Summary: Cellulose binding domain
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Carbohydrate-binding module Edit Wikipedia article
three-dimensional structures of three engineered cellulose-binding domains of cellobiohydrolase i from trichoderma reesei, nmr, 18 structures
solution structure of a cellulose binding domain from cellulomonas fimi by nuclear magnetic resonance spectroscopy
crystal structure of a family iiia cbd from clostridium cellulolyticum
interactions of a family 18 chitinase with the designed inhibitor hm508, and its degradation product, chitobiono-delta-lactone
cbm6ct from clostridium thermocellum in complex with xylopentaose
cbm4 structure and function
solution structure of type x cbm
family 11 carbohydrate-binding module of cellulosomal cellulase lic26a-cel5e of clostridium thermocellum
xylan-binding module cbm15
structure of fam17 carbohydrate binding module from clostridium cellulovorans
crystal structure analysis of crosslinked-wga3/glcnacbeta1,4glcnac complex
glucoamylase, granular starch-binding domain complex with cyclodextrin, nmr, minimized average structure
structural and thermodynamic dissection of specific mannan recognition by a carbohydrate-binding module, tmcbm27
crystal structure of the serratia marcescens chitin-binding protein cbp21 y54a mutant.
crystal structure of glycosyltrehalose trehalohydrolase from sulfolobus solfataricus
In molecular biology, a carbohydrate-binding module (CBM) is a protein domain found in carbohydrate-active enzymes (for example glycoside hydrolases). The majority of these domains have carbohydrate-binding activity. Some of these domains are found on cellulosomal scaffoldin proteins. CBMs were previously known as cellulose-binding domains. CBMs are classified into numerous families, based on amino acid sequence similarity. There are currently (June 2011) 64 families of CBM in the CAZy database.
CBMs of microbial glycoside hydrolases play a central role in the recycling of photosynthetically fixed carbon through their binding to specific plant structural polysaccharides. CBMs can recognise both crystalline and amorphous cellulose forms. CBMs are the most common non-catalytic modules associated with enzymes active in plant cell-wall hydrolysis. Many putative CBMs have been identified by amino acid sequence alignments but only a few representatives have been shown experimentally to have a carbohydrate-binding function.
Carbohydrate-binding module family 2 (CBM2) contains two conserved cysteines - one at each extremity of the domain - which have been shown  to be involved in a disulfide bond. There are also four conserved tryptophans, two of which are involved in cellulose binding.
Carbohydrate-binding module family 3 (CBM3) is involved in cellulose binding  and is found associated with a wide range of bacterial glycosyl hydrolases. The structure of this domain is known; it forms a beta sandwich.
Carbohydrate-binding module family 4 (CBM4) includes the two cellulose-binding domains, CBD(N1) and CBD(N2), arranged in tandem at the N terminus of the 1,4-beta-glucanase, CenC, from Cellulomonas fimi. These homologous CBMs are distinct in their selectivity for binding amorphous and not crystalline cellulose. Multidimensional heteronuclear nuclear magnetic resonance (NMR) spectroscopy was used to determine the tertiary structure of the 152 amino acid N-terminal cellulose-binding domain from C. fimi 1,4-beta-glucanase CenC (CBDN1). The tertiary structure of CBDN1 is strikingly similar to that of the bacterial 1,3-1,4-beta-glucanases, as well as other sugar-binding proteins with jelly-roll folds. CBM4 and CBM9 are closely related.
Carbohydrate-binding module family 5 (CBM5) binds chitin. CBM5 and CBM12 are distantly related.
Carbohydrate-binding module family 6 (CBM6) is unusual in that is contains two substrate-binding sites, cleft A and cleft B. Cellvibrio mixtus endoglucanase 5A contains two CBM6 domains, the CBM6 domain at the C-terminus displays distinct ligand binding specificities in each of the sustrate-binding clefts. Both cleft A and cleft B can bind cello-oligosaccharides, laminarin preferentially binds in cleft A, xylooligosaccharides only bind in cleft A and beta1,4,-beta1,3-mixed linked glucans only bind in cleft B.
Carbohydrate-binding module family 9 (CBM9) binds to crystalline cellulose. CBM4 and CBM9 are closely related.
Carbohydrate-binding module family 10 (CBM10) is found in two distinct sets of proteins with different functions. Those found in aerobic bacteria bind cellulose (or other carbohydrates); but in anaerobic fungi they are protein binding domains, referred to as dockerin domains. The dockerin domains are believed to be responsible for the assembly of a multiprotein cellulase/hemicellulase complex, similar to the cellulosome found in certain anaerobic bacteria.
In anaerobic bacteria that degrade plant cell walls, exemplified by Clostridium thermocellum, the dockerin domains of the catalytic polypeptides can bind equally well to any cohesin from the same organism. More recently, anaerobic fungi, typified by Piromyces equi, have been suggested to also synthesise a cellulosome complex, although the dockerin sequences of the bacterial and fungal enzymes are completely different. For example, the fungal enzymes contain one, two or three copies of the dockerin sequence in tandem within the catalytic polypeptide. In contrast, all the C. thermocellum cellulosome catalytic components contain a single dockerin domain. The anaerobic bacterial dockerins are homologous to EF hands (calcium-binding motifs) and require calcium for activity whereas the fungal dockerin does not require calcium. Finally, the interaction between cohesin and dockerin appears to be species specific in bacteria, there is almost no species specificity of binding within fungal species and no identified sites that distinguish different species.
