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0  structures 3544  species 0  interactions 8110  sequences 113  architectures

Family: Yip1 (PF04893)

Summary: Yip1 domain

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.

Yip1 domain Provide feedback

The Yip1 integral membrane domain contains four transmembrane alpha helices. The domain is characterised by the motifs DLYGP and GY. The Yip1 protein is a golgi protein involved in vesicular transport that interacts with GTPases [1].

Literature references

  1. Yang X, Matern HT, Gallwitz D; , EMBO J 1998;17:4954-4963.: Specific binding to a novel and essential Golgi membrane protein (Yip1p) functionally links the transport GTPases Ypt1p and Ypt31p. PUBMED:9724632 EPMC:9724632


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006977

This entry contains proteins belonging to the Yip1 family and represents the Yip1 domain. The Yip1 integral membrane domain contains four transmembrane alpha helices. The domain is characterised by the motifs DLYGP and GY. The Yip1 protein is a Golgi protein involved in vesicular transport that interacts with GTPases [ PUBMED:9724632 ].

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 Yip1 (CL0112), which has the following description:

Yip1 and YIF1 are members of an integral membrane complex which bind to Ras-like GTPases and are required for membrane fusion of ER derived vesicles with the Golgi [1].

The clan contains the following 6 members:

DUF1048 DUF1129 DUF1189 DUF1700 YIF1 Yip1

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
(213)
Full
(8110)
Representative proteomes UniProt
(25303)
RP15
(1351)
RP35
(3758)
RP55
(7082)
RP75
(10668)
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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
(213)
Full
(8110)
Representative proteomes UniProt
(25303)
RP15
(1351)
RP35
(3758)
RP55
(7082)
RP75
(10668)
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
(213)
Full
(8110)
Representative proteomes UniProt
(25303)
RP15
(1351)
RP35
(3758)
RP55
(7082)
RP75
(10668)
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: Pfam-B_5598 (release 7.6)
Previous IDs: DUF649;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Bateman A
Number in seed: 213
Number in full: 8110
Average length of the domain: 167.40 aa
Average identity of full alignment: 15 %
Average coverage of the sequence by the domain: 60.94 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 28.6 28.6
Trusted cut-off 28.6 28.6
Noise cut-off 28.5 28.5
Model length: 173
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

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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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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
A0A096Q578 View 3D Structure Click here
A0A0R0EFE0 View 3D Structure Click here
A0A0R0FK88 View 3D Structure Click here
A0A0R0I509 View 3D Structure Click here
A0A1D6G7X0 View 3D Structure Click here
A0A1D6M5F8 View 3D Structure Click here
A0A1D6M5Q5 View 3D Structure Click here
A0A1D6PYC9 View 3D Structure Click here
A0A1D8PFI0 View 3D Structure Click here
A4I064 View 3D Structure Click here
A4I509 View 3D Structure Click here
A5PEX8 View 3D Structure Click here
A8MSE3 View 3D Structure Click here
B4FUR9 View 3D Structure Click here
B6T5J1 View 3D Structure Click here
C6KRN3 View 3D Structure Click here
C6S3G6 View 3D Structure Click here
C6TH62 View 3D Structure Click here
F4K4B8 View 3D Structure Click here
H2KY99 View 3D Structure Click here
I1JI27 View 3D Structure Click here
I1JQ07 View 3D Structure Click here
I1JRD4 View 3D Structure Click here
I1LVR5 View 3D Structure Click here
I1NAM3 View 3D Structure Click here
I1NC02 View 3D Structure Click here
K7VZB8 View 3D Structure Click here
O64614 View 3D Structure Click here
O94348 View 3D Structure Click here
P0AD17 View 3D Structure Click here
P53039 View 3D Structure Click here
P53108 View 3D Structure Click here
Q10MY7 View 3D Structure Click here
Q4CYS0 View 3D Structure Click here
Q4DFE5 View 3D Structure Click here
Q4DQH6 View 3D Structure Click here
Q4QQU5 View 3D Structure Click here
Q54QY3 View 3D Structure Click here
Q54RZ2 View 3D Structure Click here
Q54TS4 View 3D Structure Click here

trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;