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0  structures 90  species 0  interactions 127  sequences 31  architectures

Family: CoV_NSP6 (PF19213)

Summary: Coronavirus replicase NSP6

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Coronavirus replicase NSP6 Provide feedback

This entry represents proteins found in Coronaviruses and includes the Non-structural Protein 6 (NSP6). Coronaviruses encode large replicase polyproteins which are proteolytically processed by viral proteases to generate mature Nonstructural Proteins (NSPs) [1]. NSP6 is a membrane protein containing 6 transmembrane domains with a large C-terminal tail [1]. NSP6 from the avian coronavirus, infectious bronchitis virus (IBV) and the mouse hepatitis virus (MHV) have been shown to localise to the ER and to generate autophagosomes [2]. Coronavirus NSP6 proteins have also been shown to limit autophagosome expansion. This may favour coronavirus infection by reducing the ability of autophagosomes to deliver viral components to lysosomes for degradation [2]. NSP6 from IBV, MHV and severe acute respiratory syndrome coronavirus (SARS-CoV) have also been found to activate autophagy [2,3].

Literature references

  1. Baliji S, Cammer SA, Sobral B, Baker SC;, J Virol. 2009;83:6957-6962.: Detection of nonstructural protein 6 in murine coronavirus-infected cells and analysis of the transmembrane topology by using bioinformatics and molecular approaches. PUBMED:19386712 EPMC:19386712

  2. Cottam EM, Whelband MC, Wileman T;, Autophagy. 2014;10:1426-1441.: Coronavirus NSP6 restricts autophagosome expansion. PUBMED:24991833 EPMC:24991833

  3. Cottam EM, Maier HJ, Manifava M, Vaux LC, Chandra-Schoenfelder P, Gerner W, Britton P, Ktistakis NT, Wileman T;, Autophagy. 2011;7:1335-1347.: Coronavirus nsp6 proteins generate autophagosomes from the endoplasmic reticulum via an omegasome intermediate. PUBMED:21799305 EPMC:21799305


This tab holds annotation information from the InterPro database.

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Domain organisation

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(35)
Full
(127)
Representative proteomes UniProt
(3037)
NCBI
(3141)
Meta
(0)
RP15
(125)
RP35
(125)
RP55
(125)
RP75
(125)
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PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(35)
Full
(127)
Representative proteomes UniProt
(3037)
NCBI
(3141)
Meta
(0)
RP15
(125)
RP35
(125)
RP55
(125)
RP75
(125)
Alignment:
Format:
Order:
Sequence:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(35)
Full
(127)
Representative proteomes UniProt
(3037)
NCBI
(3141)
Meta
(0)
RP15
(125)
RP35
(125)
RP55
(125)
RP75
(125)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download    
Gzipped Download   Download   Download   Download   Download   Download   Download   Download    

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

This family is new in this Pfam release.

Seed source: Jackhmmer:P0DTC1
Previous IDs: DUF5881;
Type: Family
Sequence Ontology: SO:0100021
Author: Mistry J , Williams LS
Number in seed: 35
Number in full: 127
Average length of the domain: 261.90 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 4.50 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 116.9 116.9
Noise cut-off 24.9 24.3
Model length: 268
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

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Viroids Viroids Unclassified sequence Unclassified sequence

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