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.
0  structures 128  species 0  interactions 444  sequences 10  architectures

Family: B9-C2 (PF07162)

Summary: Ciliary basal body-associated, B9 protein

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.

Ciliary basal body-associated, B9 protein Provide feedback

The B9-C2 domain is found in proteins associated with the ciliary basal body. B9 domains were identified as a specific family of C2 domains [1]. There are three sub-families represented by this family, notably, Mks1-Xbx7, Stumpy-Tza1 and Tza2 groups of proteins. Mutations in human Mks1 result in the developmental disorder Mechler-Gruber syndrome [2]; mutations in mouse Stumpy lead to perinatal hydrocephalus and severe polycystic kidney disease [3]. All the three distinct types of B9-C2 proteins cooperatively localise to the basal body or centrosome of cilia.

Literature references

  1. Zhang D, Aravind L;, Gene. 2010;469:18-30.: Identification of novel families and classification of the C2 domain superfamily elucidate the origin and evolution of membrane targeting activities in eukaryotes. PUBMED:20713135 EPMC:20713135

  2. Kyttala M, Tallila J, Salonen R, Kopra O, Kohlschmidt N, Paavola-Sakki P, Peltonen L, Kestila M;, Nat Genet. 2006;38:155-157.: MKS1, encoding a component of the flagellar apparatus basal body proteome, is mutated in Meckel syndrome. PUBMED:16415886 EPMC:16415886

  3. Town T, Breunig JJ, Sarkisian MR, Spilianakis C, Ayoub AE, Liu X, Ferrandino AF, Gallagher AR, Li MO, Rakic P, Flavell RA;, Proc Natl Acad Sci U S A. 2008;105:2853-2858.: The stumpy gene is required for mammalian ciliogenesis. PUBMED:18287022 EPMC:18287022


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR010796

B9 domain containing proteins are found in flagellar or cilia-containing species. Although its function is unknown, a cilia-specific role has been suggested for the poorly characterised B9 domain [PUBMED:16415886, PUBMED:17127412, PUBMED:18337471]. Some proteins known to contain a B9 domain are listed below:

  • Mammalian Meckel syndrome 1 (MKS1) protein, which may be related to the ciliary basal body.
  • Mammalian protein B9D1 and B9D2.
  • Caenorhabditis elegans X-box promoter element regulated protein 7 (xbx-7). It corresponds to mammalian MKS1.
  • Caenorhabditis elegans ciliary transition zone associate protein 1 (tza-1). It corresponds to mammalian B9D2.
  • Caenorhabditis elegans ciliary transition zone associate protein 2 (tza-2). It corresponds to mammalian B9D1.
  • Paramecium tetraurelia ICIS-1 (Involved in Cilia Stability-1), the B9D2 homolog.

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 C2 (CL0154), which contains the following 9 members:

Aida_C2 B9-C2 C2 CC2D2AN-C2 CEP76-C2 DOCK-C2 NT-C2 PI3K_C2 PTEN_C2

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
(45)
Full
(444)
Representative proteomes NCBI
(416)
Meta
(10)
RP15
(122)
RP35
(153)
RP55
(228)
RP75
(283)
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
(45)
Full
(444)
Representative proteomes NCBI
(416)
Meta
(10)
RP15
(122)
RP35
(153)
RP55
(228)
RP75
(283)
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
(45)
Full
(444)
Representative proteomes NCBI
(416)
Meta
(10)
RP15
(122)
RP35
(153)
RP55
(228)
RP75
(283)
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.

Pfam alignments:

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_12595 (release 10.0)
Previous IDs: B9;
Type: Family
Author: Vella Briffa B, Coggill P
Number in seed: 45
Number in full: 444
Average length of the domain: 153.90 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 49.58 %

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 20.8 20.8
Trusted cut-off 20.9 21.1
Noise cut-off 20.7 20.0
Model length: 168
Family (HMM) version: 6
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.