a) Annotation

In Swiss-Prot, as in many sequence databases, two classes of data can be distinguished: the core data and the annotation.

For each sequence entry the core data consists of:

• The sequence data;
• The citation information (bibliographical references);
• The taxonomic data (description of the biological source of the protein).

The annotation consists of the description of the following items:

• Function(s) of the protein;
• Posttranslational modification(s) such as carbohydrates, phosphorylation, acetylation and GPI-anchor;
• Domains and sites, for example, calcium-binding regions, ATP-binding sites, zinc fingers, homeoboxes, SH2 and SH3 domains and kringle;
• Secondary structure, e.g. alpha helix, beta sheet;
• Quaternary structure, i.g. homodimer, heterotrimer, etc.;
• Similarities to other proteins;
• Disease(s) associated with any number of deficiencies in the protein;
• Sequence conflicts, variants, etc.

We try to include as much annotation information as possible in Swiss-Prot. To obtain this information we use, in addition to the publications that report new sequence data, review articles to periodically update the annotations of families or groups of proteins. We also make use of external experts, who have been recruited to send us their comments and updates concerning specific groups of proteins.

We believe that having systematic recourse both to publications other than those reporting the core data and to subject referees represents a unique and beneficial feature of Swiss-Prot.

In Swiss-Prot, annotation is mainly found in the comment lines (CC), in the feature table (FT) and in the keyword lines (KW). Most comments are classified by 'topics'; this approach permits the easy retrieval of specific categories of data from the database.

b) Minimal redundancy

Many sequence databases contain, for a given protein sequence, separate entries which correspond to different literature reports. In Swiss-Prot we try as much as possible to merge all these data so as to minimize the redundancy of the database. If conflicts exist between various sequencing reports, they are indicated in the feature table of the corresponding entry.

c) Integration with other databases

It is important to provide the users of biomolecular databases with a degree of integration between the three types of sequence-related databases (nucleic acid sequences, protein sequences and protein tertiary structures) as well as with specialized data collections. Swiss-Prot is currently cross-referenced to more than 50 different databases. Cross-references are provided in the form of pointers to information related to Swiss-Prot entries and found in data collections other than Swiss-Prot. This extensive network of cross-references allows Swiss-Prot to play a major role as a focal point of biomolecular database interconnectivity.

d) Documentation

Swiss-Prot is distributed with a large number of index files and specialized documentation files. Some of these files have been available for a long time (this user manual, the release notes, the various indices for authors, citations, keywords, etc.), but many have been created recently and we are continuously adding new files. 'Documentation files' section contains an up-to-date descriptive list of all distributed document files.

a) Automatic annotation

Records waiting in TrEMBL for full manual annotation are enhanced by automatic annotation. Information is transferred from well-characterised entries in Swiss-Prot to unannotated entries in TrEMBL which belong to groups defined by InterPro, a database of protein families, domains and functional sites. This process brings the standard of annotation in TrEMBL closer to that found in Swiss-Prot through the addition of accurate, high-quality information to TrEMBL entries, thus improving the quality of data available to the user.

b) Redundancy removal

Sequences from the same organism which are full-length and which have 100% identity are merged into a single entry to reduce redundancy.

c) Evidence attribution

TrEMBL contains data from a variety of sources including data which have been imported from the underlying nucleotide databases, data from specific programs, data from automatic annotation procedures, and some manual annotation. As it is essential for users to be able to identify the source of individual data items, a system of evidence attribution has been introduced. This system also allows UniProtKB staff to automatically update data if the underlying data source changes. This is ongoing internally and the evidence tags are currently visible in the XML version of TrEMBL. For more information, please see http://www.uniprot.org/support/docs/evidence.shtml.

3.1.1. Entry name

The first item on the ID line is the entry name of the sequence. This name is a useful means of identifying a sequence, but it is not a stable identifier as is the accession number (see 3.2). The ID tracker ascertains the relevant accession numbers for Swiss-Prot entry names that are no longer in use.

3.1.2. Status

The second item on the ID line indicates the status of the entry (see section 2.2).

3.1.3. Length of the molecule

The third and last item of the ID line is the length of the molecule, which is the total number of amino acids in the sequence. This number includes the positions reported to be present but which have not been determined (coded as 'X'). The length is followed by the letter code 'AA' (Amino Acids).

3.1.4. Examples of identification lines

Two examples of Swiss-Prot ID lines are shown below:

ID   CYC_BOVIN               Reviewed;         104 AA.

ID   GIA2_GIALA              Reviewed;         296 AA.

Example of a TrEMBL ID line:

ID   Q5JU06_HUMAN            Unreviewed;       268 AA.

a) The DE line in Swiss-Prot

The description always starts with the recommended name of the protein. Alternative names are indicated between brackets. Example:

DE   Annexin A5 (Annexin V) (Lipocortin V) (Endonexin II) (Calphobindin I)
DE   (CBP-I) (Placental anticoagulant protein I) (PAP-I) (PP4)
DE   (Thromboplastin inhibitor) (Vascular anticoagulant-alpha) (VAC-alpha)
DE   (Anchorin CII).

Protein naming guidelines are described in the document file nameprot.txt.

