Protein variety and functional diversity: Swiss-Prot annotation in its biological context Brigitte Boeckmann, Marie-Claude Blatter, Livia Famiglietti, Ursula Hinz, Lydie Lane, Bernd Roechert, Amos Bairoch C. R. Biologies 328:882-899(2005) Updated version (Sep-2007) Annotation examples

Content:

Introduction
Formation of the nascent protein sequence
Protein sorting and associated sequence modifications
Protein folding and structure
Function-related protein modifications (PTMs)
Protein-protein interaction
Protein function and disease-association

The UniProtKB/Swiss-Prot Protein Knowledgebase is a manually annotated protein sequence database which provides a wealth of information regarding protein variety, protein function and associated disorders. An article in C. R. Biologies gives an overview on cellular processes that can lead to sequence variety and structural diversity in eukaryotes, as well as how such processes are annotated in UniProtKB/Swiss-Prot. The many examples given therein can be accessed below: the UniProtKB/Swiss-Prot examples (dark blue) are linked via their accession numbers to the most recent version of the database entries (UniProt web site view); the same entry in the original UniProtKB/Swiss-Prot raw format is provided. Terms in light blue indicate the annotation topics, under which the information of interest can be found in the UniProtKB/Swiss-Prot entry. Other links provide lists of further examples via queries, using specific keywords, combination of keywords and/or other annotation.

Note: The ongoing evolution of the database can lead to changes in the annotation, thus the examples might differ soon from those printed in the corresponding article. Recent changes and forthcoming changes of UniProtKB are announced. Details on the format of UniProtKB/Swiss-Prot entries are provided in the user manual.

• Alternative promoter usage
  Alternative products (CC), Ontologies (KW): Alternative promoter usage, Sequence annotation (FT): Alternative sequence
• Q9S7T7 (raw format)
• List of all relevant entries
• Alternative splicing
  Alternative products (CC), Ontologies (KW): Alternative splicing, Sequence annotation (FT): Alternative sequence
• P30429 (raw format)
• List of all relevant entries
• mRNA editing
  General annotation (CC): RNA editing, Ontologies (KW): RNA editing, Sequence annotation (FT): Natural variant (obtional)
• P04114 (raw format) creation of a STOP codon
• P42262 (raw format) modification of the protein function
• List of all relevant entries
• Alternative translation initiation
  Alternative products (CC), Ontologies (KW): Alternative initiation, Sequence annotation (FT): Alternative sequence
• P19970 (raw format)
• P08037 (raw format) isoforms with distinct subcellular location
• P04862 (raw format) usage of distinct initiator methionines; virus
• List of all relevant entries
• Ribosomal frameshifting
  General annotation (CC): Miscellaneous, Ontologies (KW): Ribosomal frameshifting
• O95190 (raw format)
• List of all relevant entries
• Stop codon readthrough
  Ontologies (KW): Selenocysteine; Pyrrolysine, Sequence annotation (FT): Modified residue
• P07203 (raw format) selenocysteine
• P24183 (raw format) selenocysteine; prokaryotes
• O30642 (raw format) pyrrolysine; prokaryotes
• List of all sequence entries containing a selenocysteine
• List of all sequence entries containing a pyrrolysine
• Combinations of events
• P04150 (raw format) alternative splicing and alternative initiation
• Some examples of protein sequences derived from alternative promoter usage & alternative splicing
• Some examples of protein sequences derived from alternative splicing & alternative initiation
• Some examples of protein sequences derived from alternative splicing & RNA editing
• List of all keywords related to coding sequence diversity

