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10  structures 513  species 0  interactions 767  sequences 4  architectures

Family: HrpJ (PF07201)

Summary: HrpJ-like domain

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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.

HrpJ-like domain Provide feedback

This family represents a conserved region approximately 200 residues long within a number of bacterial hypersensitivity response secretion protein HrpJ and similar proteins. HrpJ forms part of a type III secretion system through which, in phytopathogenic bacterial species, virulence factors are thought to be delivered to plant cells [1]. This family also includes the InvE invasion protein from Salmonella. This protein is involved in host parasite interactions and mutations in the InvE gene render Salmonella typhimurium non-invasive [2]. InvE S. typhimurium mutants fail to elicit a rapid Ca2+ increase in cultured cells, an important event in the infection procedure and internalisation of S. typhimurium into epithelial cells [2]. This family includes bacterial SepL and SsaL proteins. SepL plays an essential role in the infection process of enterohemorrhagic Escherichia coli and is thought to be responsible for the secretion of EspA, EspD, and EspB [3]. SsaL of Salmonella typhimurium is thought to be a component of the type III secretion system [4].

Literature references

  1. Hirano SS, Charkowski AO, Collmer A, Willis DK, Upper CD; , Proc Natl Acad Sci U S A 1999;96:9851-9856.: Role of the Hrp type III protein secretion system in growth of Pseudomonas syringae pv. syringae B728a on host plants in the field. PUBMED:10449783 EPMC:10449783

  2. Ginocchio C, Pace J, Galan JE; , Proc Natl Acad Sci U S A 1992;89:5976-5980.: Identification and molecular characterization of a Salmonella typhimurium gene involved in triggering the internalization of salmonellae into cultured epithelial cells. PUBMED:1631083 EPMC:1631083

  3. Kresse AU, Beltrametti F, Muller A, Ebel F, Guzman CA; , J Bacteriol 2000;182:6490-6498.: Characterization of SepL of enterohemorrhagic Escherichia coli. PUBMED:11053395 EPMC:11053395

  4. Hensel M, Shea JE, Raupach B, Monack D, Falkow S, Gleeson C, Kubo T, Holden DW; , Mol Microbiol 1997;24:155-167.: Functional analysis of ssaJ and the ssaK/U operon, 13 genes encoding components of the type III secretion apparatus of Salmonella Pathogenicity Island 2. PUBMED:9140973 EPMC:9140973


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR010812

This entry represents a conserved region approximately 200 residues long within a number of bacterial hypersensitivity response secretion protein HrpJ and similar proteins. HrpJ forms part of a type III secretion system through which, in phytopathogenic bacterial species, virulence factors are thought to be delivered to plant cells [PUBMED:10449783]. This entry also includes the InvE invasion protein from Salmonella. This protein is involved in host parasite interactions and mutations in the InvE gene render Salmonella typhimurium non-invasive [PUBMED:10449783]. InvE S. typhimurium mutants fail to elicit a rapid Ca2+ increase in cultured cells, an important event in the infection procedure and internalisation of S. typhimurium into epithelial cells [PUBMED:10449783]. This family includes bacterial SepL and SsaL proteins. SepL plays an essential role in the infection process of enterohemorrhagic Escherichia coli and is thought to be responsible for the secretion of EspA, EspD, and EspB [PUBMED:11053395]. SsaL of Salmonella typhimurium is thought to be a component of the type III secretion system [PUBMED:9140973].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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
(36)
Full
(767)
Representative proteomes NCBI
(405)
Meta
(7)
RP15
(16)
RP35
(26)
RP55
(41)
RP75
(60)
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Format an alignment

  Seed
(36)
Full
(767)
Representative proteomes NCBI
(405)
Meta
(7)
RP15
(16)
RP35
(26)
RP55
(41)
RP75
(60)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(36)
Full
(767)
Representative proteomes NCBI
(405)
Meta
(7)
RP15
(16)
RP35
(26)
RP55
(41)
RP75
(60)
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: Pfam-B_16649 & Pfam-B_11026(release 10.0) & Pfam-B_1285(release 5.4)
Previous IDs: none
Type: Domain
Author: Vella Briffa B, Moxon SJ, Bashton M, Bateman A
Number in seed: 36
Number in full: 767
Average length of the domain: 160.10 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 46.32 %

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 22.3 22.3
Trusted cut-off 25.4 23.0
Noise cut-off 22.2 22.2
Model length: 166
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the HrpJ domain has been found. There are 10 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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