-Prot | EC 3.6 Hydrolase of acid anhydrides (99.0%) | + |
| RNA-binding protein (58.6%) | |||
| Peptide-N(4)-(N-acetyl-β-d-glucosaminyl)asparagine amidase F precursor (EC 3.5.1.52) [P21163] | Swiss-Prot | EC 3.5 Hydrolase of non-peptide carbon–nitrogen bonds (99.0%) | + |
| Beta-Barrel porin (58.6%) | |||
| S-Adenosyl-l-methionine hydrolase (EC 3.3.1.2) [P07693] | Swiss-Prot | EC 3.3 Hydrolase of ether bonds (99.0%) | + |
| EC 2.7 Transferase of phosphorus-containing groups (71.3%) | |||
| DNA-binding protein (65.4%) | |||
| Hypothetical 52.8 kDa protein in VPS15-YMC2 intergenic region. (EC 3.1.22.-) [P38257] | Swiss-Prot | DNA-binding protein (89.3%) | − |
| Outer membrane (58.6%) | |||
| Hypothetical protein BBB03 (EC3.1.22.-) [O50979]. | Swiss-Prot | EC 2.7 Transferase of phosphorus-containing groups (88.1%) | − |
| EC 3.4 Peptidase (86.8%) | |||
| EC 2.3 Acyltransferase (71.3%) | |||
| EC 4.1 Carbon–carbon lyase (65.4%) | |||
| Telomere elongation protein (EC2.7.7.-) [P17214]. | Swiss-Prot | EC 2.7 Transferase of phosphorus-containing groups (99.1%) | + |
| DNA-binding protein (78.4%) | |||
| Fucose-1-phosphate guanylyltransferase (EC 2.7.7.30) [O14772] | Swiss-Prot | EC 2.7 Transferase of phosphorus-containing groups (99.1%) | + |
| 7 transmembrane receptor metabotropic glutamate family (58.6%) | |||
| DNA-directed RNA polymerase I 14 kDa polypeptide (EC 2.7.7.6) [P50106]. | Swiss-Prot | EC 2.7 Transferase of phosphorus-containing groups (99%) | + |
| DNA-binding protein (62.2%) | |||
| Beta-Barrel porin (58.6%) | |||
| EC 3.4 Peptidase (58.6%) | |||
| DNA polymerase III, theta subunit (EC 2.7.7.7) [P28689]. | Swiss-Prot | EC 2.7 Transferase of phosphorus-containing groups (99.0%) | + |
| EC 4.2 Carbon–oxygen lyase (58.6%) | |||
| Cytochrome c oxidase polypeptide IV (EC 1.9.3.1) [P77921] | Swiss-Prot | EC 1.9 Oxidoreductase of a heme group of donors (97.0%) | + |
| Envelope protein (58.6%) | |||
| Transmembrane (58.6%) | |||
| Cytochrome c oxidase polypeptide VII (EC 1.9.3.1) [P10174]. | Swiss-Prot | EC 1.9 Oxidoreductase of a heme group of donors (98.3%) | + |
| Transmembrane (58.6%) | |||
| Cytochrome c oxidase polypeptide VIII, mitochondrial precursor (EC 1.9.3.1) [P04039]. | Swiss-Prot | EC 1.9 Oxidoreductase of a heme group of donors (99.0%) | + |
| Transmembrane (58.6%) | |||
| RNA-binding protein (58.6%) | |||
| Cytochrome c oxidase polypeptide VIIA precursor (EC1.9.3.1) [P07255]. | Swiss-Prot | EC 1.9 Oxidoreductase of a heme group of donors (97.8%) | + |
| Transmembrane (93.8%) | |||
| EC 1.10 Oxidoreductase of diphenols and related substances as donors (58.6%) | |||
| Alpha-type channel (58.6%) | |||
| Heme-copper oxidase subunit IV (EC 1.9.3.-) [Q9YDX4]. | Swiss-Prot | EC 1.9 Oxidoreductase of a heme group of donors (99.0%) | + |
| Transmembrane (99.0%) | |||
| Aminoglycoside 2′-N-acetyltransferase (EC 2.3.1.-) [P95219] | Swiss-Prot | EC 2.7 Transferase of phosphorus-containing groups (78.4%) | − |
| EC 4.2 Carbon–oxygen lyase (58.6%) | |||
| Glycosyl transferase alg8 (EC2.4.1.-) [Q887P9]. | Swiss-Prot | Transmembrane (99.0%) | * |
| EC 2.4 Glycosyltransferase (98.6%) | |||
| Beta-agarase B (EC 3.2.1.81) [P48840]. | Swiss-Prot | Outer membrane (58.6%) | − |
| Beta-Barrel porin (58.6%) | |||
