HMDB

Site updated: 2023/8/07, GMT+8 [New downloadable files provided: individual_FAAs.tar.gz]
! Importance: Don't be ashamed to sent email to [shaojingwang@tmu.edu.cn] when you encounter any problems about the usage of HMDB.
Introduction

The investigation of hydrocarbon degradation potential of environmental microorganisms is an important research topic, whether for the global carbon cycle or oil pollution remediation. Under aerobic conditions, the microorganisms employ a range of monooxygenases to use hydrocarbons substrates as a source of carbon and energy. With the explosion of sequencing data, mining genes in genomes or metagenomes has become computationally expensive and time-consuming.

We proposed the HMDB, which is a professional gene database of hydrocarbon monooxygenases. HMDB contains 38 genes, which encode 11 monooxygenases responsible for the hydroxylation of 8 hydrocarbons. To reduce false positives, the strategy of using homologous genes as background noise was applied for HMDB. We added 10,095 gene sequences of enzymes which took non-hydrocarbon as substrate to HMDB.

The classic BLAST method and best-hit strategy were recommended for HMDB usage, but not limited. The performance of HMDB was validated using 264,402 prokaryote genomes from RefSeq and 51 metagenomes from SRA. The results showed that HMDB database had high sensitivity and low false positive rate. We release the HMDB database here, hoping to speed up the process for investigation of hydrocarbon monooxygenases in massive metagenomic data.

HMDB is freely available:
HMDB_v1.1.faa.gz (1.47Mb downloads) Download individual_FAAs.tar.gz (1.47Mb downloads) Download

BLAST_tabular_assistant.pl (6Kb downloads) Download
Recommended pipeline:
Here is the recommended pipeline for metagenomes investigation under linux environment.
Let's assume that the BLAST v2.9.0+ and Perl v5.26.2 have been installed in your system path.

step 1: makeblastdb -in $path/HMDB_v1.1.faa -input_type fasta -dbtype prot -out $path/HMDB_v1.1

step 2: blastp -db $path/HMDB_v1.1 -query $path/xxx.faa -evalue 1e-10 -num_threads [Integer] -outfmt 6 -out $path/xxx_vs_HMDB_v1.1.bsp

step 3: perl $path/BLAST_tabular_assistant.pl $path/HMDB_v1.1.faa $path/xxx_vs_HMDB_v1.1.bsp -meta > $path/xxx_vs_HMDB_v1.1.txt

Tips:
The "$path" represents the readable path of the corresponding file.
The "xxx" represents the prefix of the metagenome sample.

Tips：If you use HMDB in your research, please cite:
Wang, S. et al. HMDB: A curated database of genes involved in hydrocarbon monooxygenation reaction with homologous genes as background. Journal of Hazardous Materials 460(2023).