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5  structures 579  species 0  interactions 3002  sequences 56  architectures

Family: Spc97_Spc98 (PF04130)

Summary: Spc97 / Spc98 family

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.

Spc97 / Spc98 family Provide feedback

The spindle pole body (SPB) functions as the microtubule-organising centre in yeast. Members of this family are spindle pole body (SBP) components such as Spc97 and Spc98 that form a complex with gamma-tubulin. This family of proteins includes the grip motif 1 and grip moti 2 [1]. Members of this family all form components of the gamma-tubulin complex, GCP [2].

Literature references

  1. Gunawardane RN, Martin OC, Cao K, Zhang L, Dej K, Iwamatsu A, Zheng Y; , J Cell Biol. 2000;151:1513-1524.: Characterization and reconstitution of Drosophila gamma-tubulin ring complex subunits. PUBMED:11134079 EPMC:11134079

  2. Kikuchi M, Nishima T;, Nihon Eiseigaku Zasshi. 1975;30:108.: [Correlation of concentrations of gamma aminolevulinic acid and creatinine in the urine (screening test for lead exposure by urinary spot samples)]. PUBMED:1169457 EPMC:1169457


This tab holds annotation information from the InterPro database.

InterPro entry IPR007259

The microtubule organizing centres (MTOCs) of eukaryotic cells are the sites of nucleation of microtubules, and are known as the centrosome in animal cells and the spindle pole body in yeast. Gamma tubulin, which is 30% identical to alpha and beta tubulins that form microtubules, appears to be a key protein involved in nucleation of microtubules.

Gamma tubulin is found in two complexes, the large gamma tubulin ring complex (gamma TuRC) and the gamma tubulin small complex (gamma TuSC). Gamma TuSC is a subunit of gamma TuRC, and is composed of only three proteins: gamma tubulin and gamma-tubulin complex protein 2 and 3 (GCP2 and GCP3). GCP2 and 3 are also known as Spc97 and Spc98 proteins in budding yeast, Dgrip84 and Dgrip91 in Drosophila melanogaster (Fruit fly), and Xgrip109 and Xgrip110 in Xenopus laevis (African clawed frog) [PUBMED:11297925]. Gamma TuSC is able to only weakly nucleate microtubules, and it is believed that assembly into the larger gamma TuRC complex is necessary for efficient nucleation [PUBMED:10037793].

Members of this family are gamma-tubulin complex components such as GCP2/3/4/5 and Spc97/98 [PUBMED:11950928].

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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Pfam Clan

This family is a member of clan GCP (CL0540), which has the following description:

This superfamily carries families of proteins all derived via gene-duplication events that act together in the gamma-tubulin complex. This complex is required for microtubule nucleation at the centrosome.

The clan contains the following 2 members:

GCP5-Mod21 Spc97_Spc98

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...

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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
(90)
Full
(3002)
Representative proteomes UniProt
(5391)
NCBI
(6525)
Meta
(20)
RP15
(819)
RP35
(1603)
RP55
(2286)
RP75
(2922)
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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
(90)
Full
(3002)
Representative proteomes UniProt
(5391)
NCBI
(6525)
Meta
(20)
RP15
(819)
RP35
(1603)
RP55
(2286)
RP75
(2922)
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
(90)
Full
(3002)
Representative proteomes UniProt
(5391)
NCBI
(6525)
Meta
(20)
RP15
(819)
RP35
(1603)
RP55
(2286)
RP75
(2922)
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_3531 (release 7.3)
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 90
Number in full: 3002
Average length of the domain: 535.60 aa
Average identity of full alignment: 16 %
Average coverage of the sequence by the domain: 65.17 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.5 26.8
Model length: 540
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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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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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 Spc97_Spc98 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.

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