| CM (EC 5.4.99.5) [P19080] | Swiss-Prot | EC 5.4. Intramolecular transferase (99.0%) | + |
| EC 4.2. Carbon–oxygen lyase (58.6%) | |||
| Outer membrane (58.6%) | |||
| DNA β-glucosyltransferase (EC 2.4.1.27) [P04547] | Swiss-Prot | EC 2.4 Glycosyltransferases (95.7%); | + |
| EC 2.5 Transferase of alkyl or aryl groups, other than methyl groups (80.4%) | |||
| dNMPkinase (EC 2.7.4.13) [P04531] | Swiss-Prot | EC 2.7 Transferase of phosphorus-containing groups (99.0%); | + |
| EC 2.4 Glycosyltransferase (96.4%); | |||
| EC 1.1 Oxidoreductase of the CH-OH group of donors (71.3%) | |||
| Endonuclease II (EC 3.1.21.1) [P07059] | Swiss-Prot | EC 3.1 Hydrolase of ester bonds (99.0%) | + |
| Endonuclease V (EC 3.1.25.1) [P04418] | Swiss-Prot | EC 3.1 Hydrolase of ester bonds (99.0%) | + |
| Exonuclease (EC 3.1.11.3) [P03697] | Swiss-Prot | EC 3.1 Hydrolase of ester bonds (99.0%); | + |
| EC 4.1 Carbon–carbon lyases (88.1%); | |||
| EC 2.7 Transferase of phosphorus-containing groups (68.5%); | |||
| EC 1.1 Oxidoreductase of the CH-OH group of donors (58.6%) | |||
| Ribonuclease (EC 3.1.-.-)[P13312] | Swiss-Prot | EC 3.1 Hydrolase of ester bonds (99.0%) | + |
| Intron-associated endonuclease 1 (EC 3.1.-.-) [P13299] | Swiss-Prot | EC 3.1 Hydrolase of ester bonds (99.0%); | + |
| DNA-binding protein (83.9%) | |||
| Intron-associated endonuclease 2 (EC 3.1.-.-) [P07072] | Swiss-Prot | EC 3.1 Hydrolase of ester bonds (99.0%) | + |
| Putative adenine-specific methylase (EC 2.1.1.72) [P51715] | Swiss-Prot | EC 2.1 Transferase of one-carbon groups (99.0%); | + |
| Outer membrane (58.6%); | |||
| mRNA-binding protein (58.6%) | |||
| Protein kinase (EC 2.7.1.37) [P00513] | Swiss-Prot | EC 2.7 Transferase of phosphorus-containing groups (99.0%) | + |
| Slt35 (EC 3.2.1.-) [P41052] | Swiss-Prot | Outer membrane (99.0%) | − |
| EC 1.1. Oxidoreductase acting on the CH-OH group of donors (89.3%) | |||
| EC 4.1. Carbon–carbon lyase (62.2%) | |||
| Ammonia monooxygenase (EC 1.13.12.-)[Q04508] | Swiss-Prot | EC 1.13. oxygenase (99.0%) | + |
| Transmembrane (99.0%) | |||
| EC 2.4. Glycosyltransferases (83.9%) | |||
| 2-Aminomuconate deaminase (EC 3.5.99.5) [P81593] | Swiss-Prot | EC 3.5. Hydrolase acting on carbon–nitrogen bonds, other than peptide bonds (99.0%) | + |
| EC 3.4. Peptidase (58.6%) | |||
| ADP-ribosyltransferase (EC2.4.2.37) [P14299] | Swiss-Prot | Transmembrane (92.9%) | * |
| EC 2.4. Glycosyltransferase (90.3%) | |||
| Outer membrane (58.6%) | |||
| Alpha-N-AFase II (EC 3.2.1.55) [P82594] | Swiss-Prot | EC 3.4. Peptidase (91.3%) | − |
| Aminopeptidase G (EC 3.4.11.-) [Q54340] | Swiss-Prot | EC 3.4. Peptidase (99.0%) | + |
| TC 1.C. Channels/pores—pore-forming toxins (proteins and peptides) (58.6%) | |||
| Alginate lyase (EC 4.2.2.3) [Q59478] | Swiss-Prot | Transmembrane (96.4%) | − |
| EC 3.1. Hydrolase of ester bonds (78.4%) | |||
| Outer membrane (58.6%) | |||
| ATPE_YEAST (EC 3.6.3.14) [P21306] | Swiss-Prot | RNA-binding proteins (58.6%) | − |
| AhdA2cA1c (EC1.14.-.-) [BAC65427.1] | Swiss-Prot | EC 3.1. Hydrolase of ester bonds (82.2%) | − |
| DNA-binding protein (80.4%) | |||
| Transmembrane (58.6%) |
The symbol +, * and − represent the cases that the top of the predicted family, one of the predicted families, and none of the predicted families matches the enzyme function, respectively.