Summary: Polysaccharide deacetylase
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.
Polysaccharide deacetylase Provide feedback
This domain is found in polysaccharide deacetylase. This family of polysaccharide deacetylases includes NodB (nodulation protein B from Rhizobium) which is a chitooligosaccharide deacetylase . It also includes chitin deacetylase from yeast  and endoxylanases which hydrolyses glucosidic bonds in xylan .
C. Mishra, C. E. Semino, K. J. McCreath, H. de la Vega, B. J. Jones, C. A. Specht & P. W. Robbins; , Yeast 1996;13:327-336.: Cloning and expression of two chitin deacetylase genes of Saccharomyces cerevisiae. PUBMED:9133736 EPMC:9133736
S. J. Millward-Sadler, D. M. Poole, B. Henrissat, G. P. Hazlewood, J. H. Clarke & H. J. Gilbert; , Mol Microbiol 1994;11:375-382.: Evidence for a general role for high-affinity non-catalytic cellulose binding domains in microbial plant cell wall hydrolases. PUBMED:8170399 EPMC:8170399
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR002509This domain is found in polysaccharide deacetylase. This family of polysaccharide deacetylases includes NodB (nodulation protein B from Rhizobium) which is a chitooligosaccharide deacetylase [PUBMED:9163424]. It also includes chitin deacetylase from yeast [PUBMED:9133736], and endoxylanases which hydrolyses glucosidic bonds in xylan [PUBMED:8170399].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds (GO:0016810)|
|Biological process||carbohydrate metabolic process (GO:0005975)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Loading domain graphics...
This superfamily contains diverse enzymes that act on carbohydrates including both hydrolases and deacetylases.
The clan contains the following 6 members:DUF2334 Glyco_hydro_38 Glyco_hydro_57 LamB_YcsF Polysacc_deac_1 Polysacc_deac_3
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
If you find these logos useful in your own work, please consider citing the following article:
Note: You can also download the data file for the tree.
Curation and family details
|Seed source:||Pfam-B_502 (release 4.0)|
|Author:||Bashton M, Bateman A|
|Number in seed:||80|
|Number in full:||52617|
|Average length of the domain:||140.20 aa|
|Average identity of full alignment:||20 %|
|Average coverage of the sequence by the domain:||40.18 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||17|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
How the sunburst is generated
Colouring and labels
Anomalies in the taxonomy tree
Missing taxonomic levels
Unmapped species names
Too many species/sequences
The tree shows the occurrence of this domain across different species. More...
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 Polysacc_deac_1 domain has been found. There are 83 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.
Loading structure mapping...