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6  structures 788  species 0  interactions 1142  sequences 5  architectures

Family: T6SS-SciN (PF12790)

Summary: Type VI secretion lipoprotein, VasD, EvfM, TssJ, VC_A0113

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Type VI secretion lipoprotein, VasD, EvfM, TssJ, VC_A0113 Provide feedback

One of the virulence mechanisms of E coli is the production of toxins which it produces from dedicated machineries called secretion systems. Seven secretion systems have been described, which assemble from 3 to up to more than 20 subunits. These secretion systems derive from or have co-evolved with bacterial organelles such as ABC transporters (type I), type IV pili (type 2), flagella (type 3), or conjugative machines (type IV). The type VI secretion system (T6SS) is present in most pathogens that have contact with animals, plants, or humans. SciN is a lipoprotein tethered to the outer membrane and expressed in the periplasm of E coli and is essential for T6S-dependent secretion of the Hcp-like SciD protein and for biofilm formation.

Literature references

  1. Aschtgen MS, Bernard CS, De Bentzmann S, Lloubes R, Cascales E;, J Bacteriol. 2008;190:7523-7531.: SciN is an outer membrane lipoprotein required for type VI secretion in enteroaggregative Escherichia coli. PUBMED:18805985 EPMC:18805985

  2. Zhou Y, Tao J, Yu H, Ni J, Zeng L, Teng Q, Kim KS, Zhao GP, Guo X, Yao Y;, Infect Immun. 2012;80:1243-1251.: Hcp family proteins secreted via the type VI secretion system coordinately regulate Escherichia coli K1 interaction with human brain microvascular endothelial cells. PUBMED:22184413 EPMC:22184413


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR017734

One of the virulence mechanisms of Escherichia coli is the production of toxins from dedicated machineries called secretion systems. Seven secretion systems have been described, which assemble from 3 to up-to more than 20 subunits. These secretion systems derive from or have co-evolved with bacterial organelles such as ABC transporters (type I), type IV pili (type 2), flagella (type 3), or conjugative machines (type IV).

The type VI secretion system (T6SS) is present in most pathogens that have contact with animals, plants, or humans. T6SS exports Hcp (Haemolysin-Coregulated Protein) and a class of proteins named Vgr (Val-Gly Repeats), whose exact function is still speculative. In addition to Vgr and Hcp proteins, T6SS is characterised by the presence of an AAA+ Clp-like ATPase and of two additional genes icmF and dotU, encoding homologues of T4SS stabilising proteins [PUBMED:15385502].

SciN is a lipoprotein tethered to the outer membrane and expressed in the periplasm of E. coli, and is essential for T6SS-dependent secretion of the Hcp-like SciD protein and for biofilm formation [PUBMED:18805985].

Domain organisation

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Pfam Clan

This family is a member of clan Transthyretin (CL0287), which has the following description:

This clan unifies several SCOP superfamilies that all share a 7 stranded beta sandwich fold.

The clan contains the following 33 members:

CarbopepD_reg_2 CarboxypepD_reg Cna_B CooC_C Dioxygenase_C DUF1416 DUF2012 DUF2606 DUF3823 DUF3869 DUF4139 DUF4198 DUF4458 DUF5300 FctA Fimbrillin_C fn3_3 GramPos_pilinD1 GramPos_pilinD3 Lipase_C MetallophosN PapC_C PEGA phage_tail_N Pollen_Ole_e_I PUD SdrD_B SpaA T6_Ig_like T6SS-SciN Transthyretin TTR-52 VHL

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
(92)
Full
(1142)
Representative proteomes UniProt
(5111)
NCBI
(8852)
Meta
(20)
RP15
(117)
RP35
(507)
RP55
(1102)
RP75
(2242)
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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
(92)
Full
(1142)
Representative proteomes UniProt
(5111)
NCBI
(8852)
Meta
(20)
RP15
(117)
RP35
(507)
RP55
(1102)
RP75
(2242)
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
(92)
Full
(1142)
Representative proteomes UniProt
(5111)
NCBI
(8852)
Meta
(20)
RP15
(117)
RP35
(507)
RP55
(1102)
RP75
(2242)
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: Pfam-B_27 (release 24.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Coggill P
Number in seed: 92
Number in full: 1142
Average length of the domain: 122.00 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 67.60 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.6 21.6
Trusted cut-off 21.7 22.8
Noise cut-off 21.5 21.5
Model length: 120
Family (HMM) version: 7
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 T6SS-SciN domain has been found. There are 6 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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