Pfam annotation





choosefile  example




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 32.0updated 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.



Example file

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.