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dbPPT: a comprehensive database of protein phosphorylation in plants.

Cheng H, Deng W, Wang Y, Ren J, Liu Z, Xue Y - Database (Oxford) (2014)

Bottom Line: The proportions of residue types including serine, threonine and tyrosine were 77.99, 17.81 and 4.20%, respectively.All the phosphoproteins and phosphorylation sites in the database were critically annotated.Since the phosphorylation signaling in plants attracted great attention recently, such a comprehensive resource of plant protein phosphorylation can be useful for the research community.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China.

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The search options in the dbPPT database. (A) dbPPT can be queried with a simple keyword. (B) The results of simple search for ‘snrk2’ in the area ‘Protein Name’. (C) Advanced search allows users to perform a complex search using multiple keywords in several areas and three operators including ‘and’, ‘or’ and ‘exclude’. (D) Advanced search result of ‘SnRK2’ in wheat while its full-length sequence was retrieved from UniProt. (E) Multiple search allows user to search multiple keywords in one query event. (F) The results of searching ‘C8CBK4’ and ‘SnRK’ in any field. (G) BLAST search was implemented for search similar phosphoproteins with FASTA format protein sequence. (H) BLAST search for SNF1-type serine–threonine protein kinase in wheat.
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bau121-F3: The search options in the dbPPT database. (A) dbPPT can be queried with a simple keyword. (B) The results of simple search for ‘snrk2’ in the area ‘Protein Name’. (C) Advanced search allows users to perform a complex search using multiple keywords in several areas and three operators including ‘and’, ‘or’ and ‘exclude’. (D) Advanced search result of ‘SnRK2’ in wheat while its full-length sequence was retrieved from UniProt. (E) Multiple search allows user to search multiple keywords in one query event. (F) The results of searching ‘C8CBK4’ and ‘SnRK’ in any field. (G) BLAST search was implemented for search similar phosphoproteins with FASTA format protein sequence. (H) BLAST search for SNF1-type serine–threonine protein kinase in wheat.

Mentions: To provide convenient querying services, four search options are implemented in dbPPT. In the home page of dbPPT, a simple search option is provided, which allows user to perform keyword-based search in specific area (Figure 3A). An example with SNF1-type serine–threonine protein kinase SnRK2.4 is shown by searching the keyword ‘snrk2’ in the ‘Protein Name’ area. After submitting the query, the results will be shown in a tabular format with dbPPT ID, Sequence ID and protein/gene names/synonyms (Figure 3B). Furthermore, three additional search options including advanced search, multiple search, BLAST search are also implemented and available in the ‘SEARCH’ page of dbPPT. In advanced search option, three keywords can be used to perform a complex search in three areas through combination with three operators of ‘and’, ‘or’ and ‘exclude’ (Figure 3C), while the results are shown in the format as the simple search option (Figure 3D). In multiple search option, several keywords such as a list of gene names can be used to search one area (Figure 3E), all the proteins hits any one of these keywords will be presented in the results (Figure 3F). In addition, the BLAST search option is designed to search phosphoproteins in dbPPT with a protein sequence in the FASTA format. User could submit a protein sequence to run a homologous search through NCBI BLAST packages (33) with a specified E-Value threshold (Figure 3G). Search results of BLAST search is presented in a tabular format with dbPPT ID, sequence similarity evaluations including identity, E-value and score, sequence ID and protein/gene name/synonyms (Figure 3H). Furthermore, all the phosphoproteins in the dbPPT database could be accessed directly through the link of ‘http://dbppt.biocuckoo.org/getTable. php?seqID=accession’, while the ‘accession’ is the sequence accession such as UniProt accession.Figure 3.


dbPPT: a comprehensive database of protein phosphorylation in plants.

Cheng H, Deng W, Wang Y, Ren J, Liu Z, Xue Y - Database (Oxford) (2014)

The search options in the dbPPT database. (A) dbPPT can be queried with a simple keyword. (B) The results of simple search for ‘snrk2’ in the area ‘Protein Name’. (C) Advanced search allows users to perform a complex search using multiple keywords in several areas and three operators including ‘and’, ‘or’ and ‘exclude’. (D) Advanced search result of ‘SnRK2’ in wheat while its full-length sequence was retrieved from UniProt. (E) Multiple search allows user to search multiple keywords in one query event. (F) The results of searching ‘C8CBK4’ and ‘SnRK’ in any field. (G) BLAST search was implemented for search similar phosphoproteins with FASTA format protein sequence. (H) BLAST search for SNF1-type serine–threonine protein kinase in wheat.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4273206&req=5

bau121-F3: The search options in the dbPPT database. (A) dbPPT can be queried with a simple keyword. (B) The results of simple search for ‘snrk2’ in the area ‘Protein Name’. (C) Advanced search allows users to perform a complex search using multiple keywords in several areas and three operators including ‘and’, ‘or’ and ‘exclude’. (D) Advanced search result of ‘SnRK2’ in wheat while its full-length sequence was retrieved from UniProt. (E) Multiple search allows user to search multiple keywords in one query event. (F) The results of searching ‘C8CBK4’ and ‘SnRK’ in any field. (G) BLAST search was implemented for search similar phosphoproteins with FASTA format protein sequence. (H) BLAST search for SNF1-type serine–threonine protein kinase in wheat.
Mentions: To provide convenient querying services, four search options are implemented in dbPPT. In the home page of dbPPT, a simple search option is provided, which allows user to perform keyword-based search in specific area (Figure 3A). An example with SNF1-type serine–threonine protein kinase SnRK2.4 is shown by searching the keyword ‘snrk2’ in the ‘Protein Name’ area. After submitting the query, the results will be shown in a tabular format with dbPPT ID, Sequence ID and protein/gene names/synonyms (Figure 3B). Furthermore, three additional search options including advanced search, multiple search, BLAST search are also implemented and available in the ‘SEARCH’ page of dbPPT. In advanced search option, three keywords can be used to perform a complex search in three areas through combination with three operators of ‘and’, ‘or’ and ‘exclude’ (Figure 3C), while the results are shown in the format as the simple search option (Figure 3D). In multiple search option, several keywords such as a list of gene names can be used to search one area (Figure 3E), all the proteins hits any one of these keywords will be presented in the results (Figure 3F). In addition, the BLAST search option is designed to search phosphoproteins in dbPPT with a protein sequence in the FASTA format. User could submit a protein sequence to run a homologous search through NCBI BLAST packages (33) with a specified E-Value threshold (Figure 3G). Search results of BLAST search is presented in a tabular format with dbPPT ID, sequence similarity evaluations including identity, E-value and score, sequence ID and protein/gene name/synonyms (Figure 3H). Furthermore, all the phosphoproteins in the dbPPT database could be accessed directly through the link of ‘http://dbppt.biocuckoo.org/getTable. php?seqID=accession’, while the ‘accession’ is the sequence accession such as UniProt accession.Figure 3.

Bottom Line: The proportions of residue types including serine, threonine and tyrosine were 77.99, 17.81 and 4.20%, respectively.All the phosphoproteins and phosphorylation sites in the database were critically annotated.Since the phosphorylation signaling in plants attracted great attention recently, such a comprehensive resource of plant protein phosphorylation can be useful for the research community.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China.

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Related in: MedlinePlus