Proteome-wide functional classification and identification of prokaryotic transmembrane proteins by transmembrane topology similarity comparison.
We propose a new method for classifying and identifying transmembrane (TM) protein functions in proteome-scale by applying a single-linkage clustering method based on TM topology similarity, which is calculated simply from comparing the lengths of loop regions. In this study, we focused on 87 prokaryotic TM proteomes consisting of 31 proteobacteria, 22 gram-positive bacteria, 19 other bacteria, and 15 archaea. Prior to performing the clustering, we first categorized individual TM protein sequences as "known," "putative" (similar to "known" sequences), or "unknown" by using the homology search and the sequence similarity comparison against SWISS-PROT to assess the current status of the functional annotation of the TM proteomes based on sequence similarity only. More than three-quarters, that is, 75.7% of the TM protein sequences are functionally "unknown," with only 3.8% and 20.5% of them being classified as "known" and "putative," respectively. Using our clustering approach based on TM topology similarity, we succeeded in increasing the rate of TM protein sequences functionally classified and identified from 24.3% to 60.9%. Obtained clusters correspond well to functional superfamilies or families, and the functional classification and identification are successfully achieved by this approach. For example, in an obtained cluster of TM proteins with six TM segments, 109 sequences out of 119 sequences annotated as "ATP-binding cassette transporter" are properly included and 122 "unknown" sequences are also contained.
Arai
Masafumi
M
Department of Electronic and Information System Engineering, Faculty of Science and Technology, Hirosaki University, Hirosaki 036-8561, Japan.
Okumura
Kosuke
K
Satake
Masanobu
M
Shimizu
Toshio
T
D000465:Algorithms; D019295:Computational Biology; D030541:Databases, Genetic; D008565:Membrane Proteins / Q000737:chemistry* / Q000145:classification*; D011387:Prokaryotic Cells / Q000737:chemistry*; D017434:Protein Structure, Tertiary; D020543:Proteome / Q000737:chemistry*; D017386:Sequence Homology, Amino Acid
D008565:Membrane Proteins; D020543:Proteome