DOI: 10.6084/m9.figshare.19358117.v1
title: NOD1 LRR6 Copies - HMMER Results, AliView Visualizations, and Percent Amino Acid Identity

description: Using AliView, we translated the sequences into one position per amino acid format. We ran each translated sequence through HMMER program to identify the start and stop locations of each domain. HMMER provided the locations of each domain for every species and shows that each ungulate has 3-4 copies of LRR6. We were looking into LRR6 data specifically because of our hypothesis relating to the conservation of LRRs in NOD1 domain and their role in binding to iE-DAP. After locating the LRR6 domains, we ran each LRR6 sequence translated to one position per amino acid in through a Sequence Identity and Similarity program to determine the similarity of each LRR6 copy among species. We chose to focus on percent identity, which is the percent of amino acids identical in aligned sequences. We compiled all of our LRR6 sequences, ran each copy of LRR6 through the program to find percent identity across the species. Attached are the AliView visualizations and the results from the percent identity for each copy of LRR6 found in ungulates. In amino acid identity results, the green box denotes terrestrial ungulates and the blue box denotes aquatic ungulates. <br>LRR6 Copy 1The first copy of LRR6 is located from approximately amino acid position 728-749. As we expected, the percent identity was very high when all species are compared, which is consistent with our hypothesis that LRR regions would remain fairly conserved. The only outlier in this data set is the horse, which has a very low percent identity in comparison with all other ungulates. This is likely because of the insertion in their first LRR6 copy, which you can see in the AliView visualization. <br>LRR6 Copy 2The second LRR6 domain is located from approximately amino acid position 782-806. The domain is largely conserved as well, however there is a change from lysine to threonine in the fifth amino acid of the second copy of the LRR6 domain between terrestrial to aquatic ungulates. For this domain, we got high rates of amino acid percent identity within groups of terrestrial and aquatic, but when comparing the results between these groups the percent identity is much lower. <br>LRR6 Copy 3The third LRR6 domain is located between approximately amino acid position 817-834. The domain is also largely conserved when looking at AliView. Dolphin NOD1 lacks a third LRR6 domain. This domain also showed a high percent amino acid identity between all ungulates. <br>LRR Copy 4The fourth LRR6 domain is located between approximately amino acid position 838-862. The wild yak and cow both do not have a LRR6 domain, which you can visualize in AliView. The horse sequence also was shown in HMMER to not have a fourth LRR6 domain, but because our sequences are aligned in AliView and the horse had the insertion early on in the first LRR6 domain, you are unable to see that loss in the screenshot. This LRR6 domain also has high rates of similarity within aquatic and terrestrial ungulates, but when these two groups are compared, the percent amino acid identity is much lower. <br>