In Neurospora and other fungi, the protein frequency (FRQ) is an integral part and a negative element in the fungal circadian oscillator. In Drosophila and many other higher organisms, the protein period (PER) is an integral part and a negative element of their circadian oscillator. Employing bioinformatic techniques, such as BLAST, CLUSTAL, and MEME (Multiple Em for Motif Elicitation), 11 regions (sequences) of potential similarity were found between the fungal FRQ and the Drosophila PER. Many of these FRQ regions are conserved in many fungal FRQ(s). Many of these PER regions are conserved in many insects. In addition, these regions are also of biological significance since mutations in these regions lead to changes in the circadian clock of Neurospora and Drosophila. Many of these regions of similarity between FRQ and PER are also conserved between the Drosophila PER and the mouse PER (mPER2). This suggests conserved and important regions for all 3 proteins and a common ancestor, possibly in those amoeba, such as Capsaspora, that sits at the base of the phylogenetic tree where fungi and animals diverged. Two additional examples of a possible common ancestor between Neurospora and Drosophila were found. One, the white collar (WC-1) protein of Neurospora and the Drosophila PER, shows significant similarity in its Per/Arnt/Sim (PAS) motifs to the PAS motif of an ARNT-like protein found in the amoeba, Capsaspora. Two, both of the positive elements in each system (i.e., WC-1 in Neurospora and cycle [CYC] in Drosophila), show significant similarity to this Capsaspora ARNT protein. A discussion of these findings centers on the long-time debate about the origins of the many different clock systems (i.e., independent evolution or common ancestor as well as to the question of how new genes are formed).

在Neurospora和其他真菌中，蛋白质频率（FRQ）是真菌昼夜节律振荡器中不可或缺的一部分，是一种负向元素。在果蝇和许多其他高等生物中，蛋白质周期（PER）是其昼夜节律振荡器不可或缺的一部分，也是其负面因素。使用BLAST，CLUSTAL和MEME（母题激发的多重Em）等生物信息技术，在真菌FRQ和果蝇PER之间发现了11个潜在相似性区域（序列）。这些FRQ区域中的许多在许多真菌FRQ中都是保守的。这些PER区域中有许多在许多昆虫中都是保守的。此外，这些区域也具有生物学意义，因为这些区域的突变会导致生物钟的昼夜变化。神经孢子和果蝇。果蝇PER和小鼠PER（mPER2）之间在FRQ和PER之间的许多相似性区域中也有许多是保守的。这表明了所有3种蛋白质的保守重要区域和一个共同祖先，可能在那些变形虫（如Capsaspora）中，位于植物和真菌分化的系统发生树的底部。发现了神经孢菌和果蝇之间可能的共同祖先的另外两个例子。一是神经孢子虫和果蝇的白领（WC-1）蛋白PER的Per / Arnt / Sim（PAS）主题与在变形虫Capsaspora中发现的ARNT样蛋白的PAS主题非常相似。每个系统中的两个阳性元件（即Neurospora中的WC-1和果蝇中的周期[CYC] ）中的两个都与Capsaspora ARNT蛋白具有显着相似性。对这些发现的讨论集中在关于许多不同时钟系统的起源（即独立进化或共同祖先以及如何形成新基因的问题）的长期辩论上。