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83  structures 1239  species 2  interactions 4255  sequences 172  architectures

Family: Glyco_hydro_16 (PF00722)

Summary: Glycosyl hydrolases family 16

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This is the Wikipedia entry entitled "Glycoside hydrolase family 16". More...

Glycoside hydrolase family 16 Edit Wikipedia article

Glycosyl hydrolase family 16
PDB 1dyp EBI.jpg
1,3-alpha-1,4-beta-d-galactose-4-sulfate-3,6-anhydro-d-galactose 4 galactohydrolase
Identifiers
Symbol Glyco_hydro_16
Pfam PF00722
Pfam clan CL0004
InterPro IPR000757
PROSITE PDOC00794
SCOP 1cpn
SUPERFAMILY 1cpn
CAZy GH16

In molecular biology, Glycoside hydrolase family 16 is a family of glycoside hydrolases.

Glycoside hydrolases EC 3.2.1. are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycoside hydrolases, based on sequence similarity, has led to the definition of >100 different families.[1][2][3] This classification is available on the CAZy(http://www.cazy.org/GH1.html) web site,[4] and also discussed at CAZypedia, an online encyclopedia of carbohydrate active enzymes.[5]

Glycoside hydrolase family 16 CAZY GH_16 comprises enzymes with a number of known activities; lichenase (EC 3.2.1.73); xyloglucan xyloglucosyltransferase (EC 2.4.1.207); agarase (EC 3.2.1.81); kappa-carrageenase (EC 3.2.1.83); endo-beta-1,3-glucanase (EC 3.2.1.39); endo-beta-1,3-1,4-glucanase (EC 3.2.1.6); endo-beta-galactosidase (EC 3.2.1.103).

References[edit]

This article incorporates text from the public domain Pfam and InterPro IPR000757

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000757

O-Glycosyl hydrolases (EC) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [PUBMED:7624375, PUBMED:8535779]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site.

Glycoside hydrolase family 16 CAZY comprises enzymes with a number of known activities; lichenase (EC); xyloglucan xyloglucosyltransferase (EC); agarase (EC); kappa-carrageenase (EC); endo-beta-1,3-glucanase (EC); endo-beta-1,3-1,4-glucanase (EC); endo-beta-galactosidase (EC).

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 Concanavalin (CL0004), which has the following description:

This superfamily includes a diverse range of carbohydrate binding domains and glycosyl hydrolase enzymes that share a common structure.

The clan contains the following 16 members:

DUF1080 DUF2401 Gal-bind_lectin Glyco_hydro_11 Glyco_hydro_12 Glyco_hydro_16 Glyco_hydro_7 Laminin_G_1 Laminin_G_2 Laminin_G_3 Lectin_leg-like Lectin_legB Pentaxin Sialidase SKN1 Toxin_R_bind_N

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...

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
(120)
Full
(4255)
Representative proteomes NCBI
(4494)
Meta
(761)
RP15
(645)
RP35
(1357)
RP55
(1879)
RP75
(2173)
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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
(120)
Full
(4255)
Representative proteomes NCBI
(4494)
Meta
(761)
RP15
(645)
RP35
(1357)
RP55
(1879)
RP75
(2173)
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
(120)
Full
(4255)
Representative proteomes NCBI
(4494)
Meta
(761)
RP15
(645)
RP35
(1357)
RP55
(1879)
RP75
(2173)
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.

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_759 (release 2.1)
Previous IDs: glycosyl_hydro9;
Type: Domain
Author: Bateman A
Number in seed: 120
Number in full: 4255
Average length of the domain: 179.30 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 46.71 %

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 20.3 20.3
Trusted cut-off 20.3 20.3
Noise cut-off 20.2 20.2
Model length: 185
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 2 interactions for this family. More...

XET_C Glyco_hydro_16

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 Glyco_hydro_16 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.

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