EffectiveDB—updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems

@article{Eichinger2016EffectiveDBupdatesAN,
  title={EffectiveDB—updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems},
  author={Valerie Eichinger and Thomas Nussbaumer and Alexander Platzer and Marc-Andr{\'e} Jehl and Roland Arnold and Thomas Rattei},
  journal={Nucleic Acids Research},
  year={2016},
  volume={44},
  pages={D669 - D674}
}
Protein secretion systems play a key role in the interaction of bacteria and hosts. EffectiveDB (http://effectivedb.org) contains pre-calculated predictions of bacterial secreted proteins and of intact secretion systems. Here we describe a major update of the database, which was previously featured in the NAR Database Issue. EffectiveDB bundles various tools to recognize Type III secretion signals, conserved binding sites of Type III chaperones, Type IV secretion peptides, eukaryotic-like… 

Figures from this paper

An account of in silico identification tools of secreted effector proteins in bacteria and future challenges
TLDR
The mechanism, contribution and deficiency of previous developed detection tools are presented, and potential improvements of the prediction performance are discussed, which include more informative features for discriminating the effectors from non‐effectors.
Comprehensive assessment and performance improvement of effector protein predictors for bacterial secretion systems III, IV and VI
TLDR
A comprehensive survey and benchmarking of currently available tools for the prediction of effector proteins of bacterial types III, IV and VI secretion systems (T3SS, T4SS and T6SS) and three ensemble models based on ML algorithms are constructed.
A systematic analysis of the RNA-targeting potential of secreted bacterial effector proteins
TLDR
This study presents the first systematic evaluation of the RNA-targeting potential of bacterial effectors, and obtained evidence that PipB2 and Lpg2844, effector proteins of Salmonella and Legionella species, respectively, may harbor novel biochemical activities.
PredT4SE-Stack: Prediction of Bacterial Type IV Secreted Effectors From Protein Sequences Using a Stacked Ensemble Method
TLDR
A stacked ensemble model PredT4SE-Stack was developed to predict T4SEs, which utilized an ensemble of base-classifiers implemented by various machine learning algorithms, such as support vector machine, gradient boosting machine, and extremely randomized trees, to generate outputs for the meta-classifier in the classification system.
BastionHub: a universal platform for integrating and analyzing substrates secreted by Gram-negative bacteria
TLDR
Gram-negative bacteria utilize secretion systems to export substrates into their surrounding environment or directly into neighboring cells, and BastionHub is the first to incorporate substrates secreted by type I or type II secretion systems, which is also the most comprehensive online database available.
Structural Profiling of Bacterial Effectors Reveals Enrichment of Host-Interacting Domains and Motifs
TLDR
This study lends novel quantitative insight into the structural basis of effector-induced perturbation of host-endogenous PPIs and may aid in the design of selective inhibitors ofhost-pathogen interactions.
Comparative Genome Analyses Reveal the Genomic Traits and Host Plant Adaptations of Flavobacterium akiainvivens IK-1T
  • Xuehua Wan
  • Biology
    International journal of molecular sciences
  • 2019
The genus Flavobacterium contains a large group of commensal bacteria identified in diverse terrestrial and aquatic habitats. We compared the genome of a new species Flavobacterium akiainvivens IK-1T
Identification and characterization of putative Aeromonas spp. T3SS effectors
TLDR
A bioinformatics pipeline to identify T3SS effector proteins is developed, applied to the genomes of 105 Aeromonas strains isolated from environmental, mutualistic, or pathogenic contexts and evaluated the cytotoxicity of the identified effectors through their heterologous expression in yeast.
Genome Mining Shows Ubiquitous Presence and Extensive Diversity of Toxin-Antitoxin Systems in Pseudomonas syringae
TLDR
Using bioinformatic search and prediction tools, it is shown that P. syringae strains encode 26 different families of TA systems targeting diverse cellular functions, and type II TA systems in this species are almost exclusively type II.
...
...

References

SHOWING 1-10 OF 35 REFERENCES
Prediction of bacterial type IV secreted effectors by C-terminal features
TLDR
T4SEpre, as an effective inter-species T4 SS effector prediction software package, will help find new pathogenic T4SS effectors efficiently in a variety of pathogenic bacteria.
Effective—a database of predicted secreted bacterial proteins
TLDR
Effective (effectors.org) is a database of predicted bacterial secreted proteins, implementing two complementary prediction strategies for protein secretion: the identification of eukaryotic-like protein domains and the recognition of signal peptides in amino acid sequences.
Sequence-Based Prediction of Type III Secreted Proteins
TLDR
A strong type III secretion signal in the N-terminus that can be used to detect effectors with sensitivity of ∼71% and selectivity of ∼85%.
SecReT6: a web-based resource for type VI secretion systems found in bacteria.
TLDR
A broad range of T 6SS gene cluster detection and comparative analysis tools are readily accessible via SecReT6, which may aid identification of effectors and immunity proteins around the T6SS core components.
Computational Prediction of Type III and IV Secreted Effectors in Gram-Negative Bacteria
TLDR
The results show that there may be classes of effectors in which the signal has a loosely defined motif and others in which secretion is dependent only on compositional biases, which represents an important step toward better understanding the interaction between pathogens and hosts.
T346Hunter: A Novel Web-Based Tool for the Prediction of Type III, Type IV and Type VI Secretion Systems in Bacterial Genomes
TLDR
This work constructed a database of hidden Markov model (HMM) protein profiles and sequences representing the various components of T3SS, T4SS and T6SS, which offers great help to researchers in advancing their understanding of the biological mechanisms in which these sophisticated molecular machines are involved.
Accurate prediction of bacterial type IV secreted effectors using amino acid composition and PSSM profiles
TLDR
T4EffPred can discriminate IVA and IVB effectors in benchmark datasets with positive rates of 76.7% and 89.7%, respectively, and the overall accuracy shows that the present method is accurate for distinguishing the T4SS effector in unidentified sequences.
T3SEdb: data warehousing of virulence effectors secreted by the bacterial Type III Secretion System
TLDR
The T3SEdb represents a platform for inclusion of additional annotations of metadata for future developments of sophisticated effector prediction models for screening and selection of putative novel effectors from bacterial genomes/proteomes that can be validated by a small number of key experiments.
A New Means To Identify Type 3 Secreted Effectors: Functionally Interchangeable Class IB Chaperones Recognize a Conserved Sequence
ABSTRACT Many Gram-negative bacteria utilize specialized secretion systems to inject proteins (effectors) directly into host cells. Little is known regarding how bacteria ensure that only small
SecReT4: a web-based bacterial type IV secretion system resource
TLDR
It is proposed that SecReT4 will facilitate efficient investigation of large numbers of type IV secretion systems, recognition of diverse patterns of sequence-, gene- and/or functional conservation and an improved understanding of the biological roles and significance of these versatile molecular machines.
...
...