• Cytosolic protein
  General annotation (CC): Subcellular location, Ontologies (KW): Cytoplasm
• P07327 (raw format) cleavage of the initiator methionine, N-terminal acetylation
• List of proteins found in the cytoplasm
• Some additional proteins found in the cytosol only
• Nuclear and cytosolic protein
  General annotation (CC): Subcellular location, Ontologies (KW): Nucleus, Sequence annotation (FT): Motif
• Q9NRA8 (raw format)
• Some additional proteins found in the cytoplasm and nucleus
• Mitochondrial matrix protein
  General annotation (CC): Subcellular location, Ontologies (KW): Mitochondrion; Transit peptide, Sequence annotation (FT): Transit peptide
• P28330 (raw format)
• Some additional proteins found in the mitochondrial matrix
• Chloroplast thylakoid lumen protein
  General annotation (CC): Subcellular location, Ontologies (KW): Chloroplast; Thylakoid, Sequence annotation (FT): Transit peptide
• O82660 (raw format)
• Some additional proteins found in the chloroplast thylakoid
• Membrane protein
  General annotation (CC): Subcellular location, Ontologies (KW): Transmembrane, Sequence annotation (FT): Transmembrane
• P02724 (raw format) single-pass type I membrane protein
• P10852 (raw format) single-pass type II membrane protein
• P07550 (raw format) multi-pass membrane protein
• List of all transmembrane proteins
• Proteins attached to the membrane by a lipophil group
  General annotation (CC): Subcellular location (lipid-anchor), Ontologies (KW): Lipoprotein; GPI-anchor; Prenylation; Myristate; Palmitate, Sequence annotation (FT): Lipidation
• P04058 (raw format) glycosylphosphatidylinositol anchor (GPI-anchor)
• P40855 (raw format) prenylation
• P62330 (raw format) myristate
• O43687 (raw format) myristate and palmitate
• List of all sequence entries containing a GPI-anchor
• List of all sequence entries containing an isoprenoid group (prenylation)
• List of all sequence entries containing a palmitate
• List of all sequence entries containing a myristate
• Secreted protein
  General annotation (CC): Subcellular location, Ontologies (KW): Signal, Sequence annotation (FT): Signal peptide
• P80035 (raw format) cleaved signal peptide
• P27169 (raw format) uncleaved signal peptide
• List of all proteins with a N-terminal signal peptide
• List of all cellular component-related keywords

• Protein with a determined 3D-structure
  Ontologies (KW): 3D-structure, Sequence annotation (FT): Turn; Helix; Strand (optional)
• P26882 (raw format) to see the 3D-structure, click here
• P29972 (raw format) alpha-helical structure; to see the 3D-structure, click here
• P02931 (raw format) beta-barrel structure; to see the 3D-structure, click here
• P00489 (raw format) allosteric enzyme
• List of all sequence entries with a determined 3D structure
• List of all allosteric enzymes

• Propeptide cleavage
  General annotation (CC): Post-translational modification (optional), Sequence annotation (FT): Chain
• P46531 (raw format) Notch signaling
• P22895 (raw format) enzyme
• P09802 (raw format) storage
• P01308 (raw format) hormone
• Amidation
  Ontologies (KW): Amidation, Sequence annotation (FT): Modified residue
• P21591 (raw format)
• List of all amidated proteins
• Glycosylation
  Ontologies (KW): Glycoprotein, Sequence annotation (FT): Glycosylation
• O95445 (raw format) N-Glycosylation
• P19785 (raw format) O-Glycosylation
• List of all glycoproteins
• Palmitoylation
  Ontologies (KW): Lipoprotein; Palmitate, Sequence annotation (FT): Lipidation
• P07550 (raw format)
• List of all proteins with palmitoylation
• Disulfide bond
  Sequence annotation (FT): Disulfide bond
• P09931 (raw format) interchain
• P14046 (raw format) intrachain
• P01089 (raw format) intra- and interchain
• Some examples of proteins with disulfide bond(s)
• Binding a metal ligand
  Ontologies (KW): Metal-binding, Sequence annotation (FT): Metal binding
• P0ABD4 (raw format)
• Binding pyridoxal phosphate
  Ontologies (KW): Pyridoxal phosphate, Sequence annotation (FT): Binding site
• P18485 (raw format)
• Other examples
• List of all PTM-related keywords
• List the controlled PTM vocabularies

• Proteins forming stable complexes
  General annotation (CC): Subunit, Binary interactions (CC)
• P33204 (Subunit) and P33204 (Binary interaction) (raw format) ARPC4 subunit of the ARP2/3 complex
• P40337 (raw format) complex formation prevented by a mutation see Natural variant at position 158
• Other examples
• List of proteins found in the proteasome
• List of proteins found in the spliceosome
• List of proteins found in the ribosome

• Multisulfatase deficiency
  General annotation (CC): Function, Involvement in disease, Ontologies (KW): Disease mutation, Sequence annotation (FT): Natural variant
• Q8NBK3 (raw format) SUMF1
• P15289 (raw format) sulfatase
• P15848 (raw format) sulfatase
• P08842 (raw format) sulfatase
• A same mutation causes different phenotypes
  General annotation (CC): Function, Involvement in disease, Ontologies (KW): Disease mutation , Sequence annotation (FT): Natural variant
• P21802 (raw format)
• Other examples
• List of proteins involved in Alzheimer's disease
• List of proteins involved in Diabetes mellitus
• List of proteins involved in Epilepsy
• List of allergens General annotation (CC): Allergen, Ontologies (KW): Allergen
• List of all proteins with known disease mutation
• List of all medical-oriented keywords