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0  structures 12  species 0  interactions 37  sequences 1  architecture

Family: Pneumo_NS1 (PF03438)

Summary: Pneumovirus NS1 protein

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Pneumovirus NS1 protein Provide feedback

This non-structural protein is one of two found in pneumoviruses. The protein is about 140 amino acids in length. The NS1 protein appears to be important for efficient replication but not essential [1]. The NS1 protein has been shown by yeast two-hybrid to interact with the viral P protein [2]. This protein is also known as the 1C protein. It has also been shown that NS1 can potently inhibit transcription and RNA replication [3].

Literature references

  1. Teng MN, Whitehead SS, Bermingham A, St Claire M, Elkins WR, Murphy BR, Collins PL; , J Virol 2000;74:9317-9321.: Recombinant respiratory syncytial virus that does not express the NS1 or M2-2 protein is highly attenuated and immunogenic in chimpanzees. PUBMED:10982380 EPMC:10982380

  2. Hengst U, Kiefer P; , Virus Genes 2000;20:221-225.: Domains of human respiratory syncytial virus P protein essential for homodimerization and for binding to N and NS1 protein. PUBMED:10949949 EPMC:10949949

  3. Atreya PL, Peeples ME, Collins PL; , J Virol 1998;72:1452-1461.: The NS1 protein of human respiratory syncytial virus is a potent inhibitor of minigenome transcription and RNA replication. PUBMED:9445048 EPMC:9445048


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005099

This non-structural protein is one of two found in pneumoviruses. The protein is about 140 amino acids in length. The NS1 protein appears to be important for efficient replication but not essential [PUBMED:10982380]. The NS1 protein has been shown by yeast two-hybrid to interact with the viral P protein [PUBMED:10949949]. This protein is also known as the 1C protein. It has also been shown that NS1 can potently inhibit transcription and RNA replication [PUBMED:9445048].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(2)
Full
(37)
Representative proteomes NCBI
(30)
Meta
(1)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
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PP/heatmap 1 View             
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(2)
Full
(37)
Representative proteomes NCBI
(30)
Meta
(1)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
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
(2)
Full
(37)
Representative proteomes NCBI
(30)
Meta
(1)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
Raw Stockholm Download   Download           Download   Download  
Gzipped Download   Download           Download   Download  

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

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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.

Note: You can also download the data file for the tree.

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

Seed source: Pfam-B_3221 (release 6.6)
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 2
Number in full: 37
Average length of the domain: 136.00 aa
Average identity of full alignment: 85 %
Average coverage of the sequence by the domain: 98.24 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.5 20.5
Trusted cut-off 21.7 266.1
Noise cut-off 19.6 18.8
Model length: 136
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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