NMGFam

Adjustable parameters

Specificity

Coverage

Adjustable parameters

Conservation

Min relative distance

Project description

Welcome! This resource allows you to iteratively explore the genomic context, functional associations, phylogenetic information and ecological distribution of 413,335 novel and highly curated protein families, identified from thousands of uncultivated microbial organisms.

All data is derived from the systematic analysis of the so-called microbial dark matter of a multi-habitat metagenomics dataset.

You can search novel protein families by their genomic context (e.g. associated to specific KEGG functions or eggNOG orthologs), by taxa conservation (i.e., by finding rank-specific protein families), or even by association with fitness experiments.

Citation

Functional and evolutionary significance of unknown genes from uncultivated taxa

Álvaro Rodríguez del Río, Joaquín Giner-Lamia, Carlos P. Cantalapiedra, Jorge Botas, Ziqi Deng, Ana Hernández-Plaza, Lucas Paoli, Thomas S.B. Schmidt, Shinichi Sunagawa, Peer Bork, Luis Pedro Coelho, Jaime Huerta-Cepas

GO TO PREPRINT

Browse novel families by
Synapomorphy
Hits to fitness experiments
or by conserved genomic context linked to
KEGG functions
Antibiotic resistance

[[ info.level ]] [[ tax | trimTaxa ]] [[ info.nfam ]] fams

[[ ko ]] [[ info.nfam ]] fams

[[ info.desc ]] [[ ec ]]

[[ card ]]

[[ info.nfam ]] fams

[[ info.desc ]] [[ info.accession ]]

[[ condtype ]]

[[ info.nfam ]] fams

[[ info.desc ]]

Showing results from [[ (currentPage - 1) * perPage + 1 ]] to [[ Math.min(currentPage * perPage, totalItems) ]]. Total hits: [[ totalItems ]].

[[ tdata.code ]]

[[ tdata.n_members ]] members [[ tdata.nspecies ]] species [[ tdata.signalp.n_genes_sp ]] genes with signal peptide [[ tdata.mean_nh | toRounded ]] mean num. of TM domains

Sequence information

members	length (aa)	signal peptide (gram+)	signal peptide (gram-)	topology	sequence	neighbor sequences
[[ m ]]	[[ tdata.domains \| getLen(m) ]]	[[ tdata.signalp.genes[m] \| signalp('pos') ]]	[[ tdata.signalp.genes[m] \| signalp('neg') ]]

Taxonomic assignation

Taxonomic level	Number	Most common	Coverage	Specificity	Score	Total genomes	RefSeq genomes
[[ l ]]	[[ tdata["n_"+l[0]+''] ]]	[[ tdata[l[0]+'_mostcommon'] \| trimTaxa]]	[[ tdata[l[0]+'_coverage'] \| toFixed ]]	[[ tdata[l[0]+'_specificity'] \| toFixed ]]	[[ tdata[l[0]+'_score'] \| toFixed ]]	[[ tdata[l[0]+'_total_genomes'] ]]	[[ tdata[l[0]+'_refseq_genomes'] ]]

Experimentally tested

Condition	Condition type	Fitness variation	T score	Identity	Novel family coverage	Original gene coverage	e-value
[[ c.condition ]]	[[ c.condition_type ]]	[[ c.fitness_delta \| toFixed ]]	[[ c.t_score \| toFixed ]]	[[ c.identity ]]	[[ c.cov_fam ]]	[[ c.cov_gene ]]	[[ c.evalue ]]

Biome mapping distribution