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0  structures 170  species 0  interactions 189  sequences 2  architectures

Family: SPAN (PF02510)

Summary: Surface presentation of antigens protein

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Surface presentation of antigens protein Provide feedback

Surface presentation of antigens protein (SPAN), also know as invasion protein invJ, is a Salmonella secretory pathway protein involved in presentation of determinants required for mammalian host cell invasion.

Literature references

  1. Collazo CM, Zierler MK, Galan JE; , Mol Microbiol 1995;15:25-38.: Functional analysis of the Salmonella typhimurium invasion genes invl and invJ and identification of a target of the protein secretion apparatus encoded in the inv locus. PUBMED:7752894 EPMC:7752894


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003066

The Salmonella typhimurium surface presentation of antigens N/invasion protein J gene (SpaN/InvJ) is one of 12 that form a cluster responsible for invasion properties. The gene product is required for entry by the bacterium into epithelial cells, and is thus considered to be a virulence factor [PUBMED:8404849]. Other Spa genes in the cluster are related to invasion (Inv) genes in similar Salmonella and Shigella species [PUBMED:9068645], and to flagella biosynthesis genes in Helicobacter pylori [PUBMED:10066464].

Functional analysis of the gene product from SpaN/InvJ has revealed the protein to have a molecular weight of 36.4 kDa [PUBMED:7752894]. It is required by the organism to gain access to mammalian epithelial cells, and cellular mutants (InvJ-) fail successfully to infect these cells. It has been found, also, that the inv-spa loci of Salmonella species encode a type III protein secretion system, essential to the bacterium's host cell invasion process [PUBMED:8751894]. Suprisingly, type III-secreted proteins lack the customary signal sequence characteristic of most bacterial secretory peptides [PUBMED:7752894].

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
(189)
Representative proteomes NCBI
(96)
Meta
(0)
RP15
(2)
RP35
(3)
RP55
(4)
RP75
(7)
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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
(189)
Representative proteomes NCBI
(96)
Meta
(0)
RP15
(2)
RP35
(3)
RP55
(4)
RP75
(7)
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
(189)
Representative proteomes NCBI
(96)
Meta
(0)
RP15
(2)
RP35
(3)
RP55
(4)
RP75
(7)
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.

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: Pfam-B_1678 (release 5.4)
Previous IDs: none
Type: Family
Author: Mian N, Bateman A
Number in seed: 2
Number in full: 189
Average length of the domain: 271.70 aa
Average identity of full alignment: 61 %
Average coverage of the sequence by the domain: 90.70 %

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 20.1 20.1
Trusted cut-off 20.9 20.6
Noise cut-off 19.8 19.7
Model length: 336
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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