T3SSscan and FLAGscan use hmm profiles to scan a set of bacterial protein sequences for the presence of key components of: non-flagellar type III secretion systems (“NF-T3SS” database), flagella (“Flagellum”) or both (“NF-T3SS+Flagellum”).
Eight proteins have homologs in both systems and are ubiquitous (“common proteins”: SctJ, SctN, SctQ, SctR, SctS, SctT, SctU, SctV in NF-T3SS ; FliF, FliI, FliN, FliP, FliQ, FliR, FlhB, FlhA in flagellum –referred in the profile databases for instance as “SctJ_FLG” for FliF, the SctJ homolog). Thus positive hits can occur for genes of both systems, but these hits would be more significant (better e-value and score) for gene profiles of the correct system.
The secretin gene (SctC) is ubiquitous in NF-T3SS and absent from flagella, and conversely FliE, FlgB, FlgC are found in flagella but not in T3SS. Ideally, a given system would present genes with positive hits for the “common genes” homologs of the system, plus positive hits for the system-specific genes. Please note that we used a stringent best-1-domain evalue (or “independent E-value”, “i-Evalue” in the output) threshold of 0.001 to consider a hit as significant.
The output consists of three sections: a ranked list of the best scoring HMMs, a list of the best scoring domains in order of their occurrence in the sequence, and alignments for all the best scoring domains. A sequence score may be higher than a domain score for the same sequence if there is more than one domain in the sequence; the sequence score takes into account all the domains. All sequences scoring above the -E and -T cutoffs are shown in the first list, then every domain found in this list is shown in the second list of domain hits. If desired, E-value and score thresholds may also be applied to the domain list using the –domE and –domT options.
Authors: Sophie Abby, Eduardo Rocha.