Secondary metabolite biosynthetic gene clusters (BGCs) can often be identified within DNA sequences by various sequence similarity tools, but determining the exact functions of genes in the pathway and predicting their chemical products can often only be done by careful, manual comparative analysis. ...
Comparisons to the Minimum Information about a Biosynthetic Gene cluster (MIBiG) database of characterized BGCs were also performed by passing the –mibig parameter to BiG-SCAPE. KEGG functional annotations for genes across the entire genomes were obtained using METABOLIC [24]. Metatranscriptomic ...
23). By comparing the Stachelhaus codes of each A domain in the cmx gene cluster to a manually constructed database of codes with known substrates, the following peptide sequence was predicted for 2: Thr1-Hpg2-Thr3-Gly4-Leu5-Pro6-Leu7-Gly8-Tyr9-Asn10. The first and last modules ...
Subsequently, the antiSMASH job IDs were utilized to explore and classify the BGCs using the biosynthetic gene cluster family's database, BiG-FAM 1.0.068, providing preliminary insights. To refine the analysis, BiG-SCAPE 1.0.068 was employed with a cutoff value of 0.65. The resulting gene ...
these serve as allelochemicals, the importance of which is reflected in the presence of a dedicated momilactone biosynthetic gene cluster in the rice genome... H Kato-Noguchi,RJ Peters - 《Journal of Chemical Ecology》 被引量: 82发表: 2013年 The Role of Momilactones in Rice Allelopathy these...
To identify the mys gene cluster encoding MAA biosynthesis in the Subsection V cyanobacterial genomes, PCC9339DRAFT_04157 (encoding 3DHQS) of the previously identified MAA gene cluster in Fischerella sp. PCC 9339 [37] was used to performed a BLASTp search in the JGI/IMG database. Any positiv...
Within the Natural Products Atlas, information that was cross-linked to MIBiG database (the Minimum Information about a Biosynthetic Gene cluster) was retrieved for all archaeal SMs. This step was performed to determine the BGCs which were characterized for each known archaeal SM, that were previou...
Benzoxazinoids are a class of protective and allelopathic plant secondary metabolites that have been identified in multiple grass species and are encoded by the Bx biosynthetic gene cluster(BGC)in maize.Data mining of 41 high-quality grass genomes identified complete Bx clusters(containing genes Bx1...
(A) Genetic map of the vin gene cluster. Each arrow represents the direction of transcription of ORF. (B) The modular architecture of polyketide synthases for vicenistatin aglycon. Table 1. Summary of the vin Genes and Comparison with Database ProteinAmino AcidsProposed FunctionSequence Similarity...
The bio- synthetic gene cluster families (BiG-FAM) database25 for gene clus- ter family (GCF) explorations suggests that 58% of the XP GCFs are exclusive (Supplementary Table 3). Therefore, XP could be a distinct source for experimental natural product discovery. Conserved XP BGCs. In the ...