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12  structures 1879  species 2  interactions 3549  sequences 32  architectures

Family: FKBP_N (PF01346)

Summary: Domain amino terminal to FKBP-type peptidyl-prolyl isomerase

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Domain amino terminal to FKBP-type peptidyl-prolyl isomerase Provide feedback

This family is only found at the amino terminus of PF00254. This entry represents the N-terminal domain found in FKBP-type peptidylprolyl isomerases (PPIase). The N-terminal domain forms the dimer interface by the mutual exchange of two beta-strands between monomers [1].

Literature references

  1. Saul FA, Arie JP, Vulliez-le Normand B, Kahn R, Betton JM, Bentley GA;, J Mol Biol. 2004;335:595-608.: Structural and functional studies of FkpA from Escherichia coli, a cis/trans peptidyl-prolyl isomerase with chaperone activity. PUBMED:14672666 EPMC:14672666


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000774

Peptidyl-prolyl cis-trans isomerase (PPIase) catalyses the cis-trans isomerisation of proline imidic peptide bonds in oligopeptides [PUBMED:2644542]. This alpha helical domain is found at the N terminus of proteins belonging to the FKBP-type peptidyl-prolyl cis-trans isomerase family.

Peptidyl-prolyl cis-trans isomerase has been shown to accelerate the refolding of several proteins in vitro [PUBMED:6395866, PUBMED:3306408, PUBMED:3277061]; the FKPB-type enzymes probably act in the folding of extracytoplasmic proteins.

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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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 (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
(414)
Full
(3549)
Representative proteomes UniProt
(13441)
NCBI
(16246)
Meta
(295)
RP15
(771)
RP35
(2090)
RP55
(3605)
RP75
(5914)
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PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(414)
Full
(3549)
Representative proteomes UniProt
(13441)
NCBI
(16246)
Meta
(295)
RP15
(771)
RP35
(2090)
RP55
(3605)
RP75
(5914)
Alignment:
Format:
Order:
Sequence:
Gaps:
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Download options

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
(414)
Full
(3549)
Representative proteomes UniProt
(13441)
NCBI
(16246)
Meta
(295)
RP15
(771)
RP35
(2090)
RP55
(3605)
RP75
(5914)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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: Pfam-B_402 (release 3.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , El-Gebali S
Number in seed: 414
Number in full: 3549
Average length of the domain: 91.90 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 39.55 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.6 20.6
Trusted cut-off 20.6 20.6
Noise cut-off 20.5 20.5
Model length: 97
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

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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Interactions

There are 2 interactions for this family. More...

FKBP_N FKBP_C

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 FKBP_N domain has been found. There are 12 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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