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10  structures 1122  species 0  interactions 1599  sequences 8  architectures

Family: T2SG (PF08334)

Summary: Type II secretion system (T2SS), protein G

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Type II secretion system (T2SS), protein G Provide feedback

The Type II secretion system, also called Secretion-dependent pathway (SDP), is responsible for the transport of proteins across the outer membrane first exported to the periplasm by the Sec or Tat translocon in Gram-negative (diderm) bacteria [1,2]. The T2SG family includes proteins such as EpsG (P45773) in Vibrio cholera, XcpT also called PddA (Q00514) in Pseudomonas aeruginosa or PulG (P15746)in Klebsiella pneumoniae. The PulG is thought to be anchored in the inner membrane with its C-terminus directed towards the periplasme [3]. Together with other members of the Type II secretion machinery, it is thought to assemble into a pilus-like structure that may function as a dynamic mechanism to push secreted proteins out of the cell. The polypeptide is organized into a long N-terminal alpha-helix followed by a loop region that separates it from a C-terminal anti-parallel beta-sheet [1].

Literature references

  1. Kohler R, Schafer K, Muller S, Vignon G, Diederichs K, Philippsen A, Ringler P, Pugsley AP, Engel A, Welte W; , Mol Microbiol 2004;54:647-664.: Structure and assembly of the pseudopilin PulG. PUBMED:15491357 EPMC:15491357

  2. Bally M, Filloux A, Akrim M, Ball G, Lazdunski A, Tommassen J; , Mol Microbiol 1992;6:1121-1131.: Protein secretion in Pseudomonas aeruginosa: characterization of seven xcp genes and processing of secretory apparatus components by prepilin peptidase. PUBMED:1588814 EPMC:1588814

  3. Reyss I, Pugsley AP; , Mol Gen Genet 1990;222:176-184.: Five additional genes in the pulC-O operon of the gram-negative bacterium Klebsiella oxytoca UNF5023 which are required for pullulanase secretion. PUBMED:2129543 EPMC:2129543

  4. Desvaux M, Parham NJ, Scott-Tucker A, Henderson IR;, Trends Microbiol. 2004;12:306-309.: The general secretory pathway: a general misnomer?. PUBMED:15223057 EPMC:15223057

  5. Peabody CR, Chung YJ, Yen MR, Vidal-Ingigliardi D, Pugsley AP, Saier MH Jr;, Microbiology. 2003;149:3051-3072.: Type II protein secretion and its relationship to bacterial type IV pili and archaeal flagella. PUBMED:14600218 EPMC:14600218

  6. Desvaux M, Hebraud M, Talon R, Henderson IR;, Trends Microbiol. 2009;17:139-145.: Secretion and subcellular localizations of bacterial proteins: a semantic awareness issue. PUBMED:19299134 EPMC:19299134


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013545

The general secretion pathway, or type II pullulanase-like machinery, is responsible for the transport of proteins from the periplasm across the outer membrane in Gram-negative bacteria [PUBMED:15491357, PUBMED:1588814]. This entry includes protein G (e.g. SWISSPROT, SWISSPROT) involved in this pathway. The PulG protein (SWISSPROT) is thought to be anchored in the inner membrane with its C terminus directed towards the periplasm [PUBMED:2129543]. Together with other members of the secretion machinery, it is thought to assemble into a pilus-like structure that may function as a dynamic mechanism to push secreted proteins out of the cell. The polypeptide is organised into a long N-terminal alpha-helix followed by a loop region that separates it from a C-terminal anti-parallel beta-sheet [PUBMED:15491357].

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 Pilus (CL0327), which has the following description:

This is a clan contains bacterial pilus subunits and proteins involved in secretion. Pili proteins enable the transfer of plasmid between bacteria. The families in this clan adopt an alpha helical structure which is packed against a beta sheet [2-3].

The clan contains the following 10 members:

Bundlin N_methyl N_methyl_2 N_methyl_3 Pilin PilS T2SG T2SI TcpA YadA_anchor

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.

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(175)
Full
(1599)
Representative proteomes NCBI
(1149)
Meta
(368)
RP15
(154)
RP35
(301)
RP55
(395)
RP75
(474)
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Format an alignment

  Seed
(175)
Full
(1599)
Representative proteomes NCBI
(1149)
Meta
(368)
RP15
(154)
RP35
(301)
RP55
(395)
RP75
(474)
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
(175)
Full
(1599)
Representative proteomes NCBI
(1149)
Meta
(368)
RP15
(154)
RP35
(301)
RP55
(395)
RP75
(474)
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_1144 (release 18.0)
Previous IDs: GSPII_G;
Type: Family
Author: Fenech M, Desvaux M
Number in seed: 175
Number in full: 1599
Average length of the domain: 105.00 aa
Average identity of full alignment: 40 %
Average coverage of the sequence by the domain: 69.58 %

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 20.6 20.6
Trusted cut-off 20.6 20.6
Noise cut-off 20.5 20.4
Model length: 108
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 T2SG 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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