Release 4 (2022-09-03)

Computed from databases (SwissPalm and external databases) available on 2022-07-30.

Pre-release. This release may be subject of an update regarding to the predictions that didn't finish to run for Palmpred. As well, CSS-Palm 4.0 was used instead of the last version GPS-palm because we couldn't install the software.

Tool Type Description Version
RefSeq Database Set of reference sequences (genomic, transcript, and protein) 213
PhosphoSite Database Protein post-translational modifications v6.6.0.4
TAIR Database The Arabidopsis Information Resource: Genetic and molecular biology data for Arabidopsis thaliana 2019-07-11
UniProt Database Database on protein sequence and function 2022_02
Ensembl Genomes Database Taxonomically extended set of genomes from Ensembl 54
Ensembl Database Database on vertebrate (mainly) genomes 107
IPI Database International Protein Index: Protein database (closed) latest
Gene Ontology Database Ontologies describing molecular functions, biological processes an subcellular locations 2022-07-01
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 852 829 57 751 849 471 821
1 Number of experiments 1368 1277 91 1191 1364 783 1331
2 Number of organisms defining experiments 57 54 14 50 54 15 44
3 Number of organisms 72 64 21 64 67 13 54
4 Number of cell types 249 238 43 226 248 162 241
5 Number of subcellular fractions 0 0 0 0 0 0 0
6 Number of techniques 98 92 20 91 98 88 96
7 Number of hits 61541 1857 59684 33644 55291 54355 30886
8 Number of individual genes related to palmitoylated proteins 13720 766 13448 7511 11341 10982 3943
9 Number of palmitoylated proteins 19272 866 18895 9976 13914 13437 4154
10 Number of sites (unique pairs (protein, position)) 7612 1490 6122 4997 6474 5736 3941
11 Number of sites identification techniques 25 25 2 24 25 24 25
12 Number of proteins associated to sites 3633 477 3220 2194 2823 2542 1484
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 5338 20223 26.4 6329 23898 26.5 26963 1319 2157 2807
Mus musculus 6919 18084 38.3 8686 21838 39.8 29284 2158 3916 4357
Rattus norvegicus 945 12905 7.3 959 14303 6.7 1367 51 95 161
Arabidopsis thaliana 495 16352 3.0 598 19899 3.0 620 14 30 34
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 59 6721 0.9 59 6722 0.9 115 16 24 46
Cricetulus griseus 2 2644 0.1 2 6756 0.0 2 0 0 0
Plasmodium falciparum (isolate 3D7) 53 237 22.4 421 1685 25.0 489 0 0 0
Chlorocebus aethiops 1 127 0.8 1 128 0.8 1 0 0 0
Bos taurus 132 11532 1.1 134 12717 1.1 171 10 23 40
Schizosaccharomyces pombe 240 5091 4.7 240 5179 4.6 244 2 2 3
Canis familiaris 468 7037 6.7 468 7712 6.1 474 5 8 10
Drosophila melanogaster 161 8531 1.9 164 9156 1.8 186 5 11 12
Danio rerio 3 12403 0.0 3 14210 0.0 3 1 2 2
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 6271 0.0 1 6558 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 6683 0.1 7 6879 0.1 8 5 30 30
Sus scrofa 4 7090 0.1 4 7357 0.1 7 4 7 10
Toxoplasma gondii 280 365 76.7 443 594 74.6 454 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 49 2.0 3 94 3.2 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 1919 0.1 1 0 0 0
Medicago truncatula 1 2825 0.0 1 3556 0.0 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 55.0 426 487 87.5 780 0 0 0
Trypanosoma brucei brucei 2 82 2.4 125 296 42.2 125 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 4042 0.0 1 4276 0.0 1 1 1 1
Friend murine leukemia virus 1 3 33.3 2 14 14.3 5 1 1 2
Leishmania major 1 371 0.3 1 3196 0.0 1 1 1 1
Ross river virus (strain T48) 0 0 0 1 2 50.0 1 1 1 1
Caenorhabditis elegans 3 7503 0.0 3 9524 0.0 3 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 4 1 3 3
Vesicular Stomatitis Virus 0 0 0 1 1 100.0 1 0 0 0
Solanum lycopersicum 1 5059 0.0 1 5216 0.0 1 0 0 0
Neosartorya fumigata (strain CEA10 / CBS 144.89 / FGSC A1163) 0 191 0 113 357 31.7 113 0 0 0
Trypanosoma brucei brucei (strain 927/4 GUTat10.1) 1 67 1.5 1 1624 0.1 1 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) 18 711 2.5 20 2900 0.7 20 0 0 0
Human cytomegalovirus 1 206 0.5 1 403 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 6283 0.0 1 10339 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 1 280 0.4 1 2856 0.0 1 1 3 3
Autographa californica nuclear polyhedrosis virus 1 85 1.2 1 155 0.6 1 1 1 1
Dictyostelium discoideum 1 3261 0.0 1 6826 0.0 1 1 1 1
Hepatitis C virus genotype 1a (isolate H) 0 0 0 1 2 50.0 3 1 2 3
Human SARS coronavirus 0 0 0 1 1 100.0 1 1 5 5
Lithobates catesbeiana 1 1 100.0 1 100 1.0 1 0 0 0
Beet curly top virus (strain California/Logan) 1 1 100.0 1 7 14.3 1 1 1 1
Hepatitis E virus genotype 3 (isolate Human/United States/US2) 1 1 100.0 1 3 33.3 2 1 8 8
Hepatitis E virus genotype 1 (isolate Human/Myanmar/HEVNE8L) 1 1 100.0 1 3 33.3 1 0 0 0
Mungbean yellow mosaic virus (strain Vigna) 1 1 100.0 1 8 12.5 1 1 1 1
Chikungunya virus 0 0 0 1 4 25.0 1 0 0 0
Chikungunya virus (strain S27-African prototype) 0 0 0 1 3 33.3 1 1 1 1
Plasmodium falciparum (isolate Palo Alto / Uganda) 0 4 0 1 697 0.1 1 0 0 0
Severe acute respiratory syndrome coronavirus 1 1 100.0 1 15 6.7 1 0 0 0
Spodoptera frugiperda 0 37 0 0 49 0 0 0 0 0
Nicotiana benthamiana 0 11 0 0 16 0 0 0 0 0
Escherichia coli (strain B / BL21-DE3) 0 22 0 0 24 0 0 0 0 0
Mesocricetus auratus 0 5234 0 0 5251 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 6078 0 0 0 0 0
Macaca mulatta 0 7296 0 0 8936 0 0 0 0 0
Equus caballus 0 7015 0 0 7153 0 0 0 0 0
Toxoplasma gondii (strain ATCC 50611 / Me49) 0 102 0 0 823 0 0 0 0 0
Trichomonas vaginalis 0 35 0 0 10160 0 0 0 0 0
Gekko gecko 0 0 0 0 2 0 0 0 0 0
Arabidopsis lyrata 0 18 0 0 23 0 0 0 0 0