Statistics-BactMentha

On this page, you can explore graphical statistical summaries of the BactMentha database.
You can also display a table by selecting a specific statistics for a taxon (or for all taxa).

The BactMentha database stores 12544 bacteria-host protein-protein interactions (PPIs) entries for 11776 binary interactions distributed as follows:
• 11612 entries for 11004 interactions (human),
• 897 entries for 751 interactions (mouse),
• 35 entries for 21 interactions (rat).

These interactions involve 5088 distinct host proteins (respectively 4554 for human, 521 for mice and 13 for rat) and 2970 distinct bacterial proteins (2914 interacting with human proteins, 98 with mouse proteins, and 12 with rat proteins).

In total, 102 bacterial strains from 39 distinct families are represented in BactMentha:
• 97 strains from 38 families (human),
• 27 strains from 16 families (mouse),
• 6 strains from 4 families (rat).

Number of bacteria-host protein-protein interactions per host

Number of full annotated, partially annotated or unannotated interactions per host

Global

Human

Mouse

Rat

BactMentha provides different types of additional annotations for protein-protein interactons (PPIs) that can be displayed in the "Annotation" column of the result tables:

• Bacterial Protein Annotations (PA):
Bacterial proteins have been annotated as virulence factors or effectors after perfomring BLASTp sequences searches against Virulence Factor Database (VFDB) and BastionHub databases.

• Cellular Components (CC):
Uniprot subcellular localization data have been gathered for all the interactors when available.

• Binding Regions (BR):
Available experimental interaction binding regions have been retreived from IMEx databases for either the host or the bacterial protein (or both).

• MimicINT Interfaces (MI):
MimicINT was used to infer interaction interfaces for bacteria-host interactions using known interaction templates (domain-domain or motif-domain). More details about the mimicINT workflow can be found in the documentation.

• Alphafold Complexes (AF):
SFor a subset of protein interaction complex structures have been predicted using AlphaFold3 via MassiveFold workflow. An archive with all the predicted complexes can be downloaded directly on the download page.

The graphs on the left reports statistics on three subsets of BactMentha interaction data:
• Fully annotated interactions correspond to interactions for which the five possible annotations are present.
• Partially annotated interactions correspond to interactions for which at least one of the five types of possible annotations is present.
• Unannotated interactions correspond to interactions for which none of the five possible annotations are present.

N.B.: mimicINT and AlphaFold predictions are only available for the Human host.

On the right, the plots display the proportions of interaction annotations in the whole dataset and for each host.

• ___ Bacterial Protein Annotation (PA): The bacterial protein in the interaction is annotated as virulence factor or effector.

• ___ Cellular Components (CC): The subcellular localization is known for at least one of the interactors.

• ___ Binding Regions (BR): An expermiental binding region exist for at least one of the interactors.

• ___ MimicINT Interfaces (MI): MimicINT interfaces are available for the interaction partners (always both sided and only for human host).

• ___ AlphaFold Complexes (AF): The interaction complex have been predicted with AlphaFold3 (only for some bacteria-human interactions).

Proportions of interactions annotation types (among annotated interactions) per host

Global

Human

Mouse

Rat

Number of interactions (and their proportion of bacterial protein annotations) for the 10 first bacterial taxa

Global

Human

Mouse

Rat

Bacterial Protein Annotation generation:

To better understand how bacterial proteins interact with host proteins, we annotated bacterial proteins using data from the Virulence Factor Database (VFDB) and BastionHub. These annotations were assigned through BLASTp similarity searches between each bacterial protein in BactMentha and the proteins in these databases.

A given annotation was assigned to a bacterial protein if it meets the following criteria:
• Sequence Identity ≥ 30%: The bacterial protein needed to be at least 30% identical to a known protein in the database.
• Alignment Coverage ≥ 75%: At least 75% of the bacterial protein sequence should be aligned with the reference protein.

If a bacterial protein meetst both conditions, it is annotated with the given functional category such as secreted effectors, immune modulation, adherence, or motility.

BactMentha Database Statistics

Select a table to display :