Metamenu

Effective job submission

Prediction of secreted proteins and protein secretion systems

Main input for your job
FASTA formatted protein sequences
Upload a FASTA formatted protein sequence file
EffectiveT3: predicts Type III secreted proteins based on their signal peptide
Specify the minimal score of a secreted protein (allowed range 0.0 ... 1.0; see score plot in EffectiveT3 documentation).
Select the version of the EffectiveT3 model.
T4SEpre (beta): predicts Type IV secreted proteins based on amino acid composition in C-termini
Specify the minimal score (allowed range 0.0 ... 1.0; higher score, higher selectivity; default: 0.5).
EffectiveCCBD: predicts Type III secreted proteins based on their secretion chaperon binding site
EffectiveELD: predicts secreted proteins based on eukaryotic-like domains
Select the minimal Z-score of a protein domain enrichment in pathogenic bacteria (or your proteins in complete genome mode).
Predotar: predicts subcellular localization of secreted proteins in the host cell
Select the appropriate model for your host organism.
Genome mode: for protein sequences from (nearly) complete genomes
Select if your proteins represent a genome. This will enable Z-score refinement in EffectiveELD and allows the activation of EffectiveS346.
If CheckM is enabled, this threshold is used to decide whether a genome is complete or not. The recommended value for a reasonable application of EffectiveS346 is 85%.
Alternative to COGnitor: upload a file listing all eggNOG 4.0 COGs/NOGs that are present in your genome (one COG/NOG accession per line; only NOGs on root level - no bactNOGs, gproNOGs etc.). As second column, delimited by tab, the protain name can be provided (optional). Example file
Predicts Type III, IV, VI secretion systems for protein sequences from (nearly) complete genomes. If no COG/NOG assignment file is given, orthologous groups will be predicted by using COGnitor and eggNOG 4.0