Metamenu

Methods

Effective bundles various tools to predict bacterial secreted proteins based on their sequence:

  • EffectiveT3: prediction of Type III secretion signals
  • EffectiveCCBD: detection of conserved binding domains of Type III chaperones
  • EffectiveELD: secretion system independent prediction of secreted proteins based on eukaryotic-like domains

Type IV secreted proteins can be recognized by their C-terminal signal sequence. The program T4SEpre contains multiple models representing C-terminal sequential and position-specific amino acid compositions, possible motifs and structural features. Due to the very high computational costs of the T4SEpre model based on protein secondary structure (Sse), we have only used the sequence-based models T4SEpre_psAac and T4SEpre_bpbAac.

Multiple evidence suggested organelles as targets of bacterial secreted proteins. Effective therefore includes the program Predotar, a tool that allows to rapidly screen N-terminal targeting sequences and to predict their subcellular localization in eukaryotic host cells.

Beyond the analysis of arbitrary protein sequence collections, the new release of Effective also provides a “genome-mode”, in which protein sequences from nearly complete genomes and or metagenomic bins can be screened for the presence of three important secretion systems (type III, IV, VI). The genome mode utilizes several programs and databases:

  • EffectiveELD: secretion system independent prediction of secreted proteins based on eukaryotic-like domains with Z-score refinement
  • CheckM: estimates the completeness of a genome based on single-copy marker genes
  • COGnitor: predicts orthologous group assignments of protein sequences
  • EggNOG 4.0: database of Clusters of Orthologous Groups (COGs) and Non-supervised Orthologous Groups (NOGs)
  • EffectiveS346: predicts the presence and putative functionality of type III, IV, VI secretion systems

Find below documentation and supplementary data for methods that were specifically developed for Effective.

Specific methods in Effective

  • EffectiveT3

    An updated version of EffectiveT3 facilitates the recognition of N-terminal signal peptide in Effective. For the update we have assembled new training datasets, combining 504 verified secreted proteins from T3SEdb along with our original training data. Also the new model [...]

  • EffectiveCCBD

    Complementing the signal peptide based prediction of Type III secreted proteins we have integrated a novel method for class 1B chaperone prediction. Those chaperones facilitate the correct selection and unfolding of type III dependent effector proteins. A commonly shared sequence [...]

  • EffectiveELD

    EffectiveELD predicts secreted proteins based on eukaryotic-like domains (ELD). These domains, occur in eukaryotic genomes and have a higher frequency in genomes of host-associated bacteria compared to non host-associated bacteria. This observation indicates that proteins encoding such domains might be [...]

  • EffectiveS346

    The “EffectiveS346” software has been implemented for the Effective database in order to predict secretion systems encoded in bacterial genomes and to provide a clear “yes/no” prediction on whether they are sufficiently complete or not. This method predicts type III, [...]