Figure 1

The flowchart for constructing the secretome LaCOGs. The completely sequenced LAB genomes are used as input data. No plasmid sequences were used for the Inparanoid search. The squares with dash-line frames are intermediate products that are not user-queryable from the LAB-Secretome interface; the squares with full-line frames are the final information stored in LAB-Secretome database. The upper left frame shows the processes that produce new LACOGs; the upper right frame shows the processes that extend existing LaCOGs. The new LaCOGs are coded starting with "9", the extended existing LaCOGs retain the original names from Makarova et.al [43]. BlastP¹: the Blast results were processed by a revised criterion "uniform top 3" (see Material and Methods); BlastP²: the Blast results were processed by cut-off of 1e-3 and aligned sequence coverage of 60% for distant homolog identification. This work scheme can be used to update the LAB-Secretome database when new bacterial genomes are available.