Links

T6SS core components available at KEGG
T6SS descriptions available at MicrobeWiki
Bioinformatics tools used by SecReT6

  • PostgreSQL, an open source relational database management system
  • HMMER, Biosequence analysis using profile hidden Markov models
  • WU-BLAST, the Washington University improved version of BLAST
  • MUSCLE, protein multiple sequence alignment
  • Jalview, a multiple alignment editor written in Java
  • CGview, generate circular genome maps
Public database, to which SecReT6 has a hyperlink path

Other tools or servers of interest

  • NCBI Microbial Genomes
  • VFDB, Virulence Factor database
  • Effective, a database of predicted secreted bacterial proteins
  • PhyML, New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies
  • iTOL, Interactive Tree Of Life is an online tool for the display and manipulation of phylogenetic trees
  • T3DB, an integrated database for bacterial Type III Secretion System and cognate effectors
  • T3SEdb, data warehousing of virulence effectors secreted by the bacterial Type III Secretion System
  • CONJscan, Search for relaxases and key components of type IV secretion systems in proteomes using an HMM profiles database
  • AtlasT4SS, a curated database for type IV secretion systems
  • CONJdb, allows searching and browsing Conjugative Type IV Secretion and Mobilization Systems via a graphical interface
  • SecReT4, a database for gene clusters encoding type IV secretion system
  • MultiGeneBlast, an open source tool for identification of homologs of multigene modules such as operons and gene clusters. It is based on a reformatting of the FASTA headers of NCBI GenBank protein entries, using which it can track down their source nucleotide and coordinates.
  • SSPred, a prediction server based on SVM for the identification and classification of proteins involved in bacterial secretion systems.
  • SCRATCH, a protein structure and structural feature prediction server.
  • GOLD, Genomes Online Database, is a World Wide Web resource for comprehensive access to information regarding genome and metagenome sequencing projects, and their associated metadata, around the world.