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0  structures 64  species 0  interactions 542  sequences 3  architectures

Family: LCE (PF14672)

Summary: Late cornified envelope

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.

Late cornified envelope Provide feedback

This is a family of late cornified envelope proteins that are expressed in skin [1].

Literature references

  1. Jackson B, Tilli CM, Hardman MJ, Avilion AA, MacLeod MC, Ashcroft GS, Byrne C;, J Invest Dermatol. 2005;124:1062-1070.: Late cornified envelope family in differentiating epithelia--response to calcium and ultraviolet irradiation. PUBMED:15854049 EPMC:15854049


This tab holds annotation information from the InterPro database.

InterPro entry IPR028205

This is a family of late cornified envelope proteins that are expressed in skin [ PUBMED:15854049 ]. They are precursors of the cornified envelope of the stratum corneum, the outermost layer of the epidermis.

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 and the UniProtKB 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
(19)
Full
(542)
Representative proteomes UniProt
(812)
RP15
(91)
RP35
(120)
RP55
(330)
RP75
(538)
Jalview View  View  View  View  View  View  View 
HTML View  View           
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
(19)
Full
(542)
Representative proteomes UniProt
(812)
RP15
(91)
RP35
(120)
RP55
(330)
RP75
(538)
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
(19)
Full
(542)
Representative proteomes UniProt
(812)
RP15
(91)
RP35
(120)
RP55
(330)
RP75
(538)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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: Jackhmmer:Q5TA76
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Eberhardt R
Number in seed: 19
Number in full: 542
Average length of the domain: 64.70 aa
Average identity of full alignment: 55 %
Average coverage of the sequence by the domain: 93.72 %

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 28.3 28.3
Trusted cut-off 28.5 28.4
Noise cut-off 25.8 28.2
Model length: 93
Family (HMM) version: 8
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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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.

AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0A6YVV1 View 3D Structure Click here
A0A0G2KAB7 View 3D Structure Click here
A0A3B3IT34 View 3D Structure Click here
B9EJP6 View 3D Structure Click here
B9EJP6 View 3D Structure Click here
D3YUU5 View 3D Structure Click here
D3YUU5 View 3D Structure Click here
D3ZFL2 View 3D Structure Click here
D3ZFL2 View 3D Structure Click here
D3ZG26 View 3D Structure Click here
D3ZG46 View 3D Structure Click here
D3ZG46 View 3D Structure Click here
D3ZQB8 View 3D Structure Click here
D3ZQB8 View 3D Structure Click here
D3ZQC0 View 3D Structure Click here
D3ZQC0 View 3D Structure Click here
D3ZYD4 View 3D Structure Click here
D3ZYD4 View 3D Structure Click here
D4A973 View 3D Structure Click here
D4A973 View 3D Structure Click here
E9Q8V1 View 3D Structure Click here
F8VQJ0 View 3D Structure Click here
J3QP15 View 3D Structure Click here
J3QP15 View 3D Structure Click here
J3QP15 View 3D Structure Click here
M0R5D9 View 3D Structure Click here
M0R5D9 View 3D Structure Click here
M0R5X4 View 3D Structure Click here
M0R5X4 View 3D Structure Click here
M0R9P6 View 3D Structure Click here
M0R9P6 View 3D Structure Click here
O14633 View 3D Structure Click here
O14633 View 3D Structure Click here
O14633 View 3D Structure Click here
Q497I5 View 3D Structure Click here
Q5T5A8 View 3D Structure Click here
Q5T5B0 View 3D Structure Click here
Q5T751 View 3D Structure Click here
Q5T751 View 3D Structure Click here
Q5T751 View 3D Structure Click here
Q5T752 View 3D Structure Click here
Q5T752 View 3D Structure Click here
Q5T753 View 3D Structure Click here
Q5T753 View 3D Structure Click here
Q5T753 View 3D Structure Click here
Q5T754 View 3D Structure Click here
Q5T754 View 3D Structure Click here
Q5T7P2 View 3D Structure Click here
Q5T7P2 View 3D Structure Click here
Q5T7P3 View 3D Structure Click here
Q5T7P3 View 3D Structure Click here
Q5TA76 View 3D Structure Click here
Q5TA77 View 3D Structure Click here
Q5TA78 View 3D Structure Click here
Q5TA79 View 3D Structure Click here
Q5TA79 View 3D Structure Click here
Q5TA81 View 3D Structure Click here
Q5TA81 View 3D Structure Click here
Q5TA82 View 3D Structure Click here
Q5TA82 View 3D Structure Click here
Q5TCM9 View 3D Structure Click here
Q5TCM9 View 3D Structure Click here
Q6PAI4 View 3D Structure Click here
Q91V05 View 3D Structure Click here
Q9BYE3 View 3D Structure Click here
Q9CQH5 View 3D Structure Click here
Q9CQH5 View 3D Structure Click here
Q9CQM7 View 3D Structure Click here
Q9CR91 View 3D Structure Click here
Q9D139 View 3D Structure Click here
Q9D139 View 3D Structure Click here
Q9D139 View 3D Structure Click here
Q9D149 View 3D Structure Click here
Q9D149 View 3D Structure Click here
Q9D149 View 3D Structure Click here
Q9D195 View 3D Structure Click here
Q9D195 View 3D Structure Click here
Q9D1C5 View 3D Structure Click here
Q9D1C5 View 3D Structure Click here
Q9D1G7 View 3D Structure Click here
Q9D1G7 View 3D Structure Click here
Q9D1G7 View 3D Structure Click here
Q9D1K4 View 3D Structure Click here
Q9D1K4 View 3D Structure Click here
Q9D6P5 View 3D Structure Click here
Q9D6P5 View 3D Structure Click here
Q9D6R3 View 3D Structure Click here
Q9D6R3 View 3D Structure Click here
Q9D731 View 3D Structure Click here
Q9D731 View 3D Structure Click here

trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;