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