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0  structures 35  species 0  interactions 63  sequences 2  architectures

Family: FTA2 (PF13095)

Summary: Kinetochore Sim4 complex subunit FTA2

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Kinetochore Sim4 complex subunit FTA2 Provide feedback

Fission yeast has three kinetochore protein complexes. Two complexes, Sim4 and Ndc80-MIND-Spc7 (NMS), are constitutive components, whereas the third complex, DASH, is transiently associated with kinetochores only in mitosis and is required for precise chromosome segregation. The Sim4 complex functions as a loading dock for the DASH complex. Sim4 consists of a number of different proteins including Ftas 1-7 and Dad1 [1]. The equivalent higher eukaryotic protein is CENP-P. The centromere, which is the basic element of chromosome inheritance, is epigenetically determined in mammals. CENP-A, the centromere-specific histone H3 variant, assembles an array of nucleosomes and it is this that seems to be the prime candidate for specifying centromere identity. CENP-A nucleosomes directly recruit a proximal CENP-A nucleosome associated complex (NAC) comprised of CENP-M, CENP-N and CENP-T, CENP-U(50), CENP-C and CENP-H. Assembly of the CENP-A NAC at centromeres is dependent on CENP-M, CENP-N and CENP-T. Additionally, there are seven other subunits which make up the CENP-A-nucleosome distal (CAD) centromere, CENP-K, CENP-L, CENP-O, CENP-P, CENP-Q, CENP-R and CENP-S, also assembling on the CENP-A NAC [2].

Literature references

  1. Liu X, McLeod I, Anderson S, Yates JR 3rd, He X; , EMBO J. 2005;24:2919-2930.: Molecular analysis of kinetochore architecture in fission yeast. PUBMED:16079914 EPMC:16079914

  2. Foltz DR, Jansen LE, Black BE, Bailey AO, Yates JR 3rd, Cleveland DW; , Nat Cell Biol. 2006;8:458-469.: The human CENP-A centromeric nucleosome-associated complex. PUBMED:16622419 EPMC:16622419


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR025213

Fission yeast has three kinetochore protein complexes. Two complexes, Sim4 and Ndc80-MIND-Spc7 (NMS), are constitutive components, whereas the third complex, DASH, is transiently associated with kinetochores only in mitosis and is required for precise chromosome segregation. The Sim4 complex functions as a loading dock for the DASH complex. Sim4 consists of a number of different proteins including Ftas 1-7 and Dad1 [PUBMED:16079914].

This entry represents Fta2.

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
(13)
Full
(63)
Representative proteomes NCBI
(62)
Meta
(2)
RP15
(3)
RP35
(27)
RP55
(48)
RP75
(56)
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Format an alignment

  Seed
(13)
Full
(63)
Representative proteomes NCBI
(62)
Meta
(2)
RP15
(3)
RP35
(27)
RP55
(48)
RP75
(56)
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
(13)
Full
(63)
Representative proteomes NCBI
(62)
Meta
(2)
RP15
(3)
RP35
(27)
RP55
(48)
RP75
(56)
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: Wood V
Previous IDs: none
Type: Family
Author: Coggill P
Number in seed: 13
Number in full: 63
Average length of the domain: 191.60 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 60.04 %

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 20.7 20.7
Trusted cut-off 21.4 21.4
Noise cut-off 20.5 19.8
Model length: 209
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

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