Table 1.
A comparison of OMPdb to other databases that include β-barrel outer membrane proteins, in terms of total entries, method of data retrieval, existence of literature references, annotation of important sequence features (such as the signal peptide and the TM segments), interconnection to other public databases related to β-barrel proteins and availability of prediction/search tools
| Database features | OMPdb (current work) | PFAM (MBB clan) (41) | TCDB (30) | PDB_TM (nr set) (31) | TOPDB (32) | ePSORTdb (33) | TMBETA GENOME (34) | OPM (35) | MPdb (37) | PRNDS (38) | TMPDB (39) | HHompDB (13) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Total entries | 69 354 | 38 595 | 348 | 49 | 45 | 480 | 36 095 | 73 | 148 | 3182 | 17 | 54 184 |
| Total families | 85 | 36 | 57 | − | − | − | − | 26 | 25 | − | − | − |
| Data retrieval | Semi- automated | Semi- automated | Manual | Semi- automated | Semi- automated | Manual | Automated | Semi- automated | Manual | Automated | Manual | Automated |
| Literature references | + | + | + | − | + | + | − | − | + | − | + | − |
| Signal peptide/ TM segments annotation | +/+ | −/− | −/− | −/+ | +/+ | −/− | −/− | −/+ | −/− | −/− | +/+ | −/− |
| Number of databases cross-referenced | 13 | 5 | 1 | 1 | 2 | 2 | − | 3 | 2 | 2 | 3 | − |
| Prediction/search tools | BLAST/ HMMER/ PRED-TMBB/ Text search | Text search/ HMMER | Text search/ BLAST | Text search | Text search | Psortb/ BLAST | Search by organism | Text search | Text search | Text search/ BSS/BBF | Text search | HHsearch |