Release 3 (2019-09-08)
Computed from databases (SwissPalm and external databases) available on 2019-06-28.
2019 release
Tool | Type | Description | Version |
---|---|---|---|
RefSeq | Database | Set of reference sequences (genomic, transcript, and protein) | 94 |
PhosphoSite | Database | Protein post-translational modifications | 2017_may |
TAIR | Database | The Arabidopsis Information Resource: Genetic and molecular biology data for Arabidopsis thaliana | 2017_may |
UniProt | Database | Database on protein sequence and function | 2019_05 |
Ensembl Genomes | Database | Taxonomically extended set of genomes from Ensembl | 43 |
Ensembl | Database | Database on vertebrate (mainly) genomes | 96 |
IPI | Database | International Protein Index: Protein database (closed) | latest |
Gene Ontology | Database | Ontologies describing molecular functions, biological processes an subcellular locations | 2017_may |
Protein dataset | Palmitoylation validated or in palmitoyl-proteome(s) (SPalm dataset) | Validation experiments | Palmitoyl-proteomes | Predicted palmitoylation | 2 independent methods in palmitoyl-proteomes or validation experiment(s) | 2 independent methods in palmitoyl-proteomes | Same as previous column but grouped by gene | |
---|---|---|---|---|---|---|---|---|
0 | Number of articles | 760 | 745 | 45 | 676 | 757 | 278 | 732 |
1 | Number of experiments | 1198 | 1133 | 65 | 1048 | 1194 | 445 | 1164 |
2 | Number of organisms defining experiments | 57 | 54 | 13 | 51 | 54 | 16 | 44 |
3 | Number of organisms | 68 | 61 | 19 | 63 | 64 | 11 | 53 |
4 | Number of cell types | 225 | 218 | 35 | 204 | 224 | 114 | 217 |
5 | Number of subcellular fractions | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
6 | Number of techniques | 94 | 88 | 18 | 86 | 94 | 72 | 92 |
7 | Number of hits | 30142 | 1626 | 28516 | 16704 | 19870 | 18585 | 18923 |
8 | Number of individual genes related to palmitoylated proteins | 8869 | 687 | 8565 | 4952 | 3827 | 3362 | 3886 |
9 | Number of palmitoylated proteins | 12688 | 778 | 12278 | 6818 | 4721 | 4151 | 4087 |
10 | Number of sites (unique pairs (protein, position)) | 7459 | 1337 | 6122 | 4878 | 4627 | 3625 | 3781 |
11 | Number of sites identification techniques | 24 | 24 | 2 | 23 | 24 | 20 | 24 |
12 | Number of proteins associated to sites | 3603 | 438 | 3220 | 2173 | 2028 | 1683 | 1450 |
Set | Palmitoyl-transferases | Acyl-Protein Thioesterases | |
---|---|---|---|
0 | Has a DHHC motif (for DHHC-PATs) | 101 | - |
1 | Has a DHHC domain (for DHHC-PATs) | 108 | - |
