Comprehensive Functional Identification of Transmembrane Proteins Using the BTP Method
نویسندگان
چکیده
It has been revealed that TM protein functions correspond well to the TM topologies [the number of TM segments (tms), the loop length and the N-terminus location] [4, 5] and long loop regions contain functional domains. Recently, our group proposed a novel approach for classifying and identifying the functional classification and identification of TM protein functions based on TM topology information (the binary TM topology pattern (BTP) method) [4], where each loop length is expressed as ‘1’ for a long loop or ‘0’ for a short loop, and BTP is described as a string of binary loop length. By applying the BTP method to TM protein sequences encoded in 12 eukaryotic and 87 prokaryotic genomes, in this study, we have identified and classified comprehensively functions of TM proteins of these genomes.
منابع مشابه
Identification of transmembrane protein functions by binary topology patterns.
We propose a novel method for identifying and classifying the functions of transmembrane (TM) proteins based on their TM topology [the number of TM segments (tms), the loop length and the N-terminus location]. In this method, the TM topology is expressed as a string of '0' and '1', and this is designated the binary topology pattern (BTP). We focused on TM proteins with up to 12 tms, with the ex...
متن کاملDeciphering the functional role of hypothetical proteins from Chloroflexus aurantiacs J-10-f1 using bioinformatics approach
Chloroflexus aurantiacus J-10-f1 is an anoxygenic, photosynthetic, facultative autotrophic gram negative bacterium found from hot spring at a temperature range of 50-60°C. It can sustain itself in dark only if oxygen is available thereby exhibiting a dark orange color, however display a dark green color when grown in sunlight. Genome of the organism contains total of 3853 proteins out ...
متن کاملComprehensive Functional Identification of Prokaryotic Transmembrane Proteins by Binary Topology Pattern
متن کامل
Genome-Wide Functional Classification/Identification of Prokaryotic Transmembrane Proteins Based on Transmembrane Topology Similarity
Functions of transmembrane (TM) proteins holding 20-30% [1] in individual proteomes are difficult to be inferred comprehensively based on only sequence similarity, which is partly because TM protein sequences of known function are lacking. Recent studies, however, revealed that TM protein functions are closely correlated to their TM topologies, i.e., the number of TM segments (TMSs), positions ...
متن کاملComprehensive Functional Classification/Identification of Prokaryotic Transmembrane Proteins by Sequence and Topology Similarities
About one fourth of genes in genomes has been known to encode transmembrane (TM) proteins (TMPs) [2, 6, 8]. Although TMPs have important functions playing an essential role in life, detailed and comprehensive analysis of their functions haven’t been carried out yet. In this study, we tried to develop a novel method to classify and identify TMP functions with use of TM topology similarity in add...
متن کامل