Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, No. 185, Donghu Road, Wuchang, Wuhan 430071, China.
School of Life Science and Technology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China.
Database (Oxford). 2022 Mar 28;2022. doi: 10.1093/database/baac010.
We previously released the Anti-CRISPRdb database hosting anti-CRISPR proteins (Acrs) and associated information. Since then, the number of known Acr families, types, structures and inhibitory activities has accumulated over time, and Acr neighbors can be used as a candidate pool for screening Acrs in further studies. Therefore, we here updated the database to include the new available information. Our newly updated database shows several improvements: (i) it comprises more entries and families because it includes both Acrs reported in the most recent literatures and Acrs obtained via performing homologous alignment; (ii) the prediction of Acr neighbors is integrated into Anti-CRISPRdb v2.2, and users can identify novel Acrs from these candidates; and (iii) this version includes experimental information on the inhibitory strength and stage for Acr-Cas/Acr-CRISPR pairs, motivating the development of tools for predicting specific inhibitory abilities. Additionally, a parameter, the rank of codon usage bias (CUBRank), was proposed and provided in the new version, which showed a positive relationship with predicted result from AcRanker; hence, it can be used as an indicator for proteins to be Acrs. CUBRank can be used to estimate the possibility of genes occurring within genome island-a hotspot hosting potential genes encoding Acrs. Based on CUBRank and Anti-CRISPRdb, we also gave the first glimpse for the emergence of Acr genes (acrs).
我们之前发布了 Anti-CRISPRdb 数据库，其中包含抗 CRISPR 蛋白（Acr）及其相关信息。自那时以来，已知的 Acr 家族、类型、结构和抑制活性数量随着时间的推移而不断增加，并且 Acr 邻居可用作进一步研究中筛选 Acrs 的候选池。因此，我们在此更新了数据库以包含新的可用信息。我们新更新的数据库显示了几个改进：（i）它包含更多的条目和家族，因为它包括最近文献中报道的 Acrs 和通过同源比对获得的 Acrs；（ii）Acr 邻居的预测已集成到 Anti-CRISPRdb v2.2 中，用户可以从这些候选者中识别新的 Acrs；（iii）此版本包括 Acr-Cas/Acr-CRISPR 对抑制强度和阶段的实验信息，这激发了用于预测特定抑制能力的工具的开发。此外，新版本中提出并提供了一个参数，即密码子使用偏性（CUBRank）的等级，它与 AcRanker 的预测结果呈正相关；因此，它可以用作 Acrs 蛋白的指标。CUBRank 可用于估计基因在基因组岛（包含潜在编码 Acrs 的基因的热点）中出现的可能性。基于 CUBRank 和 Anti-CRISPRdb，我们还首次观察到了 Acr 基因（acrs）的出现。
