Release 2 (2018-02-18)

Major update of the application, the website and the database.

Tool Type Description Version
RefSeq Database Set of reference sequences (genomic, transcript, and protein) 86
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 2018_01
Ensembl Genomes Database Taxonomically extended set of genomes from Ensembl 35
Ensembl Database Database on vertebrate (mainly) genomes 91
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 661 647 38 537 657 213 638
1 Number of experiments 949 901 48 765 944 319 921
2 Number of organisms defining experiments 41 38 11 22 38 11 34
3 Number of organisms 55 48 17 19 48 4 41
4 Number of cell types 168 159 28 142 166 87 161
5 Number of subcellular fractions 0 0 0 0 0 0 0
6 Number of techniques 71 66 11 67 71 58 71
7 Number of hits 19159 1293 17866 9497 8630 7512 8689
8 Number of individual genes related to palmitoylated proteins 7207 603 6930 3637 1891 1455 1975
9 Number of palmitoylated proteins 9796 670 9440 4285 2072 1557 2117
10 Number of sites (unique pairs (protein, position)) 5426 1103 4323 3070 2479 1660 2458
11 Number of sites identification techniques 18 18 0 18 18 16 18
12 Number of proteins associated to sites 2612 375 2269 1247 989 690 981
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 2880 19899 14.5 2999 22456 13.4 7389 342 617 804
Mus musculus 2938 17509 16.8 3590 19713 18.2 7802 2150 3872 4293
Rattus norvegicus 672 10980 6.1 684 12290 5.6 905 42 81 130
Arabidopsis thaliana 491 14567 3.4 595 16632 3.6 610 13 26 30
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 58 6721 0.9 58 6721 0.9 109 15 23 42
Cricetulus griseus 2 295 0.7 2 4042 0.0 2 0 0 0
Plasmodium falciparum (isolate 3D7) 53 229 23.1 421 1475 28.5 488 0 0 0
Bos taurus 12 8289 0.1 13 10710 0.1 29 7 15 27
Schizosaccharomyces pombe 240 5085 4.7 240 5140 4.7 244 2 2 3
Canis familiaris 3 6139 0.0 3 6901 0.0 3 2 4 4
Drosophila melanogaster 7 4553 0.2 7 6849 0.1 9 3 4 4
Danio rerio 2 6796 0.0 2 10674 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 3984 0.0 1 4161 0.0 1 0 0 0
Human herpesvirus 1 2 74 2.7 2 127 1.6 4 1 1 1
Semliki forest virus 0 0 0 2 3 66.7 6 2 4 7
Sindbis virus 0 0 0 2 4 50.0 2 2 3 3
Oryctolagus cuniculus 5 825 0.6 5 4634 0.1 5 4 28 28
Sus scrofa 3 1373 0.2 3 4921 0.1 6 3 4 7
Toxoplasma gondii 280 361 77.6 443 567 78.1 454 2 4 4
Torpedo californica 4 9 44.4 4 21 19.0 4 0 0 0
Landoltia punctata 1 2 50.0 1 2 50.0 1 0 0 0
Influenza A virus (A/udorn/1972(H3N2)) 1 1 100.0 1 1 100.0 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 1826 0.1 1 1903 0.1 1 0 0 0
Medicago truncatula 1 60 1.7 1 1607 0.1 1 1 1 1
Influenza C virus (strain C/Johannesburg/1/1966) 1 6 16.7 1 7 14.3 4 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 3 119 2.5 126 322 39.1 126 0 0 0
Xenopus laevis 1 3222 0.0 1 3404 0.0 1 1 1 1
Friend murine leukemia virus 1 3 33.3 2 11 18.2 3 1 1 2
Leishmania major 1 299 0.3 1 1783 0.1 1 1 1 1
Ross river virus (strain T48) 0 0 0 1 2 50.0 1 1 1 1
Caenorhabditis elegans 1 5835 0.0 1 6789 0.0 1 1 1 1
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 1 0 0 0
Vaccinia Virus 0 0 0 1 1 100.0 1 0 0 0
Influenza A virus (strain A/Fowl plague virus/Rostock/8/1934 H7N1) 1 1 100.0 1 1 100.0 1 1 3 3
Solanum lycopersicum 1 4117 0.0 1 4117 0.0 1 0 0 0
Neosartorya fumigata (strain CEA10 / CBS 144.89 / FGSC A1163) 0 0 0 115 115 100.0 115 0 0 0
Mink cell focus-forming murine leukemia viru 1 1 100.0 1 1 100.0 1 0 0 0
Moloney murine leukemia virus (strain neuropathogenic variant ts1-92b) 1 1 100.0 1 1 100.0 1 0 0 0
Moloney murine leukemia virus (isolate Shinnick) 1 1 100.0 1 1 100.0 1 0 0 0
Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) 18 22 81.8 18 1684 1.1 18 0 0 0
Murine coronavirus (strain A59) 1 1 100.0 1 1 100.0 1 1 5 5
Oryza sativa subsp. japonica 1 3201 0.0 1 5217 0.0 1 1 2 2
Rous sarcoma virus (strain Prague C) 1 1 100.0 1 1 100.0 1 1 2 2
Human herpesvirus 8 type P (isolate GK18) 1 1 100.0 1 1 100.0 1 1 1 1
Anas platyrhynchos 1 1 100.0 1 534 0.2 1 1 3 3
Autographa californica nuclear polyhedrosis virus 1 1 100.0 1 1 100.0 1 1 1 1
Dictyostelium discoideum 1 131 0.8 1 1291 0.1 1 1 1 1
Chlorocebus aethiops 0 127 0 0 128 0 0 0 0 0
Spodoptera frugiperda 0 37 0 0 46 0 0 0 0 0
Nicotiana benthamiana 0 10 0 0 11 0 0 0 0 0
Escherichia coli (strain B / BL21-DE3) 0 17 0 0 17 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) (HIV-1) 0 6 0 0 6 0 0 0 0 0
Human immunodeficiency virus type 1 group M subtype B (isolate BH10) (HIV-1) 0 9 0 0 9 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 4446 0 0 5970 0 0 0 0 0
Macaca mulatta (Rhesus macaque) 0 4392 0 0 4475 0 0 0 0 0
Trypanosoma brucei brucei (strain 927/4 GUTat10.1) 0 10 0 0 1295 0 0 0 0 0
Equus caballus 0 4572 0 0 4572 0 0 0 0 0
Toxoplasma gondii (strain ATCC 50611 / Me49) 0 14 0 0 155 0 0 0 0 0
Medicago sativa subsp. falcata 0 0 0 0 1 0 0 0 0 0