Help and Information

This website is actively searching through 22 motif(s).
So far 7469 unique visitors have seen Motlook and have completed 2815 searches.

HELP:

MotLook takes your protein of interest and attempts to find protein seqence motifs within it. To use MotLook, simply paste your protein sequence in single amino acid (fasta) format into the box labeled "insert protein". Parameters can then be adjusted which include strigency or DISPHOS Phosphorylation Prediction (see below).

Strigency will adjust the scope of motif search. Search under "Exact" will look for motifs only as they are written in the literature. The "Literature" option will look for exact searches plus any execeptions as indicated by the authors of the paper who discussed the motif. "BLOSUM80-Strong", "BLOSUM80-Weak", "BLOSUM35-Strong" and "BLOSUM35-Weak" searches will look for the "Exact" motifs extended with BLOSUM80 or BLOSUM35 based amino acid similarity. Additionally, "Strong" or "Weak" indicates whether the BLOSUM matrix will use only strongly similar amino acids or strong and weak amino acids in the motif search.

ADDITIONAL INFORMATION:

BLOSUM80 Amino Acid Similarity (Info) includes:
       (Strong similar bold / Weakly similar in italics)

A {A,S}
C {C}
D {D,N,E}
E {E,D,Q,K}
F {F,Y}
G {G}
H {H,Y,N,Q}
I {I,L,M,V}
K {K,R,Q,E}
L {L,I,M,V}
M {M,I,L,V}
N {N,D,E,S}
P {P}
Q {Q,E,K,R,H}
R {R,K,Q}
S {S,A,T,N}
T {T,S}
V {V,I,L,M}
W {W,Y}
Y {Y,H,F}

BLOSUM35 Amino Acid Similarity (Info) includes:

A {A,S}
C {C}
D {D,E,N}
E {E,D,Q,K}
F {F,Y,L,I,W,V}
G {G,N,S}
H {H,M,N}
I {I,L,V,M,F}
K {K,R,E}
L {L,I,M,F,V}
M {M,L,H,I,W,V}
N {N,D,Q,G,H}
P {P}
Q {Q,R,E,N}
R {R,Q,K}
S {S,T,A,G}
T {T,S,V}
V {V,I,L,M,F,T}
W {W,Y,M,F}
Y {Y,F,W}

All motif searches use the following information:

Aliphatic Amino acids: {G,A,V,L,I}1
Hydrophobic Amino Acids: {A,V,F,P,M,I,L}2
Hydrophilic Amino Acids: {R,N,D,Q,E,H,K,S,T}3
Acidic Amino Acids: {D,E,N,Q}1
Basic Amino Acids: {H,K,R}1
Charged Amino Acids: {D,E,K,R}2
Aromatic Amino Acids: {F,Y,W}1
Polar Amino Acids: {S,T,Y,H,C,N,Q,W}2

Sources:
1)The Biology Project, The Chemistry of Amino Acids (Link), University of Arizona Department of Biochemistry (Link)
2)Brandon C., Tooze J., Introduction to Protein Structure, Second Edition, Garland Publishing, 1991/1999
3)Lodish, H. Et. al., Molecular Cell Biology, Fifth Edition, W.H. Freeman and Company, 2004

DISPHOS:

MotLook has been enhanced with phosphorylation prediction by concurrently running an inputted protein on the website DISPHOS 1.3. http://core.ist.temple.edu/pred/pred.html. Results of the search are returned and included in the results of Motlook.

Citation:
Iakoucheva LM, Radivojac P, Brown CJ, et al. The importance of intrinsic disorder for protein phosphorylation. Nucleic Acids Res. 2004;32(3):10371049. [PubMed]

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