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41  structures 1475  species 0  interactions 21184  sequences 502  architectures

Family: ArfGap (PF01412)

Summary: Putative GTPase activating protein for Arf

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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.

Putative GTPase activating protein for Arf Provide feedback

Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.

Literature references

  1. Hammonds-Odie LP, Jackson TR, Profit AA, Blader IJ, Turck CW, Prestwich GD, Theibert AB; , J Biol Chem 1996;271:18859-18868.: Identification and cloning of centaurin-alpha. A novel phosphatidylinositol 3,4,5-trisphosphate-binding protein from rat brain. PUBMED:8702546 EPMC:8702546

  2. Tanaka K, Imajoh-Ohmi S, Sawada T, Shirai R, Hashimoto Y, Iwasaki S, Kaibuchi K, Kanaho Y, Shirai T, Terada Y, Kimura K, Nagata S, Fukui Y; , Eur J Biochem 1997;245:512-519.: A target of phosphatidylinositol 3,4,5-trisphosphate with a zinc finger motif similar to that of the ADP-ribosylation -factor GTPase-activating protein and two pleckstrin homology domains. PUBMED:9151987 EPMC:9151987

  3. Vitale N, Moss J, Vaughan M; , J Biol Chem 1998;273:2553-2560.: Molecular characterization of the GTPase-activating domain of ADP-ribosylation factor domain protein 1 (ARD1). PUBMED:9446556 EPMC:9446556


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001164

Proteins containing this domain include ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins [ PUBMED:9446556 ]. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins.

The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved [ PUBMED:10601011 ]. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis [ PUBMED:10102276 ].

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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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 and the UniProtKB 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
(117)
Full
(21184)
Representative proteomes UniProt
(37693)
RP15
(2889)
RP35
(8083)
RP55
(17088)
RP75
(23594)
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HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(117)
Full
(21184)
Representative proteomes UniProt
(37693)
RP15
(2889)
RP35
(8083)
RP55
(17088)
RP75
(23594)
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
(117)
Full
(21184)
Representative proteomes UniProt
(37693)
RP15
(2889)
RP35
(8083)
RP55
(17088)
RP75
(23594)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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: SMART
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Ponting CP , Schultz J, Bork P
Number in seed: 117
Number in full: 21184
Average length of the domain: 114.30 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 17.34 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 28.7 28.7
Trusted cut-off 28.7 28.7
Noise cut-off 28.6 28.6
Model length: 117
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

