Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
5  structures 223  species 1  interaction 235  sequences 5  architectures

Family: Cyclophil_like (PF04126)

Summary: Cyclophilin-like

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Cyclophilin-like Provide feedback

This domain has a cyclophilin-like fold, consisting of an eight-stranded beta-barrel with an alpha helix located between the beta-2 and beta-3 strands and a 310 helix located between the beta-7 and beta-8 strands. The catalytic site found in human cyclophilin is not conserved in this domain, suggesting a different function for this domain [1,2].

Literature references

  1. Jin KK, Krishna SS, Schwarzenbacher R, McMullan D, Abdubek P, Agarwalla S, Ambing E, Axelrod H, Canaves JM, Chiu HJ, Deacon AM, DiDonato M, Elsliger MA, Feuerhelm J, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Haugen J, Hornsby M, Jaroszewski L, Klock HE, Knuth MW, Koesema E, Kreusch A, Kuhn P, Lesley SA, Miller MD, Moy K, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Quijano K, Reyes R, Rife C, Stevens RC, Spraggon G, van den Bedem H, Velasquez J, White A, Wolf G, Han GW, Xu Q, Hodgson KO, Wooley J, Wilson IA;, Proteins. 2006;63:1112-1118.: Crystal structure of TM1367 from Thermotoga maritima at 1.90 A resolution reveals an atypical member of the cyclophilin (peptidylprolyl isomerase) fold. PUBMED:16544291 EPMC:16544291

  2. Ai X, Li L, Semesi A, Yee A, Arrowsmith CH, Li SS, Choy WY;, J Biomol NMR. 2007;38:353-358.: Hypothetical protein AF2241 from Archaeoglobus fulgidus adopts a cyclophilin-like fold. PUBMED:17610131 EPMC:17610131


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR025658

This entry represent a TM1367-type cyclophilin-like domain. The crystal structure of protein TM1367 from Thermotoga maritima revealed an atypical cyclophilin (peptidylprolyl isomerase) fold [PUBMED:16544291]. The catalytic site found in human cyclophilin is not conserved in this domain, suggesting a different function for this domain [PUBMED:16544291, PUBMED:17610131].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...

Pfam Clan

This family is a member of clan Cyclophil-like (CL0475), which has the following description:

This superfamily is characterised by being the core, closed, beta barrel of cyclophilin with complex topology, with some family members lacking the N-terminal strand of cyclophilin but retaining a closed barrel.

The clan contains the following 6 members:

AHS1 Cyclophil_like DUF3830 DUF871 PIF Pro_isomerase

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(14)
Full
(235)
Representative proteomes NCBI
(217)
Meta
(103)
RP15
(35)
RP35
(56)
RP55
(71)
RP75
(81)
Jalview View  View  View  View  View  View  View  View 
HTML View  View  View  View  View  View     
PP/heatmap 1 View  View  View  View  View     
Pfam viewer View  View             

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

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

Format an alignment

  Seed
(14)
Full
(235)
Representative proteomes NCBI
(217)
Meta
(103)
RP15
(35)
RP35
(56)
RP55
(71)
RP75
(81)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(14)
Full
(235)
Representative proteomes NCBI
(217)
Meta
(103)
RP15
(35)
RP35
(56)
RP55
(71)
RP75
(81)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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: COG2164
Previous IDs: DUF369;
Type: Family
Author: Kerrison ND, Finn RD, Eberhardt R
Number in seed: 14
Number in full: 235
Average length of the domain: 113.10 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 69.69 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.3 20.3
Trusted cut-off 20.3 20.3
Noise cut-off 20.1 20.2
Model length: 120
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Show

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Interactions

There is 1 interaction for this family. More...

Cyclophil_like

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 Cyclophil_like domain has been found. There are 5 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.

Loading structure mapping...