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UniProt release 6.0

Published September 13, 2005

Headlines

UniProtKB/Swiss-Prot major release (48.0)

Release 48.0 of 13-Sep-2005 of UniProtKB/Swiss-Prot contains 194'317 sequence entries, comprising 70'391'852 amino acids abstracted from 133'723 references. 11'963 sequences have been added since release 47, the sequence data of 1'095 existing entries has been updated and the annotations of 93'692 entries have been revised. This represents an increase of 7%.

Many improvements were carried out in the last 4 months. In particular, we have expanded our system of feature identifiers (FTIds): Feature keys concerning protein processing (CHAIN, PEPTIDE, PROPEP) have been tagged by a new feature identifier with the prefix PRO. We also changed the format of the OG Chloroplast and Cyanelle lines, to be able to indicate more precisely the kind of plastid organelle.

UniProt Knowledgebase release 6.0 includes Swiss-Prot release 48.0 and TrEMBL release 31.0. For more information you can also read the Full statistics and release notes for the UniProt Knowledgebase, i.e. Swiss-Prot and TrEMBL.


UniProtKB News

Changes in the OG (OrGanelle) line

We changed the format of the OG Chloroplast and Cyanelle lines, to be able to indicate more precisely the kind of plastid organelle. So far we defined the following lines:

OG   Plastid.
OG   Plastid; Apicoplast.
OG   Plastid; Chloroplast.
OG   Plastid; Cyanelle.
OG   Plastid; Non-photosynthetic plastid.

The line "OG Plastid" is used when the type of plastid - from which the gene coding for a protein originates - is unknown. This will be the case for most TrEMBL entries.

The line "OG Plastid; Apicoplast" is used for plastid-type organelles from the apicocomplexan parasites. These plastids are not photosynthetic, and encode a different suite of proteins than do photosynthetic organisms.

The line "OG Plastid; Chloroplast" is used for plastids from all organisms able to perform photosynthesis except the glaucophyte algae (see next).

The line "OG Plastid; Cyanelle" is used for plastids from the glaucophyte algae.

The line "OG Plastid; Non-photosynthetic plastid" is used for plastids derived from non-photosynthetic, but not apicocomplexan organisms. Examples of such organisms are the land plant Epifagus virginiana, the chlorophyte algae Prototheca wickerhamii and the euglenoid Astasia longa, none of which encode the genes necessary for photosynthesis on their plastid genome.

Cross-references to TAIR

Cross-references have been added to TAIR, The Arabidopsis Information Resource, which is a model organism database providing a centralized, curated gateway to Arabidopsis biology. TAIR is available at http://arabidopsis.org. Implicit links to this database have already been provided before in the NiceProt view of relevant Swiss-Prot entries on ExPASy.

The format of the explicit links in the flat file is:

Resource abbreviation TAIR
Resource identifier TAIR unique locus identifier.
Example
P33487:
DR   TAIR; At4g02980; -.

Introduction of a new feature identifier

The system of feature identifiers has been expanded. All feature keys concerning protein processing (CHAIN, PEPTIDE, PROPEP) have been tagged with the new feature identifier with the prefix PRO. We now have 4 types of feature identifiers:

  • prefix CAR relevant to the feature key CARBOHYD (e.g. /FTId=CAR_123456.)
  • prefix VAR relevant to the feature key VARIANT (e.g. /FTId=VAR_123456.)
  • prefix VSP relevant to the feature key VARSPLIC (e.g. /FTId=VSP_123456.)
  • new prefix PRO relevant to CHAIN, PEPTIDE, PROPEP (e.g. /FTId=PRO_1234567890.)

Examples:

Q9W568: 
FT   CHAIN        23    611       Halfway protein.
FT                                /FTId=PRO_0000021413.
P15515: 
FT   PEPTIDE      20     57       Histatin 1.
FT                                /FTId=PRO_0000021416.
Q7XAD0: 
FT   PROPEP       25     48
FT                                /FTId=PRO_0000021449.

Changes concerning keywords

New keywords:

Deleted keywords:

  • Bombesin family
  • Bradykinin
  • Embryo
  • Erythrocyte
  • Galectin
  • Glucagon family
  • Insulin family
  • Lipocalin
  • Macrophage
  • Pancreas
  • Pentaxin
  • Phytochrome
  • Pituitary
  • Placenta
  • Platelet
  • Pyrokinin
  • Rubredoxin
  • Selectin
  • Serpin
  • Tachykinin
  • Thionin
  • Thymus
  • Whey