TABLE 2.
Examples of the predicted true positive (TP), true negative (TN), false positive (FP), false negative (FN) protein sequences and host species of different RNA-binding classes
| Protein class | Prediction category | Example of predicted protein (host species) |
| RNA-binding | TP | 30S ribosomal protein S3 (Anaeroplasma abactoclasticum) |
| 30S ribosomal protein S4 (Chlorobium tepidum) | ||
| 30S ribosomal protein S5 (Shewanella oneidensis) | ||
| 30S ribosomal protein S11 (Mycoplasma penetrans) | ||
| 30S ribosomal protein S12 (Leptospira interrogans) | ||
| Matrix protein M1 (Influenza A virus [strain A/Bangkok/1/79], Influenza A virus [strain A/Wilson-Smith/33]) | ||
| Methionyl-tRNA synthetase | ||
| Nonstructural RNA-binding protein 53 (Simian 11 rotavirus [serotype 3/strain SA11-Patton]) | ||
| Ribonuclease P protein component (Bifidobacterium longum) | ||
| Transactivating regulatory protein (Bovine immunodeficiency virus [isolate 106]) | ||
| TN | DNA-binding 11 kDa phosphoprotein (Vaccinia virus [strain Copenhagen]) | |
| DNA polymerase V (Schizosaccharomyces pombe) | ||
| Hypothetical AL4 protein (Indian cassava mosaic virus) | ||
| Mating type protein mtA-1 (Sordaria fimicola) | ||
| NGFI-A binding protein 1 (Mus musculus) | ||
| Nonstructural protein 2 (Human coronavirus [strain OC43]) | ||
| Nucleolar phosphoprotein p130 (Homo sapiens) | ||
| Virulence-associated V antigen (Yersinia pestis) | ||
| XAP-5 protein (Homo sapiens) | ||
| FP | Arsenate reductase (Acidiphilium multivorum) | |
| Delta-atracotoxin-Hv1b (Hadronyche versuta) | ||
| DNA-binding protein HU 2 (Bacillus subtilis) | ||
| Cytochrome c oxidase polypeptide VIII, mitochondrial precursor (Candida albicans) | ||
| Elongation factor 1-beta (Methanobacterium thermoautotrophicum) | ||
| Hypothetical protein AF1917 (Archaeoglobus fulgidus) | ||
| Hypothetical protein HP0309 | ||
| Hypothetical protein PH0461 (Pyrococcus horikoshii) | ||
| Hypothetical protein yhbY (Escherichia coli) | ||
| Insecticidal toxin fragment | ||
| Nerve growth factor fragment | ||
| Nitrogenase GLNBA subunit | ||
| Prefoldin subunit 6 (Homo sapiens) | ||
| Putative cell surface protein homolog | ||
| Putative nucleolar protein K01G5.5 (Caenorhabditis elegans) | ||
| Putative MUDRA-like RETROTRANSPOSON-associated protein | ||
| Ribosomal protein L13A fragment | ||
| Zinc finger protein 263 (Homo sapiens) | ||
| FN | 2′,5′-oligoadenylate synthetase-like 11 | |
| 30S ribosomal protein S7P fragment (Methanosarcina thermophila) | ||
| 30S ribosomal protein S6, chloroplast precursor fragment | ||
| Bicoid protein fragment | ||
| Coat protein (Bacteriophage Q-beta) | ||
| Hypothetical 56.7 kD protein | ||
| Matrix protein M1 fragment (Influenza A virus [strain A/Camel/Mongolia/82]) | ||
| Putative heterogeneous nuclear ribonucleoprotein X fragment | ||
| RNA helicase DbpA | ||
| U2 small nuclear ribonucleoprotein 40K | ||
| rRNA-binding | TP | 30S ribosomal protein S1 (Escherichia coli, Helicobacter pylori J99, Mycobacterium tuberculosis) |
| 30S ribosomal protein S3 (Anaeroplasma abactoclasticum) | ||