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Selections

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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 ArfGap domain has been found. There are 41 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 sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0A0MPV6 View 3D Structure Click here
A0A0G2K2D4 View 3D Structure Click here
A0A0G2K5N8 View 3D Structure Click here
A0A0G2K7G2 View 3D Structure Click here
A0A0G2K7I9 View 3D Structure Click here
A0A0G2K7U5 View 3D Structure Click here
A0A0G2K808 View 3D Structure Click here
A0A0G2K847 View 3D Structure Click here
A0A0G2L9G1 View 3D Structure Click here
A0A0R0FEV9 View 3D Structure Click here
A0A0R0I2Q8 View 3D Structure Click here
A0A0R0KF93 View 3D Structure Click here
A0A0R4IAC2 View 3D Structure Click here
A0A0R4IM47 View 3D Structure Click here
A0A0R4IPR8 View 3D Structure Click here
A0A0R4IV74 View 3D Structure Click here
A0A140LH27 View 3D Structure Click here
A0A143ZVA6 View 3D Structure Click here
A0A1D6E1X2 View 3D Structure Click here
A0A1D6EEH5 View 3D Structure Click here
A0A1D6EEN2 View 3D Structure Click here
A0A1D6EHC3 View 3D Structure Click here
A0A1D6EMB9 View 3D Structure Click here
A0A1D6EYB4 View 3D Structure Click here
A0A1D6F5L2 View 3D Structure Click here
A0A1D6F9C1 View 3D Structure Click here
A0A1D6FJ31 View 3D Structure Click here
A0A1D6G4I8 View 3D Structure Click here
A0A1D6H0Z0 View 3D Structure Click here
A0A1D6H4U9 View 3D Structure Click here
A0A1D6H7G4 View 3D Structure Click here
A0A1D6I8A5 View 3D Structure Click here
A0A1D6IFU2 View 3D Structure Click here
A0A1D6IX43 View 3D Structure Click here
A0A1D6JYA9 View 3D Structure Click here
A0A1D6K164 View 3D Structure Click here
A0A1D6K975 View 3D Structure Click here
A0A1D6LDD0 View 3D Structure Click here
A0A1D6LS08 View 3D Structure Click here
A0A1D6MV52 View 3D Structure Click here
A0A1D6NRL0 View 3D Structure Click here
A0A1D6P636 View 3D Structure Click here
A0A1D6P636 View 3D Structure Click here
A0A1D6PDH1 View 3D Structure Click here
A0A1D6PYH0 View 3D Structure Click here
A0A1D6Q5I5 View 3D Structure Click here
A0A1D6Q972 View 3D Structure Click here
A0A1D6QQV7 View 3D Structure Click here
A0A1D8PCP6 View 3D Structure Click here
A0A1D8PD25 View 3D Structure Click here
A0A1D8PIG1 View 3D Structure Click here
A0A1D8PTP5 View 3D Structure Click here
A0A286YBU1 View 3D Structure Click here
A1L1F5 View 3D Structure Click here
A1Z7A6 View 3D Structure Click here
A1Z7K6 View 3D Structure Click here
A2BG45 View 3D Structure Click here
A2BIM6 View 3D Structure Click here
A4HVJ9 View 3D Structure Click here
A4I3Q4 View 3D Structure Click here
A4I485 View 3D Structure Click here
A4I7U0 View 3D Structure Click here
A4I7X2 View 3D Structure Click here
A4IAS7 View 3D Structure Click here
A4IDA3 View 3D Structure Click here
A6NIR3 View 3D Structure Click here
A8JNX0 View 3D Structure Click here
B0UXL9 View 3D Structure Click here
B1WBX6 View 3D Structure Click here
B3H5G3 View 3D Structure Click here
B4F9F9 View 3D Structure Click here
B4FDU5 View 3D Structure Click here
B4FK00 View 3D Structure Click here
B4FY47 View 3D Structure Click here
B6TSD4 View 3D Structure Click here
B8JLA1 View 3D Structure Click here
C0H4G3 View 3D Structure Click here
C0HEL3 View 3D Structure Click here
C0PAH7 View 3D Structure Click here
C0PDH5 View 3D Structure Click here
C6T8G3 View 3D Structure Click here
D4ABD3 View 3D Structure Click here
E1JHR0 View 3D Structure Click here
E7F7Y0 View 3D Structure Click here
