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]. 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
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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
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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
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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
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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
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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
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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
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 Concanavalin (CL0004), which has the following description:
This superfamily includes a diverse range of carbohydrate binding domains and glycosyl hydrolase enzymes that share a common structure.
The clan contains the following 49 members:
Alginate_lyase2 ArabFuran-catal Arabino_trans_N Bac_rhamnosid Bact_lectin bCoV_S1_N Calreticulin Cleaved_Adhesin DUF1080 DUF1349 DUF1583 DUF1961 DUF2401 DUF3472 DUF4975 Exotox-A_bind Gal-bind_lectin GalBD_like GH131_N GH43_C2 Glyco_hydro_11 Glyco_hydro_12 Glyco_hydro_16 Glyco_hydro_32C Glyco_hydro_7 HA1 Laminin_G_1 Laminin_G_2 Laminin_G_3 Lectin_leg-like Lectin_legB MAM Methyltransf_FA Neuralized Pentaxin Peptidase_A4 Polysacc_lyase PRY Reoviridae_Vp9 Sial-lect-inser Sialidase SKN1 SPRY TgMIC1 Toxin_R_bind_N TSP_C VP4_haemagglut XET_C YrpDAlignments
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 (4) |
Full (515) |
Representative proteomes | UniProt (2083) |
NCBI (3330) |
Meta (75) |
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RP15 (40) |
RP35 (254) |
RP55 (601) |
RP75 (960) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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Seed (4) |
Full (515) |
Representative proteomes | UniProt (2083) |
NCBI (3330) |
Meta (75) |
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RP15 (40) |
RP35 (254) |
RP55 (601) |
RP75 (960) |
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Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | Yeats C |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Yeats C |
Number in seed: | 4 |
Number in full: | 515 |
Average length of the domain: | 142.70 aa |
Average identity of full alignment: | 16 % |
Average coverage of the sequence by the domain: | 21.40 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 174 | ||||||||||||
Family (HMM) version: | 12 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
There is 1 interaction for this family. More...
Cleaved_AdhesinStructures
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 7 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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