2 | Has a known thioesterase activity (for APTs) | - | 55 |
3 | Curated in SwissPalm (at least one substrate reported) | 68 | 3 |
4 | All | 120 | 55 |
Categories
Proteins in
Organism | Genes with hit(s) | All genes in SwissPalm | Percent genes with hits(s) in SwissPalm (%) | Proteins with hit(s) | All proteins in SwissPalm | Percent proteins with hits(s) in SwissPalm (%) | Hits | Proteins with site(s) | Unique sites | Sites |
---|---|---|---|---|---|---|---|---|---|---|
Homo sapiens | 3593 | 20140 | 17.8 | 4587 | 23484 | 19.5 | 14645 | 1298 | 2096 | 2696 |
Mus musculus | 3764 | 17781 | 21.2 | 4647 | 20377 | 22.8 | 11189 | 2153 | 3890 | 4330 |
Rattus norvegicus | 680 | 11472 | 5.9 | 693 | 12774 | 5.4 | 942 | 50 | 94 | 160 |
Arabidopsis thaliana | 494 | 16012 | 3.1 | 597 | 17874 | 3.3 | 618 | 13 | 26 | 30 |
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | 59 | 6721 | 0.9 | 59 | 6721 | 0.9 | 115 | 16 | 24 | 46 |
Cricetulus griseus | 2 | 309 | 0.6 | 2 | 4626 | 0.0 | 2 | 0 | 0 | 0 |
Plasmodium falciparum (isolate 3D7) | 53 | 236 | 22.5 | 421 | 1593 | 26.4 | 488 | 0 | 0 | 0 |
Chlorocebus aethiops | 1 | 127 | 0.8 | 1 | 128 | 0.8 | 1 | 0 | 0 | 0 |
Bos taurus | 63 | 10113 | 0.6 | 65 | 11287 | 0.6 | 90 | 10 | 23 | 38 |
Schizosaccharomyces pombe | 240 | 5091 | 4.7 | 240 | 5173 | 4.6 | 244 | 2 | 2 | 3 |
Canis familiaris | 7 | 7018 | 0.1 | 7 | 7674 | 0.1 | 8 | 5 | 8 | 8 |
Drosophila melanogaster | 159 | 7032 | 2.3 | 164 | 7532 | 2.2 | 185 | 5 | 11 | 12 |
Danio rerio | 2 | 9835 | 0.0 | 2 | 11475 | 0.0 | 2 | 0 | 0 | 0 |
Human immunodeficiency virus type 1 group M subtype B (isolate HXB2) | 1 | 9 | 11.1 | 1 | 9 | 11.1 | 1 | 1 | 2 | 2 |
Gallus gallus | 1 | 4627 | 0.0 | 1 | 4812 | 0.0 | 1 | 0 | 0 | 0 |
Human herpesvirus 1 | 2 | 74 | 2.7 | 2 | 127 | 1.6 | 4 | 1 | 1 | 1 |
Semliki forest virus | 1 | 1 | 100.0 | 3 | 4 | 75.0 | 7 | 3 | 5 | 8 |
Sindbis virus | 0 | 0 | 0 | 3 | 5 | 60.0 | 3 | 3 | 8 | 8 |
Oryctolagus cuniculus | 7 | 5502 | 0.1 | 7 | 5642 | 0.1 | 8 | 5 | 30 | 30 |
Sus scrofa | 3 | 5565 | 0.1 | 3 | 5757 | 0.1 | 6 | 3 | 4 | 7 |
Toxoplasma gondii | 280 | 366 | 76.5 | 443 | 579 | 76.5 | 454 | 2 | 4 | 4 |
Torpedo californica | 5 | 9 | 55.6 | 5 | 21 | 23.8 | 5 | 1 | 13 | 13 |
Landoltia punctata | 1 | 2 | 50.0 | 1 | 2 | 50.0 | 1 | 0 | 0 | 0 |
Influenza A virus (A/udorn/1972(H3N2)) | 1 | 3 | 33.3 | 1 | 4 | 25.0 | 1 | 1 | 1 | 1 |
Giardia intestinalis | 1 | 39 | 2.6 | 3 | 76 | 3.9 | 5 | 1 | 1 | 1 |
Pectobacterium carotovorum subsp. carotovorum | 1 | 634 | 0.2 | 1 | 644 | 0.2 | 1 | 1 | 1 | 1 |
