PPLRE SprotProteinProkaryote Table
The PPLRE SprotProteinProkaryote Table is a PPLRE Table that contains a recent snapshot of the protein data maintained by SwissProt for the organisms in the PPLRE NCBIOrganismProkaryote Table.
Attribute Descriptions
|
Attribute Name |
Description |
|
SprotID |
A primary key. “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. a) Swiss-Prot entry names The Swiss-Prot entry name consists of up to 11 uppercase alphanumeric characters…. The TrEMBL entry name consists of up to 12 uppercase alphanumeric characters.” |
|
ProteinPA |
A primary key. The “Primary Accession” number. A foreign key to Proteins table. … “The purpose of accession numbers is to provide a stable way of identifying entries from release to release. It is sometimes necessary for reasons of consistency to change the names of the entries, for example, to ensure that related entries have similar names. However, an accession number is always conserved, and therefore allows unambiguous citation of entries. Researchers who wish to cite entries in their publications should always cite the first accession number. This is commonly referred to as the 'primary accession number'. 'Secondary accession numbers' are sorted alphanumerically. We strongly advise those users who have programs performing mappings of Swiss-Prot to another data resource to use Swiss-Prot accession numbers to identify an entry. Entries will have more than one accession number if they have been merged or split. For example, when two entries are merged into one, the accession numbers from both entries are stored in the AC line(s).” |
|
OrganismId |
The organism’s identifier. (aka NCBI tax_id) |
|
OrganismName |
A name that the organism is known by. |
|
SprotProteinNameID |
The identifier of the official SwissProt name for the protein. A foreign key to SprotProteinName. |
|
ProteinName |
The official SwissProt name for the protein. |
|
SprotGeneNameID |
An identifier to the official SwissProt name of the gene. A foreign key to the SprotGeneName. |
|
GeneName |
One or more names that the gene is known by. Multiple values are separated by semicolons. |
|
|
|
|
|
|
|
Keywords (future) |
May be extracted in a future release. (see sample) |
|
Function |
May be extracted in a future release. (see sample) |
Summary Statistics:
- 112,809
Source
- uniprot_sprot_archaea.dat
- uniprot_sprot_bacteria.dat
- ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz
Expected Data Role
- Populate the PPLRE Protein Table.
Notes
- Basic UniProtKB Entry Viewer http://www.uniprot.org/entry/P23189
- ExPASy interface http://www.expasy.org/cgi-bin/niceprot.pl?P23189 The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE
- http://www.pir.uniprot.org/cgi-bin/upEntry?id=P23189
- http://pir.georgetown.edu/cgi-bin/ipcEntry?id=GSHR_PSEAE
- http://www.expasy.org/uniprot/ELAS_PSEAE
- http://www.expasy.org/sprot/userman.html
- http://www.pir.uniprot.org/start/faq.shtml
- Organisms:
- only in NCBI: 64,295 (e.g. strains P. aureginosa PA01)
- only in Sprot: 8,019 (e.g. Eukaryotes)
- in both: 1,795 (e.g. P. aureginosa)
- n.b.
5,671,77016,597,981 rows in the raw file.
See Also
- Swiss-Prot.
- TrEMBL (Translation of EMBL)
- UniProtKB (Universal Protein Knowledge Base)
- Swiss-Prot Accession Format.
Example 1
|
SprotID |
ELAS_PSEAE |
BLAC_STAAU |
GSHR_PSEAE |
|
ProteinPA |
P14756 |
P00807 |
P23189 |
|
OrganismID |
|||
|
OrganismName |
Pseudomonas aeruginosa |
Staphylococcus aureus |
Pseudomonas aeruginosa |
|
SprotProteinNameID |
|
|
|
|
ProteinName |
Pseudolysin
precursor |
Beta-lactamase
precurso |
Glutathione reductase |
|
SprotGeneNameID |
|
|
|
|
GeneName |
lasB |
blaZ |
gor |
|
Keywords (future) |
3d-structure; calcium; complete proteome;
direct protein sequencing; extracellular protein; hydrolase; metal-binding; metalloprotease;
metalloproteinase; protease; signal; zinc; zymogen |
3d-structure; antibiotic resistance;
direct protein sequencing; extracellular protein; hydrolase; plasmid;
signal; transposable element |
FAD; NADP; complete proteome; fad;
flavoprotein; nadp; oxidoreductase; redox-active center; redox-active
disulfide |
|
Function (future) |
Cleaves elastin, collagen, IgG, and
several complement components. Involved in the pathogenesis of P.aeruginosa
infections. |
NULL |
Maintains high levels of reduced glutathione
in the cytosol. |
Example 2
|
SprotID |
CSG_METFE |
SECG_METJA |
|
ProteinPA |
P27373 |
P60460 |
|
OrganismID |
2180 |
2190 |
|
OrganismName |
Methanothermus fervidus ?? |
?? |
|
SprotProteinNameID |
|
|
|
ProteinNames |
Cell surface glycoprotein precursor |
Preprotein translocase secG subunit |
|
SprotGeneNameID |
|
|
|
GeneName |
slgA |
secG |
|
Keywords (future) |
Cell wall; Direct protein sequencing; Glycoprotein;
S-layer; Signal |
3D-structure; Complete proteome; Membrane; Protein
transport; Translocation; Transmembrane; Transport |
|
Function (future) |
The S-layer is a paracrystalline mono-layered
assembly of proteins which coat the surface of the cell. |
Involved in protein export. The function of the beta
subunit is unknown, but it may be involved in stabilization of the trimeric
complex. |
Example 3
% head ./data/ontology/v1.2/SprotProteinProkaryote.tab
- SprotID ProteinPA OrganismID OrganismName ProteinNameID ProteinName SprotGeneNameID GeneName
1A1D_PYRAB Q9V2L2 29292 Pyrococcus abyssi 0 Putative 1-aminocyclopropane-1-carboxylate deaminase
1A1D_PYRFU Q8U4R3 2261 Pyrococcus furiosus 0 Putative 1-aminocyclopropane-1-carboxylate deaminase
1A1D_PYRHO O57809 53953 Pyrococcus horikoshii 0 Putative 1-aminocyclopropane-1-carboxylate deaminase
3MGH_AERPE Q9Y9P1 56636 Aeropyrum pernix 2 Putative 3-methyladenine DNA glycosylase
AAT1_METJA Q60317 2190 Methanococcus jannaschii 3 aspartate aminotransferase 1
AAT2_METJA Q58097 2190 Methanococcus jannaschii 6 aspartate aminotransferase 2
AAT_PYRAB Q9V0L2 29292 Pyrococcus abyssi 7 Aspartate aminotransferase 0 aspC
AAT_PYRHO O58489 53953 Pyrococcus horikoshii 7 Aspartate aminotransferase 0 aspC
AAT_PYRKO O93744 69014 Pyrococcus kodakaraensis 7 Aspartate aminotransferase 0 aspC
% head ./data/ontology/v1.2/SprotProteinProkaryote.tab
112809 1345999 10897810 SprotProteinProkaryote.tab