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11  structures 1382  species 0  interactions 2824  sequences 38  architectures

Family: Mod_r (PF07200)

Summary: Modifier of rudimentary (Mod(r)) protein

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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.

Modifier of rudimentary (Mod(r)) protein Provide feedback

This family represents a conserved region approximately 150 residues long within a number of eukaryotic proteins that show homology with Drosophila melanogaster Modifier of rudimentary (Mod(r)) proteins. The N-terminal half of Mod(r) proteins is acidic, whereas the C-terminal half is basic [1] and both of these regions are represented in this family. Members of this family include the Vps37 subunit of the endosomal sorting complex ESCRT-I, a complex involved in recruiting transport machinery for protein sorting at the multivesicular body (MVB). The yeast ESCRT-I complex consists of three proteins (Vps23, Vps28 and Vps37). The mammalian homologue of Vps37 interacts with Tsg101 (Pfam: PF05743) through its mod(r) domain and its function is essential for lysosomal sorting of EGF receptors [2].

Literature references

  1. Begley D, Murphy AM, Hiu C, Tsubota SI; , Mol Gen Genet 1995;248:69-78.: Modifier of rudimentary p1, mod(r)p1, a trans-acting regulatory mutation of rudimentary. PUBMED:7651329 EPMC:7651329

  2. Bache KG, Slagsvold T, Cabezas A, Rosendal KR, Raiborg C, Stenmark H; , Mol Biol Cell 2004;15:4337-4346.: The growth-regulatory protein HCRP1/hVps37A is a subunit of mammalian ESCRT-I and mediates receptor down-regulation. PUBMED:15240819 EPMC:15240819


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR009851

This entry represents a conserved region approximately 150 residues long within a number of eukaryotic proteins that show homology with Drosophila melanogaster Modifier of rudimentary (Mod(r)) proteins. The N-terminal half of Mod(r) proteins is acidic, whereas the C-terminal half is basic [ PUBMED:7651329 ], and both of these regions are represented in this 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 VPS23_C (CL0596), which has the following description:

The clan contains the following 3 members:

Mod_r Vps23_core VPS28

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
(145)
Full
(2824)
Representative proteomes UniProt
(4952)
RP15
(475)
RP35
(1163)
RP55
(2169)
RP75
(2921)
Jalview View  View  View  View  View  View  View 
HTML View  View           
PP/heatmap 1 View           

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

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

Format an alignment

  Seed
(145)
Full
(2824)
Representative proteomes UniProt
(4952)
RP15
(475)
RP35
(1163)
RP55
(2169)
RP75
(2921)
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
(145)
Full
(2824)
Representative proteomes UniProt
(4952)
RP15
(475)
RP35
(1163)
RP55
(2169)
RP75
(2921)
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_16631 (release 10.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Vella Briffa B , Wood V , Mistry J
Number in seed: 145
Number in full: 2824
Average length of the domain: 139.80 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 48.91 %

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 30.1 30.1
Trusted cut-off 30.3 30.3
Noise cut-off 30.0 30.0
Model length: 146
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

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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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 Mod_r domain has been found. There are 11 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
A0A0R0GNX9 View 3D Structure Click here
A0A0R0J4U3 View 3D Structure Click here
A0A0R4IIN4 View 3D Structure Click here
A0A1D6JR08 View 3D Structure Click here
A0A1D6MBY1 View 3D Structure Click here
A0A1D6PIN9 View 3D Structure Click here
A0JPF7 View 3D Structure Click here
A3KGZ5 View 3D Structure Click here
A4I3D0 View 3D Structure Click here
A5D8V6 View 3D Structure Click here
B2GV76 View 3D Structure Click here
B5DFF4 View 3D Structure Click here
D3ZU64 View 3D Structure Click here
I1JPT7 View 3D Structure Click here
I1NAF3 View 3D Structure Click here
K7LHR2 View 3D Structure Click here
K7LZU1 View 3D Structure Click here
O44158 View 3D Structure Click here
O77259 View 3D Structure Click here
Q10HX5 View 3D Structure Click here
Q10QR4 View 3D Structure Click here
Q3EBL9 View 3D Structure Click here
Q4CYE2 View 3D Structure Click here
Q4DKE7 View 3D Structure Click here
Q4V794 View 3D Structure Click here
Q55DV8 View 3D Structure Click here
Q5AEC8 View 3D Structure Click here
Q5R9T2 View 3D Structure Click here
Q6P3K6 View 3D Structure Click here
Q810I0 View 3D Structure Click here
Q86XT2 View 3D Structure Click here
Q8CHS8 View 3D Structure Click here
Q8NEZ2 View 3D Structure Click here
Q8R0J7 View 3D Structure Click here
Q8R105 View 3D Structure Click here
Q99176 View 3D Structure Click here
Q9H9H4 View 3D Structure Click here
Q9SCP9 View 3D Structure Click here
Q9VN88 View 3D Structure Click here
X1WEV5 View 3D Structure Click here