Influenza A virus (strain A/Duck/Ukraine/1/1963 H3N8) | 1 | 4 | 25.0 | 1 | 5 | 20.0 | 1 | 0 | 0 | 0 |
Salmonella typhimurium | 1 | 1835 | 0.1 | 1 | 1917 | 0.1 | 1 | 0 | 0 | 0 |
Medicago truncatula | 1 | 1647 | 0.1 | 1 | 1950 | 0.1 | 1 | 1 | 1 | 1 |
Influenza C virus (strain C/Johannesburg/1/1966) | 1 | 6 | 16.7 | 1 | 7 | 14.3 | 5 | 1 | 1 | 2 |
Simian immunodeficiency virus (isolate mac239) | 1 | 1 | 100.0 | 1 | 1 | 100.0 | 1 | 1 | 1 | 1 |
Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487) | 22 | 40 | 55.0 | 426 | 444 | 95.9 | 780 | 0 | 0 | 0 |
Trypanosoma brucei brucei | 3 | 125 | 2.4 | 126 | 330 | 38.2 | 126 | 0 | 0 | 0 |
Human immunodeficiency virus type 1 group M subtype B (isolate BH10) | 1 | 9 | 11.1 | 1 | 9 | 11.1 | 4 | 1 | 1 | 1 |
Xenopus laevis | 1 | 3245 | 0.0 | 1 | 3428 | 0.0 | 1 | 1 | 1 | 1 |
Friend murine leukemia virus | 1 | 3 | 33.3 | 2 | 14 | 14.3 | 5 | 1 | 1 | 2 |
Leishmania major | 1 | 308 | 0.3 | 1 | 1947 | 0.1 | 1 | 1 | 1 | 1 |
Ross river virus (strain T48) | 0 | 0 | 0 | 1 | 2 | 50.0 | 1 | 1 | 1 | 1 |
Caenorhabditis elegans | 2 | 6353 | 0.0 | 2 | 7369 | 0.0 | 2 | 2 | 3 | 3 |
Epstein-Barr virus (strain B95-8) | 2 | 79 | 2.5 | 2 | 79 | 2.5 | 7 | 2 | 6 | 6 |
Kirsten murine sarcoma virus | 1 | 1 | 100.0 | 1 | 1 | 100.0 | 1 | 0 | 0 | 0 |
Harvey murine sarcoma virus | 1 | 1 | 100.0 | 1 | 1 | 100.0 | 4 | 0 | 0 | 0 |
Vaccinia virus (strain Western Reserve) | 0 | 47 | 0 | 1 | 230 | 0.4 | 2 | 1 | 2 | 2 |
Influenza A virus (strain A/Fowl plague virus/Rostock/8/1934 H7N1) | 1 | 7 | 14.3 | 1 | 10 | 10.0 | 1 | 1 | 3 | 3 |
Vesicular Stomatitis Virus | 0 | 0 | 0 | 1 | 1 | 100.0 | 1 | 0 | 0 | 0 |
Solanum lycopersicum | 1 | 4477 | 0.0 | 1 | 4585 | 0.0 | 1 | 0 | 0 | 0 |
Neosartorya fumigata (strain CEA10 / CBS 144.89 / FGSC A1163) | 0 | 191 | 0 | 115 | 338 | 34.0 | 115 | 0 | 0 | 0 |
Mink cell focus-forming murine leukemia virus | 1 | 2 | 50.0 | 2 | 3 | 66.7 | 5 | 0 | 0 | 0 |
Moloney murine leukemia virus (strain neuropathogenic variant ts1-92b) | 1 | 1 | 100.0 | 1 | 1 | 100.0 | 4 | 0 | 0 | 0 |
Moloney murine leukemia virus (isolate Shinnick) | 3 | 3 | 100.0 | 3 | 3 | 100.0 | 7 | 0 | 0 | 0 |
Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) | 18 | 708 | 2.5 | 18 | 2670 | 0.7 | 18 | 0 | 0 | 0 |
Human cytomegalovirus | 1 | 206 | 0.5 | 1 | 402 | 0.2 | 2 | 1 | 1 | 2 |
Murine coronavirus (strain A59) | 1 | 6 | 16.7 | 1 | 11 | 9.1 | 1 | 1 | 5 | 5 |
Medicago sativa subsp. falcata | 0 | 3 | 0 | 1 | 5 | 20.0 | 1 | 1 | 1 | 1 |
Oryza sativa subsp. japonica | 1 | 6253 | 0.0 | 1 | 9444 | 0.0 | 1 | 1 | 2 | 2 |
