Posts Tagged ‘COVID-19’

Pfam SARS-CoV-2 special update (part 2)

April 6, 2020

This post presents an update to last week’s post. Since the initial release of the 40 Pfam profile HMMs that match SARS-CoV-2, we have now produced a set of flatfiles that are more typical of a Pfam release.  These files make our updated annotations that describe the entries available for download, prior to being released via the Pfam website. Moreover, you can now use the multiple sequence alignments to investigate the conserved positions across different coronavirus proteins. Figure 1 shows the alignment of the SARS-CoV-2 receptor binding domain (PF09408 N.B. the Pfam website still shows the old alignment).

pf09408-spike

Figure 1 – Excerpt of the Betacoronavirus spike glycoprotein S1, receptor binding domain alignment (Pfam accession PF09408), rendered using Jalview. The SARS-CoV-2 sequence is the last sequence in the alignment.

Finally, we have made some very minor changes to the family descriptions and one name change from the last release.  You can now access all the updated files here:

ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam_SARS-CoV-2_2.0/

In this directory you can find the updated seed (Pfam-A.SARS-CoV-2.seed) and full alignments (Pfam-A.SARS-CoV-2.full) in Stockholm format based on the Pfamseq database, which contains sequences of the UniProt Reference Proteomes.  We provide a file with matches to UniProtKB 2019_08 (Pfam-A.SARS-CoV-2.full.uniprot). We also provide a set of alignments for each of the families which include matches to the SARS-CoV-2 sequences which are not as yet present in the Pfamseq database. These alignments can be found in aligned fasta format here or as a tar gzipped library here.

Posted by The Pfam team

Pfam SARS-CoV-2 special update

April 2, 2020

The SARS-CoV-2 pandemic has mobilised a worldwide research effort to understand the pathogen itself and the mechanism of COVID-19 disease, as well as to identify treatment options. Although Pfam already provided useful annotation for SARS-CoV-2, we decided to update our models and annotations for this virus in an effort to help the research community. This post explains what was done and how we are making the data available as quickly as possible.

What have we done?

We assessed all the protein sequences provided by UniProt via its new COVID-19 portal (https://covid-19.uniprot.org/), identified those which lacked an existing Pfam model, and set about building models as required. In some cases we built families based on recently solved structures of SARS-CoV-2 proteins. For example, we built three new families representing the three structural domains of the NSP15 protein (Figure 1) based on the structure by Youngchang Kim and colleagues (http://europepmc.org/article/PPR/PPR115432). In other cases, such as Pfam’s RNA dependent RNA polymerase family (PF00680), we took our existing family and extended its taxonomic range to ensure it included the new SARS-CoV-2 sequences.

Figure 1. The structure of NSP15 (PDB:6VWW) from Kim et al. shows the three new Pfam domains. (1) CoV_NSP15_N (PF19219) Coronavirus replicase NSP15, N-terminal oligomerisation domain in red, (2) CoV_NSP15_M (PF19216) Coronavirus replicase NSP15, middle domain in blue and (3) CoV_NSP15_C (PF19215) Coronavirus replicase NSP15, uridylate-specific endoribonuclease in green.

We have also stratified our ID nomenclature and descriptions of the families to ensure they are both correct and consistent. The majority of the family identifiers now begin with either CoV, for coronavirus specific families, or bCoV for the families which are specific to the betacoronavirus clade, which SARS-CoV-2 belongs to. We have also fixed inconsistencies in the naming and descriptions of the various non-structural proteins, using NSPx for those proteins encoded by the replicase polyprotein, and NSx for those encoded by other ORFs. We are grateful to Philippe Le Mercier from the Swiss Institute of Bioinformatics who gave us valuable guidance for our nomenclature.

Where are the data?

You can access a small HMM library (Pfam-A.SARS-CoV-2.hmm) for all the Pfam families that match the SARS-CoV-2 protein sequences on the Pfam FTP site:

ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam_SARS-CoV-2_1.0/

You can also find a file (matches.scan) showing the matches of the models against the SARS-CoV-2 sequences in the same FTP location. These updates are not yet available on the Pfam website. We anticipate making them available in 6-8 weeks.  We hope you find our SARS-CoV-2 models useful for your research, and as always we welcome your feedback via email at pfam-help@ebi.ac.uk.

How to use this library?

This library is not compatible with the pfam_scan software that we normally recommend to reproduce Pfam matches, as this library only contains a small subset of models.  If you wish to compare these models to your own sequences, please use the following HMMER commands:

$ hmmpress  Pfam-A.SARS-CoV-2.hmm

This only needs to be performed once. Then to compare your sequences (in a file called my.fasta) to this special Pfam profile HMM library, then:

$ hmmscan --cut_ga --domtblout matches.scan Pfam-A.SARS-CoV-2.hmm my.fasta

The –domtblout option enables you to save the matches in a more convenient tabular form, if you do not want to parse the HMMER output.

And finally

We will be making Pfam alignments available during the next week and will produce another blog post describing them.

Posted by The Pfam team