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NMPFamsDB

A database of Novel Metagenome Protein Families

A database of Novel Metagenome Protein Clusters

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Protein Families

Full Database
Full database	All Sequences (FASTA)	Consensus Sequences (FASTA)	Full Alignments (FASTA)	Seed Alignments (FASTA)	HMM profiles (HMMER)	AlphaFold2 3D models (PDB)	AlphaFold2 Input Alignments (FASTA)
Clustered based on habitat distribution
Environmental	All Sequences (FASTA)	Consensus Sequences (FASTA)	Full Alignments (FASTA)	Seed Alignments (FASTA)	HMM profiles (HMMER)	AlphaFold2 3D models (PDB)	AlphaFold2 Input Alignments (FASTA)
Host-associated	All Sequences (FASTA)	Consensus Sequences (FASTA)	Full Alignments (FASTA)	Seed Alignments (FASTA)	HMM profiles (HMMER)	AlphaFold2 3D models (PDB)	AlphaFold2 Input Alignments (FASTA)
Engineered	All Sequences (FASTA)	Consensus Sequences (FASTA)	Full Alignments (FASTA)	Seed Alignments (FASTA)	HMM profiles (HMMER)	AlphaFold2 3D models (PDB)	AlphaFold2 Input Alignments (FASTA)
Clustered based on phylogeny
Bacteria	All Sequences (FASTA)	Consensus Sequences (FASTA)	Full Alignments (FASTA)	Seed Alignments (FASTA)	HMM profiles (HMMER)	AlphaFold2 3D models (PDB)	AlphaFold2 Input Alignments (FASTA)
Archaea	All Sequences (FASTA)	Consensus Sequences (FASTA)	Full Alignments (FASTA)	Seed Alignments (FASTA)	HMM profiles (HMMER)	AlphaFold2 3D models (PDB)	AlphaFold2 Input Alignments (FASTA)
Eukaryota	All Sequences (FASTA)	Consensus Sequences (FASTA)	Full Alignments (FASTA)	Seed Alignments (FASTA)	HMM profiles (HMMER)	AlphaFold2 3D models (PDB)	AlphaFold2 Input Alignments (FASTA)
Viruses	All Sequences (FASTA)	Consensus Sequences (FASTA)	Full Alignments (FASTA)	Seed Alignments (FASTA)	HMM profiles (HMMER)	AlphaFold2 3D models (PDB)	AlphaFold2 Input Alignments (FASTA)
Unclassified	All Sequences (FASTA)	Consensus Sequences (FASTA)	Full Alignments (FASTA)	Seed Alignments (FASTA)	HMM profiles (HMMER)	AlphaFold2 3D models (PDB)	AlphaFold2 Input Alignments (FASTA)
Clustered based on sample type
Metagenome Families	All Sequences (FASTA)	Consensus Sequences (FASTA)	Full Alignments (FASTA)	Seed Alignments (FASTA)	HMM profiles (HMMER)	AlphaFold2 3D models (PDB)	AlphaFold2 Input Alignments (FASTA)
Metatranscriptome Families	All Sequences (FASTA)	Consensus Sequences (FASTA)	Full Alignments (FASTA)	Seed Alignments (FASTA)	HMM profiles (HMMER)	AlphaFold2 3D models (PDB)	AlphaFold2 Input Alignments (FASTA)
Metagenome/Metatranscriptome Families	All Sequences (FASTA)	Consensus Sequences (FASTA)	Full Alignments (FASTA)	Seed Alignments (FASTA)	HMM profiles (HMMER)	AlphaFold2 3D models (PDB)	AlphaFold2 Input Alignments (FASTA)

Other Downloads

Metagenome Families (Tab-delimited): The protein clusters/families obtained from JGI IMG's Metagenomes and Metatranscriptomes, as described in Pavlopoulos et al, 2021. The sequences are given in a tab-delimited format with the following columns:
1. Family index
2. Sequence header (Taxon OID | Scaffold ID | Gene/Protein ID)
3. Protein sequence
Reference Genome Families (Tab-delimited): The protein clusters/families obtained from JGI IMG's reference genomes, as described in Pavlopoulos et al, 2021. The sequences are given in a tab-delimited format with the following columns:
1. Family index
2. Sequence header (taxonomy superkingdom | Gold Genome ID | Gene/Protein ID)
3. Protein sequence

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