If a protein is known to be cleaved into multiple functional components, the description starts with the name of the precursor protein, followed by a section delimited by '[Contains: ...]'. All the individual components are listed in that section and are separated by semi-colons (';'). Synonyms are allowed at the level of the precursor and for each individual component. Example:

DE   Corticotropin-lipotropin precursor (Pro-opiomelanocortin) (POMC)
DE   [Contains: NPP; Melanotropin gamma (Gamma-MSH); Potential peptide;
DE   Corticotropin (Adrenocorticotropic hormone) (ACTH); Melanotropin alpha
DE   (Alpha-MSH); Corticotropin-like intermediary peptide (CLIP);
DE   Lipotropin beta (Beta-LPH); Lipotropin gamma (Gamma-LPH); Melanotropin
DE   beta (Beta-MSH); Beta-endorphin; Met-enkephalin].

If a protein is known to include multiple functional domains each of which is described by a different name, the description starts with the name of the overall protein, followed by a section delimited by '[Includes: ]'. All the domains are listed in that section and are separated by semi-colons (';'). Synonyms are allowed at the level of the protein and for each individual domain. Example:

DE   CAD protein [Includes: Glutamine-dependent carbamoyl-phosphate
DE   synthase (EC 6.3.5.5); Aspartate carbamoyltransferase (EC 2.1.3.2);
DE   Dihydroorotase (EC 3.5.2.3)].

In rare cases, the functional domains of an enzyme are cleaved, but the catalytic activity can only be observed, when the individual chains reorganize in a complex. Such proteins are described in the DE line by a combination of both '[Includes:...]' and '[Contains:...]', in the order given in the following example:

DE   Arginine biosynthesis bifunctional protein argJ [Includes: Glutamate
DE   N-acetyltransferase (EC 2.3.1.35) (Ornithine acetyltransferase)
DE   (Ornithine transacetylase) (OATase); Amino-acid acetyltransferase
DE   (EC 2.3.1.1) (N-acetylglutamate synthase) (AGS)] [Contains: Arginine
DE   biosynthesis bifunctional protein argJ alpha chain; Arginine
DE   biosynthesis bifunctional protein argJ beta chain].

If the complete sequence is not determined, the last information given on the DE lines is '(Fragment)' or '(Fragments)'. Example:

DE   Dihydrodipicolinate reductase (EC 1.3.1.26) (DHPR) (Fragment).

b) The DE line in TrEMBL

The format of the DE line in TrEMBL follows closely the format used in Swiss-Prot. However, as TrEMBL is not manually annotated, the description is derived directly from the underlying nucleotide entry and its accuracy relies on the information provided by the submitter of the nucleotide entry. The description may later be improved by automatic annotation procedures (see section Automatic annotation) but if not, it remains as provided by the submitter until the entry is manually annotated and added to Swiss-Prot.

These lines comprise the literature citations. The citations indicate the sources from which the data has been abstracted. The reference lines for a given citation occur in a block, and are always in the order RN, RP, RC, RX, RG, RA, RT and RL. Within each such reference block, the RN line occurs once, the RC, RX and RT lines occur zero or more times, and the RP, RG/RA and RL lines occur one or more times. If several references are given, there will be a reference block for each.

An example of a complete reference is:

RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS A AND C), FUNCTION, INTERACTION
RP   WITH PKC-3, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, DEVELOPMENTAL
RP   STAGE, AND MUTAGENESIS OF PHE-175 AND PHE-221.
RC   STRAIN=Bristol N2;
RX   PubMed=11134024; DOI=10.1074/jbc.M008990200;
RA   Zhang L., Wu S.-L., Rubin C.S.;
RT   "A novel adapter protein employs a phosphotyrosine binding domain and
RT   exceptionally basic N-terminal domains to capture and localize an
RT   atypical protein kinase C: characterization of Caenorhabditis elegans
RT   C kinase adapter 1, a protein that avidly binds protein kinase C3.";
RL   J. Biol. Chem. 276:10463-10475(2001).

The formats of the individual lines are explained below.

3.11.2. The RN line

The RN (Reference Number) line gives a sequential number to each reference citation in an entry. This number is used to indicate the reference in comments and feature table notes. The format of the RN line is:

RN   [n]

where 'n' denotes the n^th reference for this entry. The reference number is always between square brackets.

3.11.3. The RP line

The RP (Reference Position) lines describe the extent of the work relevant to the entry carried out by the authors. The format of the RP line is:

RP   COMMENT.

It should contain a description of the information that has been propagated in the Swiss-Prot entry.

A typical comment is "NUCLEOTIDE SEQUENCE". This item might be tagged with a qualifier, indicating the origin of the sequence data. Valid names of this qualifiers are:

• GENOMIC DNA: the individual gene has been sequenced
• GENOMIC RNA: the individual gene has been sequenced
• MRNA: the individual cDNA has been sequenced
• LARGE SCALE GENOMIC DNA: the gene has been sequenced as part of a genome project
• LARGE SCALE MRNA: the cDNA has been sequenced as part of a large-scale cDNA project

If 2 qualifiers apply, both are indicated, separated by a '/'.

The 'LARGE SCALE ANALYSIS' is another typical tag added in references that report large screen results to indicate that results have not been extensively studied.

Typical examples of RP lines are shown below:

RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] (ISOFORM 1).

RP   NUCLEOTIDE SEQUENCE [GENOMIC RNA / MRNA].

RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 21-35.