Rous sarcoma virus (strain Prague C) | 1 | 4 | 25.0 | 1 | 4 | 25.0 | 1 | 1 | 2 | 2 |
Human herpesvirus 8 type P (isolate GK18) | 1 | 83 | 1.2 | 1 | 85 | 1.2 | 2 | 1 | 1 | 1 |
Anas platyrhynchos | 1 | 127 | 0.8 | 1 | 832 | 0.1 | 1 | 1 | 3 | 3 |
Autographa californica nuclear polyhedrosis virus | 1 | 85 | 1.2 | 1 | 155 | 0.6 | 1 | 1 | 1 | 1 |
Dictyostelium discoideum | 1 | 3190 | 0.0 | 1 | 5591 | 0.0 | 1 | 1 | 1 | 1 |
Hepatitis C virus genotype 1a (isolate H) | 0 | 0 | 0 | 1 | 1 | 100.0 | 2 | 1 | 1 | 2 |
Human SARS coronavirus | 0 | 0 | 0 | 1 | 1 | 100.0 | 1 | 1 | 5 | 5 |
Lithobates catesbeiana | 1 | 1 | 100.0 | 1 | 1 | 100.0 | 1 | 0 | 0 | 0 |
Beet curly top virus (strain California/Logan) | 1 | 1 | 100.0 | 1 | 1 | 100.0 | 1 | 1 | 1 | 1 |
Hepatitis E virus genotype 3 (isolate Human/United States/US2) | 1 | 1 | 100.0 | 1 | 1 | 100.0 | 2 | 1 | 8 | 8 |
Hepatitis E virus genotype 1 (isolate Human/Myanmar/HEVNE8L) | 1 | 1 | 100.0 | 1 | 1 | 100.0 | 1 | 0 | 0 | 0 |
Mungbean yellow mosaic virus (strain Vigna) | 1 | 1 | 100.0 | 1 | 1 | 100.0 | 1 | 1 | 1 | 1 |
Chikungunya virus (strain S27-African prototype) | 0 | 0 | 0 | 1 | 1 | 100.0 | 1 | 1 | 1 | 1 |
Spodoptera frugiperda | 0 | 37 | 0 | 0 | 46 | 0 | 0 | 0 | 0 | 0 |
Nicotiana benthamiana | 0 | 11 | 0 | 0 | 12 | 0 | 0 | 0 | 0 | 0 |
Escherichia coli (strain B / BL21-DE3) | 0 | 22 | 0 | 0 | 22 | 0 | 0 | 0 | 0 | 0 |
Mesocricetus auratus | 0 | 259 | 0 | 0 | 274 | 0 | 0 | 0 | 0 | 0 |
Human immunodeficiency virus type 1 group M subtype B (isolate NY5) | 0 | 6 | 0 | 0 | 6 | 0 | 0 | 0 | 0 | 0 |
Human adenovirus C serotype 5 | 0 | 10 | 0 | 0 | 31 | 0 | 0 | 0 | 0 | 0 |
Escherichia coli (strain K12) | 0 | 4456 | 0 | 0 | 5987 | 0 | 0 | 0 | 0 | 0 |
Macaca mulatta | 0 | 5692 | 0 | 0 | 5938 | 0 | 0 | 0 | 0 | 0 |
Trypanosoma brucei brucei (strain 927/4 GUTat10.1) | 0 | 11 | 0 | 0 | 1454 | 0 | 0 | 0 | 0 | 0 |
Equus caballus | 0 | 5768 | 0 | 0 | 5846 | 0 | 0 | 0 | 0 | 0 |
Toxoplasma gondii (strain ATCC 50611 / Me49) | 0 | 14 | 0 | 0 | 163 | 0 | 0 | 0 | 0 | 0 |
Trichomonas vaginalis | 0 | 28 | 0 | 0 | 3298 | 0 | 0 | 0 | 0 | 0 |
The SwissPalm database content is provided under a Creative Commons Attribution-Non Commercial-NoDerivatives 4.0 International License.
Experiments | Tab-separated file | JSON file |
Proteins | Tab-separated file | JSON file |
Hits | Tab-separated file | JSON file |
Sites | Tab-separated file | JSON file |
DHHC-PATs and APTs | Tab-separated file | JSON file |
Palmitoyl-proteome comparisons | ZIP file |