User's Guide
Browse Search Tools Statistical Info People Disclaimer
The need to develop new classes of antibiotics with novel mechanisms of action against drug-resistant pathogens is becoming very urgent. Enzybiotics are becoming increasingly recognized as potential alternative therapies for drug-resistant bacteria. Enzybiotics are referred to as bacterial cell wall-degrading enzymes, including lysins, bacteriocins, autolysins, and lysozymes. Fischetti and coworkers coined the term "enzybiotics" for these proteins, describing both enzymatic and antibacterial properties. The most important characteristics of enzybiotics are their novel mechanisms of antibacterial action and capacity to kill antibiotic-resistant bacteria. Another significant feature of certain enzybiotics is their low probability of developing bacterial resistance.
Enzybiotics have been optimized through evolution to cause fast and efficient lysis of the host cell from within, thereby ensuring the phage's survival. However, this does not preclude that there is still potential for important when it comes to application from without, especially in complex environments such as certain food matrics, blood or on mucous membranes. Protein engineering strategies such as domain swapping or random mutagenesis can alter binding and lytic properies of PGHs and thereby potentially optimize these proteins for specific applications.
collect the genetically modified enzybiotics(GMEs) from the scientific literature.As a result, it is difficult to find information on enzybiotics for recent users. Developing a central database that stores information on enzybiotics is warranted by investigators to promote their research on enzybiotics discovery and design.
Browse
The database browse interface provides the users with a function of navigating the entire database and supply a download link for the download all genetically modified enzybiotics stored in GMEnzy.
Search
We classified search into simple search and complex search in GMEnzy. Simple search allows users to search based on keywords like "clys" or string searches like "HydH5 Lyso" 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 |
| GM Id | The unique identifier in GMEnzy. E.g. L01A003147
|
| GME name | The name of genetically modified enzybiotics, such as Clys or P128. |
| Parent Enzybiotic | Parent Enzybiotic, such aslysostaphin. |
| Domain | The name of domain consists a GME, such as SH3b. |
| Strategy Modified | The strategy used to product GMEs. |
| Target Organism | The Target organism of GMEs against. E.g. E.coli
|
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 GMEnzy on Web Server. And we supply a link to NCBI BLASTP if you want to blast full datasets in NCBI.
BLASTP AGAINST GMEnzy: Users can search for similar sequences in GMEnzy.
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 :
>GM0001|ClyS|Domains Assembly
MKTLKQAESYIKSKVNTGTDFDGLYGYQCMDLAVDYIYHVTDGKIRMWGNAKDAINNSFGGTATVYKNYPAFRPKYGDVVVWTTGNFA
TYGHIAIVTNPDPYGDLQYVTVLEQNWNGNGIYKTELATIRTHDYTGITHFIRPNFATESSVKKKDTKKKPKPSNRDGINKDKIVYDRTNINY
NMVKRGKSASKITVGSKAPYNLKWSKGAYFNAKIDGLGATSATRYGDNRTNYRFDVGQAVYAPGTLIYVFEIIDGWCRIYWNNHNEWIW
HERLIVKEVF
Statistical Info
The statical info interface provides data on distribution of sequence length, protein mass, isoelectric point and rank of domains and sources.
People involved:
| Mr. Hongyu Wu |
| Dr. Jinjiang Huang |
| Dr. Hairong Lu |
| Mr. Guodong Li |
| Dr. Qingshan Huang |
| at SLS, Fudan University |
Disclaimer
The authors do not assume any responsibility for losses of any kind incurred by use of this database.
This work has been partly funded by the plan 2012 for Science and technology innovation action of Shanghai, China (grant 12DE1940500) and the ‘Yangtze river delta’ joint scientific and technological project of China (grant 10495810600).