|Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)||Crenarchaeota||801||1675|
|Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)||Crenarchaeota||536||1238|
|Escherichia coli (strain K12)||Proteobacteria||332||648|
|Escherichia coli O157:H7||Proteobacteria||295||442|
|Synechococcus sp. (strain ATCC 27264 / PCC 7002 / PR-6) (Agmenellum quadruplicatum)||Cyanobacteria||245||521|
In dbPSP database, we have tried to develop a friendly user interface which can be convenient to be used. The database also provides the search and advance options.
1. Search. You can input one or multiple keywords (separated by space character) to search the dbPSP database. The search fields including dbPSP ID, UniProt Accession, Species, Protein Name, Protein Alias, Gene Name, Gene Alias, and Function.
EXAMPLE: Please click on the "Example"
button to search "era" in GeneName field. By clicking
on the "Submit" button, the related dbPSP proteins will be
2. Browse. Two simple ways have been provided for users to browse phosphorylation proteins or residues in the database. Users can browse by phyla or by residue type. Type browse allows user to select interested type. Phyla browse allows user to choose interested phyla.
3. Advance Options. Three advance options are provided, including advance search, browse, BLAST search.
(1) Advance search allows you to input up to three terms to find the information more specifically. The querying fields can be empty if less terms are needed. The three terms could be connected by the following operators:
exclude: If selected, the
term following this operator must be not contained in the specified field(s)
and: the term following this operator has to be included in the specified field(s)
or: either the preceding or the following term to this operator should occur in the specified field(s)
EXAMPLE: You can click on the "Example" button to load an instance, which could search era for Gene Name. The GLYA_ECOLI (P0A825) will be shown by clicking on the "Submit" button.
(2) Batch Search It can be employed to find a number of proteins such as protein list. You can input keyword list, for example, a list UniprotIDs to search the database. The list should be inputed as one key one line.
(3) BLAST search could be used to find the specific protein and/or related homologues by sequence alignment. This search-option will help you to find the querying protein accurately and fast. Only one protein sequence in FASTA format is allowed per time. The E-value threshold could be user-defined, while the phyla information could be specified. The default parameters of E-value and phyla are 0.01 and All phyla, respectively.
EXAMPLE: You can click on the "Example" button to load the protein sequence of Chemotaxis protein CheY. By clicking on the "Submit" button, you can find the related homologues.