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216  structures 2216  species 0  interactions 121459  sequences 4450  architectures

Family: HemolysinCabind (PF00353)

Summary: RTX calcium-binding nonapeptide repeat (4 copies)

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RTX calcium-binding nonapeptide repeat (4 copies) Provide feedback

No Pfam abstract.

Literature references

  1. Economou A, Hamilton WD, Johnston AW, Downie JA; , EMBO J 1990;9:349-354.: The Rhizobium nodulation gene nodO encodes a Ca2(+)-binding protein that is exported without N-terminal cleavage and is homologous to haemolysin and related proteins. PUBMED:2303029 EPMC:2303029

  2. Baumann U, Wu S, Flaherty KM, McKay DB; , EMBO J 1993;12:3357-3364.: Three-dimensional structure of the alkaline protease of Pseudomonas aeruginosa: a two-domain protein with a calcium binding parallel beta roll motif. PUBMED:8253063 EPMC:8253063

  3. Chung YJ, Steen MT, Hansen JN; , J Bacteriol 1992;174:1417-1422.: The subtilin gene of Bacillus subtilis ATCC 6633 is encoded in an operon that contains a homolog of the hemolysin B transport protein. PUBMED:1735728 EPMC:1735728

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001343

Gram-negative bacteria produce a number of proteins that are secreted into the growth medium by a mechanism by the type I secretion system that does not require a cleaved N-terminal signal sequence. These proteins, while having different functions, share two properties: they bind calcium and they contain a multiple tandem repeat of a nonapeptide [ PUBMED:2303029 ]. The nonapeptide is found in a group of bacterial exported proteins that includes haemolysin, cyclolysin, leukotoxin and metallopeptidases belonging to MEROPS peptidase family M10 (clan MA(M)), subfamily 10B (serralysin).

It has been suggested that the internally repeated domain of haemolysin may be involved in Ca-mediated binding to erythrocytes. It has been shown that such a domain is involved in the binding of calcium ions in a parallel beta roll structure [ PUBMED:8253063 ].

The Bordetella pertussis adenylate cyclase toxin tertiary structure has been solved. The C-terminal RTX repeats are Asp-rich, which bind calcium ions as the protein moves from the low calcium intercellular environment to a higher extracellular concentration of calcium ions. The C-terminal assembly containing the RTX repeats has been shown to form beta rolls, which prevent backsliding of the protein in the type I sectretion system conduits and accelerating secretion of the large toxin [ PUBMED:27058787 ].

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 beta_Roll (CL0592), which has the following description:

This superfamily is characterised by families of a short nonarepeat unit. The beta-roll is made up of a super-helix of beta-strand-turns of two short strands each, and the loops are stabilised by Ca2+ ions. The region of a protein with this beta-roll is often termed the R-module, and it can frequently be found in metalloproteases of the serralysin type and in epimerases [1]. The nonarepeat is also found multiple times in haemolysins, where the structure is again stabilised by binding Ca2+ ions.

The clan contains the following 2 members:

HemolysinCabind Peptidase_M10_C


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 and the UniProtKB sequence database. More...

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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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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.

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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: Prosite
Previous IDs: hemolysinCabind;
Type: Repeat
Sequence Ontology: SO:0001068
Author: Finn RD , Bateman A
Number in seed: 254
Number in full: 121459
Average length of the domain: 34.00 aa
Average identity of full alignment: 37 %
Average coverage of the sequence by the domain: 26.04 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.0 7.0
Trusted cut-off 23.0 7.0
Noise cut-off 22.9 6.9
Model length: 36
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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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 HemolysinCabind domain has been found. There are 216 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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