Table 5.
Features of databases and tools available for the effectors, secreted proteins, and virulence factors identified in bacterial genomes.
| Database (specificity) | Important features | Reference/website |
|---|---|---|
| AtlasT4SS [Database for type IV secretion system (T4SS) related proteins] | Describes a large number of proteins related to the type IV secretion system reported in Gram-negative, Gram-positive bacteria, and Archaea | Souza et al., 2012 |
| http://www.t4ss.lncc.br/ | ||
| DBSecSys (Database of Burkholderia mallei Secretion Systems) | Provides a database for computationally predicted bacterial secretion system proteins and their host factors | Memi et al., 2014 |
| LAB-Secretome [Database for the extracellular and surface-associated proteins of Lactic Acid Bacteria (LAB)] | Provides a database comparison of the secretomes from 26 sequenced LAB genomes | Zhou et al., 2010 |
| www.cmbi.ru.nl/lab_secretome/ | ||
| Mycosec (A database for signal peptide bearing genes of mycobacterium) | Provides computationally predicted signal peptides in the 21 different strains of Mycobacterium genome | Sen, 2011 |
| www.bicnbu.in/mycosec/ | ||
| SecReT4 | Provides a web-based bacterial type IV secretion system resource. T4SSs are versatile assemblages that promote genetic exchange and/or effector translocation with consequent impacts on pathogenesis and genome plasticity | Bi et al., 2012 |
| http://db-mml.sjtu.edu.cn/SecReT4/ | ||
| BEAN (Bacterial effector analyzer) | Provides an integrated web resource to predict, analyze, and store type III secreted effectors (T3SEs) | Dong et al., 2013 |
| http://protein.cau.edu.cn:8080/bean/. | ||
| BPBAac (Bacterial type III secreted protein identifier) | Provides a tool that was developed and trained using Support Vector Machine (SVM) based on the Aac feature extracted using a Bi-profile Bayes model. BPBAac classifies T3S and non-T3S proteins very effectively | Wang et al., 2011 |
| http://biocomputer.bio.cuhk.edu.hk/softwares/BPBAac. | ||
| SIEVE Server (Web tool for prediction of type III secreted effectors) | Provides computational prediction of type III and IV secreted effectors in gram-negative bacteria | Samudrala et al., 2009 |
| http://www.sysbep.org/sieve/ | ||
| T3SEdb [Database for effectors of Type III secretion system (T3SS)] | Provides keyword as well as sequence searches. More than 171 clusters of T3SEs have been detected based on sequence identity comparisons | Tay et al., 2010 |
| http://effectors.bic.nus.edu.sg/T3SEdb/index.php | ||
| T3SS effector prediction tool | Presents a signal prediction method together with comprehensive survey of potential type III secretion system effectors extracted from 918 published bacterial genomes | Lower and Schneider, 2009 |
| http://www.modlab.org/ | ||