Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
0  structures 6168  species 0  interactions 12967  sequences 32  architectures

Family: Virul_fac_BrkB (PF03631)

Summary: Virulence factor BrkB

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.

Virulence factor BrkB Provide feedback

This family acts as a virulence factor. In Bordetella pertussis, Q45339 is essential for resistance to complement-dependent killing by serum [1]. This family was originally predicted to be ribonuclease BN [2] but this prediction has since been shown to be incorrect [3].

Literature references

  1. Fernandez RC, Weiss AA;, Infect Immun. 1994;62:4727-4738.: Cloning and sequencing of a Bordetella pertussis serum resistance locus. PUBMED:7927748 EPMC:7927748

  2. Callahan C, Deutscher MP; , J Bacteriol 1996;178:7329-7332.: Identification and characterization of the Escherichia coli rbn gene encoding the tRNA processing enzyme RNase BN. PUBMED:8955422 EPMC:8955422

  3. Ezraty B, Dahlgren B, Deutscher MP;, J Biol Chem. 2005;280:16542-16545.: The RNase Z homologue encoded by Escherichia coli elaC gene is RNase BN. PUBMED:15764599 EPMC:15764599


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR017039

Members of this family include the largely uncharacterised BrkB (Bordetella resist killing by serum B) from Bordetella pertussis. It is essential for resistance to complement-dependent killing by serum in Bordetella pertussis [ PUBMED:7927748 ]. Some members have an additional C-terminal domain. Paralogs from E. coli (yhjD) and Mycobactrium tuberculosis (Rv3335c) are part of a smaller, related subfamily that form their own cluster [ PUBMED:1400219 ].

This family was originally predicted to be ribonuclease BN [ PUBMED:15764599 ] but this prediction has since been shown to be incorrect [ PUBMED:8955422 ].

Domain organisation

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

Loading domain graphics...

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 and the UniProtKB sequence database. More...

View options

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
(93)
Full
(12967)
Representative proteomes UniProt
(58385)
RP15
(1249)
RP35
(5675)
RP55
(13737)
RP75
(24745)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

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

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

Format an alignment

  Seed
(93)
Full
(12967)
Representative proteomes UniProt
(58385)
RP15
(1249)
RP35
(5675)
RP55
(13737)
RP75
(24745)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(93)
Full
(12967)
Representative proteomes UniProt
(58385)
RP15
(1249)
RP35
(5675)
RP55
(13737)
RP75
(24745)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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_4424 (release 7.0)
Previous IDs: Ribonuclease_BN;
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A , Eberhardt R
Number in seed: 93
Number in full: 12967
Average length of the domain: 253.5 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 75.53 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 33.7 33.7
Trusted cut-off 33.8 33.7
Noise cut-off 33.6 33.6
Model length: 258
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0H3GPK4 View 3D Structure Click here
A0A0H3GZU5 View 3D Structure Click here
A1BGZ7 View 3D Structure Click here
A1KAC6 View 3D Structure Click here
A1SB50 View 3D Structure Click here
A1T0A0 View 3D Structure Click here
A1WPD7 View 3D Structure Click here
A1WUX4 View 3D Structure Click here
A2SFP5 View 3D Structure Click here
A3N3P2 View 3D Structure Click here
A3QIW3 View 3D Structure Click here
A4VNB9 View 3D Structure Click here
A4XWM7 View 3D Structure Click here
A6TG76 View 3D Structure Click here
A6VL73 View 3D Structure Click here
A8AL54 View 3D Structure Click here
A8H9I2 View 3D Structure Click here
A9BMQ0 View 3D Structure Click here
A9IT56 View 3D Structure Click here
A9MIA4 View 3D Structure Click here
B0UTI5 View 3D Structure Click here
B1KLY8 View 3D Structure Click here
B2FQ10 View 3D Structure Click here
B3EDE6 View 3D Structure Click here
B3PJS2 View 3D Structure Click here
B4S8V4 View 3D Structure Click here
B4SAH4 View 3D Structure Click here
B6IRC8 View 3D Structure Click here
B7VHE7 View 3D Structure Click here
B8F6K4 View 3D Structure Click here
C1D515 View 3D Structure Click here
C4L9W1 View 3D Structure Click here
C5BNZ4 View 3D Structure Click here
C7RCQ5 View 3D Structure Click here
I6YE67 View 3D Structure Click here
K0ETH3 View 3D Structure Click here
K0ETM4 View 3D Structure Click here
K0F8Q0 View 3D Structure Click here
O25957 View 3D Structure Click here
O34437 View 3D Structure Click here

trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;