E7F871 View 3D Structure Click here
E7FD04 View 3D Structure Click here
E7FF53 View 3D Structure Click here
E9PY16 View 3D Structure Click here
E9QE78 View 3D Structure Click here
E9QHH4 View 3D Structure Click here
F1LM60 View 3D Structure Click here
F1Q973 View 3D Structure Click here
F1Q975 View 3D Structure Click here
F1QCL0 View 3D Structure Click here
F1QX54 View 3D Structure Click here
F1QYT8 View 3D Structure Click here
F1R254 View 3D Structure Click here
F1R9R7 View 3D Structure Click here
F1RB32 View 3D Structure Click here
I1J6C3 View 3D Structure Click here
I1JK49 View 3D Structure Click here
I1JPD0 View 3D Structure Click here
I1JXQ4 View 3D Structure Click here
I1K1U8 View 3D Structure Click here
I1K469 View 3D Structure Click here
I1K5T7 View 3D Structure Click here
I1K6T3 View 3D Structure Click here
I1KQ36 View 3D Structure Click here
I1KWR3 View 3D Structure Click here
I1KX25 View 3D Structure Click here
I1L8K7 View 3D Structure Click here
I1LIX1 View 3D Structure Click here
I1LUW6 View 3D Structure Click here
I1LYU3 View 3D Structure Click here
I1M3D5 View 3D Structure Click here
I1MG37 View 3D Structure Click here
I1N9Z5 View 3D Structure Click here
K7K9C3 View 3D Structure Click here
K7KVG3 View 3D Structure Click here
K7KXB2 View 3D Structure Click here
K7L0I1 View 3D Structure Click here
K7L557 View 3D Structure Click here
K7L688 View 3D Structure Click here
K7LEB1 View 3D Structure Click here
K7LER1 View 3D Structure Click here
K7LQK9 View 3D Structure Click here
K7LSS6 View 3D Structure Click here
K7M0S1 View 3D Structure Click here
K7M627 View 3D Structure Click here
K7M6G6 View 3D Structure Click here
K7MDG6 View 3D Structure Click here
K7MIZ2 View 3D Structure Click here
K7MMV3 View 3D Structure Click here
K7MX33 View 3D Structure Click here
M0R5J1 View 3D Structure Click here
M0RC57 View 3D Structure Click here
O18181 View 3D Structure Click here
O43150 View 3D Structure Click here
O74345 View 3D Structure Click here
O75689 View 3D Structure Click here
O80925 View 3D Structure Click here
O82171 View 3D Structure Click here
O94601 View 3D Structure Click here
O95081 View 3D Structure Click here
P32572 View 3D Structure Click here
P35197 View 3D Structure Click here
P38682 View 3D Structure Click here
P40529 View 3D Structure Click here
P40956 View 3D Structure Click here
P52594 View 3D Structure Click here
P90904 View 3D Structure Click here
Q04412 View 3D Structure Click here
Q09531 View 3D Structure Click here
Q0DSA0 View 3D Structure Click here
Q0J0G6 View 3D Structure Click here
Q0J435 View 3D Structure Click here
Q0WQQ1 View 3D Structure Click here
Q10165 View 3D Structure Click here
Q10367 View 3D Structure Click here
Q10N88 View 3D Structure Click here
Q14161 View 3D Structure Click here
Q15027 View 3D Structure Click here
Q15057 View 3D Structure Click here
Q19467 View 3D Structure Click here
Q1AAU6 View 3D Structure Click here
Q1LXU3 View 3D Structure Click here
Q1ZXH8 View 3D Structure Click here
Q3MID3 View 3D Structure Click here
Q3UHD9 View 3D Structure Click here
Q4CSB1 View 3D Structure Click here
Q4CTU1 View 3D Structure Click here
Q4D8K1 View 3D Structure Click here
Q4DAT5 View 3D Structure Click here
Q4DID1 View 3D Structure Click here
Q4DJC3 View 3D Structure Click here
Q4DJV1 View 3D Structure Click here
Q4DNL0 View 3D Structure Click here
Q4DNS1 View 3D Structure Click here
Q4DST2 View 3D Structure Click here
Q4DU40 View 3D Structure Click here
Q4DWS4 View 3D Structure Click here
Q4DXC4 View 3D Structure Click here
