Summary: Periplasmic glucan biosynthesis protein, MdoG
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Periplasmic glucan biosynthesis protein, MdoG Provide feedback
This family represents MdoG, a protein that is necessary for the synthesis of periplasmic glucans. The function of MdoG remains unknown. It has been suggested that it may catalyse the addition of branches to a linear glucan backbone.
Literature references
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Bohin JP; , FEMS Microbiol Lett 2000;186:11-19.: Osmoregulated periplasmic glucans in Proteobacteria. PUBMED:10779706 EPMC:10779706
This tab holds annotation information from the InterPro database.
InterPro entry IPR007444
Membrane-derived oligosaccharides (MDO) are members of a family of glucans found in the periplasmic space of Gram-negative bacteria. MdoG has been shown to be necessary for the synthesis of MDO [PUBMED:7934824], but its exact function is not known yet. MdoD, an MdoG paralog, is a twin-arginine-dependent periplasmic protein that controls osmoregulated periplasmic glucan backbone structures [PUBMED:15175282]. This entry represents the functional portion of the protein and excludes the N-terminal signal sequence.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Cellular component | periplasmic space (GO:0042597) |
Biological process | carbohydrate biosynthetic process (GO:0016051) |
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 Gal_mutarotase (CL0103), which has the following description:
This clan is composed of a beta-sandwich that was first observed in domain 5 of beta-galactosidase, then as the central domain of copper amine oxidase, the C-terminal domain of chondroitinase, the C-terminal domain of hyaluronate lyase, the N-terminal domain of maltose phosphorylase and in Galactose Mutarotase [1]. All these enzymes act on a sugar substrate.
The clan contains the following 17 members:
Aldose_epim Bgal_small_N DUF1926 DUF4432 DUF5054 DUF5107 Gal_mutarotas_2 Glucodextran_N Glyco_hyd_65N_2 Glyco_hydro_38C Glyco_hydro_65N Glyco_transf_36 Lyase_8 MdoG Rhamnogal_lyase RhgB_N YidC_periplasAlignments
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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 (174) |
Full (829) |
Representative proteomes | UniProt (3956) |
NCBI (6981) |
Meta (66) |
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RP15 (114) |
RP35 (391) |
RP55 (842) |
RP75 (1735) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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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 (174) |
Full (829) |
Representative proteomes | UniProt (3956) |
NCBI (6981) |
Meta (66) |
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RP15 (114) |
RP35 (391) |
RP55 (842) |
RP75 (1735) |
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Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | COG3131 |
Previous IDs: | none |
Type: | Family |
Author: | Mifsud W |
Number in seed: | 174 |
Number in full: | 829 |
Average length of the domain: | 465.10 aa |
Average identity of full alignment: | 39 % |
Average coverage of the sequence by the domain: | 90.69 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 476 | ||||||||||||
Family (HMM) version: | 11 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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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Interactions
There is 1 interaction for this family. More...
MdoGStructures
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 MdoG domain has been found. There are 2 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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