The Pfam protein families database

Bateman, Alex; Coin, Lachlan; Durbin, Richard; Finn, Robert D.; Hollich, Volker; Griffiths-Jones, Sam; Khanna, Ajay K.; Marshall, Mhairi; Moxon, Simon; Sonnhammer, Erik L. L.; Studholme, David J.; Yeats, Corin; Eddy, Sean R.

doi:10.1093/nar/gkh121

Cited by 3,192 publications

(1,500 citation statements)

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“…The conserved domains of inserts were analysed using the CD search module in NCBI (https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi). Their structure and putative function were annotated based on similarities to the sequences in the Clusters of Orthologous Groups (COG) [21], Protein Families (Pfam) [22] (http://xfam.org/), and Blocks [23] (InterPro http://www.ebi.ac.uk/interpro/) databases and based on the results of BLAST searches in UniProt (http://www.uniprot.org/). If the similarity of the protein sequence alignment was less than 30%, it was considered to be an unknown sequence.…”

Section: Methodsmentioning

confidence: 99%

Acid-resistant genes of oral plaque microbiome from the functional metagenomics

Zhang

Zheng

et al. 2018

Journal of Oral Microbiology

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Acid resistance is one of key properties assisting the survival of cariogenic bacteria in a dental caries environment, but only a few genes conferring acid resistance have been identified to data. Functional metagenomics provides a systematic method for investigating commensal DNA to identify genes that encode target functions. Here, the host strain Escherichia coli DH10B and a constructed bidirectional transcription vector pSKII+-lacZ contributed to the construction of a metagenomic library, and 46.6 Mb of metagenomic DNA was cloned from carious supragingival plaque of 8children along with screening for lethal functionality. The screen identified 2 positive clones that exhibited a similar aciduric phenotype to that of the positive controls. Bioinformatic analysis revealed that these two genes encoded an ATP/GTP-binding protein and a malate dehydrogenase. Moreover, we also performed functional screening of Streptococcus mutans, since it is one of the predominant cariogenic strains but was not identified in our initial screening. Five positive clones were retrieved. In conclusion, our improved functional metagenomics screening method helped in the identification of important acid resistance genes, thereby providing new insights into the mechanism underlying caries formation as well as in the prevention and treatment of early childhood caries (ECC).

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Section: Methodsmentioning

confidence: 99%

Acid-resistant genes of oral plaque microbiome from the functional metagenomics

Zhang

Zheng

et al. 2018

Journal of Oral Microbiology

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“…Community driven databases such as GNPS (Wang et al, 2016) provide a good platform for researchers to contribute to the growth of spectral library knowledge, much like how nucleotide or protein databases were established in recent years (Bateman et al, 2004;Sayers et al, 2012).…”

Section: Tandem Mass Spectrometry and Spectral Networkingmentioning

confidence: 99%

High-Resolution Liquid Chromatography Tandem Mass Spectrometry Enables Large Scale Molecular Characterization of Dissolved Organic Matter

et al. 2017

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Dissolved organic matter (DOM) is arguably one of the most complex exometabolomes on earth, and is comprised of thousands of compounds, that together contribute more than 600 × 10 15 g carbon. This reservoir is primarily the product of interactions between the upper ocean's microbial food web, yet abiotic processes that occur over millennia have also modified many of its molecules. The compounds within this reservoir play important roles in determining the rate and extent of element exchange between inorganic reservoirs and the marine biosphere, while also mediating microbe-microbe interactions. As such, there has been a widespread effort to characterize DOM using high-resolution analytical methods including nuclear magnetic resonance spectroscopy (NMR) and mass spectrometry (MS). To date, molecular information in DOM has been primarily obtained through calculated molecular formulas from exact mass. This approach has the advantage of being non-targeted, accessing the inherent complexity of DOM. Molecular structures are however still elusive and the most commonly used instruments are costly. More recently, tandem mass spectrometry has been employed to more precisely identify DOM components through comparison to library mass spectra. Here we describe a data acquisition and analysis workflow that expands the repertoire of high-resolution analytical approaches available to access the complexity of DOM molecules that are amenable to electrospray ionization (ESI) MS. We couple liquid chromatographic separation with tandem MS (LC-MS/MS) and a data analysis pipeline, that integrates peak extraction from extracted ion chromatograms (XIC), molecular formula calculation and molecular networking. This provides more precise structural characterization. Although only around 1% of detectable DOM compounds can be annotated through publicly available spectral libraries, community-wide participation in populating and annotating DOM datasets could rapidly increase the annotation rate and should be broadly encouraged. Our analysis also identifies shortcomings of the current Petras et al. LC-MS/MS Analysis of DOMdata analysis workflow that need to be addressed by the community in the future. This work will lay the foundation for an integrative, non-targeted molecular analysis of DOM which, together with next generation sequencing, meta-proteomics and physical data, will pave the way to a more comprehensive understanding of the role of DOM in structuring marine ecosystems.

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“…Single-copy gene analysis was performed to infer biogeographical patterns by (1) selecting 47 conserved single-copy gene families in isolate genomes in the Integrated Microbial Genomes (IMG) database (Markowitz et al 2006) using PFAM (Bateman et al 2004) profile searches with rps-BLAST (Altschul et al 1997), (2) identifying members of these families in the bacterial sludge metagenomes, (3) aligning each family with ClustalX ( Thompson et al 1994), and (4) generating neighbor-joining trees using ClustalX. See Supplemental Research Data for details.…”

Section: Bioinformatic Analysesmentioning

confidence: 99%

A bacterial metapopulation adapts locally to phage predation despite global dispersal

Kunin¹,

He²,

Warnecke³

et al. 2007

Genome Res.

141

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Using a combination of bacterial and phage-targeted metagenomics, we analyzed two geographically remote sludge bioreactors enriched in a single bacterial species Candidatus Accumulibacter phosphatis (CAP). We inferred unrestricted global movement of this species and identified aquatic ecosystems as the primary environmental reservoirs facilitating dispersal. Highly related and geographically remote CAP strains differed principally in genomic regions encoding phage defense mechanisms. We found that CAP populations were high density, clonal, and nonrecombining, providing natural targets for “kill-the-winner” phage predation. Community expression analysis demonstrated that phages were consistently active in the bioreactor community. Genomic signatures linking CAP to past phage exposures were observed mostly between local phage and host. We conclude that CAP strains disperse globally but must adapt to phage predation pressure locally.

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The Pfam protein families database

Cited by 3,192 publications

References 0 publications

Acid-resistant genes of oral plaque microbiome from the functional metagenomics

Acid-resistant genes of oral plaque microbiome from the functional metagenomics

High-Resolution Liquid Chromatography Tandem Mass Spectrometry Enables Large Scale Molecular Characterization of Dissolved Organic Matter

A bacterial metapopulation adapts locally to phage predation despite global dispersal

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