Model organism list
Record selection uses this hierarchical set of 33 model organisms across 6 taxonomic groups as its primary species filter. Counts below are computed from the curated dataset at build time, so they always reflect the records actually published.
33Model organisms listed
26Represented in the dataset
1000Records from listed species
1874Records from other species
How the list is applied. The list is a starting point for
selection, not a restriction on the dataset. Listed species contribute
1000 records (35%); the remaining 1874 come from other
species admitted under the secondary and relaxed criteria described in
Curation & Methods. 7 of the 33 listed
organisms have no record in the current dataset — the list states the intended
sampling frame, and those gaps mark where no member met the annotation threshold.
Animals
| Species | Records | GT families |
|---|---|---|
| Homo sapiens | 252 | 49 |
| Gallus gallus | 26 | 10 |
| Xenopus laevis | 26 | 13 |
| Danio rerio | 53 | 16 |
| Petromyzon marinus | 1 | 1 |
| Ciona intestinalis | 2 | 2 |
| Branchiostoma floridae | 0 | 0 |
| Drosophila melanogaster | 77 | 31 |
| Caenorhabditis elegans | 54 | 27 |
Plants
| Species | Records | GT families |
|---|---|---|
| Arabidopsis thaliana | 221 | 39 |
| Oryza sativaOryza sativa subsp. indica; Oryza sativa subsp. japonica | 44 | 11 |
| Zea mays | 4 | 2 |
| Populus spp. | 0 | 0 |
| Glycine max | 1 | 1 |
| Physcomitrium patens | 0 | 0 |
Fungi
| Species | Records | GT families |
|---|---|---|
| Saccharomyces cerevisiaeSaccharomyces cerevisiae (strain ATCC 204508 / S288c) | 64 | 22 |
| Neurospora crassaNeurospora crassa; Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) | 5 | 3 |
Protists
| Species | Records | GT families |
|---|---|---|
| Dictyostelium discoideum | 9 | 7 |
| Trypanosoma cruzi | 0 | 0 |
| Leishmania major | 11 | 4 |
| Euglena gracilis | 0 | 0 |
Bacteria
| Species | Records | GT families |
|---|---|---|
| Escherichia coliEscherichia coli; Escherichia coli (strain 55989 / EAEC); Escherichia coli (strain K12); Escherichia coli O127:H6 (strain E2348/69 / EPEC); Escherichia coli O139:H28 (strain E24377A / ETEC); Escherichia coli O157 typing phage 7; Escherichia coli O157:H7; Escherichia coli O18:K1:H7 (strain RS218 / NMEC); Escherichia coli O1:K1 / APEC; Escherichia coli O45:K1 (strain S88 / ExPEC); Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC); Escherichia coli O78:H11 (strain H10407 / ETEC); Escherichia coli O83:H1 (strain NRG 857C / AIEC); Escherichia coli SMS-3-5 | 110 | 45 |
| Pseudomonas aeruginosaPseudomonas aeruginosa; Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1); Pseudomonas aeruginosa (strain UCBPP-PA14) | 9 | 6 |
| Bacillus subtilisBacillus subtilis (strain 168) | 11 | 6 |
| Staphylococcus aureusStaphylococcus aureus (strain COL); Staphylococcus aureus (strain MW2); Staphylococcus aureus (strain Mu50 / ATCC 700699); Staphylococcus aureus (strain N315); Staphylococcus aureus (strain NCTC 8325 / PS 47) | 7 | 4 |
| Mycobacterium smegmatis | 0 | 0 |
| Corynebacterium glutamicumCorynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534) | 3 | 2 |
| Synechocystis spp.Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa) | 1 | 1 |
Archaea
| Species | Records | GT families |
|---|---|---|
| Haloferax volcaniiHaloferax volcanii (strain ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2) | 2 | 2 |
| Methanococcus spp.Methanococcus voltae | 3 | 2 |
| Pyrococcus furiosusPyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) | 3 | 3 |
| Saccharolobus (Sulfolobus) solfataricus | 0 | 0 |
| Sulfolobus acidocaldariusSulfolobus acidocaldarius DSM 639 | 1 | 1 |
Why records come from unlisted species
Two gaps make a strict model-organism filter unworkable, and both are visible in the dataset:
- 23 of 138 families contain no listed model organism at all, so a strict filter would leave them empty.
- 47 families contain no member at UniProt annotation level 4 or 5 in any species, so representation there required accepting lower annotation depth.
Records admitted this way are still the best-annotated available for their family. The annotation level is shown on every record page, and the 116 records below level 4 (4.0% of the dataset) carry a badge marking their enzymology as provisional.
Species matching. Species are matched against the
workbook's
Species column as case-insensitive substrings, so a
genus-level entry such as Populus spp. counts every species in that genus, and
strain-qualified UniProt names (for example
Saccharomyces cerevisiae strain ATCC 204508 / S288c) count toward the parent
species. Where the dataset holds more than one strain string for a listed organism, the
strings are shown beneath the species name.