Summary: Alpha-L-arabinofuranosidase C-terminal domain
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Alpha-L-arabinofuranosidase C-terminal domain Provide feedback
This family represents the C-terminus (approximately 200 residues) of bacterial and eukaryotic alpha-L-arabinofuranosidase ( EC:3.2.1.55). This catalyses the hydrolysis of nonreducing terminal alpha-L-arabinofuranosidic linkages in L-arabinose-containing polysaccharides [1].
Literature references
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Gilead S, Shoham Y; , Appl Environ Microbiol 1995;61:170-174.: Purification and characterization of alpha-L-arabinofuranosidase from Bacillus stearothermophilus T-6. PUBMED:7887599 EPMC:7887599
Internal database links
SCOOP: | 3keto-disac_hyd Glyco_hydro_39 |
External database links
SCOP: | 1pz2 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR010720
This entry represents the C terminus (approximately 200 residues) of bacterial and eukaryotic alpha-L-arabinofuranosidase ( EC ). This catalyses the hydrolysis of non-reducing terminal alpha-L-arabinofuranosidic linkages in L-arabinose-containing polysaccharides [ PUBMED:7887599 ].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | alpha-L-arabinofuranosidase activity (GO:0046556) |
Biological process | L-arabinose metabolic process (GO:0046373) |
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 GHD (CL0369), which has the following description:
This domain is C-terminal to the catalytic beta/alpha barrel domain. The superfamily includes the C-terminal domain of a number of sugar-lytic families.
The clan contains the following 40 members:
A_amylase_dom_C Alpha-amy_C_pro Alpha-amyl_C Alpha-amyl_C2 Alpha-amylase_C Alpha-L-AF_C AMPK1_CBM AMT4_dom_C Bac_A_amyl_C BetaGal_dom2 CBM_20 CBM_48 Collagen_bind_2 Cyc-maltodext_C DUF1923 DUF1953 DUF1964 DUF3459 DUF5597 Fucosidase_C GH97_C GHD GlgX_C Glyc_hyd_38C_2 Glyco_hyd_101C Glyco_hydro38C2 Glyco_hydro_30C Glyco_hydro_36C Glyco_hydro_42C Glyco_hydro_5_C HepII_C hGDE_central Lact_bio_phlase LBP_C Malt_amylase_C Melibiase_2_C Melibiase_C MGTA_C Pullul_strch_C SpuA_CAlignments
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 and the UniProtKB 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 (229) |
Full (5869) |
Representative proteomes | UniProt (18357) |
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RP15 (529) |
RP35 (2522) |
RP55 (5511) |
RP75 (9234) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
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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 (229) |
Full (5869) |
Representative proteomes | UniProt (18357) |
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RP15 (529) |
RP35 (2522) |
RP55 (5511) |
RP75 (9234) |
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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: | Pfam-B_3625 (release 10.0) |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Vella Briffa B |
Number in seed: | 229 |
Number in full: | 5869 |
Average length of the domain: | 200.2 aa |
Average identity of full alignment: | 21 % |
Average coverage of the sequence by the domain: | 33.99 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 168 | ||||||||||||
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 Alpha-L-AF_C domain has been found. There are 117 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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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.