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0  structures 2171  species 0  interactions 3289  sequences 2  architectures

Family: Bac_export_3 (PF01313)

Summary: Bacterial export proteins, family 3

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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.

Bacterial export proteins, family 3 Provide feedback

This family includes the following members; FliQ, MopD, HrcS, Hrp, YopS and SpaQ All of these members export proteins, that do not possess signal peptides, through the membrane. Although the proteins that these exporters move may be different, the exporters are thought to function in similar ways [1].

Literature references

  1. Zhuang WY, Shapiro L; , J Bacteriol 1995;177:343-356.: Caulobacter FliQ and FliR membrane proteins, required for flagellar biogenesis and cell division, belong to a family of virulence factor export proteins. PUBMED:7814323 EPMC:7814323


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002191

The fliL operon of Escherichia coli contains seven genes (including fliO, fliP, fliQ and fliR) involved in the biosynthesis and functioning of the flagellar organelle [PUBMED:8282695]. The fliO, fliP, fliQ and fliR genes encode highly hydrophobic polypeptides. The fliQ gene product, a small integral membrane protein that contains two putative transmembrane (TM) regions, is required for the assembly of the rivet at the earliest stage of flagellar biosynthesis.

Proteins sharing an evolutionary relationship with FliQ have been found in a range of bacteria: these include Yop translocation protein S from Yersinia pestis [PUBMED:8300512]; surface antigen-presentation protein SpaQ from Salmonella typhimurium and Shigella flexneri [PUBMED:8404849]; and probable translocation protein Y4YM from Rhizobium sp. (strain NGR234) [PUBMED:9163424]. All of these members export proteins, that do not possess signal peptides, through the membrane. Although the proteins that these exporters move may be different, the exporters are thought to function in similar ways [PUBMED:7814323].

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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Pfam Clan

This family is a member of clan Gx_transp (CL0315), which has the following description:

This superfamily includes a wide range of transporters that contain many conserved glycine residues in the presumed transmembrane regions.

The clan contains the following 12 members:

5TM-5TMR_LYT Bac_export_3 BioY CbiM DUF2232 DUF3816 ECF-ribofla_trS Hpre_diP_synt_I MreD QueT Thia_YuaJ ThiW

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
(202)
Full
(3289)
Representative proteomes NCBI
(1501)
Meta
(334)
RP15
(203)
RP35
(390)
RP55
(513)
RP75
(652)
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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
(202)
Full
(3289)
Representative proteomes NCBI
(1501)
Meta
(334)
RP15
(203)
RP35
(390)
RP55
(513)
RP75
(652)
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
(202)
Full
(3289)
Representative proteomes NCBI
(1501)
Meta
(334)
RP15
(203)
RP35
(390)
RP55
(513)
RP75
(652)
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_898 (release 3.0)
Previous IDs: none
Type: Family
Author: Finn RD, Bateman A
Number in seed: 202
Number in full: 3289
Average length of the domain: 75.20 aa
Average identity of full alignment: 37 %
Average coverage of the sequence by the domain: 85.64 %

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 25.0 25.0
Trusted cut-off 25.0 25.3
Noise cut-off 23.6 24.9
Model length: 76
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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