We will update this page with the most frequently asked questions and answers.
If you don't find any answer to your question here, you can contact us !

BactMentha data come from multiple databases. First protein-protein interaction data are taken from IMEx Consortium for each host taxon. A lot of complementary informations concerning the interacting proteins are taken from Uniprot. Moreover, NCBI blastp has been used against Virulence Factor Database (VFDB) and BastionHub content to annotate the bacterial proteins. Some informations such has the detection method, the interaction type and the PubMed ID are also retrieved. Finally, binding interfaces are inferred in addition to experimentally detected binding regions thanks to the mimicINT tool.

You can use the Advanced Search to create custom search query, using a list of values separed by a comma. To do that, you can use the operators 'like (..., ..., ...)' or 'not like (..., ..., ...)'. For example, you can create a custom query by first selecting (bacterial) Uniprot AC, then select like (..., ..., ...), and finally type in the search bar the Uniprot identifiers like this: P0ABE7, Q8CZU2, A0A6L8PTK5. This will allows you to search for interactions that involve bacterial proteins corresponding to these Uniprot accession numbers.

PA or 'Protein Annotation' concern the bacterial annotation available in BactMentha Database. Those informations come from Virulence Factor Database (VFDB) and BastionHub.
BR or 'Binding Regions' concern the known binding regions between two interactors (detected experimentaly). Those informations are taken directly from the publications.
MI or 'mimicINT Interface' concern the predicted binding interfaces between two interactors. Those informations are produced by the prediction tool mimicINT.

When the table is displayed after your search, you can see some buttons at the upper right corner.
The 'Show/Hide columns' button allows you to mask or display some columns on the current resulting table. The second, button, 'CSV + annotations to CSV' allows you to download the current table (after filtering in the headers for exemple) and the annotations tables (bacterial protein annotations, binding regions and mimicINT interfaces) for the corresponding interactions in the filtered table. The 'CSV' button allows you to download only the current filtered table (without the additionnal annotations tables). Finally, the 'Excel' button permits also to download only the current table in an Excel format.

The units are in base pairs. For exemple for with this Binding Region table:

Identifier A	Feature A	Feature start A	Feature end A	Identifier B	Feature B	Feature start B	Feature end B
Q8X482	binding-associated region	221	314	O08816	binding-associated region	193	501

We can see that there is an interaction between the bacterial protein (always in A columns) Q8X482 and the host protein (always in B columns) O08816.
The detected binding region seem to bury the protein Q8X482 from the amino acid position 221 to the amino acid position 314, and the protein O08816 from the position 193 to the position 501.

The units used for mimicINT Interfaces tables are the same, at the only difference that the interfaces are inferred instead of being found in the literature.

BactMentha follows the HUPO Proteomics Standards Initiative on Molecular Interactions. You can find the tree view and definitions of the different terms here.

The confidence score used on BatcMentha is not a significance score but an heuristic score based on three factors : the detection method, the interaction type, and the number of publication that catalog this interaction. For more information see the Intact Interaction Scoring documentation.

The percentage of BactMentha interactions for which a Binding Region has been described in the litterature for at least one of the two interactors is about 1.3% in February 2024. Adding the mimicINT interfaces inference, the number of interactions for which we have the positions of either a binding region or an interface is around 6.13% of BactMentha interations. That represent an icrease of more than 470%. Unfortunaly, except for those interactions that enables you to refer to some database such as Pfam, ELM or InterPro (based on the given positions or interfaces), it is not possible to give more details on the way the interactions occur than the ones given in the table based on curation of the literature.

Yes, you can add a condition based on the WHO priority level or the Hazard group of the bacterial pathogen in the Advanced Search form.

WHO priority groups aims to guide/promote research of new antibiotics for multidrug resistant bacteria so it consists in a list of antibiotic-resistant "priority pathogens". On the other side, pathogens are classified into an hazard group depending on their level of risk of infections to humans and the availability of a vaccine or treatment.