RP   PROTEIN SEQUENCE OF 39-76; 95-118 AND 125-138, AND DISULFIDE BONDS.

RP   SEQUENCE REVISION TO 76-84 AND 129.

RP   STRUCTURE BY NMR.

RP   X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).

RP   CHARACTERIZATION.

RP   MUTAGENESIS OF TYR-65.

RP   REVIEW.

RP   VARIANT ALA-1368.

RP   VARIANTS HDLD1 ARG-597 AND ARG-1477, AND VARIANT HDLD2 LEU-693 DEL.

RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-22; 2-17;
RP   240-256; 318-339 AND 381-390, AND CHARACTERIZATION.

RP   NUCLEOTIDE SEQUENCE [MRNA], PROTEIN SEQUENCE OF 154-171; 302-308;
RP   312-328; 377-384 AND 419-431, FUNCTION, SUBCELLULAR LOCATION, AND
RP   MUTAGENESIS OF ARG-331; GLY-332 AND ARG-333.

RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-387 AND SER-391, AND
RP   MASS SPECTROMETRY.

3.11.4. The RC line

The RC (Reference Comment) lines are optional lines which are used to store comments relevant to the reference cited. The format of the RC line is:

RC   TOKEN1=Text; TOKEN2=Text; ...

The currently defined tokens and their order in the RC line are:

STRAIN

PLASMID

TRANSPOSON

TISSUE

Reference comment line topics may span lines. Examples of RC lines:

RC   STRAIN=Sprague-Dawley; TISSUE=Liver;

RC   STRAIN=Holstein; TISSUE=Lymph node, and Mammary gland;

RC   STRAIN=301 / Serotype 2a;

RC   STRAIN=cv. SP753012-O; TISSUE=Leaf;

RC   PLASMID=R1 (R7268); TRANSPOSON=Tn3;

RC   STRAIN=AL.012, AZ.026, AZ.180, DC.005, GA.039, GA2181, IL.014, IL2.17,
RC   IN.018, KY.172, KY2.37, LA.013, MI.035, MN.001, MNb027, MS.040,
RC   NY.016, OH.036, TN.173, TN2.38, UT.002, and VA.015;

3.11.5. The RX line

The RX (Reference cross-reference) line is an optional line which is used to indicate the identifier assigned to a specific reference in a bibliographic database. The format of the RX line is:

RX   Bibliographic_db=IDENTIFIER[; Bibliographic_db=IDENTIFIER...];

Where the valid bibliographic database names and their associated identifiers are:

Name	Identifier
MEDLINE	Eight-digit MEDLINE Unique Identifier (UI)
PubMed	PubMed Unique Identifier (PMID)
DOI	Digital Object Identifier (DOI)

Example of RX lines:

RX   MEDLINE=83283433; PubMed=6688356;

RX   PubMed=15626370; DOI=10.1016/j.toxicon.2004.10.011;

RX   MEDLINE=22709107; PubMed=12788972; DOI=10.1073/pnas.1130426100;

3.11.6. The RG line

The Reference Group (RG) line lists the consortium name associated with a given citation. The RG line is mainly used in submission reference blocks, but can also be used in paper references, if the working group is cited as an author in the paper. RG line and RA line (Reference Author) can be present in the same reference block; at least one RG or RA line is mandatory per reference block. An example of the use of RG lines is shown below:

RG   The mouse genome sequencing consortium;

3.11.7. The RA line

The RA (Reference Author) lines list the authors of the paper (or other work) cited. The RA line is present in most references, but might be missing in references that cite a reference group (see RG line). At least one RG or RA line is mandatory per reference block.

All of the authors are included, and are listed in the order given in the paper. The names are listed surname first followed by a blank, followed by initial(s) with periods. The authors' names are separated by commas and terminated by a semicolon. Author names are not split between lines. An example of the use of RA lines is shown below:

RA   Galinier A., Bleicher F., Negre D., Perriere G., Duclos B.,
RA   Cozzone A.J., Cortay J.-C.;

As many RA lines as necessary are included in each reference. All initials of the author names are indicated and hyphens between initials are kept.

An author's initials can be followed by an abbreviation such as 'Jr' (for Junior), 'Sr' (Senior), 'II', 'III' or 'IV' (2nd, 3rd and 4th). Example:

RA   Nasoff M.S., Baker H.V. II, Wolf R.E. Jr.;

3.11.8. The RT line

The RT (Reference Title) lines give the title of the paper (or other work) cited as exactly as possible given the limitations of the computer character set. The format of the RT line is:

RT   "Title.";

Example of a set of RT lines:

RT   "New insulin-like proteins with atypical disulfide bond pattern
RT   characterized in Caenorhabditis elegans by comparative sequence
RT   analysis and homology modeling.";

It should be noted that the format of the title is not always identical to that displayed at the top of the published work:

• Major title words are not capitalized;
• The text of a title ends with either a period '.', a question mark '?' or an exclamation mark '!';
• Double quotation marks ' " ' in the text of the title are replaced by single quotation marks;
• Titles of articles published in a language other than English have been translated into English;
• Greek letters are written in full (alpha, beta, etc.).

3.11.9. The RL line

The RL (Reference Location) lines contain the conventional citation information for the reference. In general, the RL lines alone are sufficient to find the paper in question.