| 30S ribosomal protein S4 (Chlorobium tepidum, Shigella flexneri) | ||
| 30S ribosomal protein S5 (Shewanella oneidensis) | ||
| 30S ribosomal protein S7 (Rhodobacter capsulatus) | ||
| 30S ribosomal protein S20 fragment | ||
| 30S ribosomal protein S12 fragment | ||
| 50S ribosomal protein L2 (Aquifex pyrophilus) | ||
| 50S ribosomal protein L3 (Aquifex pyrophilus) | ||
| TN | Apolipoprotein B mRNA editing enzyme (Rattus norvegicus) | |
| Aspartoacylase (Bos taurus) | ||
| DNA-directed RNA polymerase III 80 kD polypeptide (Mus musculus) | ||
| DNA polymerase V (Schizosaccharomyces pombe) | ||
| Hypothetical protein MG248 homolog (Mycoplasma pneumoniae) | ||
| Membrane protein C21orf4 (Homo sapiens) | ||
| Mitochondrial 24 kD protein (Zea mays) | ||
| Probable RNA 3′-terminal phosphate cyclase (Methanobacterium thermoautotrophicum) | ||
| RNA-binding protein VP2 (Bovine rotavirus [strain RF]) | ||
| RNA polymerase transcriptional regulation mediator, subunit 6 homolog (Homo sapiens) | ||
| FP | Bcn92 protein (Drosophila melanogaster) | |
| Cell division topological specificity factor (Escherichia coli) | ||
| DNA-directed RNA polymerases I, II, and III 7.0 kD polypeptide (Homo sapiens) | ||
| DNA repair protein radC homolog (Aquifex aeolicus) | ||
| GyrA fragment | ||
| Hypothetical protein AQ_1922 (Aquifex aeolicus) | ||
| Hypothetical protein C24H6.02c in chromosome I (Schizosaccharomyces pombe) | ||
| Hypothetical protein Rv2842c (Mycobacterium tuberculosis) | ||
| Imidazoleglycerol-phosphate dehydratase [Archaeoglobus fulgidus] | ||
| Photosystem I reaction center subunit IV, chloroplast precursor (Chlamydomonas reinhardtii) | ||
| Putative RNA binding protein KOC | ||
| RlpA-like lipoprotien precursor (Aquifex aeolicus) | ||
| FN | 30S ribosomal protein S6, chloroplast precursor fragment | |
| 50S ribosomal protein L23 (Aquifex pyrophilus) | ||
| 50S ribosomal protein L4 (Aquifex pyrophilus) | ||
| Chloroplast 50S ribosomal protein L1 fragment | ||
| Chloroplast 50S ribosomal protein L29 fragment | ||
| mRNA-binding | TP | 30S ribosomal protein S1 (Escherichia coli, Helicobacter pylori J99, Mycobacterium tuberculosis) |
| 30S ribosomal protein S3 (Acholeplasma axanthum, Acholeplasma sp. [strain ATCC J233], Alder yellows phytoplasma, Aquifex aeolicus, Bacillus halodurans) | ||
| 30S ribosomal protein S4 (Chlorobium tepidum, Shigella flexneri) | ||
| Cap specific mRNA (nucleoside-2′-O)-methyltransferase (Variola virus, Swinepox virus [strain Kasza]) | ||
| Eukaryotic translation initiation factor 3 subunit 4 (Homo sapiens, Mus musculus, Arabidopsis thaliana, Medicago truncatula) | ||
| Fertility inhibition protein | ||
| Fragile X mental retardation protein 1 homolog | ||
| Heterogeneous nuclear ribonucleoprotein D0 (Homo sapiens) | ||
| Heterogeneous nuclear ribonucleoprotein F (Homo sapiens) | ||
| Interleukin enhancer-binding factor 3 (Mus musculus) | ||
| Iron-responsive element binding protein 2 (Homo sapiens) | ||
| Maternal exuperantia protein | ||
| Polyadenylate-binding protein 1 (Homo sapiens) | ||