Q4KLH5 View 3D Structure Click here
Q4KLN7 View 3D Structure Click here
Q4LDD4 View 3D Structure Click here
Q54DK4 View 3D Structure Click here
Q54DK9 View 3D Structure Click here
Q54LD4 View 3D Structure Click here
Q54TP9 View 3D Structure Click here
Q54WI0 View 3D Structure Click here
Q54YF3 View 3D Structure Click here
Q551Q8 View 3D Structure Click here
Q553M5 View 3D Structure Click here
Q55GS5 View 3D Structure Click here
Q5A7M1 View 3D Structure Click here
Q5FVC7 View 3D Structure Click here
Q5N770 View 3D Structure Click here
Q5RG20 View 3D Structure Click here
Q5TZC7 View 3D Structure Click here
Q5U464 View 3D Structure Click here
Q5VTM2 View 3D Structure Click here
Q5VUJ5 View 3D Structure Click here
Q5VW22 View 3D Structure Click here
Q5W7F2 View 3D Structure Click here
Q62848 View 3D Structure Click here
Q66H91 View 3D Structure Click here
Q68FF6 View 3D Structure Click here
Q69QY4 View 3D Structure Click here
Q6DG41 View 3D Structure Click here
Q6H462 View 3D Structure Click here
Q6H738 View 3D Structure Click here
Q6H8D8 View 3D Structure Click here
Q6L4C8 View 3D Structure Click here
Q6NXL5 View 3D Structure Click here
Q6Z653 View 3D Structure Click here
Q6ZQK5 View 3D Structure Click here
Q7SIG6 View 3D Structure Click here
Q7TN29 View 3D Structure Click here
Q7XBX2 View 3D Structure Click here
Q80WC7 View 3D Structure Click here
Q84T71 View 3D Structure Click here
Q86H99 View 3D Structure Click here
Q8BXK8 View 3D Structure Click here
Q8BZ05 View 3D Structure Click here
Q8CGU4 View 3D Structure Click here
Q8H100 View 3D Structure Click here
Q8I4Y5 View 3D Structure Click here
Q8IAP4 View 3D Structure Click here
Q8IYB5 View 3D Structure Click here
Q8K2H4 View 3D Structure Click here
Q8K2K6 View 3D Structure Click here
Q8L7A4 View 3D Structure Click here
Q8LFN9 View 3D Structure Click here
Q8N6H7 View 3D Structure Click here
Q8N6T3 View 3D Structure Click here
Q8R2V5 View 3D Structure Click here
Q8R5G7 View 3D Structure Click here
Q8RXE7 View 3D Structure Click here
Q8RZA2 View 3D Structure Click here
Q8SSP5 View 3D Structure Click here
Q8TDY4 View 3D Structure Click here
Q8TF27 View 3D Structure Click here
Q8VHH5 View 3D Structure Click here
Q8W4K6 View 3D Structure Click here
Q8WU79 View 3D Structure Click here
Q8WWN8 View 3D Structure Click here
Q8WZ64 View 3D Structure Click here
Q91VZ6 View 3D Structure Click here
Q95RG8 View 3D Structure Click here
Q96P47 View 3D Structure Click here
Q96P48 View 3D Structure Click here
Q96P50 View 3D Structure Click here
Q96P64 View 3D Structure Click here
Q99490 View 3D Structure Click here
Q99K28 View 3D Structure Click here
Q9C6C3 View 3D Structure Click here
Q9D8S3 View 3D Structure Click here
Q9EPJ9 View 3D Structure Click here
Q9FIQ0 View 3D Structure Click here
Q9FIT8 View 3D Structure Click here
Q9FL69 View 3D Structure Click here
Q9FVJ3 View 3D Structure Click here
Q9JK15 View 3D Structure Click here
Q9JLQ2 View 3D Structure Click here
Q9M354 View 3D Structure Click here
Q9NGC3 View 3D Structure Click here
Q9NP61 View 3D Structure Click here
Q9NPF8 View 3D Structure Click here
Q9QWY8 View 3D Structure Click here
Q9SMX5 View 3D Structure Click here
Q9ULH1 View 3D Structure Click here
Q9UPQ3 View 3D Structure Click here
Q9UT34 View 3D Structure Click here
Q9UUE2 View 3D Structure Click here
Q9VCQ6 View 3D Structure Click here
Q9VTX5 View 3D Structure Click here
Q9XX14 View 3D Structure Click here
Q9XXH8 View 3D Structure Click here
Q9Y2X7 View 3D Structure Click here
Q9Z272 View 3D Structure Click here
X1WEM9 View 3D Structure Click here