BATMAS30: Amino acid substitution matrix for alignment of bacterial transporters
نویسندگان
چکیده
منابع مشابه
BATMAS30: amino acid substitution matrix for alignment of bacterial transporters.
Aligned amino acid sequences of three functionally independent samples of transmembrane (TM) transport proteins have been analyzed. The concept of TM-kernel is proposed as the most probable transmembrane region of a sequence. The average amino acid composition of TM-kernels differs from the published amino acid composition of transmembrane segments. TM-kernels contain more alanines, glycines, a...
متن کاملAn Amino Acid Substitution Matrix for Protein Conformation Identification
Amino acid substitution matrices play an essential role in protein sequence alignment, a fundamental task in bioinformatics. Most widely used matrices, such as PAM matrices derived from homologous sequences and BLOSUM matrices derived from aligned segments of PROSITE, did not integrate conformation information in their construction. There are a few structure-based matrices, which are derived fr...
متن کاملCationic Amino Acid Transporters
We have identified the third member of a family of cationic amino acid transporters in lipopolysaccharidestimulated murine macrophages. The deduced amino acid sequence of this transporter is the same as MCAT-2 (mouse cationic amino acid transporter-Z), the low affinity transporter expressed in hepatocytes, except for a stretch of 41 amino acids that connects the eighth and ninth membrane-spanni...
متن کاملHeteromeric Amino Acid Transporters
• The heavy subunits (molecular mass of ~90 and ~80 kDa for rBAT and 4F2hc, respectively) are type II membrane N-glycoproteins with a single transmembrane domain, an intracellular NH2 terminus, and an extracellular COOH terminus significantly homologous to insect and bacterial glucosidases (FIGURE 1). Recently, X-ray diffraction of the extracellular domain of human 4F2hc revealed a three-dimens...
متن کاملAmino Acid Substitution Scores
GNPKVKAH Here we discuss standard ways of assigning a score to each amino acid pair, i.e., to each possible column of a gap-free pairwise protein alignment. Examples of such scoring matrices include the PAM30, PAM70, BLOSUM80, BLOSUM62 and BLOSUM45 matrices that are available on NCBI’s blastp server. Such scores are appropriate for comparing two sequences about which we have no other informatio...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Proteins: Structure, Function, and Genetics
سال: 2003
ISSN: 0887-3585,1097-0134
DOI: 10.1002/prot.10308