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Pfam database introduction
Proteins are generally composed of one or more functional regions, commonly termed domains. Different combinations of domains give rise to the diverse range of proteins found in nature. The identification of domains that occur within proteins can therefore provide insights into their function. Pfam (Protein families database of alignments and hidden Markov models), a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs).Pfam-A is a high quality and HMM based hand curated Pfam entry which is built using a small number of representative sequences.
Pfam_Scan (https://www.ebi.ac.uk/Tools/pfa/pfamscan/) was used for sequences mapping and annotation based on database (version 32.0，updated on September 2018), with default parameters.
Input files
fasta file of amino acid query sequences.
Results
1. Mapping and annotation results
2. Statistics of alignment
showing the distribution of mapped and unmapped results.
1. Mapping and annotation results
Seq id : ID of query sequences
Alignment start : the start position of domain on query sequence in the alignment results
Alignment end : the end position of domain on query sequence in the alignment results
Envelope start : the start position of domain on query sequence preticted by HMM module
Envelope end : the end position of domain on query sequence preticted by HMM module
Hmm acc: ID of mapped module in database
Hmm name : name of mapped module in database
Type : classificaion, family or domain of mapped module in database
Hmm start : the start position of subject sequences covered by alignment
Hmm end : the end position of subject sequences covered by alignment
Hmm length：the length of sequences covered by alignment
bit score：Score of alignment, the higher the better
E value ：Expcet values of alignment, the lower the better
Significance : number of mapping domains
Clan : A clan is a collection of Pfam entries which are related by similarity of sequence, structure or profile-HMM
PfamA definition：description of mapped module in PfamA database
2. Statistics of alignment
showing the distribution of mapping and unmapping results.