| Pyrimidine operon regulatory protein | ||
| PyrR bifunctional protein (Bacillus caldolyticus, Clostridium acetobutylicum, Listeria monocytogenes, Thermoanaerobacter tengcongensis) | ||
| Pre-mRNA splicing factor PRP9 (Candida albicans) | ||
| Splicing factor 3A subunit 3 (Drosophila melanogaster) | ||
| Splicing factor SC35 | ||
| Transcription termination factor rho | ||
| U1 small nuclear ribonucleoprotein A (Drosophila melanogaster) | ||
| TN | 3-deoxy-D-manno-octulosonic acid kinase (Pasteurella multocida) | |
| Adenosylhomocysteinase (Sulfolobus tokodaii) | ||
| Decarboxylase DEC1 (Cochliobolus heterostrophus) | ||
| DNA replication terminus site-binding protein | ||
| DNA terminal protein | ||
| Holliday junction DNA helicase ruvB (Staphylococcus aureus [strain Mu50/ATCC 700699]) | ||
| rRNA processing protein EBP2 (Candida albicans) | ||
| Transcription factor-like protein MORF4 (Homo sapiens) | ||
| Virion membrane protein FPV182 (Fowlpox virus) | ||
| FP | 40S ribosomal protein S25 (Arabidopsis thaliana) | |
| 50S ribosomal protein L22 (Mycoplasma gallisepticum) | ||
| Cell division protein ftsB homolog (Xanthomonas axonopodis [pv. citri]) | ||
| DNA mismatch repair protein MutS fragment | ||
| Hypothetical protein TC0713 (Chlamydia muridarum) | ||
| Hypothetical protein yjiX (Escherichia coli) | ||
| Hypothetical protein in LEU2 3′ region fragment (Pichia angusta) | ||
| Opioid growth factor receptor (Homo sapiens) | ||
| Putative metal-dependent hydrolase | ||
| Putative transition state regulator abh (Bacillus subtilis) | ||
| Squamosa-promoter binding protein 1 (Antirrhinum majus) | ||
| Trimethylamine methyltransferase mttB (Methanosarcina barkeri) | ||
| FN | 30S ribosomal protein S1 (Rickettsia prowazekii) | |
| Cap specific mRNA (Capripoxvirus [strain KS-1]) | ||
| Double-stranded RNA-binding protein Staufen homolog (Homo sapiens) | ||
| Eukaryotic translation initiation factor 3 RNA-binding subunit (Candida albicans) | ||
| Heterogenous nuclear ribonucleoprotein U (Homo sapiens) | ||
| Polyadenylate-binding protein 5 (Homo sapiens) | ||
| Putative eukaryotic translation initiation factor 3 subunit 7 (Caenorhabditis elegans) | ||
| U1 small nuclear ribonucleoprotein A (Candida albicans) | ||
| U6 snRNA-associated Sm-like protein LSm4 (Candida albicans) | ||
| tRNA-binding | TP | 30S ribosomal protein S7 (Haemophilus ducreyi, Chlamydia pneumoniae, Vibrio cholerae, Campylobacter jejuni) |
| 30S ribosomal protein S12 (Spirulina platensis, Mycobacterium gordonae, Leptospira interrogans, Streptococcus mutans, Bartonella henselae) | ||
| 60S ribosomal protein L35a | ||
| Methionyl-tRNA synthetase (Xanthomonas campestris, [pv. campestris], Pyrococcus furiosus) | ||
| Multisynthetase complex auxiliary component p43 | ||
| Phenylalanyl-tRNA synthetase beta chain (Chlamydia pneumoniae, Rickettsia prowazekii) | ||
| Zipcode-binding protein | ||
| TN | 4-hydroxythreonine-4-phosphate dehydrogenase (Sphingomonas aromaticivorans) | |
| Capsid protein VP26 | ||
| DNA repair protein RAD9 (Schizosaccharomyces octosporus) | ||
