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0  structures 255  species 0  interactions 283  sequences 2  architectures

Family: SrfB (PF07520)

Summary: Virulence factor SrfB

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 SrfB Provide feedback

This family includes homologues of SsrAB is a two-component regulatory system encoded within the Salmonella pathogenicity island SPI-2. Among the products of genes activated by SsrAB within epithelial and macrophage cells is Q9KIJ9 [1]. Homologues are found in several other proteobacteria.

Literature references

  1. Worley MJ, Ching KH, Heffron F; , Mol Microbiol 2000;36:749-761.: Salmonella SsrB activates a global regulon of horizontally acquired genes. PUBMED:10844662 EPMC:10844662


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR009216

This entry represents proteins of unknown function. It has been shown in Salmonella enterica that srfB is one of the genes activated by the global signal transduction/regulatory system SsrA/B [PUBMED:10844662]. This activation takes place within eukaryotic cells. The activated genes include pathogenicity island 2 (SPI-2) genes and at least 10 other genes (srfB is one of them) which are believed to be horizontally acquired, and to be involved in virulence/pathogenicity [PUBMED:10844662].

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...

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
(12)
Full
(283)
Representative proteomes NCBI
(223)
Meta
(26)
RP15
(4)
RP35
(17)
RP55
(37)
RP75
(53)
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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
(12)
Full
(283)
Representative proteomes NCBI
(223)
Meta
(26)
RP15
(4)
RP35
(17)
RP55
(37)
RP75
(53)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(12)
Full
(283)
Representative proteomes NCBI
(223)
Meta
(26)
RP15
(4)
RP35
(17)
RP55
(37)
RP75
(53)
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.

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.

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: Manual
Previous IDs: none
Type: Family
Author: Studholme D
Number in seed: 12
Number in full: 283
Average length of the domain: 878.30 aa
Average identity of full alignment: 58 %
Average coverage of the sequence by the domain: 97.93 %

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 19.1 19.1
Trusted cut-off 19.6 20.6
Noise cut-off 18.1 19.0
Model length: 1002
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

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