EnzyBase2: An update of EnzyBase database for enzybiotic studies
User's Guide
Browse Search Tools Statistical Info Disclaimer
Enzybiotics in EnzyBase refer to bacterial cell wall-degrading enzymes including lysins, bacteriocins, autolysins, and lysozymes. The most important characteristics of enzybiotics are a novel mode of antibacterial action, different from those typical of antibiotics, and the capacity to kill antibiotic-resistant bacteria. Another significant feature of some enzybiotics is the low probability of developing bacterial resistance.
EnzyBase2 (Collection of enzybiotics) has been created with an objective to provide a useful resource for study of enzybiotics. This manually curated database currently holds 2039 enzybiotics sequences, contains not only 1844 enzybiotics from 217 nature sources but also 195 synthetic enzybiotics. Information related to protein name, protein full name, producer organism, simple function annotation and protein sequence, domains, Go term prediction, 3D-structure and regarding references, target organisms with MIC values, and links to external databases like UniProt, PDB and InterPro. PubMed links are included here.
Browse
The database browse interface provides the users with a function of navigating the entire database.
Search
We classified search into simple search and complex search in EnzyBase. Simple search allows users to search based on keywords like "lysosyaphin" or string searches like "lysozyme g" in full name or function field in main table.
Complex search allows users restrict the search to a particular field descriptor or a combination of varied field description.
All searches are case insensitive. A complete list of the field descriptors and their description is given below:
DESCRIPTORS |
DESCRIPTION |
| EnzyBase Id | The unique identifier in EnzyBase. Start with EN and 6 -8 digital number.
E.g. EN81226619 |
| Protein name | The name of Enzybiotic protein, such as lysostaphin. |
| Uniprot Id | UniprotKB entry name, like P10547. |
| Producer Organism | The source of the enzybiotics origin from. |
| Domains | The name of domain, such as Peptidase_M23. |
| Target Organism | Target organism can be searched as shown in the example. |
| MIC | Minimum inhibitory concentration [MIC values] . |
Tools
Currently, the tools interface only implements two tools: ClustalW and BlastP.
ClustalW
We supply a simple ClustalW service for users to alignment the enzybiotics by ClustalW. And we provide a link to EBI ClustalW which supplied more options for multiple sequence alignment.
Reference:
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. (2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.
BLASTP
We only construct BLASTP AGAINST EnzyBase on Web Server. And we supply a link to NCBI BLASTP if you want to blast full datasets in NCBI.
BLASTP AGAINST EnzyBase: Users can search for similar sequences in EnzyBase.
Reference:
Altschul, S. F. et al. (1997), Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 25:3389-3402.
FASTA format for sequences begins with a single-line description, followed by lines of sequence data. The description line is demarked from the sequence data by a greater-than ('>') symbol in the first column.
For example :
>EN10753092|P10547|Lysostaphin
MKKTKNNYYTRPLAIGLSTFALASIVYGGIQNETHASEKSNMDVSKKVAEVETSKAPVENTAEVETSKAPVENTAEVET
SKAPVENTAEVETSKAPVENTAEVETSKAPVENTAEVETSKAPVENTAEVETSKAPVENTAEVETSKAPVENTAEVE
TSKAPVENTAEVETSKAPVENTAEVETSKAPVENTAEVETSKAPVENTAEVETSKAPVENTAEVETSKAPVENTAEV
ETSKALVQNRTALRAATHEHSAQWLNNYKKGYGYGPYPLGINGGMHYGVDFFMNIGTPVKAISSGKIVEAGWSNYGGG
NQIGLIENDGVHRQWYMHLSKYNVKVGDYVKAGQIIGWSGSTGYSTAPHLHFQRMVNSFSNSTAQDPMPFLKSAGYG
KAGGTVTPTPNTGWKTNKYGTLYKSESASFTPNTDIITRTTGPFRSMPQSGVLKAGQTIHYDEVMKQDGHVWVGYTGN
SGQRIYLPVRTWNKSTNTLGVLWGTIK
Statistical Info
The statical info interface provides data on distribution of sequence length, protein mass, isoelectric point and domains.
Disclaimer
The authors do not assume any responsibility for losses of any kind incurred by use of this database.
This work has been funded by the Major scientific and technological specialized project of China for ‘significant new formulation of new drugs’ (grant 2008ZX09101-032) and ‘Yangtze river delta’ joint scientific and technological project of China (grant 10495810600).