UniProt Proteome Removal Impact Assessment

Overview

UniProt is removing TrEMBL entries from non-Reference Proteomes by release 2026_02.

Sources:
- Protein removal list: https://ftp.ebi.ac.uk/pub/contrib/UniProt/proteomes/proteins_to_remove_from_UniProtKB.txt
- Proteins retained: https://ftp.ebi.ac.uk/pub/contrib/UniProt/proteomes/proteins_retained_in_UniProtKB.txt
- Help doc: https://www.uniprot.org/help/proteome_redundancy

What happens:
- TrEMBL entries from "Redundant Proteomes" and "Other Proteomes" will be removed from UniProtKB
- They will be archived in UniParc (still accessible via UniParc, but not in UniProtKB)
- SwissProt entries are NOT affected
- ~253M entries dropping to ~141M entries (~58M being removed)

Impact Summary

VERIFIED against proteins_to_remove_from_UniProtKB.txt (58M entries):

We have 15 entries that WILL BE REMOVED from UniProtKB.

Entries Being Removed

UniProt ID	Gene	Organism	Review File
A0A1S7IWC7	M2	Influenza A	9INFA/M2
A0A1V0M5B3	merB	Pseudomonas aeruginosa	PSEAI/merB
A0A1Y0Y121	xdhB	Acetobacter pasteurianus	ACEPA/xdhB
A0A2Z5TSL2	fae1A	Ruminiclostridium josui	RUMJO/fae1A
A0A9Q6Z964	stx2A	E. coli O157:H7	ECO57/stx2A
D2STP8	PGRPS3	Anopheles gambiae	ANOGA/PGRPS3
D2SU82	PGRPS2	Anopheles gambiae	ANOGA/PGRPS2
D9J262	amoA	Nitrobacter sp.	NITRP/amoA
O30741	dorR	Cereibacter sphaeroides	CERSP/dorR
Q1IFG0	Q1IFG0	Pseudomonas entomophila	PSEEN/Q1IFG0
Q6DTY2	Q6DTY2	Clostridium cellulovorans	CLOCL/Q6DTY2
Q9RGE6	Q9RGE6	Clostridium cellulovorans	CLOCL/Q9RGE6
Q9RGE7	Q9RGE7	Clostridium cellulovorans	CLOCL/Q9RGE7
Q9RGE8	Q9RGE8	Clostridium cellulovorans	CLOCL/Q9RGE8
Q9XJG2	darB	Bacteriophage	9CAUD/darB

Action Required

[ ] Find alternative entries or archive affected reviews
[ ] Consider if UniParc references are acceptable for these use cases

Tooling

Download the removal list and check entries:

just fetch-uniprot-removal-list       # Download ~578MB file to cache/uniprot/
just check-uniprot-removal ID1 ID2    # Check specific IDs
just check-all-uniprot-removal        # Check all gene reviews

STATUS

[x] Download protein removal list (58M entries, 578MB)
[x] Set up cache directory and just targets
[x] Comprehensive check of all 896 gene review UniProt IDs
[x] Identify 15 entries being removed
[ ] Find alternative entries or archive affected reviews

NOTES

2026-02-03

Methodology

Downloaded proteins_to_remove_from_UniProtKB.txt (578MB, 58M entries)
Created cache/uniprot/ directory (gitignored)
Added just targets for automated checking
Extracted all 896 UniProt IDs from gene reviews
Used LC_ALL=C comm -12 for fast intersection (locale matters for sort order!)
Found 15 entries in removal list

Lessons Learned

Proteome-based inference is unreliable - use the explicit protein removal list
Sort locale matters: must use LC_ALL=C for consistent results with comm
The removal list is already sorted (alphanumeric), so comm is O(n) - much faster than grep

Full Verification Output

$ just check-all-uniprot-removal
Found 896 unique UniProt IDs in our reviews
Checking against removal list (58M entries)...

Entries being removed from UniProtKB:
  A0A1S7IWC7: 9INFA/M2
  A0A1V0M5B3: PSEAI/merB
  A0A1Y0Y121: ACEPA/xdhB
  A0A2Z5TSL2: RUMJO/fae1A
  A0A9Q6Z964: ECO57/stx2A
  D2STP8: ANOGA/PGRPS3
  D2SU82: ANOGA/PGRPS2
  D9J262: NITRP/amoA
  O30741: CERSP/dorR
  Q1IFG0: PSEEN/Q1IFG0
  Q6DTY2: CLOCL/Q6DTY2
  Q9RGE6: CLOCL/Q9RGE6
  Q9RGE7: CLOCL/Q9RGE7
  Q9RGE8: CLOCL/Q9RGE8
  Q9XJG2: 9CAUD/darB

Summary: 15 will be removed, 881 safe