Table 1.
Proteomes and structure models considered.
| Species | Common name | Reference proteome | # unique UniProt IDs | # original | # domains | # structure predictions with no domains (1D) |
|---|---|---|---|---|---|---|
| Arabidopsis thaliana | Arabidopsis | UP000006548 | 27,434 | 27,434 | 37,682 | 5722 |
| Caenorhabditis elegans | Nematode worm | UP000001940 | 19,694 | 19,694 | 26,160 | 4277 |
| Candida albicans | C. albicans | UP000000559 | 5974 | 5,974 | 9,978 | 743 |
| Danio rerio | Zebrafish | UP000000437 | 24,664 | 24,664 | 42,135 | 2530 |
| Dictyostelium discoideum | Dictyostelium | UP000002195 | 12,622 | 12,622 | 18,963 | 2986 |
| Drosophila melanogaster | Fruit fly | UP000000803 | 13,458 | 13,458 | 19,881 | 2335 |
| Escherichia coli | E. coli | UP000000625 | 4363 | 4363 | 5397 | 417 |
| Glycine max | Soybean | UP000008827 | 55,799 | 55,799 | 72,217 | 14,146 |
| Homo sapiens | Human | UP000005640 | 20,504 | 23,391 | 44,827 | 3302 |
| Leishmania infantum | L. infantum | UP000008153 | 7924 | 7924 | 12,257 | 1579 |
| Methanocaldococcus jannaschii | M. jannaschii | UP000000805 | 1,773 | 1,773 | 2,097 | 131 |
| Mus musculus | Mouse | UP000000589 | 21,615 | 21,615 | 35,216 | 2477 |
| Mycobacterium tuberculosis | M. tuberculosis | UP000001584 | 3988 | 3988 | 5170 | 351 |
| Oryza sativa | Asian rice | UP000059680 | 43,649 | 43,649 | 39,775 | 19,756 |
| Plasmodium falciparum | P. falciparum | UP000001450 | 5187 | 5187 | 7283 | 1162 |
| Rattus norvegicus | Rat | UP000002494 | 21,272 | 21,272 | 33,818 | 2664 |
| Saccharomyces cerevisiae | Budding yeast | UP000002311 | 6040 | 6040 | 9837 | 967 |
| Schizosaccharomyces pombe | Fission yeast | UP000002485 | 5128 | 5128 | 8173 | 637 |
| Staphylococcus aureus | S. aureus | UP000008816 | 2888 | 2888 | 3283 | 415 |
| Trypanosoma cruzi | T. cruzi | UP000002296 | 19,036 | 19,036 | 26,205 | 5436 |
| Zea mays | Maize | UP000007305 | 39,299 | 39,299 | 48,433 | 11,582 |
For each proteome, the number of unique proteins, total original/domain models, and total original models containing no confident domains are given. The definition of the confident domains is given in the main text. The human original model count is underlined, indicating that the number of original models does not match the number of unique proteins. The human structure predictions retrieved from the AlphaFold Database contain models which are 1400-residue slices of larger proteins.