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0  structures 263  species 0  interactions 295  sequences 6  architectures

Family: BCNT (PF07572)

Summary: Bucentaur or craniofacial development

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Bucentaur or craniofacial development Provide feedback

Bucentaur or craniofacial development protein 1 (BCNT) in ruminents has a different domain architecture to that in mouse and human. For this reason it has been used as a model for molecular evolution [1-3]. Both bovine and human BCNTs are phosphorylated by casein kinase II in vitro [4].

Literature references

  1. Takahashi I, Nobukuni T, Ohmori H, Kobayashi M, Tanaka S, Ohshima K, Okada N, Masui T, Hashimoto K, Iwashita S; , Gene 1998;211:387-394.: Existence of a bovine LINE repetitive insert that appears in the cDNA of bovine protein BCNT in ruminant, but not in human, genomes. PUBMED:9602175 EPMC:9602175

  2. Iwashita S, Itoh T, Takeda H, Sugimoto Y, Takahashi I, Nobukuni T, Sezaki M, Masui T, Hashimoto K; , Gene 2001;268:59-66.: Gene organization of bovine BCNT that contains a portion corresponding to an endonuclease domain derived from an RTE-1 (Bov-B LINE), non-LTR retrotransposable element: duplication of an intramolecular repeat unit downstream of the truncated RTE-1. PUBMED:11368901 EPMC:11368901

  3. Iwashita S, Osada N, Itoh T, Sezaki M, Oshima K, Hashimoto E, Kitagawa-Arita Y, Takahashi I, Masui T, Hashimoto K, Makalowski W; , Mol Biol Evol 2003;20:1556-1563.: A transposable element-mediated gene divergence that directly produces a novel type bovine Bcnt protein including the endonuclease domain of RTE-1. PUBMED:12832649 EPMC:12832649

  4. Iwashita S, Nobukuni T, Tanaka S, Kobayashi M, Iwanaga T, Tamate HB, Masui T, Takahashi I, Hashimoto K; , Biochim Biophys Acta 1999;1427:408-416.: Partial nuclear localization of a bovine phosphoprotein, BCNT, that includes a region derived from a LINE repetitive sequence in Ruminantia. PUBMED:10350657 EPMC:10350657


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR011421

Vertebrate BCNT (named after Bucentaur) or human craniofacial development protein 1 (CFDP1) are characterised by an N-terminal acidic region, a central and single IR element (inverted repeat) from the retrotransposable element-1 family (RTE-1) and a highly conserved 82-amino acid region at the C terminus.

This entry represents the BCNT C-terminal domain that is also found in Drosophila YETI, a protein that binds to a microtubule-based motor kinesin-1, and the yeast SWR1-complex protein 5 (SWC5), a component of the SWR1 chromatin remodeling complex [PUBMED:16384818, PUBMED:14720462].

In the bovine genome recombination of BCNT through the IR element with a member of the retrotransposable element-1 family, leads to gene duplications, the insertion of the RTE-1 apurinic/apyrimidinic endonuclease (APE)-like domain (see INTERPRO) with the concomitant loss of the conserved C-terminal domain of BCNT and with the additional recruitment of either 2 (p97bcnt) or 3 (p97bcnt-2) C-terminal IR-elements [PUBMED:19393175].

For more information about this family, see http://www.intechopen.com/download/pdf/pdfs_id/21926

Domain organisation

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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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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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
(37)
Full
(295)
Representative proteomes NCBI
(299)
Meta
(2)
RP15
(71)
RP35
(117)
RP55
(177)
RP75
(214)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(37)
Full
(295)
Representative proteomes NCBI
(299)
Meta
(2)
RP15
(71)
RP35
(117)
RP55
(177)
RP75
(214)
Alignment:
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Order:
Sequence:
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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
(37)
Full
(295)
Representative proteomes NCBI
(299)
Meta
(2)
RP15
(71)
RP35
(117)
RP55
(177)
RP75
(214)
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: Pfam-B_10149 (release 12.0)
Previous IDs: none
Type: Family
Author: Studholme D
Number in seed: 37
Number in full: 295
Average length of the domain: 78.80 aa
Average identity of full alignment: 36 %
Average coverage of the sequence by the domain: 26.19 %

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 22.2 22.2
Trusted cut-off 25.3 24.2
Noise cut-off 21.5 21.5
Model length: 81
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

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