3.12.1. Examples for each comment line topic

We show here, for each of the defined topics, two examples of their usage:

CC   -!- ALLERGEN: Causes an allergic reaction in human. Binds to IgE.
CC       Partially heat-labile allergen that may cause both respiratory and
CC       food-allergy symptoms in patients with the bird-egg syndrome.

CC   -!- ALLERGEN: Causes an allergic reaction in human. Minor allergen of
CC       bovine dander.

CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=3;
CC         Comment=Additional isoforms seem to exist. Experimental
CC         confirmation may be lacking for some isoforms;
CC       Name=1; Synonyms=AIRE-1;
CC         IsoId=O43918-1; Sequence=Displayed;
CC       Name=2; Synonyms=AIRE-2;
CC         IsoId=O43918-2; Sequence=VSP_004089;
CC       Name=3; Synonyms=AIRE-3;
CC         IsoId=O43918-3; Sequence=VSP_004089, VSP_004090;

CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative initiation; Named isoforms=2;
CC       Name=Alpha;
CC         IsoId=P51636-1; Sequence=Displayed;
CC       Name=Beta;
CC         IsoId=P51636-2; Sequence=VSP_018696;

CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       pH dependence:
CC         Optimum pH is 8-10;
CC       Temperature dependence:
CC         Highly active at low temperatures, even at 0 degree Celsius.
CC         Thermolabile;

CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Kinetic parameters:
CC         KM=98 uM for ATP;
CC         KM=688 uM for pyridoxal;
CC         Vmax=1.604 mmol/min/mg enzyme;
CC       pH dependence:
CC         Optimum pH is 6.0. Active from pH 4.5 to 10.5;

CC   -!- BIOTECHNOLOGY: The effect of PG can be neutralized by introducing
CC       an antisense PG gene by genetic manipulation. The Flavr Savr
CC       tomato produced by Calgene (Monsanto) in such a manner has a
CC       longer shelf life due to delayed ripening.

CC   -!- BIOTECHNOLOGY: Used in the food industry for high temperature
CC       liquefaction of starch-containing mashes and in the detergent
CC       industry to remove starch. Sold under the name Termamyl by
CC       Novozymes.

CC   -!- CATALYTIC ACTIVITY: ATP + L-glutamate + NH(3) = ADP + phosphate +
CC       L-glutamine.

CC   -!- CATALYTIC ACTIVITY: (R)-2,3-dihydroxy-3-methylbutanoate + NADP(+)
CC       = (S)-2-hydroxy-2-methyl-3-oxobutanoate + NADPH.

CC   -!- CAUTION: It is uncertain whether Met-1 or Met-3 is the initiator.

CC   -!- COFACTOR: Pyridoxal phosphate.

CC   -!- COFACTOR: FAD (By similarity).

CC   -!- WEB RESOURCE: Name=Alzheimer Research Forum; Note=APP mutations;
CC       URL="http://www.alzforum.org/res/com/mut/app/default.asp".

CC   -!- DEVELOPMENTAL STAGE: Expressed early during conidial (dormant
CC       spores) differentiation.

CC   -!- DEVELOPMENTAL STAGE: Detected in embryonic skin (E12.5 and E14.5)
CC       during the formation of hair follicles and at E15.5 in the enamel
CC       knot of the developing tooth. Detected in the basal layer of the
CC       epidermis and hair follicles of P2 mice.

CC   -!- DISEASE: Defects in PHKA1 are linked to X-linked muscle
CC       glycogenosis [MIM:311870]. It is a disease characterized by slowly
CC       progressive, predominantly distal muscle weakness and atrophy.

CC   -!- DISEASE: Defects in ABCD1 are the cause of recessive X-linked
CC       adrenoleukodystrophy (X-ALD) [MIM:300100]. X-ALD is a rare
CC       peroxisomal metabolic disorder that occurs in boys and is
CC       characterized by progressive multifocal demyelination of the
CC       central nervous system and by adrenocortical insufficiency. It
CC       produces mental deterioration, corticospinal tract dysfunction,
CC       and cortical blindness. There is laboratory evidence of adrenal
CC       cortical dysfunction. Different clinical manifestations exist
CC       like: cerebral childhood ALD (CALD), adult cerebral ALD (ACALD),
CC       adrenomyeloneuropathy (AMN) and "Addison disease only" (ADO)
CC       phenotype.

CC   -!- DOMAIN: Contains a coiled-coil domain essential for vesicular
CC       transport and a dispensable C-terminal region.

CC   -!- DOMAIN: The B chain is composed of two domains, each domain
CC       consists of 3 homologous subdomains (alpha, beta, gamma).

CC   -!- ENZYME REGULATION: The activity of this enzyme is controlled by
CC       adenylation under conditions of abundant glutamine. The fully
CC       adenylated enzyme complex is inactive (By similarity).

CC   -!- ENZYME REGULATION: Activated by Gram-negative bacterial
CC       lipopolysaccharides and chymotrypsin.

CC   -!- FUNCTION: Binds to actin and affects the structure of the
CC       cytoskeleton. At high concentrations, profilin prevents the
CC       polymerization of actin, whereas it enhances it at low
CC       concentrations. By binding to PIP2, it inhibits the formation of
CC       IP3 and DG.

