Reference proteomes
UniProt proteomes used for source-protein lookup and peptide-flank extraction. All gzipped, git-LFS tracked.
human.fasta.gz (UP000005640, 147,506 seqs) and mouse.fasta.gz (UP000000589, 54,857 seqs) are the full
proteomes including isoforms and TrEMBL entries. The files below are canonical reference proteomes,
fetched from UniProt (REST ?query=(proteome:<UPID>)&format=fasta, or the reference_proteomes FTP).
| file | organism | proteome | taxid | sequences | bytes (gz) |
|---|---|---|---|---|---|
ecoli_K12_UP000000625.fasta.gz |
Escherichia coli (strain K12) | UP000000625 | 83333 | 4,403 | 988,444 |
egallinarum_UP000254807.fasta.gz |
Enterococcus gallinarum | UP000254807 | 1353 | 3,635 | 775,627 |
mgnavus_UP000018690.fasta.gz |
Mediterraneibacter gnavus (strain CC55_001C) | UP000018690 | 1073375 | 2,942 | 666,125 |
saureus_UP000008816.fasta.gz |
Staphylococcus aureus (strain NCTC 8325 / PS 47) | UP000008816 | 93061 | 2,889 | 577,723 |
lreuteri_UP000001991.fasta.gz |
Limosilactobacillus reuteri (strain DSM 20016) | UP000001991 | 557436 | 1,865 | 401,750 |
cmv_HHV5_UP000000938.fasta.gz |
Human cytomegalovirus (strain Merlin) | UP000000938 | 295027 | 168 | 42,838 |
hhv6a_UP000009295.fasta.gz |
Human herpesvirus 6A (strain Uganda-1102) | UP000009295 | 10370 | 99 | 29,596 |
ebv_UP000153037.fasta.gz |
Epstein-Barr virus (strain B95-8) | UP000153037 | 10377 | 92 | 27,660 |
hhv7_UP000098510.fasta.gz |
Human herpesvirus 7 (strain RK) | UP000098510 | 262398 | 84 | 26,566 |
ebv_AG876_UP000007639.fasta.gz |
Epstein-Barr virus (strain AG876) | UP000007639 | 82830 | 79 | 26,243 |
hsv1_HHV1_UP000009294.fasta.gz |
Human herpesvirus 1 (strain 17) | UP000009294 | 10299 | 73 | 25,505 |
vzv_HHV3_UP000002602.fasta.gz |
Varicella-zoster virus (strain Dumas) | UP000002602 | 10338 | 69 | 24,236 |
adenovirusC_HAdV2_UP000008167.fasta.gz |
Human adenovirus C serotype 2 | UP000008167 | 10515 | 45 | 9,028 |
fluA_PR8_UP000009255.fasta.gz |
Influenza A virus (strain A/Puerto Rico/8/1934 H1N1) | UP000009255 | 211044 | 13 | 3,378 |
bkpyv_UP000008475.fasta.gz |
BK polyomavirus | UP000008475 | 1891762 | 6 | 1,238 |
parvoB19_UP000006624.fasta.gz |
Human parvovirus B19 (strain HV) | UP000006624 | 648237 | 5 | 1,342 |
Totals: 16,467 sequences across 16 proteomes (3,627,299 bytes gzipped).
Note on Epstein-Barr virus and HHV-7
Two EBV strains are included: B95-8 (UP000153037, taxid 10377) and AG876 (UP000007639, taxid 82830). UP000007639 is EBV strain AG876 -- not HHV-7, despite what its proteome ID may suggest by adjacency. The genuine HHV-7 reference proteome is UP000098510 (strain RK, taxid 262398, 84 proteins); UP000009246 (strain JI) exists but is flagged Non Reference by UniProt.