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0  structures 258  species 0  interactions 306  sequences 2  architectures

Family: GHL1-3 (PF11308)

Summary: Glycosyl hydrolases related to GH101 family, GHL1-GHL3

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This is the Wikipedia entry entitled "Glycoside hydrolase family 101". More...

Glycoside hydrolase family 101 Edit Wikipedia article

Endo-alpha-N-acetylgalactosaminidase
Identifiers
Symbol Glyco_hydro_101
Pfam PF12905
Pfam clan CL0058
CAZy GH101
Glycoside hydrolases related to GH101 family
Identifiers
Symbol GHL
Pfam PF11308
Pfam clan CL0058

In molecular biology, glycoside hydrolase family 101 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 101 CAZY GH_101 includes enzymes with endo-α-N-acetylgalactosaminidase EC 3.2.1. activity and can be split into several subfamilies.[6]

References

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

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.

Glycosyl hydrolases related to GH101 family, GHL1-GHL3 Provide feedback

This family of bacterial and lower eukaryote glycosyl hydrolases is related to CAZy family GH101, and is made up of sub-families GHL1-GHL3. In the example C02A26 the substrate-binding Asp is residue 596, the nucleophilic Asp is residue 706, and the proton donor Glu is residue 747.

Literature references

  1. Naumoff DG;, J Bioinform Comput Biol. 2010;8:437-451.: Gh101 family of glycoside hydrolases: subfamily structure and evolutionary connections with other families. PUBMED:20556855 EPMC:20556855

  2. Naumov DG;, Mol Biol (Mosk). 2011;45:1073-1083.: [GHL1-GHL15: new families of hypothetical glycoside hydrolases]. PUBMED:22295578 EPMC:22295578


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR021459

This family of predicted glycosyl hydrolases is related to CAZy family GH101, and is made up of sub-families designated GHL1-GHL4 [PUBMED:20556855].

Domain organisation

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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
(24)
Full
(306)
Representative proteomes NCBI
(239)
Meta
(5)
RP15
(16)
RP35
(23)
RP55
(29)
RP75
(36)
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Format an alignment

  Seed
(24)
Full
(306)
Representative proteomes NCBI
(239)
Meta
(5)
RP15
(16)
RP35
(23)
RP55
(29)
RP75
(36)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(24)
Full
(306)
Representative proteomes NCBI
(239)
Meta
(5)
RP15
(16)
RP35
(23)
RP55
(29)
RP75
(36)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
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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_4091 (release 23.0)
Previous IDs: DUF3111; GHL;
Type: Family
Author: Pollington J, Finn RD, Naumoff D
Number in seed: 24
Number in full: 306
Average length of the domain: 281.20 aa
Average identity of full alignment: 36 %
Average coverage of the sequence by the domain: 43.87 %

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 25.6 25.6
Trusted cut-off 25.6 28.2
Noise cut-off 23.4 24.8
Model length: 307
Family (HMM) version: 3
Download: download the raw HMM for this family

Species distribution

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