TUTORIAL


C-PAmP is a high level database for antimicrobial domain search in plant proteins and estimation of the antimicrobial potential of individual peptides.

Four modes available for searching antimicrobial peptide sequences

Search by Peptide Sequence

The user enters peptide sequence. The application searches in C-PAmP db the proteins that contain the entered peptide sequence and responds with the antimicrobial classifier's score.

The peptides are also given a CAMP antimicrobial score (CAMP), as well as existing experimental annotation (PhytAMP and CAMP).

An example of a peptide search given below

Index Species Protein Sequence Description C-PAmP Probability CAMP Probability Existing experimental annotation
1 Aesculus hippoca-
stanum
(Horse chestnut).
Q7M1F3 WSGNC
GNTAHCDK
QCQDWEKAS
RecName: Full=Defensin-like protein 1; AltName: Full=Cysteine-rich antimicrobial protein 1; AltName: Full=Defensin AMP1; Short=AhAMP1; 0.937 0.062 PhytAMP: PHYT00001
CAMP:link


If a peptide sequence is found in the PhytAMP, then the PhytAMP ID is displayed under the column 'Existing experimental annotation', for example PHYT00101. In addition, a link with the CAMP score is also provided.


Search by Protein Sequence

The user enters peptide sequence. The application searches in C-PAmP db the proteins that contain the entered protein sequence and responds with the description.

An example of a peptide search given below

Index Species Protein Sequence Description
1 Aesculus hippoca-
stanum
(Horse chestnut).
Q7M1F3 WSGNC
GNTAHCDK
QCQDWEKAS
RecName: Full=Defensin-like protein 1; AltName: Full=Cysteine-rich antimicrobial protein 1; AltName: Full=Defensin AMP1; Short=AhAMP1;


Search by Protein Accession Number (AC)

The user enters protein Accession Numbers (AC).
For each entered protein AC, there is a short protein label as follows

A0A314RecName:Full=30S ribosomal protein S12, chloroplastic;Species:Coffea arabica (Arabian coffee).

The Antimicrobial Scoring Graph button displays the antimicrobial protein domains according to the C-PAmP score. The graph shows a fixed threashold at score 0.5.
The antimicrobial profile of the protein is visualized on a chart where X-axis reports the aminoacid position in the protein and the Y-axis reports the anticrobial score at that position.

Colorscale of residue antimicrobial propensity.
MPTIKQLIRNARQPIRNVTKSPALRGCPQRRGTCTRVYTITPKKPNSALRK
FEITAYIPGIGHNLQEHSVVLVRGGRVKDLPGVRYHIVRGTLDAVGVKDRQ
KPK
0%1-20%21-40%41-60%61-80%81-100%

The Heatmap frame shows the protein sequence with a Colorscale of residue antimicrobial propensity.Each potential antimicrobial peptide contributes to increase the tension of the color in its position in the protein sequence.
High antimicrobial probability increases the color tension.

The system calculates the tension of the antimicrobial property in each amino acid position of a protein.
The heatmap value is the normalized weighted sum of all the overlapping antimicrobial peptides.

The retrieved peptides are displayed in a table. An example is given below.

Index Antimicrobial Peptide C-PAmP Probability
1PTIKQLIRNARQPIRNVTKSPALRGCPQRRGTCTRVYTIT
PKKPNSALRKVARVRLTSGFEITAYIPGIGHNLQ
0.5901

Search by Species

The user selects the plant species of interest and the system retrieves the proteins of the specified species from C-PAmP database.

An example of a protein found in the Arabian coffee(coffea arabica) which contains predicted antimicrobial peptides is displayed below. The protein link gives these peptide sequences.

Index Species Protein Description
1 Coffea arabica (Arabian coffee). A0A314 RecName: Full=30S ribosomal protein S12, chloroplastic;