This web page was produced as an assignment for Genetics 564, an undergraduate course at UW‐Madison.
What are protein sequence motifs?
Protein sequence motifs are amino acid sequence patterns that are signatures of protein families and can be used to predict protein functions. [1]
The MAOA protein sequence motifs
FASTA of human MAOA protein and its homologs of six model organisms were entered into MEME to identify 3 conserved motifs of length ranging from 30 to 80 amino acids. The three motifs detected are listed below.
Motif 1
Motif 1
Length
Expression Motif 2 |
: 80 amino acids
: [RM]K[KDR][KL]I[CD][EK][LI][YC][AW][KT][VK][LT][GA][SR]Q[EF]A[LY][HL][PF]V[HN][YI][EN][EV] [KT][NS][WE][CP][EH]E[QV][YS][SA][GL][GW][CF][YL][TW][AY][YV][FK][PQ][PC]G[IG][MT]T[QR] [YI][GF][RS]V[IT][RN][QG][PG][VQ][GE]R[IK][FY][FV][AG]G[TS][EG][TQ][AV][TS][EKQ][WR][SI] [GM]Y[ML][EL]G[AD] |
Length
Expression Motif 3 |
: 80 amino acids
: IPPTLTAKIHF[RK]PELP[ASP]ERNQLIQRLPMG[AS][IV]IKCMMYYKEAFWKKKDYCGCMIIEDE[ED]A PISITLDDTKPDGSLPAIMGF |
Length
Expression |
: 59 amino acids
: VEAGERAAREVLN[AG]LGKV[AT][EK]KDI[WK]VQEPESKDVPAVEITHTFWERNLPSV[SP]GLLK[IL] IGF |
Locations of Motif 1, 2 and 3 in protein homologs
Mouse, dog, cow, and cat all have MAOA protein sequence of the same length as human's (Isoform 1), hence it is not surprising that one site of Motif 1, one site of Motif 2 and two sites of Motif 3 were found at the exact same locations in these homologs. Chimpanzee and chicken have MAOA protein sequence of shorter length compared to human; when aligned, it can be observed that the N-terminal section of human MAOA protein sequence is missing in chimpanzee and chicken's homologs. This explains why the site of Motif 3 near the N-terminus of human homolog is missing in chimpanzee and chicken homologs. To study the functions of MAOA protein, mouse, dog, cow and cat might be a better choice of model organisms than chimpanzee and chicken, since the above three motifs are better conserved in the homologs of the former group.
References:
- Bork, P., & Koonin, E.V. (1996). Protein sequence motifs. Current Opinion in Structural Biology. 6(3):366-76.