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The text below were extracted from Swiss-Prot Manual for quick reference. Some of the text were omitted for brevity and relevance. To read the full manual, click here :


2.4. Non-experimental qualifiers
3 types of non-experimental qualifiers in comment (CC) lines and feature table (FT lines) indicate that the information given is not based on experimentally proven findings:
  • Potential
  • Probable
  • By similarity
The term 'Potential' indicates that there is some logical or conclusive evidence that the given annotation could apply. This non-experimental qualifier is often used to present the results from protein sequence analysis tools, which are only annotated, if the result makes sense in the context of a given protein. A typical example is the annotation of N-glycosylation sites in the entries of non-cytoplasmic domains or proteins.

The term 'Probable' counts stronger than the qualifier 'Potential' and there must be at least some experimental evidence, which indicates, that the given information is expected to be found in the natural environment of a protein.

'By similarity' is added to facts that were proven for a protein or part of it, and which is then transferred to the proteins of related organisms. This non-experimental qualifier is also used to transfer the information on known biological important sites within conserved domains to proteins that contain one or more copies of such a domain, e.g. active sites within an enzymatic domain or disulfide bonds, which stabilize the structure of extracellular modules.
»» To read the full Swis-Prot manual, click here

3.7. The OG line
The OG (OrGanelle) line indicates if the gene coding for a protein originates from the mitochondria, the chloroplast, the cyanelle, the nucleomorph or a plasmid.

The format of the OG line is:

OG Chloroplast.
OG Cyanelle.
OG Mitochondrion.
OG Nucleomorph.
OG Plasmid name.

Where 'name' is the name of the plasmid.
»» To read the full Swis-Prot manual, click here

3.15. The FT line
The FT (Feature Table) lines provide a precise but simple means for the annotation of the sequence data. The table describes regions or sites of interest in the sequence. In general the feature table lists posttranslational modifications, binding sites, enzyme active sites, local secondary structure or other characteristics reported in the cited references. Sequence conflicts between references are also included in the feature table.

Example of a FT line in Swiss-Prot entry :
FT   NON_TER       1      1

FT   SIGNAL       <1     10       By similarity.
The first item on each FT line is the key name, which is a fixed abbreviation (of up to 8 characters) with a defined meaning. A list of the currently defined key names can be found in Appendix A of this document.

Following the key name are the 'FROM' and 'TO' endpoint specifications. These fields designate (inclusively) the endpoints of the feature named in the key field. In general, these fields simply contain residue numbers which indicate positions in the sequence as listed. Note that these positions are always specified assuming a numbering of the listed sequence from 1 to n; this numbering is not necessarily the same as that used in the original reference(s). The following should be noted:

If the 'FROM' and 'TO' specifications are identical, the feature involves one single amino acid;

When a feature is known to extend beyond the position that is given in the feature table, the endpoint specification will be preceded by '<' for features which continue to the left end (N-terminal direction) or by '>' for features which continue to the right end (C- terminal direction);

Unknown endpoints are denoted by '?'. Uncertain endpoints are denoted by a '?' before the position, e.g. '?42'.

The remaining portion of the FT line is a description that contains additional information about the feature. For example, for a posttranslationally modified residue (key MOD_RES) the chemical nature of the modified residue is given, while for a sequence variation (key VARIANT) the nature of the variation is indicated. This portion of the line is generally in free form, and may be continued on additional lines when necessary.
»» To read the full Swis-Prot manual, click here

 

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