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0  structures 144  species 0  interactions 156  sequences 6  architectures

Family: Afi1 (PF07792)

Summary: Docking domain of Afi1 for Arf3 in vesicle trafficking

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Docking domain of Afi1 for Arf3 in vesicle trafficking Provide feedback

This domain occurs at the N-terminal of Afi1, an Arf3p-interacting protein, is a protein necessary for vesicle trafficking in yeast. This domain is the interacting region of the protein which binds to Arf3, the highly conserved small GTPases (ADP-ribosylation factors). Afi1 is distributed asymmetrically at the plasma membrane and is required for polarized distribution of Arf3 but not of an Arf3 guanine nucleotide-exchange factor, Yel1p. However, Afi1 is not required for targeting of Arf3 or Yel1p to the plasma membrane. Afi1 functions as an Arf3 polarization-specific adapter and participates in development of polarity. Although Arf3 is the homologue of human Arf6 it does not function in the same way, not being necessary for endocytosis or for mating factor receptor internalization. In the S phase, however, it is concentrated at the plasma membrane of the emerging bud. Because of its polarized localisation and its critical function in the normal budding pattern of yeast, Arf3 is probably a regulator of vesicle trafficking, which is important for polarized growth.

Literature references

  1. Tsai PC, Lee SW, Liu YW, Chu CW, Chen KY, Ho JC, Lee FJ;, J Biol Chem. 2008;283:16915-16927.: Afi1p functions as an Arf3p polarization-specific docking factor for development of polarity. PUBMED:18397879 EPMC:18397879


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR012860

This domain occurs at the N terminus of Afi1 (Arf3-interacting protein 1), a protein necessary for vesicle trafficking in yeast. This domain is the interacting region of the protein which binds to Arf3. Afi1 is distributed asymmetrically at the plasma membrane and is required for polarized distribution of Arf3 but not of an Arf3 guanine nucleotide-exchange factor, Yel1p. However, Afi1 is not required for targeting of Arf3 or Yel1p to the plasma membrane. Afi1 functions as an Arf3 polarization-specific adapter and participates in development of polarity [PUBMED:18397879]. Although Arf3 is the homologue of human Arf6 it does not function in the same way, not being necessary for endocytosis or for mating factor receptor internalisation. In the S phase, however, it is concentrated at the plasma membrane of the emerging bud. Because of its polarized localisation and its critical function in the normal budding pattern of yeast, Arf3 is probably a regulator of vesicle trafficking, which is important for polarized growth.

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 AVL9 (CL0330), which contains the following 5 members:

Afi1 Avl9 DENN DUF2347 SPA

Alignments

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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.

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(31)
Full
(156)
Representative proteomes NCBI
(210)
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RP15
(42)
RP35
(72)
RP55
(103)
RP75
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  Seed
(31)
Full
(156)
Representative proteomes NCBI
(210)
Meta
(0)
RP15
(42)
RP35
(72)
RP55
(103)
RP75
(117)
Alignment:
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  Seed
(31)
Full
(156)
Representative proteomes NCBI
(210)
Meta
(0)
RP15
(42)
RP35
(72)
RP55
(103)
RP75
(117)
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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.

Pfam alignments:

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Trees

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Curation and family details

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Curation View help on the curation process

Seed source: Pfam-B_9160 (release 14.0)
Previous IDs: DUF1630;
Type: Domain
Author: Fenech M
Number in seed: 31
Number in full: 156
Average length of the domain: 149.80 aa
Average identity of full alignment: 36 %
Average coverage of the sequence by the domain: 19.68 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.5 25.5
Trusted cut-off 26.0 25.5
Noise cut-off 24.9 25.2
Model length: 145
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

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