CC   -!- FUNCTION: Inhibitor of fungal polygalacturonase. It is an
CC       important factor for plant resistance to phytopathogenic fungi.
CC       Substrate preference is polygalacturonase (PG) from A.niger >> PG
CC       of F.oxysporum, A.solani or B.cinerea. Not active on PG from
CC       F.moniliforme.

CC   -!- INDUCTION: By heat shock, salt stress, oxidative stress, glucose
CC       limitation and oxygen limitation.

CC   -!- INDUCTION: By infection, plant wounding, or elicitor treatment of
CC       cell cultures.

CC   -!- INTERACTION:
CC       Self; NbExp=1; IntAct=EBI-123485, EBI-123485;
CC       Q9W158:CG4612; NbExp=1; IntAct=EBI-123485, EBI-89895;
CC       Q9VYI0:fne; NbExp=1; IntAct=EBI-123485, EBI-126770;

CC   -!- INTERACTION:
CC       Q9W1K5-1:CG11299; NbExp=1; IntAct=EBI-133844, EBI-212772;

CC   -!- MASS SPECTROMETRY: Mass=24948; Mass_error=6; Method=MALDI;
CC       Range=1-228; Source=PubMed:11101899;

CC   -!- MASS SPECTROMETRY: Mass=13822; Method=MALDI; Range=19-140 (P15522-
CC       2); Source=PubMed:10531593;

CC   -!- MISCELLANEOUS: Binds to bacitracin.

CC   -!- MISCELLANEOUS: Called DUO because the encoded protein is closely
CC       related to but shorter than TRIO.

CC   -!- PATHWAY: Cofactor biosynthesis; porphyrin biosynthesis; 5-
CC       aminolevulinate from L-glutamyl-tRNA(Glu): step 2/2.

CC   -!- PATHWAY: Nucleotide metabolism; purine metabolism.

CC   -!- PHARMACEUTICAL: Available under the names Avonex (Biogen),
CC       Betaseron (Berlex) and Rebif (Serono). Used in the treatment of
CC       multiple sclerosis (MS). Betaseron is a slightly modified form of
CC       IFNB1 with two residue substitutions.

CC   -!- PHARMACEUTICAL: Available under the name Proleukin (Chiron). Used
CC       in patients with renal cell carcinoma or metastatic melanoma.

CC   -!- POLYMORPHISM: The allelic form of the enzyme with Gln-191
CC       (Allozyme A) hydrolyzes paraoxon with a low turnover number and
CC       the one with Arg-191 (Allozyme B) with a high turnover number.

CC   -!- POLYMORPHISM: In the human populations there are two major allelic
CC       forms, alpha-1 with 83 residues and alpha-2 with 142 residues.
CC       These alleles determine the 3 major phenotypes HP*1F/HP*1S and
CC       HP*2FS. The two main alleles of HP*1 are called HP*1F (fast) and
CC       HP*1S (slow).

CC   -!- PTM: N-glycosylated and probably also O-glycosylated.

CC   -!- PTM: A soluble short 95 kDa form may be released by proteolytic
CC       cleavage from the long membrane-anchored form.

CC   -!- RNA EDITING: Modified_positions=393, 431, 452, 495.

CC   -!- RNA EDITING: Modified_positions=59, 78, 94, 98, 102, 121; Note=The
CC       nonsense codon at position 59 is modified to a sense codon. The
CC       stop codon at position 121 is created by RNA editing.

CC   -!- SEQUENCE CAUTION:
CC       Sequence=CAI24940.1; Type=Erroneous gene model prediction;

CC   -!- SIMILARITY: Belongs to the annexin family.

CC   -!- SIMILARITY: Contains 13 EGF-like domains.

CC   -!- SUBCELLULAR LOCATION: Bacterial cell inner membrane; Multi-pass
CC       membrane protein.

CC   -!- SUBUNIT: Homotetramer.

CC   -!- SUBUNIT: Disulfide-linked heterodimer of a light chain (L) and a
CC       heavy chain (H). The light chain has the pharmacological activity,
CC       while the N- and C-terminal of the heavy chain mediate channel
CC       formation and toxin binding, respectively.

CC   -!- TISSUE SPECIFICITY: Shoots, roots, and cotyledon from dehydrating
CC       seedlings.

CC   -!- TISSUE SPECIFICITY: Expressed at high levels in brain and ovary.
CC       Lower levels in small intestine. In brain regions, detected in all
CC       regions tested. Highest levels in the cerebellum and cerebral
CC       cortex.

CC   -!- TOXIC DOSE: PD(50) is 1.72 mg/kg by injection in blowfly larvae.

CC   -!- TOXIC DOSE: LD(50) is 0.015 mg/kg by intravenous injection for
CC       sarafotoxin-A and sarafotoxin-B, and 0.3 mg/kg for sarafotoxin-C.

CC   -!- WEB RESOURCE: Name=CD40Lbase;
CC       Note=European CD40L defect database (mutation db);
CC       URL="http://www.expasy.org/cd40lbase/".

