3PFDB+ - Database of Best Representative Profiles of Protein Families : Database Entry - PF00540

Details:

PFam ID : PF00540

PFam Domain Description : gag gene protein p17 (matrix protein)

Number of Sequence in 50% Dataset : 14

Number of Sequence in Full Dataset : 5120

Average sequence length: 124.8

Pairwise Identity of Sequence in 50% Dataset : 31.3

FASSM Based Coverage Results:

Pfam ID	Best Profile	Coverage of Best Profile
PF00540	Q00CS5_9HIV1_1_22	53.8

HMMER Based Coverage Results:

Pfam ID	Best Profile	Coverage of Best Profile
PF00540	Q99FI2_SIVCZ_2_131	99.7

Sequence based PCA Plot of the family - PF00540 :

BRP of Green color is by FASSM and of Red color is by HMMER

PSIMOT-Motifs Extracted using PSIMOT:
There are 2 motifs

Motif1 Start=10 Length=8
Motif2 Start=1 Length=8

Download PSSM/HMM Models/Alignment:

Prof. R. Sowdhamini (Contact : mini@ncbs.res.in)
Agnel P. Joseph, Prashant N. Shingate, and Atul K. Upadhyay