Does UniProtKB contain all protein sequences?

The two sections of UniProtKB - UniProtKB/Swiss-Prot and UniProtKB/TrEMBL - give access to all the protein sequences which are available to the public. However, UniProtKB excludes the following protein sequences:

1. Most non-germline immunoglobulins and T-cell receptors
2. Synthetic sequences
3. Most patent application sequences
4. Small fragments encoded from nucleotide sequence (<8 amino acids)
5. Pseudogenes
6. Fusion/truncated proteins
7. Not real proteins

The first 5 are identified automatically by the UniProtKB/TrEMBL creation program and never enter UniProtKB. However some proteins belonging to these classes are also identified during the UniProtKB/Swiss-Prot annotation process by the curators and then removed from UniProtKB.

Fusion/truncated proteins and those classified as not real proteins are only manually identified by the curators and removed from UniProtKB/TrEMBL or UniProtKB/Swiss-Prot. All these excluded sequences are available at UniParc. The corresponding UniParc entries have been flagged with the reason for the absence of that sequence from UniProtKB.

See also:

• Where do the UniProtKB protein sequences come from?
• What are UniProtKB's criteria for defining a CDS as a protein?
• Why have some UniProtKB accession numbers been deleted? How can I track them?
• Why do we keep dubious sequences in UniProtKB? How to discard them from a protein set?
• Sequences