Summary: Bacterial pre-peptidase C-terminal domain
Bacterial pre-peptidase C-terminal domain Provide feedback
This domain is normally found at the C-terminus of secreted bacterial peptidases. They are not present in the active peptidase. It is possible that they fulfill a similar role to the PKD (PF00801) domain, which also are found in this context. Visual analysis suggests that PKD and PPC are distantly related (personal obs:Bateman A, Yeats C).
Internal database links
|SCOOP:||DUF642 DUF1883 Inhibitor_I42 DUF4962 DUF5060|
External database links
|MEROPS:||S8 M9 M4|
This tab holds annotation information from the InterPro database.
InterPro entry IPR007280This domain is normally found at the C terminus of secreted archaeal and bacterial peptidases, the majority of which belong to MEROPS peptidase families M4 (vibriolysin, INTERPRO), M9A amd M9B (microbial collangenase, INTERPRO), M28 (aminopeptidase Ap1, INTERPRO) and S8 (subtilisin family peptidases, INTERPRO).
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
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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 .
The clan contains the following 32 members:Allantoicase ANAPC10 Bac_rhamnosid_N BetaGal_dom4_5 CBM-like CBM27 CBM60 CBM_11 CBM_15 CBM_17_28 CBM_35 CBM_4_9 CBM_6 CIA30 DUF5000 DUF642 Endotoxin_C Ephrin_lbd F5_F8_type_C FBA Glyco_hydro_2_N Laminin_N Lyase_N Muskelin_N NPCBM P_proprotein PA-IL PepX_C PITH PPC Sad1_UNC XRCC1_N
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
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Note: You can also download the data file for the tree.
Curation and family details
|Seed source:||Yeats C|
|Number in seed:||93|
|Number in full:||5390|
|Average length of the domain:||69.50 aa|
|Average identity of full alignment:||30 %|
|Average coverage of the sequence by the domain:||13.96 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||11|
|Download:||download the raw HMM for this family|
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a FASTA-format file
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How the sunburst is generated
Colouring and labels
Anomalies in the taxonomy tree
Missing taxonomic levels
Unmapped species names
Too many species/sequences
The tree shows the occurrence of this domain across different species. More...
You can use the tree controls to manipulate how the interactive tree is displayed:
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There are 3 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 PPC domain has been found. There are 13 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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