T346Hunter: A novel web-based tool for the prediction of T3SS, T4SS and T6SS


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Upload your sequence for secretion systems prediction

If you leave your email, you will be notified when the job is done.

DNA sequence
(sequence file [sample])
E-mail (optional)
E-value (HMMER) <= E-value (BLASTp) <=
Sequence shape      Secretion systems to predict T3SS T4SS T6SS

...or upload NCBI sequence files for a faster execution
Genes Location
(NCBI ptt file [sample])
Protein sequences
(NCBI faa file [sample])
DNA sequence
(NCBI fna file [sample])
E-mail (optional)
E-value (HMMER) <= E-value (BLASTp) <=
Sequence shape      Secretion systems to predict T3SS T4SS T6SS

About T346Hunter

T346Hunter is a web application for the identification of type III, type IV and type VI secretion systems (T3SS, T4SS and T6SS, respectively) in bacterial genomes. Non-flagellar T3SS (NF-T3SS) and T6SS are complex molecular machines that deliver effector proteins from bacterial cells into the environment or into other eukaryotic or prokaryotic cells, with significant implications for pathogenesis of the strains encoding them. Meanwhile, T4SS is a more functionally diverse system, which is involved in not only effector translocation but also conjugation and DNA uptake/release.

After inspection of the available scientific literature, we constructed a database of hidden Markov model (HMM) protein profiles and sequences representing the various components of T3SS, T4SS and T6SS. T346hunter performs BLASTp and HMMER searches of such a database against user-supplied bacterial sequences and localises enriched regions in any of these three types of secretion systems. Predicted loci are presented in a comprehensive and user-friendly formatted document. A tab-delimited summary of the gene-by-gene search, which can be easily incorporated into data pipelines, is also provided.

We expect T346hunter will offer great help to researchers in advancing their understanding of the biological mechanisms in which secretion systems are involved.

User Manual

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Methods

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Predicted clusters

T346Hunter analysed complete bacterial genomic sequences of 2,997 chromosomes and 2,164 plasmids sequenced available as of 14 February 2014 in RefSeq. In total, 2,814 clusters were identified (512 NF-T3SS, 1,466 T4SS and 836 T6SS) across 1,121 organisms. Such clusters can be queried below (we included some other predictions that do not fulfill the restrictions described in Methods but may be worth to check).

Select a sequence:

Contact us

Pablo Rodríguez-Palenzuela

Full Professor
Email: pablo.rpalenzuela@upm.es
Link: Pablo Rodriguez-Palenzuela
Phytopathogenic bacteria
Centre for Plant Biotechnology and Genomics (CBGP)
Universidad Politécnica de Madrid

Cayo Ramos Rodríguez

Full Professor
Email: crr@uma.es
Link: Cayo Ramos Rodriguez
Institute for Mediterranean and Subtropical Horticulture (IHSM-UMA-CSIC)
Department of Cellular Biology, Genetics and Physiology
Universidad de Málaga

Pedro M. Martínez García

PhD
Email: pm.martinez@uma.es
Link: Pedro M. Martinez Garcia
Institute for Mediterranean and Subtropical Horticulture (IHSM-UMA-CSIC)
Department of Cellular Biology, Genetics and Physiology
Universidad de Málaga