Background: Proteins may have none, single, double, or multiple domains, while a single domain may appear in multiple proteins. Their distribution patterns may have impacts on bacterial physi-ology and lifestyle. Objective: This study aims to understand how domains are distributed and duplicated in bacterial prote-omes, in order to better understand bacterial physiology and lifestyles. Methods: In this study, we used 16712 Hidden Markov Models to screen 944 bacterial reference prote-omes versus a threshold E-value<0.001. The number of non-redundant domains and duplication rates of redundant domains for each species were calculated. The unique domains, if any, were also identified for each species. In addition, the properties of no-domain proteins were investigated in terms of physico-chemical properties. Results: The increasing number of non-redundant domains for a bacterial proteome follows the trend of an asymptotic function. The domain duplication rate is positively correlated with proteome size and in-creases more rapidly. The high percentage of single-domain proteins is more associated with small pro-teome size. For each proteome, unique domains were also obtained. Moreover, no-domain proteins show differences with the other three groups for several physicochemical properties analysed in this study. Conclusion: The study confirmed that a low domain duplication rate and a high percentage of single-domain proteins are more likely to be associated with bacterial host-dependent or restricted niche-adapted lifestyle. In addition, the unique lifestyle and physiology were revealed based on the analysis of species-specific domains and core domain interactions or co-occurrences.

中文翻译：

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基于领域的细菌蛋白质组比较分析：独特性、相互作用和暗物质

背景：蛋白质可能没有、单一、双重或多个结构域，而单个结构域可能出现在多个蛋白质中。它们的分布模式可能对细菌生理和生活方式产生影响。目的：本研究旨在了解结构域在细菌蛋白质组中的分布和复制方式，以便更好地了解细菌生理学和生活方式。方法：在这项研究中，我们使用 16712 个隐马尔可夫模型筛选了 944 个细菌参考蛋白质组，阈值 E 值<0.001。计算了每个物种的非冗余域的数量和冗余域的重复率。还为每个物种确定了独特的域，如果有的话。此外，还根据物理化学性质研究了无结构域蛋白的性质。结果：细菌蛋白质组的非冗余结构域数量的增加遵循渐近函数的趋势。域重复率与蛋白质组大小呈正相关，并且增加得更快。单域蛋白质的高百分比与小蛋白质组大小更相关。对于每个蛋白质组，还获得了独特的结构域。此外，在本研究中分析的几种物理化学性质方面，无结构域蛋白质与其他三组蛋白质存在差异。结论：该研究证实，低域重复率和高百分比的单域蛋白更可能与细菌宿主依赖性或受限的生态位适应生活方式有关。此外，