DOI: 10.6084/m9.figshare.29878766
title: Supplementary Table S8: Results for All Rice-human Structure Pairs after Filtering (Foldseek-TM method)

description: Table data of rice-human structure pair hits in Foldseek (Foldseek-TM method) used in E, F, G, H, I, J in Supplementary Figure S4.The results of structural alignment using the Foldseek-TM method with rice structural prediction data as query, filtered based on the defined filtering conditions (more details, see Materials and Methods section), resulted in <b>4,343 / 16,068 pair hits</b> in the rice upregulated gene group and <b>5,121 / 15,367 pair hits</b> in the rice downregulated gene group.【Filtering Condition】<br>(1) The coverage of both rice and human structural alignments is greater than 50%.<br>(2) If a structure with a different UniProt accession number from the same rice gene aligns with a structure of the same human protein structure, the hit with the highest coverage from the alignment result for the rice structure is selected. The Local Distance Difference Test (lDDT) score is used if the hits are identical.<br>(3) Human protein structure information was matched to the current stable Ensembl gene ID and HUGO Gene Nomenclature Committee (HGNC) gene symbol using TogoID, an identifier (ID) conversion tool (accessed on 9 August 2025), and UniProt accessions as keys, and those that met this condition were selected.<br>Table S8-1: <b>foldseek_result_rice_up_tmalign_domain_panhomology_info_filtercondtion3_250811</b>: All structure pair data (4,343 pairs) after filtering for structure alignment using protein structure prediction data corresponding to rice upregulated genes as query. Corresponds to E, G, and I in Supplementary Figure S4.Table S8-2: <b>foldseek_result_rice_up_tmalign_domain_panhomology_info_filtercondtion3_filter1_250811</b>: Structure pairs in Table S8-1 that meet the following filtering conditions.<br>High-sequence similarity / High-structural similarity (HS-HS): global sequence alignment similarity &gt; the 75th percentile (Q3) and average lDDT ≥ the median (Q2).<br>Table S8-3: <b>foldseek_result_rice_up_tmalign_domain_panhomology_info_filtercondtion3_filter4_250811</b>: Structure pairs in Table 8-1 that meet the following filtering conditions.<br>Low-sequence similarity / High-structural similarity (LS-HS): global sequence alignment similarity ≤ Q3 and average lDDT ≥ Q2. Additionally, the rice genes identified in Table S8-2 were excluded.<br>Table S8-4: <b>foldseek_result_rice_down_tmalign_domain_panhomology_info_filtercondtion3_250811</b>: All structure pair data (5,121 pairs) after filtering for structure alignment using protein structure prediction data corresponding to rice downregulated genes as query. Corresponds to F, H, and J in Supplementary Figure S4.Table S8-5: <b>foldseek_result_rice_down_tmalign_domain_panhomology_info_filtercondtion3_filter1_250811</b>:<br>Structure pairs in Table S8-4 that meet the following filtering conditions.<br>High-sequence similarity / High-structural similarity (HS-HS): global sequence alignment similarity &gt; Q3 and average lDDT ≥ Q2.<br>Table S8-6: <b>foldseek_result_rice_down_tmalign_domain_panhomology_info_filtercondtion3_filter4_250811</b>: Structure pairs in Table 8-4 that meet the following filtering conditions.<br>Low-sequence similarity / High-structural similarity (LS-HS): global sequence alignment similarity ≤ Q3 and average lDDT ≥ Q2. Additionally, the rice genes identified in Table S8-5 were excluded.<br>