Tutorial

How to use MOBscan.

Use the submission form to upload a FASTA file containing amino acid sequences (protein sequences). MOBscan searches your input for relaxases and reports their MOB classification.

The results page typically shows two tables (unless no relaxase is detected):

Summary: inferred MOB class for the plasmid or plasmids detected in the input.
Results table: relaxase-level hits, including the assigned MOB class and additional hit details (Profile HMM, Coverage, Start/End coordinates on the profile, E-value, and i-Evalue).

The key point is that the biological meaning of the Summary depends on how your FASTA headers are structured.

Mode A — Screen an arbitrary set of proteins

Upload a standard multi-FASTA file containing any collection of protein sequences. MOBscan will detect relaxases and populate the Results table listing:

Sequence identifier
Assigned MOB class
Profile HMM producing the hit
Coverage
Alignment start and end (profile coordinates)
E-value and i-Evalue

A Summary is also produced. However, in this mode it should not be interpreted as a plasmid-level MOB classification, since the input proteins do not necessarily form a complete plasmid proteome.

Example FASTA (standard headers)

>Protein_1
ABCDEFGHIJK
>Protein_2
KJIHGFEDCBA
>Protein_3
AKBJCIDHEGF

This mode is useful for screening predicted proteins, partial datasets, or mixed protein collections.

Mode B — Classify a single plasmid proteome

If your input multi-FASTA contains the complete proteome of a single plasmid, the Summary becomes biologically meaningful and represents the plasmid MOB class, inferred from the relaxases detected in that proteome. MOBscan will:

Detect relaxases (Results table)
Infer the plasmid MOB class (Summary)

The FASTA format is identical to Mode A (standard headers); the difference is conceptual: all proteins are interpreted as belonging to the same plasmid.

Example FASTA (single plasmid proteome - standard headers)

>Protein_1
ABCDEFGHIJK
>Protein_2
KJIHGFEDCBA
>Protein_3
AKBJCIDHEGF

Mode C — Classify multiple plasmids in one submission

To classify multiple plasmids within a single job, encode plasmid membership in the FASTA headers using a vertical bar (|) separator.

Header convention:

>PlasmidID|ProteinID

Example FASTA (multiple plasmids - plasmid membership encoded in headers)

>Plasmid_1|Protein_1
ABCDEFGHIJK
>Plasmid_1|Protein_2
KJIHGFEDCBA
>Plasmid_2|Protein_1
AKBJCIDHEGF

In this mode, MOBscan groups sequences by PlasmidID and generates a Summary reporting the MOB class for each plasmid independently, in addition to the global Results table listing all relaxase hits.