MOBscan

MOBscan is a web application for identifying relaxase MOB families. It uses the hmmscan function of the HMMER3 software suite (Eddy, 2011) to search against MOBfamDB, a curated relaxase profile HMM database. If you find it useful for your work, please cite it as:

Garcillán-Barcia M.P., Redondo-Salvo S., Vielva L., de la Cruz F. (2020) "MOBscan: Automated Annotation of MOB Relaxases". In: de la Cruz F. (eds) Horizontal Gene Transfer. Methods in Molecular Biology, vol 2075. Humana, New York, NY

MOBfamDB construction information

Individual profile HMM files for relaxase families MOB_P (T4SS_MOBP1, T4SS_MOBP2, and T4SS_MOBP3), MOB_Q (T4SS_MOBQ), MOB_H (T4SS_MOBH), MOB_C (T4SS_MOBC), MOB_V (T4SS_MOBV), and MOB_B (T4SS_MOBB) have been retrieved from the TXSScan suite (Abby et al., 2016).

New profile HMMs were built for MOB_F, MOB_T, and MOB_M families from seed multiple sequence alignments generated with MUSCLE v3.8.31 (Edgar, 2004) by using the hmmbuild function of HMMER3.

• MOB_F Profile

  The profile HMM for the MOB_F relaxase family (profile_MOBF) was generated from an alignment of the N-terminal 300 residues of 146 MOB_F proteins described by (Garcillan-Barcia et al., 2009), which was previously trimmed to remove poorly aligned regions at the edges by using Trimal (Capella-Gutierrez et al., 2009).

• MOB_T Profile

  The profile HMM for the MOB_T relaxase family (profile_MOBT) was built from an alignment of 498 relaxases retrieved from a BLASTP search (Altschul et al., 1990) using as query the Orf20_Tn916 complete sequence present in Figure 3 of (Wright and Grossman, 2016). The alignment was trimmed while keeping both HTH and Rep_trans domains.

• MOB_M Profile

  For the novel family MOB_M, a profile HMM (profile_MOBM) was built based on an alignment of thirteen relaxases from Clostridium perfringens plasmids, retrieved from a BLASTP search using TcpM_pCW3 (GenBank Acc. No. WP_003479716.1) as query.