DOI: 10.5281/zenodo.14305029
title: Human Gut Microbial Protein Structure Database (GMPS) part1

description: The human gut microbiome contains numerous proteins whose functions remain elusive yet are pivotal for host health. Sequence-based methods often falter when attempting to infer functions within this microbial proteome due to evolutionary divergence. To address this challenge, we develop the Human Gut Microbial Protein Structure Database, which incorporates ~2.7 million predicted protein structures. Our findings reveal that structural analogy enhances the annotation of phage proteins. We detail the structural diversification of phage endolysins and confirm their potential in eliminating gut pathobionts. Furthermore, our structure-guided approach is effective in the identification of microbial-host isozymes. By employing structural alignments, we identify previously unrecognized bacterial enzymes involved in melatonin biosynthesis. Finally, we present an alignment-free method, Dense Enzyme Retrieval, based on structure-encoded protein language models for ultrafast and sensitive detection of remote homologs. Our research underscores the value of computational structural genomics in elucidating the functional landscape of the human gut microbiome.
description: Because of the large size of the GMPS database, it has been deposited in three separate Zenodo repositories (https://doi.org/10.5281/zenodo.14305030, https://doi.org/10.5281/zenodo.17461341; https://doi.org/10.5281/zenodo.17461360). For convenient access to structural proteomes of specific microbes, the files for the 968 bacterial genomes were divided and packaged by groups of four species per archive. Appendix figures supporting the results reported in this paper is deposited at Zenodo (https://doi.org/10.5281/zenodo.17456214).

 

 

File: GMPS_genomes_metadata.zip

Description: the metadata information of 968 human gut bacterial genomes and 1255 phage/prophage genomes, the proteins of which have been used to build the GMPS.

File: bacteria_final_annotation.zip

Description: a complete metadata file (including functional information derived from three sequence-based annotation tools (DRAM[v1.3], microbeannotator[v2.0.5], eggnog-mapper[v2.1.9]) for all the GMPS bacterial structures.

File: bacteria_N.tar.gz_Species.txt

Description: The bacterial section of GMPS was separated and packed into 8 parts. This file includes the information about the species each compressed file included.

File: bacteria_N.tar.gz

Description: Protein structure files, protein sequence files, annotation files of protein sequences (including functional information derived from three sequence-based annotation tools (DRAM[v1.3], microbeannotator[v2.0.5], eggnog-mapper[v2.1.9]), and genome files of the 968 human gut bacteria. The files are collected and separated by species. The total size of the bacteria database (.gz) is approximately 130 GB, which expands to about 1.3 TB when fully decompressed. 

File: phage_prophage_annotation.zip

Description: a complete metadata file (including functional information derived from three sequence-based annotation tools (DRAM[v1.3], microbeannotator[v2.0.5], eggnog-mapper[v2.1.9]) for all the GMPS phage/prophage structures.

File: phage.tar.gz

Description: Protein structure files, protein sequence files, annotation files of protein sequences (including functional information derived from three sequence-based annotation tools (DRAM[v1.3], microbeannotator[v2.0.5], eggnog-mapper[v2.1.9]), and genome files of the 209 previously isolated human gut phages from GPIC. The total size of the phage database is approximately 750 MB. The phage data is separated based on the host species they infect.

File: prophage.tar.gz

Description: Protein structure files, protein sequence files, annotation files of protein sequences (including functional information derived from three sequence-based annotation tools (DRAM[v1.3], microbeannotator[v2.0.5], eggnog-mapper[v2.1.9]), and genome files of 1046 predicted prophages from previously isolated human gut bacterial genomes. The total size of the phage database is approximately 2.3 GB (.gz). The phage data is separated based on the host species they infect.

File: Typephages.tar.gz

Description: Protein structure files, protein sequence files, and genome files of 12 type phages. These well-studied phage proteins are clustered together with gut phage protein structures to infer the functions of unannotated gut phage proteins. List of type phages: Escherichia phage P1、Escherichia phage P2、Bacteriophage P2、Enterobacteria phage P4、Enterobacteria phage T3、Escherichia phage T4、Escherichia phage T5、Escherichia phage T7、Escherichia phage HK97、Escherichia phage Lambda、Escherichia phage Mu、Inovirus M13.