Summary: TAP-like protein
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This is the Wikipedia entry entitled "Alpha/beta hydrolase fold". More...
Alpha/beta hydrolase fold Edit Wikipedia article
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TAP-like protein Provide feedback
This is a family of putative bacterial peptidases and hydrolases that bear similarity to a tripeptidyl aminopeptidase isolated from Streptomyces lividans (Q54410). A member of this family (Q6E3K7) is thought to be involved in the C-terminal processing of propionicin F, a bacteriocidin characterised from Propionibacterium freudenreichii [1].
Literature references
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Brede DA, Faye T, Johnsborg O, Odegard I, Nes IF, Holo H; , Appl Environ Microbiol 2004;70:7303-7310.: Molecular and genetic characterization of propionicin F, a bacteriocin from Propionibacterium freudenreichii. PUBMED:15574930 EPMC:15574930
Internal database links
SCOOP: | Abhydrolase_1 Abhydrolase_2 Abhydrolase_3 Abhydrolase_5 Abhydrolase_6 AXE1 BAAT_C DLH DUF1057 DUF2048 Esterase Esterase_PHB FSH1 Hydrolase_4 LIDHydrolase Ndr Peptidase_S15 Peptidase_S9 Ser_hydrolase Thioesterase UPF0227 |
Similarity to PfamA using HHSearch: | Peptidase_S9 Ser_hydrolase |
This tab holds annotation information from the InterPro database.
InterPro entry IPR013595
This entry represents a C-terminal domain associated with putative hydrolases and bacterial peptidases that belong to MEROPS peptidase family S33 (clan SC). They are related to a tripeptidyl aminopeptidase from Streptomyces lividans (SWISSPROT). A member of this family (SWISSPROT) is thought to be involved in the C-terminal processing of propionicin F, a bacteriocidin characterised from Propionibacterium freudenreichii [PUBMED:15574930].
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 AB_hydrolase (CL0028), which has the following description:
This catalytic domain is found in a very wide range of enzymes.
The clan contains the following 70 members:
Abhydro_lipase Abhydrolase_1 Abhydrolase_2 Abhydrolase_3 Abhydrolase_4 Abhydrolase_5 Abhydrolase_6 Abhydrolase_7 Abhydrolase_8 Abhydrolase_9 Acyl_transf_2 Asp2 AXE1 BAAT_C Chlorophyllase Chlorophyllase2 COesterase Cutinase DLH DUF1057 DUF1100 DUF1350 DUF1400 DUF1749 DUF2048 DUF2235 DUF2920 DUF2974 DUF3089 DUF3141 DUF3530 DUF452 DUF676 DUF726 DUF818 DUF829 DUF900 DUF915 EHN Esterase Esterase_PHB FSH1 Hydrolase_4 LCAT LIDHydrolase LIP Lipase Lipase3_N Lipase_2 Lipase_3 Ndr PAE PAF-AH_p_II Palm_thioest PE-PPE Peptidase_S10 Peptidase_S15 Peptidase_S28 Peptidase_S37 Peptidase_S9 PGAP1 PhaC_N PHB_depo_C PhoPQ_related Say1_Mug180 Ser_hydrolase Tannase Thioesterase UPF0227 VirJAlignments
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...
View options
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 (33) |
Full (4639) |
Representative proteomes | UniProt (12639) |
NCBI (76354) |
Meta (880) |
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RP15 (383) |
RP35 (1847) |
RP55 (4141) |
RP75 (7049) |
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Jalview | |||||||||
HTML | |||||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
Format an alignment
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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 (33) |
Full (4639) |
Representative proteomes | UniProt (12639) |
NCBI (76354) |
Meta (880) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (383) |
RP35 (1847) |
RP55 (4141) |
RP75 (7049) |
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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: | Pfam-B_3096 (release 18.0) |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Fenech M |
Number in seed: | 33 |
Number in full: | 4639 |
Average length of the domain: | 100.50 aa |
Average identity of full alignment: | 22 % |
Average coverage of the sequence by the domain: | 19.46 % |
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: | 103 | ||||||||||||
Family (HMM) version: | 11 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Selections
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...
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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 Abhydrolase_4 domain has been found. There are 8 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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