Since MalF and MalG are structurally determined membrane proteins, it was possible to draw conclusions from the publicly available coordinate sets in the Protein Data Bank (PDB), for example, from chains F and G in “2R6G” from E. coli K12. We provide evidence that the extra 2 TMSs in MalF relative to MalG are TMSs 1 and 2. The results reported here strongly suggest Capmatinib supplier that the membrane constituents of ABC uptake transporters evolved through pathways starting with a GDC941 primordial 6 TMS ABC2 porter. Multiple and pairwise alignments as well as hydropathy plots were created and analyzed to elucidate the evolutionary appearance of this topologically diverse group
of ABC uptake porters. The two primary structural repeat elements have 5 or 6 TMSs which duplicated in many such proteins and quadruplicated in a few. Although some uncertainty exists regarding the precise topologies of some of these integral membrane proteins, we could document their internal duplications and propose the routes taken during their evolutionary histories. Results Demonstration that most ABC uptake transporters are homologous The aim of this section is to establish common origins for the integral membrane constituents of most ABC uptake systems. Initially,
the integral membrane constituents of one uptake transporter from each family was blasted using the BLAST search tool in TCDB (TC-BLAST). The resulting proteins were examined, and those that belonged to uptake systems with e-values of smaller than
1e-4 were retained I-BET-762 for further studies. An example of the BLAST output is shown in Additional file 1: Table S1 where the query sequence was MalF of E. coli (TC# 3.A.1.1.1). Using the Multiple Sequence Alignment Program with Displayed TMSs (MAP-TMS) from TCDB (http://www.tcdb.org), the query sequence and the output sequences were aligned, and their transmembrane regions were predicted. If more than 60 residues containing the corresponding transmembrane α-helical segments (TMSs) aligned between two proteins, and they gave an e-value of 10-7 or smaller, they were considered homologous. If the e-value was greater than 10-7, we compared both Glutamate dehydrogenase sequences using the GAP program. By our criteria, a comparison score of ≥ 10 standard deviations (S.D.), as defined by the GAP program, indicates that the two sequences are homologous (see Methods). For instance, the sequences YfeC (TC# 3.A.1.15.4) and FhuB (TC# 3.A.1.14.3) were compared using the GAP program, and the comparison score (quality subtracted from average quality divided by the program’s S.D. value) computed was 18 S.D., well-above the value of 10 S.D. needed to establish homology (Additional file 1: Figure S1).