Sentence examples for microbial protein sequences from inspiring English sources
We performed the analyses on microbial protein sequences from 63 bacterial and archaeal genomes [see Additional file 5].
In our experiments, we used the following datasets: (i) a collection of 64 000 experimental spectra obtained from Synechococcus sp. PCC 7002; (ii) a database containing 2.65 million microbial protein sequences downloaded from NCBI GenBank; and (iii) a spectral library containing a set of 1752 S.Oneidensis MR-1 spectra.
Vaxign predicts possible vaccine targets based on various vaccine design criteria using microbial genomic and protein sequences as input data.
Microbial and metagenomic protein sequences were retrieved from IMG 3.4 and IMG/M 3.3 [ 39, 40].
A neighbor-joining phylogenetic tree was generated to establish the phylogenetic relationship of GsSGT with reported microbial and plant SGT protein sequences through MEGA 5.5 software [ 39].
The protein sequences of microbial genomes were downloaded from the Microbial Genome Database (archive no. mbgd_2011-01).
An integrated database including the human proteins and protein sequences for microbial species causing∼98% of all diagnosed UTIs was used for analysis of LC-MS data.
Without a closely related protein sequence database, however, one cannot survey the novel microbial protein profile comprehensively, and full-length sequence information of these proteins for further characterization is required, especially for enzymes present as gene families.
NarJ subfamily protein sequences present in microbial genomes were identified using tBLASTn [ 37] searches, with one of the following Escherichia coli NarJ subfamily protein query sequences: NarJ (BAL38294), NarW (AAC74548), TorD (AAC74083), DmsD (AAC74663), and YcdY (AAC74119).
The protein database included NCBI's Reference Sequence (release 42) and predicted protein sequences from recently sequenced microbial eukaryotes (JGI genome portal and Ghent University's online genome annotation server BOGAS).
Either a human UniProtKB database (Release 2013_6; 88 295 human sequences) or a database consisting of the aforementioned human proteins and all protein sequences derived from 21 microbial genomes (Supporting Information Table S-1) were used.
