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1  structure 6009  species 1  interaction 6266  sequences 5  architectures

Family: YajC (PF02699)

Summary: Preprotein translocase subunit

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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.

Preprotein translocase subunit Provide feedback

See [1].

Literature references

  1. Muller M, Koch HG, Beck K, Schafer U; , Prog Nucleic Acid Res Mol Biol 2001;66:107-157.: Protein traffic in bacteria: multiple routes from the ribosome to and across the membrane. PUBMED:11051763 EPMC:11051763


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003849

Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component [PUBMED:2202721]. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins [PUBMED:2202721]. The translocase protein subunits are encoded on the bacterial chromosome.

The translocase itself comprises 7 proteins, including a chaperone (SecB), ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) [PUBMED:2202721]. Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC [PUBMED:9305629]. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA [PUBMED:9305629].

Homologues of the YajC gene have been found in a range of pathogenic and commensal microbes. Brucella abortis YajC- and SecD-like proteins were shown to stimulate a Th1 cell-mediated immune response in mice, and conferred protection when challenged with B.abortis [PUBMED:9826342]. Therefore, these proteins may have an antigenic role as well as a secretory one in virulent bacteria [PUBMED:9826342]. A number of previously uncharacterised "hypothetical" proteins also show similarity to E.coli YajC, suggesting that this family is wider than first thought [PUBMED:9826342].

More recently, the precise interactions between the E.coli SecYEG complex, SecD, SecF, YajC and YidC have been studied [PUBMED:12068816]. Rather than acting individually, the four proteins form a heterotetrameric complex and associate with the SecYEG heterotrimeric complex [PUBMED:12068816]. The SecF and YajC subunits link the complex to the integral membrane translocase.

In Bacillus subtilis, YajC is known as YrbF.

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, 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
(726)
Full
(6266)
Representative proteomes UniProt
(28072)
NCBI
(26962)
Meta
(1631)
RP15
(684)
RP35
(2614)
RP55
(5553)
RP75
(9791)
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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
(726)
Full
(6266)
Representative proteomes UniProt
(28072)
NCBI
(26962)
Meta
(1631)
RP15
(684)
RP35
(2614)
RP55
(5553)
RP75
(9791)
Alignment:
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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
(726)
Full
(6266)
Representative proteomes UniProt
(28072)
NCBI
(26962)
Meta
(1631)
RP15
(684)
RP35
(2614)
RP55
(5553)
RP75
(9791)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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: COG1862
Previous IDs: DUF219;
Type: Family
Sequence Ontology: SO:0100021
Author: Mian N , Bateman A
Number in seed: 726
Number in full: 6266
Average length of the domain: 78.60 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 69.12 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 28.2 28.2
Trusted cut-off 28.5 29.6
Noise cut-off 27.7 26.4
Model length: 80
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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

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Interactions

There is 1 interaction for this family. More...

ACR_tran

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 YajC domain has been found. There are 1 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 sequence.

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