3.12.2. Syntax of the topic 'BIOPHYSICOCHEMICAL PROPERTIES'

CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Absorption:
CC         Abs(max)=xx nm;
CC         Note=free_text;
CC       Kinetic parameters:
CC         KM=xx unit for substrate [(free_text)];
CC         Vmax=xx unit enzyme [free_text];
CC         Note=free_text;
CC       pH dependence:
CC         free_text;
CC       Redox potential:
CC         free_text;
CC       Temperature dependence:
CC         free_text;

A BIOPHYSICOCHEMICAL PROPERTIES block must contain at least one of the properties Absorption, Kinetic parameters, pH dependence, Redox potential, Temperature dependence and may have any combination of these properties (ordered as indicated above). The meaning of these subtopics is as follows:

Property	Description
Absorption	indicates the wavelength at which photoreactive proteins such as opsins and DNA photolyases show maximal absorption
Kinetic parameters	mentions the Michaelis-Menten constant (KM) and maximal velocity (Vmax) of enzymes
pH dependence	describes the optimum pH for enzyme activity and/or the variation of enzyme activity with pH variation
Redox potential	reports the value of the standard (midpoint) oxido-reduction potential(s) for electron transport proteins
Temperature dependence	indicates the optimum temperature for enzyme activity and/or the variation of enzyme activity with temperature variation; the thermostability/thermolability of the enzyme is also mentioned when it is known

3.12.3. The topic 'INTERACTION'

The CC line topic INTERACTION conveys information relevant to binary protein-protein interaction. It is automatically derived from the IntAct database and is updated on a monthly basis. The occurrence is one INTERACTION topic per entry, with each binary interaction being presented in a separate line. Each data line can be longer than 75 characters.

Interactions can be derived by any appropriate experimental method, but must be confirmed by a second experiment, if resulting from a single yeast- two-hybrid experiment. For large-scale experiments, interactions are considered if a high confidence is assigned from the authors.

The format of the CC line topic INTERACTION is:

CC   -!- INTERACTION:
CC       {{SP_Ac:identifier[ (xeno)]}|Self}; NbExp=n; IntAct=IntAct_Protein_Ac, IntAct_Protein_Ac;

where

SP_Ac	is the Swiss-Prot or TrEMBL accession number of the interacting protein. If appropriate, the IsoId is used instead to specify the relevant interacting protein isoform.
identifier	serves to describe the interacting protein. It is derived from the Swiss-Prot or TrEMBL GN line and thus presents either a "gene name", a "ordered locus name" or a "ORF name". When no GN line is available a dash is indicated instead.
(xeno)	is an optional qualifier indicating that the interacting proteins are derived from different species. This may be due to the experimental set-up or may reflect a pathogen-host interaction.
Self	reflects a self-association; the corresponding current entry's SP_Ac and 'identifier' are not given/repeated.
NbExp=n	refers to the number of experiments in IntAct supporting the interaction.
IntAct_Protein_Ac	is the IntAct accession number of a interacting protein. The first IntAct_Protein_Ac refers to the protein or an isoform of the current entry, the second refers to the interacting protein or isoform.

Within the CC INTERACTION topic, homomeric interactions are listed before the heteromeric interactions; latter are sorted alphanumerical according the 'identifier'.

"IntAct=IntAct_Protein_Ac, IntAct_Protein_Ac" identifies the interaction in IntAct by using the two IntAct protein identifiers.

Examples of interaction lines are given below. The CC INTERACTION topics are not complete; only explained interaction lines are indicated.

CC   -!- INTERACTION:
CC       P11450:fcp3c; NbExp=1; IntAct=EBI-126914, EBI-159556;

In the typical example the current protein is interacting with P11450 which is further characterized by "fcp3c" derived from its GN line and presents its gene name "Fcp3C". The interaction is supported by one experiment stored in IntAct. Experimental details for this interaction can be found by querying IntAct with "EBI-126914, EBI-159556".

CC   -!- INTERACTION:
CC       Q9W1K5-1:CG11299; NbExp=1; IntAct=EBI-133844, EBI-212772;

The current protein interacts with an isoform of Q9W1K5 defined by the IsoID Q9W1K5-1 .

CC   -!- INTERACTION:
CC       Q8NI08:-; NbExp=1; IntAct=EBI-80809, EBI-80799;

No gene name information for the interacting protein is available.

CC   -!- INTERACTION:
CC       Self; NbExp=1; IntAct=EBI-123485, EBI-123485;

The protein self-associates.

CC   -!- INTERACTION:
CC       Q8C1S0:2410018M14Rik (xeno); NbExp=1; IntAct=EBI-394562, EBI-398761;

The source organisms of the interacting proteins are different.

CC   -!- INTERACTION:
CC       P51617:IRAK1; NbExp=1; IntAct=EBI-448466, EBI-358664;
CC       P51617:IRAK1; NbExp=1; IntAct=EBI-448472, EBI-358664;

Different isoforms of the current protein are shown to interact with the same protein (P51617). This is reflected by different IntAct_Protein_Acs for the current protein.

Example entry with many interaction lines: Q02821.

