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122  structures 1926  species 0  interactions 6020  sequences 275  architectures

Family: CBM_20 (PF00686)

Summary: Starch binding domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Carbohydrate-binding module". More...

Carbohydrate-binding module Edit Wikipedia article

In molecular biology, a carbohydrate binding module is a protein domain found in carbohydrate active enzymes (for example glycoside hydrolases).

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.

Starch binding domain Provide feedback

No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002044

This entry represents CAZY , which binds starch. The crystal structure of CBM20 has been solved [ PUBMED:1826034 ]. It consists of seven beta-stands forming an open-sided distorted beta-barrel. Several aromatic residues, especially the well-conserved Trp and Tyr residues, participate in granular starch binding.

A carbohydrate-binding module (CBM) is defined as a contiguous amino acid sequence within a carbohydrate-active enzyme with a discreet fold having carbohydrate-binding activity. A few exceptions are CBMs in cellulosomal scaffolding proteins and rare instances of independent putative CBMs. The requirement of CBMs existing as modules within larger enzymes sets this class of carbohydrate-binding protein apart from other non-catalytic sugar binding proteins such as lectins and sugar transport proteins.

CBMs were previously classified as cellulose-binding domains (CBDs) based on the initial discovery of several modules that bound cellulose [ PUBMED:3338453 , PUBMED:3134347 ]. However, additional modules in carbohydrate-active enzymes are continually being found that bind carbohydrates other than cellulose yet otherwise meet the CBM criteria, hence the need to reclassify these polypeptides using more inclusive terminology.

Previous classification of cellulose-binding domains were based on amino acid similarity. Groupings of CBDs were called "Types" and numbered with roman numerals (e.g. Type I or Type II CBDs). In keeping with the glycoside hydrolase classification, these groupings are now called families and numbered with Arabic numerals. Families 1 to 13 are the same as Types I to XIII. For a detailed review on the structure and binding modes of CBMs see [ PUBMED:15214846 ].

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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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 (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
(50)
Full
(6020)
Representative proteomes UniProt
(13337)
RP15
(1231)
RP35
(2984)
RP55
(5017)
RP75
(7254)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(50)
Full
(6020)
Representative proteomes UniProt
(13337)
RP15
(1231)
RP35
(2984)
RP55
(5017)
RP75
(7254)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(50)
Full
(6020)
Representative proteomes UniProt
(13337)
RP15
(1231)
RP35
(2984)
RP55
(5017)
RP75
(7254)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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_111 (release 2.1)
Previous IDs: CBD_2; CBD_4;
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 50
Number in full: 6020
Average length of the domain: 93.3 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 15.27 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.3 23.3
Trusted cut-off 23.3 23.3
Noise cut-off 23.2 23.2
Model length: 96
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
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Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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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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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 CBM_20 domain has been found. There are 122 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.

Protein Predicted structure External Information
A0A044SRD8 View 3D Structure Click here
A0A0D2GV95 View 3D Structure Click here
A0A0K0DTL0 View 3D Structure Click here
A0A0R0E240 View 3D Structure Click here
A0A0R0E3U7 View 3D Structure Click here
A0A0R0I7Q2 View 3D Structure Click here
A0A0R0KFG5 View 3D Structure Click here
A0A0R0KFI1 View 3D Structure Click here
A0A0R0KFY0 View 3D Structure Click here
A0A0R0KMT0 View 3D Structure Click here
A0A0R4ITF0 View 3D Structure Click here
A0A175W7Z8 View 3D Structure Click here
A0A175WAR5 View 3D Structure Click here
A0A175WE05 View 3D Structure Click here
A0A1C1CTV0 View 3D Structure Click here
A0A1D6INP8 View 3D Structure Click here
A0A1D6IVK7 View 3D Structure Click here
A0A1D6KLZ2 View 3D Structure Click here
A0A368UIB7 View 3D Structure Click here
B7ZZ23 View 3D Structure Click here
C0HDU8 View 3D Structure Click here
C0NJV0 View 3D Structure Click here
C1GVZ3 View 3D Structure Click here
D8Q9M3 View 3D Structure Click here
E9QCC5 View 3D Structure Click here
F4IV66 View 3D Structure Click here
I1J7A3 View 3D Structure Click here
I1JLH3 View 3D Structure Click here
I1JMZ7 View 3D Structure Click here
I1N8M8 View 3D Structure Click here
K7KA51 View 3D Structure Click here
K7KD84 View 3D Structure Click here
K7KD85 View 3D Structure Click here
K7L1S8 View 3D Structure Click here
K7MTG7 View 3D Structure Click here
O95210 View 3D Structure Click here
O95278 View 3D Structure Click here
P0DN29 View 3D Structure Click here
P14804 View 3D Structure Click here
P36914 View 3D Structure Click here