COMPREHENSIVE COMPUTER ANALYSIS OF E COLI GENES

大肠杆菌染色体中已知序列的比例 最近越过60大关，完整的序列预计在 几年大肠杆菌基因组DNA的未注释区域 EcoSeq6数据库中的1，278个“基因间”序列， 组合长度为359，279个碱基对）使用计算机进行分析。 辅助方法，目的是鉴定推定的未知基因。的 所提出的寻找新基因的策略包括两个关键要素：i） 使用GeneMark预测表达的开放阅读框（ORF） 基于马尔可夫链模型的编码区和非编码区的方法 大肠杆菌DNA，以及ii）搜索蛋白质序列相似性 使用基于BLAST算法的程序和基序的程序 识别.共预测了358个推定表达的ORF， 基因标记使用BLASTX和TBLASTX程序，结果表明，206 ORFs位于E.大肠杆菌染色体 与其他蛋白质序列非常相似。识别184 GeneMark和BLAST均支持ORF作为可能基因， 包括51.4%的GeneMark“命中”和89.1%的BLAST“命中”。 72个推定的新基因或20.1%的GeneMark预测属于 古老的保守蛋白家族，包括真细菌和 真核生物成员这一数值接近于 真细菌蛋白质中高度保守的序列，表明 大多数推定表达的ORF被预测为 基因标记，但没有显着的BLAST命中，但很可能是 是真实的基因。通过BLAST鉴定的大多数推定基因 自EcoSeq6数据库发布以来， 至今仍有约70个基因未被发现。在这些新 鉴定是编码具有多种预测的蛋白质的基因， 功能包括酶，激酶，几种其他代谢酶， 酶、ATP酶、rRNA甲基转移酶、膜蛋白和 不同类型的调节蛋白。一个新的细菌家族， 噬菌体转糖基酶和一个新的rRNA家族 描述了甲基转移酶。

The fraction of known sequences in the Escherichia coli chromosome has recently crossed the 60 mark and the complete sequence is expected within a few years. The unannotated regions of the Escherichia coli genome DNA sequence from the EcoSeq6 database (1,278 "intergenic" sequences of the combined length of 359,279 basepairs) were analyzed using computer- assisted methods with the aim of identifying putative unknown genes. The proposed strategy for finding new genes includes two key elements: i) prediction of expressed open reading frames (ORFs) using the GeneMark method based on Markov chain models for coding and non-coding regions of Escherichia coli DNA, and ii) search for protein sequence similarities using programs based on the BLAST algorithm and programs for motif identification. A total of 358 putative expressed ORFs were predicted by GeneMark. Using the BLASTX and TBLASTN programs, it was shown that 206 ORFs located in the unannotated regions of the E. coli chromosome are significantly similar to other protein sequences. Identification of 184 ORFs as probable genes was supported by both GeneMark and BLAST, comprising 51.4% of the GeneMark "hits" and 89.1% of the BLAST "hits". 72 putative new genes or 20.1% of the GeneMark predictions belong to ancient conserved protein families including both eubacterial and eukaryotic members. This value is close to the overall proportion of highly conserved sequences among eubacterial proteins, indicating that the majority of the putative expressed ORFs that are predicted by GeneMark, but have no significant BLAST hits, nevertheless are likely to be real genes. The majority of the putative genes identified by BLAST search have been described since the release of the EcoSeq6 database, but about 70 genes have not been detected so far. Among these new identifications are genes encoding proteins with a variety of predicted functions including dehydrogenases, kinases, several other metabolic enzymes, ATPases, rRNA methyltransferases, membrane proteins and different types of regulatory proteins. A new family of bacterial and bacteriophage transglycosylase and a new family of rRNA methyltransferases were described.