3.12.4. Syntax of the topic 'SUBCELLULAR LOCATION'

The document subcell.txt, lists the controlled vocabularies used in the comment line (CC) topic SUBCELLULAR LOCATION, their definitions and further information such as synonyms or relevant GO terms in the following format:

    ---------  -------------------------------   ----------------------------------------------
    Line code  Content                           Occurrence in an entry
    ---------  -------------------------------   ----------------------------------------------
    ID         Identifier (location)             Once; starts an entry
    IT         Identifier (topology)             Once; starts a 'topology' entry
    IO         Identifier (orientation)          Once; starts an 'orientation' entry
    AC         Accession (SL-xxxx)               Once
    DE         Definition                        Once or more
    SY         Synonyms                          Optional; Once or more
    SL         Content of subc. loc. lines       Once
    HI         Hierarchy ('is-a')                Optional; Once or more
    HP         Hierarchy ('part-of')             Optional; Once or more
    KW         Associated keyword (accession)    Optional; Once or more
    GO         Gene ontology (GO) mapping        Optional; Once or more
    WW         Interesting links or references   Optional; Once or more
    //         Terminator                        Once; ends an entry
    
   

Example:

    ID   Cyanelle.
    AC   SL-0082
    DE   A cyanelle is a photosynthetic organelle of glaucocystophyte algae.
    DE   Cyanelles are surrounded by a double membrane and, in between, a
    DE   peptidoglycan wall. Thylakoid membrane architecture and the presence
    DE   of carboxysomes are cyanobacteria-like. Historically, the term
    DE   cyanelle is derived from a classification as endosymbiotic
    DE   cyanobacteria, and thus is not fully correct.
    SY   Muroplast; Cyanoplast.
    SL   Plastid, cyanelle.
    HI   Plastid.
    KW   KW-0194
    GO   GO:0009842; cyanelle
    //
   

The format of SUBCELLULAR LOCATION is:

       CC   -!- SUBCELLULAR LOCATION:(( Molecule:)?( Location\.)+)?( Note=Free_text( Flag)?\.)?
   

• Molecule: Isoform, chain or peptide name
• Location = Subcellular_location( Flag)?(; Topology( Flag)?)?(; Orientation( Flag)?)?
  • Subcellular_location: SL-line of subcell.txt ID-record
  • Topology: SL-line of subcell.txt IT-record
  • Orientation: SL-line of subcell.txt IO-record
  • Flag = \(By similarity|Probable|Potential\)

Note: Perl-style multipliers indicate whether a pattern (as delimited by parentheses) is optional (?) or may occur 1 or more times (+).

Examples:

When no chain/peptide/isoform is specified, the subcellular location corresponds to that of the mature protein.

    CC   -!- SUBCELLULAR LOCATION: Cytoplasm. Endoplasmic reticulum membrane;
    CC       Peripheral membrane protein. Golgi apparatus membrane; Peripheral
    CC       membrane protein.
   

    CC   -!- SUBCELLULAR LOCATION: Cell membrane; Peripheral membrane protein
    CC       (By similarity). Secreted (By similarity). Note=The last 22 C-
    CC       terminal amino acids may participate in cell membrane attachment.
    CC   -!- SUBCELLULAR LOCATION: Isoform 2: Cytoplasm (Probable).
   

    CC   -!- SUBCELLULAR LOCATION: Golgi apparatus, trans-Golgi network
    CC       membrane; Multi-pass membrane protein (By similarity).
    CC       Note=Predominantly found in the trans-Golgi network (TGN). Not
    CC       redistributed to the plasma membrane in response to elevated
    CC       copper levels.
    CC   -!- SUBCELLULAR LOCATION: Isoform 2: Cytoplasm.
    CC   -!- SUBCELLULAR LOCATION: WND/140 kDa: Mitochondrion.
   

3.12.5. Syntax of the topic 'ALTERNATIVE PRODUCTS'

The format of the CC line topic ALTERNATIVE PRODUCTS is:

 CC   -!- ALTERNATIVE PRODUCTS:
 CC       Event=Event(, Event)*; Named isoforms=Number_of_isoforms;
(CC         Comment=Free_text;)?
(CC       Name=Isoform_name;( Synonyms=Synonym(, Synonym)*;)?
 CC         IsoId=Isoform_identifier(, Isoform_identifer)*;
 CC         Sequence=(Displayed|External|Not described|Feature_identifier(, Feature_identifier)*);
(CC         Note=Free_text;)?)+

Note: Variable values are represented in italics. Perl-style multipliers indicate whether a pattern (as delimited by parentheses) is optional (?), may occur 0 or more times (*), or 1 or more times (+). Alternative values are separated by a pipe symbol (|).

Topic	Description
Event	Biological process that results in the production of the alternative forms. It lists one or a combination of the following values (Alternative promoter usage, Alternative splicing, Alternative initiation, Ribosomal frameshifting). Format: Event=controlled vocabulary; Example: Event=Alternative splicing;
Named isoforms	Number of isoforms listed in the topics 'Name' currently only for 'Event=Alternative splicing'. Format: Named isoforms=number; Example: Named isoforms=6;
Comment	Any comments concerning one or more isoforms; optional; Format: Comment=free text; Example: Comment=Experimental confirmation may be lacking for some isoforms;
Name	A common name for an isoform used in the literature or assigned by Swiss-Prot; currenty only available for spliced isoforms. Format: Name=common name; Example: Name=Alpha;
Synonyms	Synonyms for an isoform as used in the literature; optional; currently only available for spliced isoforms. Format: Synonyms=Synonym_1[, Synonym_n]; Example: Synonyms=B, KL5;
IsoId	Unique identifier for an isoform, consisting of the Swiss-Prot accession number, followed by a dash and a number. Format: IsoId=acc#-isoform_number[, acc#-isoform_number]; Example: IsoId=P05067-1;
Sequence	Information on the isoform sequence; the term 'Displayed' indicates, that the sequence is shown in the entry; a lists of feature identifiers (VSP_#) indicates that the isoform is annotated in the feature table; the FTIds enable programs to create the sequence of a splice variant; if the accession number of the IsoId does not correspond to the accession number of the current entry, this topic contains the term 'External'; 'Not described' points out that the sequence of the isoform is unknown. Format: Sequence=VSP_#[, VSP_#]|Displayed|External|Not described; Example: Sequence=Displayed; Example: Sequence=VSP_000013, VSP_000014; Example: Sequence=External; Example: Sequence=Not described;
Note	Lists isoform-specific information; optional. It may specify the event(s), if there are several. Format: Note=Free text; Example: Note=No experimental confirmation available;

