TMBETADISC-MOTIF:
Discrimination of Outer Membrane Proteins using Motif (A*B) Composition.

Discriminating outer membrane proteins from other folding types of globular and membrane proteins is an important task both for dissecting outer membrane proteins (OMPs) from genomic sequences and for the successful prediction of their secondary and tertiary structures.

We observed that the motifs E*L, A*K and L*E occur frequently in globular proteins while S*S, N*S and R*D predominantly occur in OMPs. We have devised a statistical method based on frequently occurring motifs in globular and OMPs and obtained an accuracy of 96% and 82% for correctly identifying OMPs and excluding globular proteins, respectively.


TMBETADISC-MOTIF discriminates the beta-barrel membrane proteins using the motif, A*B (* denotes a gap) composition. To discriminate an outer membrane protein enter your sequence in a single letter code in the following box.


Sample sequence:
MAPKDNTWYTGAKLGWSQYHDTGLINNNGPTHENKLGAGAFGGYQVNPYVGFEMGYDWLG RMPYKGSVENGAYKAQGVQLTAKLGYPITDDLDIYTRLGGMVWRADTYSNVYGKNHDTGV SPVFAGGVEYAITPEIATRLEYQWTNNIGDAHTIGTRPDNGMLSLGVSYRFG

References:
M. Michael Gromiha and Makiko Suwa (2005) A Simple Statistical Method for Discriminating Outer Membrane Proteins with Better Accuracy. Bioinformatics 21, 961-968.

M. Michael Gromiha, S. Ahmad and M. Suwa (2005) Application of Residue Distribution Along the Sequence for Discriminating Outer Membrane Proteins. Comput. Biol. Chem. 29, 135-142.

M. Michael Gromiha, S. Ahmad and M. Suwa (2005) TMBETA-NET: Discrimination and Prediction of Membrane Spanning Beta-strands in Outer Membrane Proteins. Nucleic Acids Res. (in press).

Contributors for the Analysis and Prediction:
1. M. Michael Gromiha, Computational Biology Research Center, AIST.
2. Makiko Suwa, Computational Biology Research Center, AIST.