| Histone deacetylase HST1 (Candida albicans) | ||
| Putative RNA-directed RNA polymerase (Avian infectious bursal disease virus [strain Australian 002-73]) | ||
| Single-stranded DNA-binding protein 2 (Homo sapiens) | ||
| TAP42 protein (Candida albicans) | ||
| Transport protein particle 20 kD subunit (Candida albicans) | ||
| Zinc finger protein Rp-8 (Mus musculus) | ||
| FP | 60S ribosomal protein L18 fragment (Cicer arietinum) | |
| 40S ribosomal protein S26 (Schizophyllum commune) | ||
| SsrA-binding protein (Bacillus subtilis) | ||
| Cytochrome c oxidase polypeptide VIc-1 (Rattus norvegicus) | ||
| Thiamine biosynthesis protein, putative | ||
| FN | Phenylalanyl-tRNA synthetase beta chain (Ureaplasma parvum, Deinococcus radiodurans) | |
| Probable methionyl-tRNA synthetase (Oryza sativa) | ||
| snRNA-binding | TP | Octamer-binding transcription factor I (Homo sapiens, Sus scrofa) |
| U1 small nuclear ribonucleoprotein A (Homo sapiens) | ||
| U1 small nuclear ribonucleoprotein 70 kD (Drosophila melanogaster, Xenopus laevis) | ||
| U2 small nuclear ribonucleoprotein A′ (Mus musculus) | ||
| U6 snRNA-associated Sm-like protein LSm4 (Fagus sylvatica, Oryza sativa, Candida albicans) | ||
| TN | Acetylglutamate kinase | |
| DNA binding protein S1FA (Arabidopsis thaliana) | ||
| DNA mismatch repair protein mutS (Vibrio vulnificus) | ||
| DNA-directed RNA polymerase beta′ chain (Porphyra purpurea) | ||
| Guanine nucleotide exchange factor MSS4 homolog (Drosophila melanogaster) | ||
| Glutaminyl-tRNA synthetase (Lupinus luteus) | ||
| Heme/hemopexin-binding protein precursor (Haemophilus influenzae) | ||
| Nonstructural protein NS2 | ||
| Probable arginyl-tRNA—protein transferase (Xylella fastidiosa) | ||
| RNA polymerase sigma-54 factor (Salmonella typhimurium) | ||
| FP | CG1622 protein | |
| CG17446 protein | ||
| F46B6.3b protein | ||
| Heparan sulfate 2-sulfotransferase fragment | ||
| Homoserine dehydrogenase fragment | ||
| Hypothetical 44.5 kD protein | ||
| Hypothetical protein BH2667 (Bacillus halodurans) | ||
| Hypothetical protein PYRAB10580 (Pyrococcus abyssi) | ||
| Hypothetical protein spyM18_1551 | ||
| MiaE fragment | ||
| ORF FPV166 Molluscum contagiosum virus MC105L homolog | ||
| US3ii/US3iv protein | ||
| FN | 80 kD nuclear cap binding protein NCBP 80 kD subunit (Homo sapiens) | |
| Hypothetical 28.9 kD protein (Caenorhabditis elegans) | ||
| NHP2-like protein 1 (Homo sapiens) | ||
| Probable U6 snRNA-associated Sm-like protein LSm3 (Schizosaccaromyces pombe) | ||
| Small nuclear ribonucleoprotein E (Candida albicans) | ||
| Small nuclear ribonucleoprotein D1 homolog (Candida albicans) | ||
| U6 snRNA-associated Sm-like protein LSm2 (Homo sapiens) | ||
| U6 snRNA-associated Sm-like protein LSm3 (Candida albicans) | ||
| U6 snRNA-associated Sm-like protein LSm6 (Homo sapiens) | ||
| Zinc finger protein 143 (SPH-binding factor) (Homo sapiens) |
Only proteins in the independent evaluation sets are included. Host species of some protein sequences are not provided because the relevant information is not yet available in the protein sequence database.