pneumophila, C. burnetti and/or Plasmid Colb-P9 Dot/Icm systems; and (iv) the GI-T4SS group contains orthologs encoded on the genomic islands of H. influenza, P. aeruginosa and Salmonella enterica. The “”2nd category”":
The second category describes a well-known protein family or else an uncharacterized protein family (UPF). At present, selleck kinase inhibitor the AtlasT4SS shows a total of 119 annotated protein families. The “”3rd category”": The last category displays the classification based broadly on the function of a particular type IV secretion system. We described ten functional categories. When the function of a T4SS is well-known, we annotated it as either: (i) conjugation, (ii) effector translocator, (iii) T-DNA translocator, or (iv) DNA uptake/release. Also, when there is experimental evidence of bifunctional proteins, we annotated them with both functions, as follows: (v) conjugation and effector translocator or (vi) effector and T-DNA translocator. On the other hand, there are some uncharacterized systems, which we annotated KPT-8602 concentration as a probable function by analysis of similarity data (subject and
query coverage ≥80% and similarity ≥80%) and phylogenetic tree, as follows: (vii) probable effector translocator, (viii) probable conjugation or (ix) probable effector translocator and DNA uptake/release. Finally, when the function of a given system was not possible to predict, we annotated it as (x) unknown. The current version
of the AtlasT4SS check database contains 119 PXD101 families dispersed into 134 clusters. Each protein family can be related to one cluster (e.g. F-T4SS TraA-F family), two clusters (e.g. I-T4SS DotA family), three clusters (e.g. P-T4SS VirB7 family), or up to eight clusters (e.g. P-T4SS VirB2/TrbC family). Figure 3 shows the distribution of protein family sizes in the database, and for each of them its functional category is highlighted. This figure allows a simple identification of functional category within a given family. For example, the largest protein families (more than 10 members), in particular those belonging to the P-T4SS group contain several annotated functional categories, including the unknown function. These functional categories vary from four for Endonuclease_MobA/VirD2 Family to eight for several VirB related families and nine for VirB6/TrbL Family. Figure 3 Distribution of family sizes in the Atlas T4SS. The graphic shows the distribution of the 119 protein families annotated in the 2nd category of the Atlas T4SS according to the number of entries per family. The colors within each bar indicate the percentage of entries annotated with a known or unknown function.