Hi everyone,
I'm trying to identify the presence of all 6 types of secretion systems in a couple of bacterial genomes but the 346Hunter and Preffector server seems not to work. Is anyone familiar with other platforms or other alternatives for this kind of predictions?
McDermott et al 2010, Computational Prediction of Type III and IV Secreted Effectors in Gram-Negative Bacteria, Infection and Immunity Dec 2010, 79 (1) 23-32; DOI: 10.1128/IAI.00537-10
Xiong et al 2018, PredT4SE-Stack: Prediction of Bacterial Type IV Secreted Effectors From Protein Sequences Using a Stacked Ensemble Method, Frontiers in Microbiology, DOI=10.3389/fmicb.2018.02571
Eichinger et al 2016, EffectiveDB--updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems.Nucleic Acids Res. 2016 Jan 4;44(D1):D669-74. doi: 10.1093/nar/gkv1269. Epub 2015 Nov 20.
You can send the protein fasta file from your annotated genome to KofamKOALA. It uses HMM to annotate the metabolic pathways of your bacteria. There is a section in results to list all secretion systems found.
https://www.genome.jp/tools/kofamkoala/
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