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5  structures 326  species 0  interactions 2555  sequences 89  architectures

Family: GRAM (PF02893)

Summary: GRAM domain

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This is the Wikipedia entry entitled "GRAM domain". More...

GRAM domain Edit Wikipedia article

GRAM domain
1zvr.gif
Myotubularin-related protein 2
Identifiers
Symbol GRAM
Pfam PF02893
Pfam clan CL0266
InterPro IPR004182
SMART GRAM
SCOP 1lw3
SUPERFAMILY 1lw3
OPM superfamily 176
OPM protein 1zvr

The GRAM domain is found in glucosyltransferases, myotubularins and other membrane-associated proteins.[1] The structure of the GRAM domain is similar to that found in PH domains.[2]

Human proteins containing this domain[edit]

DIP; GRAMD1A; GRAMD1B; GRAMD1C; GRAMD2; GRAMD3; MTM1; MTMR1; MTMR2; NCOA7; NSMAF; OXR1; SBF1; SBF2; TBC1D8; TBC1D8B; TBC1D9; TBC1D9B; WBP2; WBP2NL; dJ439F8.1;

References[edit]

  1. ^ Doerks T, Strauss M, Brendel M, Bork P (October 2000). "GRAM, a novel domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins". Trends Biochem. Sci. 25 (10): 483–5. doi:10.1016/S0968-0004(00)01664-9. PMID 11050430. 
  2. ^ Begley MJ, Taylor GS, Kim SA, Veine DM, Dixon JE, Stuckey JA (December 2003). "Crystal structure of a phosphoinositide phosphatase, MTMR2: insights into myotubular myopathy and Charcot-Marie-Tooth syndrome". Mol. Cell 12 (6): 1391–402. doi:10.1016/S1097-2765(03)00486-6. PMID 14690594. 

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GRAM domain Provide feedback

The GRAM domain is found in in glucosyltransferases, myotubularins and other putative membrane-associated proteins.

Literature references

  1. Doerks T, Strauss M, Brendel M, Bork P; , Trends Biochem Sci 2000;25:483-485.: GRAM, a novel domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins. PUBMED:11050430 EPMC:11050430


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004182

The GRAM domain is found in glucosyltransferases, myotubularins and other putative membrane-associated proteins. It is normally about 70 amino acids in length. It is thought to be an intracellular protein-binding or lipid-binding signalling domain, which has an important function in membrane-associated processes. Mutations in the GRAM domain of myotubularins cause a muscle disease, which suggests that the domain is essential for the full function of the enzyme [PUBMED:11050430]. Myotubularin-related proteins are a large subfamily of protein tyrosine phosphatases (PTPs) that dephosphorylate D3-phosphorylated inositol lipids [PUBMED:14690594].

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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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.

  Seed
(33)
Full
(2555)
Representative proteomes NCBI
(2393)
Meta
(6)
RP15
(338)
RP35
(634)
RP55
(1024)
RP75
(1481)
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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
(33)
Full
(2555)
Representative proteomes NCBI
(2393)
Meta
(6)
RP15
(338)
RP35
(634)
RP55
(1024)
RP75
(1481)
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
(33)
Full
(2555)
Representative proteomes NCBI
(2393)
Meta
(6)
RP15
(338)
RP35
(634)
RP55
(1024)
RP75
(1481)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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:

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: Alignment kindly provided by SMART
Previous IDs: none
Type: Family
Author: SMART
Number in seed: 33
Number in full: 2555
Average length of the domain: 70.70 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 10.41 %

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 21.1 21.1
Trusted cut-off 21.1 21.1
Noise cut-off 21.0 21.0
Model length: 69
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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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 GRAM domain has been found. There are 5 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 seqence.

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