※ Data Summary
Species |
Protein |
Site |
Serine (Num./Per.) |
Threonine (Num./Per.) |
Tyrosine (Num./Per.) |
| Arabidopsis thaliana | 9,003 |
29,058 |
20,545 (70.70%) |
6,517 (22.43%) |
1,996 (6.87%) |
| Brachypodium distachyon | 1,680 |
3,239 |
2,861 (88.33%) |
373 (11.52%) |
5 (0.15%) |
| Brassica napus | 325 |
818 |
484 (59.17%) |
218 (26.65%) |
116 (14.18%) |
| Chlamydomonas reinhardtii | 218 |
527 |
292 (55.41%) |
181 (34.35%) |
54 (10.25%) |
| Citrus sinensis | 111 |
182 |
133 (73.08%) |
42 (23.08%) |
7 (3.85%) |
| Glycine max | 1,436 |
2,718 |
2,181 (80.24%) |
396 (14.57%) |
141 (5.19%) |
| Gossypium hirsutum | 1,474 |
2,789 |
2,491 (89.32%) |
270 (9.68%) |
28 (1.00%) |
| Hordeum vulgare | 345 |
523 |
457 (87.38%) |
66 (12.62%) |
0 (0.00%) |
| Lotus japonicus | 489 |
904 |
789 (87.28%) |
95 (10.51%) |
20 (2.21%) |
| Medicago truncatula | 4,204 |
14,836 |
12,211 (82.31%) |
2,283 (15.39%) |
342 (2.31%) |
| Nicotiana tabacum | 8 |
9 |
5 (55.56%) |
4 (44.44%) |
0 (0.00%) |
| Oryza sativa subsp. japonica | 3,746 |
8,603 |
7,048 (81.92%) |
1,243 (14.45%) |
312 (3.63%) |
| Physcomitrella patens subsp. patens | 374 |
747 |
428 (57.30%) |
230 (30.79%) |
89 (11.91%) |
| Populus trichocarpa | 200 |
297 |
243 (81.82%) |
50 (16.84%) |
4 (1.35%) |
| Selaginella moellendorffii | 716 |
730 |
634 (86.85%) |
91 (12.47%) |
5 (0.68%) |
| Solanum lycopersicum | 43 |
60 |
48 (80.00%) |
11 (18.33%) |
1 (1.67%) |
| Solanum tuberosum | 21 |
33 |
17 (51.52%) |
12 (36.36%) |
4 (12.12%) |
| Triticum aestivum | 998 |
1,499 |
1,363 (90.93%) |
130 (8.67%) |
6 (0.40%) |
| Vitis vinifera | 694 |
1,023 |
919 (89.83%) |
93 (9.09%) |
11 (1.08%) |
| Zea mays | 4,927 |
13,580 |
10,940 (80.56%) |
2,327 (17.14%) |
313 (2.30%) |
| Total | 31,012 |
82,175 |
64,089 (77.99%) |
14,632 (17.81%) |
3,454 (4.20%) |
※ Usage
In 1.0 database, we tried to make it powerful and convenient to be used. This USAGE is prepared for the online service. The dbPPT 1.0 provides the search option, browse option and advance options.
1. Search. You can input one keyword to search the dbPPT 1.0. The search fields include dbPPT ID, Squence Source Database, Reference Database ID, UniProt Accession, Gene Name, Protein Name, Taxa ID, Organism and Function.
Example: Please click on the "Example" button to search "snrk2" in "Protein Name" field. The related proteins will be shown by clicking on the "Submit" button.
2. Browse. You can select one of these twenty species listed below to browse all known proteins with p-sites of corresponding species.
3. Advance Options. Three additional advance options are provided, including Advance search, Multiple search, 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 fewer 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 the protein whose gene name is SnRK2 and sequence source from UniProt in Wheat. The Wheat SnRK2 protein (C8CBK4) will be shown by clicking on the "Submit" button.
(2) Multiple search could be used to find a number of proteins such as a protein list. You can input keyword list, for example, a list of UniProt IDs to search the database. The list should be inputted as one keyword one line.
Example: You can click on the "Example" button to load the protein UniPort ID list of F4JA42 and Q9XIC8 and you will find the regulator of Vps4 activity in the MVB pathway protein and protein CHUP1 by clicking on the "Submit" button.
(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 default is 0.01.
Example: You can click on the "Example" button to load the protein sequence of Os07g0609000 protein (Q6YTX5) and will find the related homologues in other species by clicking on the "Submit" button.
4. I have a few questions which are not listed above, how can I contact the authors of dbPPT 1.0?
Please contact the three major authors: Han Cheng, Wankun Deng, Dr. Zexian Liu and Dr. Yu Xue, for details.