Example of the CC lines and the corresponding FT lines for an entry with alternative splicing:

CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing, Alternative initiation; Named isoforms=8;
CC         Comment=Additional isoforms seem to exist;
CC       Name=1; Synonyms=Non-muscle isozyme;
CC         IsoId=Q15746-1; Sequence=Displayed;
CC       Name=2;
CC         IsoId=Q15746-2; Sequence=VSP_004791;
CC       Name=3A;
CC         IsoId=Q15746-3; Sequence=VSP_004792, VSP_004794;
CC       Name=3B;
CC         IsoId=Q15746-4; Sequence=VSP_004791, VSP_004792, VSP_004794;
CC       Name=4;
CC         IsoId=Q15746-5; Sequence=VSP_004792, VSP_004793;
CC       Name=Del-1790;
CC         IsoId=Q15746-6; Sequence=VSP_004795;
CC       Name=5; Synonyms=Smooth-muscle isozyme;
CC         IsoId=Q15746-7; Sequence=VSP_018845;
CC         Note=Produced by alternative initiation at Met-923 of isoform 1;
CC       Name=6; Synonyms=Telokin;
CC         IsoId=Q15746-8; Sequence=VSP_018846;
CC         Note=Produced by alternative initiation at Met-1761 of isoform
CC         1. Has no catalytic activity;
...
FT   VAR_SEQ       1   1760       Missing (in isoform 6).
FT                                /FTId=VSP_018846.
FT   VAR_SEQ       1    922       Missing (in isoform 5).
FT                                /FTId=VSP_018845.
FT   VAR_SEQ     437    506       VSGIPKPEVAWFLEGTPVRRQEGSIEVYEDAGSHYLCLLKA
FT                                RTRDSGTYSCTASNAQGQVSCSWTLQVER -> G (in
FT                                isoform 2 and isoform 3B).
FT                                /FTId=VSP_004791.
FT   VAR_SEQ    1433   1439       DEVEVSD -> MKWRCQT (in isoform 3A,
FT                                isoform 3B and isoform 4).
FT                                /FTId=VSP_004792.
FT   VAR_SEQ    1473   1545       Missing (in isoform 4).
FT                                /FTId=VSP_004793.
FT   VAR_SEQ    1655   1705       Missing (in isoform 3A and isoform 3B).
FT                                /FTId=VSP_004794.
FT   VAR_SEQ    1790   1790       Missing (in isoform Del-1790).
FT                                /FTId=VSP_004795.

CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing, Alternative initiation; Named isoforms=3;
CC         Comment=Isoform 1 and isoform 2 arise due to the use of two
CC         alternative first exons joined to a common exon 2 at the same
CC         acceptor site but in different reading frames, resulting in two
CC         completely different isoforms;
CC       Name=1; Synonyms=p16INK4a;
CC         IsoId=O77617-1; Sequence=Displayed;
CC       Name=3;
CC         IsoId=O77617-2; Sequence=VSP_018701;
CC         Note=Produced by alternative initiation at Met-35 of isoform 1.
CC         No experimental confirmation available;
CC       Name=2; Synonyms=p19ARF;
CC         IsoId=O77618-1; Sequence=External;
..
FT   VAR_SEQ       1     34       Missing (in isoform 3).
FT                                /FTId=VSP_004099.

3.12.6. Syntax of the topic 'MASS SPECTROMETRY'

CC   -!- MASS SPECTROMETRY: Mass=mass(; Mass_error=error)?; Method=method; Range=ranges( (IsoformID))?(; Note=free_text)?; Source=references;

Where:

• 'Mass=XXX' is the determined molecular weight (MW);
• 'Mass_error=XX' (optional) is the accuracy or error range of the MW measurement;
• 'Method=XX' is the ionization method;
• 'Range=XX-XX[ (Name)]' is used to indicate what part of the protein sequence entry corresponds to the molecular weight. In case of multiple products, the name of the relevant isoform is enclosed;
• 'Note={Free text}'. Comment in free text format;
• 'Source=PubMed:/Ref.n' indicates the relevant reference'.

3.12.7. Syntax of the topic 'SEQUENCE CAUTION'

The format of the SEQUENCE CAUTION topic is:

CC   -!- SEQUENCE CAUTION:
         Sequence=Sequence; Type=Type;[ Positions=Positions;][ Note=Note;]

Where:

• Sequence is the sequence which differs from the UniProtKB sequence. It is described by one of:
  • an EMBL protein identifier (with version number)
  • an EMBL accession number.