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0  structures 2  species 0  interactions 2  sequences 1  architecture

Family: Sec3_C_2 (PF15278)

Summary: Sec3 exocyst complex subunit

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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.

Sec3 exocyst complex subunit Provide feedback

This small Sec3 C-terminal domain family is based around the fission yeast protein, and is rather shorter than the budding yeast/vertebrate domain Sec3_C, family. PF09763. In fact it is only this coiled-coil region that they carry in common. The full length fission yeast, UniProtKB:Q10324 protein Sec3 is redundant with Exo70 for viability and for the localisation of other exocyst subunits, suggesting that these components act as exocyst tethers at the plasma membrane. Sec3, Exo70 and Sec5 are transported by the myosin V Myo52 along actin cables. The exocyst holo-complex, including Sec3 and Exo70, is present on exocytic vesicles, which can reach cell poles by either myosin-driven transport or random walk [1].

Literature references

  1. Bendezu FO, Vincenzetti V, Martin SG;, PLoS One. 2012;7:e40248.: Fission yeast sec3 and exo70 are transported on actin cables and localize the exocyst complex to cell poles. PUBMED:22768263 EPMC:22768263


External database links

This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

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 Vps51 (CL0295), which has the following description:

This clan includes an N-terminal domain from several vesicle transport proteins that are related to Vps51.

The clan contains the following 16 members:

COG2 COG5 COG6 Dor1 DUF2450 Exo70 Sec15 Sec3_C Sec3_C_2 Sec5 Sec6 Sec8_exocyst Vps51 Vps52 Vps53_N Zw10

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
(2)
Full
(2)
Representative proteomes NCBI
(3)
Meta
(0)
RP15
(1)
RP35
(1)
RP55
(2)
RP75
(2)
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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
(2)
Full
(2)
Representative proteomes NCBI
(3)
Meta
(0)
RP15
(1)
RP35
(1)
RP55
(2)
RP75
(2)
Alignment:
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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
(2)
Full
(2)
Representative proteomes NCBI
(3)
Meta
(0)
RP15
(1)
RP35
(1)
RP55
(2)
RP75
(2)
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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

This family is new in this Pfam release.

Seed source: Jackhmmer:Q10324
Previous IDs: none
Type: Domain
Author: Coggill P
Number in seed: 2
Number in full: 2
Average length of the domain: 86.00 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 14.06 %

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 27.0 27.0
Trusted cut-off 29.4 28.4
Noise cut-off 25.7 19.8
Model length: 86
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

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