6. Create MEROPS profile

Source: vignettes/06_Create_merops_profile.Rmd

The MEROPS database classifies peptidases (proteases) and their inhibitors using a hierarchical, structure-based system. Peptidases are grouped into Families based on significant sequence similarities, and related families are further grouped into Clans, indicating evolutionary relationships. This classification helps researchers understand enzyme function, structure, and evolution. The database provides sequence identifiers, structural data (if available), and literature references for deeper exploration.

Rbims also includes functions to read and explore MEROPS annotations.

To learn how to to this;

First, load the rbims package.

read_merops(): Parse MEROPS Outputs

The read_merops function is designed to parse and format raw output files from the MEROPS blast annotation tool.

Input Requirements

  • File Path: Provide the path to the directory containing your MEROPS files.

  • File Extension: The function specifically looks for files ending in *.txt.

Data Structure

The processed input contains 6 key columns:

  • qseqid: Query Sequence ID.

  • sseqid: Subject Sequence ID.

  • stitle: Subject Title.

  • pident: Percentage of identical matches.

  • evalue: Expect value.

  • bitscore: Bit score.

If you want to follow this example, you can download the raw data here.

To obtain a wide output, the argument profile = T.

merops_profile_T <- read_merops(merops_path = "../test/results/04.merops", 
                                profile = T, 
                                write = F )
head(merops_profile_T)
Table 2. MEROPS Profile Overview ( profile = T )
MEROPS_family domain_name 5mSIPHEX1_0 5mSIPHEX1_1 5mSIPHEX1_10 5mSIPHEX1_11 5mSIPHEX1_13 5mSIPHEX1_15 5mSIPHEX1_18 5mSIPHEX1_19 5mSIPHEX1_2 5mSIPHEX1_25 5mSIPHEX1_26 5mSIPHEX1_32 5mSIPHEX1_33 5mSIPHEX1_37 5mSIPHEX1_8 5mSIPHEX1_9 5mSIPHEX2_10 5mSIPHEX2_14 5mSIPHEX2_16 5mSIPHEX2_18 5mSIPHEX2_25 5mSIPHEX2_3 5mSIPHEX2_5 5mSIPHEX2_7 700mSIPHEX1_0 700mSIPHEX1_1 700mSIPHEX1_12 700mSIPHEX1_15 700mSIPHEX1_17 700mSIPHEX1_18 700mSIPHEX1_2 700mSIPHEX1_20 700mSIPHEX1_3 700mSIPHEX1_8 700mSIPHEX2_13 700mSIPHEX2_14 700mSIPHEX2_16 700mSIPHEX2_21 700mSIPHEX2_22 700mSIPHEX2_23 700mSIPHEX2_24 700mSIPHEX2_9
MER0000510 ClpA ATP-ase component of endopeptidase Clp | X20.001 1 1 0 0 1 0 0 0 0 0 0 0 0 1 1 0 1 0 0 0 1 1 0 1 1 1 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1
MER0011344 family C26 unassigned peptidases | C26.UPW 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0
MER0015597 amidophosphoribosyltransferase precursor | C44.001 1 1 0 0 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
MER0020519 TldD peptidase | M103.001 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
MER0024566 amidophosphoribosyltransferase precursor | C44.001 1 1 0 0 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
MER0024582 methionyl aminopeptidase 1 | M24.001 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
MER0025778 GMP synthase | C26.957 1 1 0 0 1 0 0 0 0 0 0 0 0 1 1 0 1 0 0 0 1 1 0 1 1 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0
MER0026061 peptidase Clp | S14.001 1 1 0 0 1 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 1 0 1 0 1 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1
MER0026064 Lon-A peptidase | S16.001 1 0 0 0 1 0 0 0 0 0 0 0 0 1 1 0 1 0 0 0 1 1 0 1 0 1 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1
MER0027987 peptidase Clp | S14.001 1 1 0 0 1 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 1 0 1 0 1 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1

Or print a long table profile = F.

merops_profile_F <-read_merops(merops_path = "../test/results/04.merops", 
                               profile = F, 
                               write = F)
head(merops_profile_F)
Table 2. MEROPS Profile Overview (profile = F)
Bin_name MEROPS_family domain_name Abundance
5mSIPHEX1_0 MER0000510 ClpA ATP-ase component of endopeptidase Clp | X20.001 1
5mSIPHEX1_0 MER0011344 family C26 unassigned peptidases | C26.UPW 1
5mSIPHEX1_0 MER0015597 amidophosphoribosyltransferase precursor | C44.001 1
5mSIPHEX1_0 MER0020519 TldD peptidase | M103.001 1
5mSIPHEX1_0 MER0024566 amidophosphoribosyltransferase precursor | C44.001 1
5mSIPHEX1_0 MER0024582 methionyl aminopeptidase 1 | M24.001 1
5mSIPHEX1_0 MER0025778 GMP synthase | C26.957 1
5mSIPHEX1_0 MER0026061 peptidase Clp | S14.001 1
5mSIPHEX1_0 MER0026064 Lon-A peptidase | S16.001 1
5mSIPHEX1_0 MER0027987 peptidase Clp | S14.001 1
5mSIPHEX1_0 MER0029893 HslV component of HslUV peptidase | T01.006 1
5mSIPHEX1_0 MER0036043 glutamate synthase | C44.003 1
5mSIPHEX1_0 MER0043258 urease | M38.982 1
5mSIPHEX1_0 MER0047854 family M41 unassigned peptidases | M41.UPW 1
5mSIPHEX1_0 MER0048082 methionyl aminopeptidase 1 | M24.001 1

You can export this profile with:

write.table(merops_profile_T, "merops.tsv", quote = F, sep = "\t", row.names = F, col.names = T)

Or setting write write = T in the function read_merops()