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Publication for MicrobeDB
Differential NtcA Responsiveness to 2 Oxoglutarate Underlies the Diversity of C/N Balance Regulation in Prochlorococcus
[…] Selected cyanobacterial ntcA sequences were retrieved from CYORF (http://cyano.genome.jp/), Cyanobase (http://genome.microbedb.jp/cyanobase/), Integrated Microbial Genomes (https://img.jgi.doe.gov) and NCBI (http://www.ncbi.nlm.nih.gov/) databases. Protein BLAST analysis were performed using NCBI BLASTp tool (http:/ […]
Transcriptomic Responses in the Bloom Forming Cyanobacterium Microcystis Induced during Exposure to Zooplankton
[…] d clade-specific microbial marker genes. Differentially expressed genes were assigned functional categories based upon categories found in CyanoBase for the Microcystis NIES-843 genome (http://genome.microbedb.jp/cyanobase/GCA_000010625.1). Full differential expression results can be found in Table S1 to S6 in the supplemental material. Principal-component analysis (PCA) for functional category si […]
Comparison of aldehyde producing activities of cyanobacterial acyl (acyl carrier protein) reductases
[…] ructed using 16S ribosomal RNA . Multiple sequence alignment of 12 representative AARs was carried out using the Clustal X software .The habitats of 128 cyanobacterial species were examined using MicrobeDB (http://microbedb.jp/), CyanoBase (http://genome.microbedb.jp/cyanobase/) , and the Pasteur Culture collection of Cyanobacteria (PCC; http://cyanobacteria.web.pasteur.fr/). Sixty-nine and […]
The Evolution of Silicon Transport in Eukaryotes
[…] ely low similarity of the bacterial SIT-L sequences to SdSITa, the Synechococcus sp. KORDI-100 SIT-L was used as a query sequence for prokaryotic database searches, including Cyanobase (http://genome.microbedb.jp/cyanobase; last accessed October 12, 2016), Cyanorak (www.sb-roscoff.fr/cyanorak/; last accessed October 12, 2016), and the Tara Oceans metaG Environmental Sequence Datasets (0.22–8-μm fr […]
Calcium impacts carbon and nitrogen balance in the filamentous cyanobacterium Anabaena sp. PCC 7120
[…] , Finland). Significantly differentially expressed genes were identified using a false discovery rate (FDR: Benjamini–Hochberg) cutoff of 0.05. Gene descriptions were collected from Cyanobase (genome.microbedb.jp/cyanobase/) and KEGG (www.genome.jp/kegg/). […]
Investigation of a Quadruplex Forming Repeat Sequence Highly Enriched in Xanthomonas and Nostoc sp.
[…] hboring ORF of 0–50 bp, 50–100 bp and > 100 bp. Functions of annotated genes and their positions on the genome were collected from KEGG (http://www.kegg.jp/), NCBI as well as Cyanobase (http://genome.microbedb.jp/cyanobase) . Repeat associated genes were sorted into functional categories using the KEGG pathway mapper (http://www.genome.jp/kegg/mapper.html) . […]
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