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6  structures 36  species 0  interactions 203  sequences 31  architectures

Family: Cleaved_Adhesin (PF07675)

Summary: Cleaved Adhesin Domain

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Cleaved Adhesin Domain Provide feedback

This is a family of bacterial protein modules thought to function in various roles including cell adhesion, cell lysis and carbohydrate binding [1]. The beta-sandwich jelly-roll topology of these modules is known as the galactose-binding domain-like superfamily, clan CL0202. A tandem repeat of these modules (either two or three repeats) constitute the haemagglutinin/adhesin (HA) regions of the gingipains, RgpA, Q51816 and Kgp, P72194 and P72197 [3] expressed by Porphyromonas gingivalis (Bacteroides gingivalis) [2]. They form components of the major extracellular virulence complex RgpA-Kgp - a mixture of proteinases and adhesin domains [4]. The adhesin domains in this complex are found in proteinase-cleaved forms when isolated from the cell surface [5]. Haemagglutinin genes of P. gingivalis [6] (hagA1 HAGA1_PORGI - P59915 - and hagA2 HAGA2_PORGI - Q51845) suggest that such proteins are composed of eight to ten tandem repeats of these adhesin modules [1]. Genomic data predicts that homologous protein modules are also expressed by a number of other bacteria and form part of putative multi-domain proteins, eg. Q26BR9 and B0VGL6. These domains may be acting in concert with other adhesion modules thought to be part of these multi-domain proteins such as fibronectin type III, PF00041 and Meprin, A5, mu (MAM), PF00629 domains.

Literature references

  1. Li N, Yun P, Nadkarni MA, Ghadikolaee NB, Nguyen KA, Lee M, Hunter N, Collyer CA;, Mol Microbiol. 2010; [Epub ahead of print]: STRUCTURE DETERMINATION AND ANALYSIS OF A HEMOLYTIC GINGIPAIN ADHESIN DOMAIN FROM PORPHYROMONAS GINGIVALIS. PUBMED:20233299 EPMC:20233299

  2. Pavloff N, Potempa J, Pike RN, Prochazka V, Kiefer MC, Travis J, Barr PJ;, J Biol Chem. 1995;270:1007-1010.: Molecular cloning and structural characterization of the Arg-gingipain proteinase of Porphyromonas gingivalis. Biosynthesis as a proteinase-adhesin polyprotein. PUBMED:7836351 EPMC:7836351

  3. Pavloff N, Pemberton PA, Potempa J, Chen WC, Pike RN, Prochazka V, Kiefer MC, Travis J, Barr PJ;, J Biol Chem. 1997;272:1595-1600.: Molecular cloning and characterization of Porphyromonas gingivalis lysine-specific gingipain. A new member of an emerging family of pathogenic bacterial cysteine proteinases. PUBMED:8999833 EPMC:8999833

  4. Bhogal PS, Slakeski N, Reynolds EC; , Microbiology 1997;143:2485-2495.: A cell-associated protein complex of Porphyromonas gingivalis W50 composed of Arg- and Lys-specific cysteine proteinases and adhesins. PUBMED:9245829 EPMC:9245829

  5. Veith PD, Talbo GH, Slakeski N, Dashper SG, Moore C, Paolini RA, Reynolds EC;, Biochem J. 2002;363:105-115.: Major outer membrane proteins and proteolytic processing of RgpA and Kgp of Porphyromonas gingivalis W50. PUBMED:11903053 EPMC:11903053

  6. Han N, Whitlock J, Progulske-Fox A;, Infect Immun. 1996;64:4000-4007.: The hemagglutinin gene A (hagA) of Porphyromonas gingivalis 381 contains four large, contiguous, direct repeats. PUBMED:8926061 EPMC:8926061


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR011628

This conserved region is found in a group of haemagglutinins and peptidases, e.g. INTERPRO, that, in Porphyromonas gingivalis (Bacteroides gingivalis), form components of the major extracellular virulence complex RgpA-Kgp - a mixture of proteinases and adhesins [PUBMED:10858222]. These domains are cleaved from the original polyprotein and form part of the adhesins [PUBMED:9245829].

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 GBD (CL0202), which has the following description:

This large superfamily contains beta sandwich domains with a jelly roll topology. Many of these families are involved in carbohydrate recognition. Despite sharing little sequence similarity they do share a weak sequence motif, with a conserved bulge in the C-terminal beta sheet. The probable role of this bulge is in bending of the beta sheet that contains the bulge. This enables the curvature of the sheet forming the sugar binding site [1].

The clan contains the following 27 members:

Allantoicase APC10 Bac_rhamnosid_N BetaGal_dom4_5 CBM_11 CBM_15 CBM_17_28 CBM_4_9 CBM_6 CIA30 Cleaved_Adhesin DUF642 Endotoxin_C Ephrin_lbd F5_F8_type_C FBA Glyco_hydro_2_N Laminin_N Lyase_N MAM Muskelin_N P_proprotein PA-IL PepX_C PITH Sad1_UNC XRCC1_N

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
(9)
Full
(203)
Representative proteomes NCBI
(218)
Meta
(69)
RP15
(29)
RP35
(40)
RP55
(40)
RP75
(40)
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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
(9)
Full
(203)
Representative proteomes NCBI
(218)
Meta
(69)
RP15
(29)
RP35
(40)
RP55
(40)
RP75
(40)
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
(9)
Full
(203)
Representative proteomes NCBI
(218)
Meta
(69)
RP15
(29)
RP35
(40)
RP55
(40)
RP75
(40)
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: Yeats C
Previous IDs: none
Type: Domain
Author: Yeats C, Collyer C
Number in seed: 9
Number in full: 203
Average length of the domain: 157.90 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 23.51 %

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 20.5 7.0
Trusted cut-off 20.8 7.1
Noise cut-off 20.1 6.9
Model length: 168
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 Cleaved_Adhesin 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 seqence.

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