The of dockerin from P. equi contains two helical stretches and four short beta-strands which form an antiparallel sheet structure adjacent to an additional short twisted parallel strand. The N- and C-termini are adjacent to each other.
Carbohydrate-binding module family 11 (CBM11) is found in a number of bacterial cellulases. One example is the CBM11 of Clostridium thermocellum Cel26A-Cel5E, this domain has been shown to bind both β-1,4-glucan and β-1,3-1,4-mixed linked glucans. CBM11 has beta-sandwich structure with a concave side forming a substrate-binding cleft.
Carbohydrate-binding module family 12 (CBM12) comprises two beta-sheets, consisting of two and three antiparallel beta strands respectively. It binds chitin via the aromatic rings of tryptophan residues. CBM5 and CBM12 are distantly related.
Carbohydrate-binding module family 14 (CBM14) is also known as the peritrophin-A domain. It is found in chitin binding proteins, particularly the peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. It is an extracellular domain that contains six conserved cysteines that probably form three disulfide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains.
Carbohydrate-binding module family 15 (CBM15), found in bacterial enzymes, has been shown to bind to xylan and xylooligosaccharides. It has a beta-jelly roll fold, with a groove on the concave surface of one of the beta-sheets.
Carbohydrate-binding module family 17 (CBM17) appears to have a very shallow binding cleft that may be more accessible to cellulose chains in non-crystalline cellulose than the deeper binding clefts of family 4 CBMs. Sequence and structural conservation in families CBM17 and CBM28 suggests that they have evolved through gene duplication and subsequent divergence. CBM17 does not compete with CBM28 modules when binding to non-crystalline cellulose. Different CBMs have been shown to bind to different sirtes in amorphous cellulose, CBM17 and CBM28 recognise distinct non-overlapping sites in amorphous cellulose.
Carbohydrate-binding module family 18 (CBM18) (also known as chitin binding 1 or chitin recognition protein) is found in a number of plant and fungal proteins that bind N-acetylglucosamine (e.g. solanaceous lectins of tomato and potato, plant endochitinases, the wound-induced proteins: hevein, win1 and win2, and the Kluyveromyces lactis killer toxin alpha subunit). The domain may occur in one or more copies and is thought to be involved in recognition or binding of chitin subunits. In chitinases, as well as in the potato wound-induced proteins, this 43-residue domain directly follows the signal sequence and is therefore at the N terminus of the mature protein; in the killer toxin alpha subunit it is located in the central section of the protein.
Carbohydrate-binding module family 25 (CBM25) binds alpha-glucooligosaccharides, particularly those containing alpha-1,6 linkages, and granular starch.
Carbohydrate-binding module family 27 (CBM27) binds to beta-1,4-mannooligosaccharides, carob galactomannan, and konjac glucomannan, but not to cellulose (insoluble and soluble) or soluble birchwood xylan. CBM27 adopts a beta sandwich structure comprising 13 beta strands with a single, small alpha-helix and a single metal atom.
Carbohydrate-binding module family 28 (CBM28) does not compete with CBM17 modules when binding to non-crystalline cellulose. Different CBMs have been shown to bind to different sirtes in amorphous cellulose, CBM17 and CBM28 recognise distinct non-overlapping sites in amorphous cellulose. CBM28 has a "beta-jelly roll" topology, which is similar in structure to the CBM17 domains. Sequence and structural conservation in families CBM17 and CBM28 suggests that they have evolved through gene duplication and subsequent divergence.
Carbohydrate-binding module family 32 (CBM32) binds to diverse substrates, ranging from plant cell wall polysaccharides to complex glycans. The module has so far been found in microorganisms, including archea, eubacteria and fungi. CBM32 adopts a beta-sandwich fold and has a bound metal atom, most often observed to be calcium. CBM32 modules are associated with catalytic modules such as sialidases, B-N-acetylglucosaminidases, α-N-acetylglucosaminidases, mannanases and galactose oxidases.
Carbohydrate-binding module family 33 (CBM33) is a chitin-binding domain. It has a budded fibronectin type III fold consisting of two beta-sheets, arranged as a beta-sheet sandwich and a bud consisting of three short helices, located between beta-strands 1 and 2. It binds chitin via conserved polar amino acids. This domain is found in isolation in baculoviral spheroidin and spindolin proteins.
Carbohydrate-binding module family 48 (CBM48) is often found in enzymes containing glycosyl hydrolase family 13 catalytic domains. It is found in a range of enzymes that act on branched substrates i.e. isoamylase, pullulanase and branching enzyme. Isoamylase hydrolyses 1,6-alpha-D-glucosidic branch linkages in glycogen, amylopectin and dextrin; 1,4-alpha-glucan branching enzyme functions in the formation of 1,6-glucosidic linkages of glycogen; and pullulanase is a starch-debranching enzyme. CBM48 binds glycogen.
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- Xu, G. Y.; Ong, E.; Gilkes, N. R.; Kilburn, D. G.; Muhandiram, D. R.; Harris-Brandts, M.; Carver, J. P.; Kay, L. E.; Harvey, T. S. (1995). "Solution structure of a cellulose-binding domain from Cellulomonas fimi by nuclear magnetic resonance spectroscopy". Biochemistry. 34 (21): 6993–7009. doi:10.1021/bi00021a011. PMID 7766609.
- Poole DM, Morag E, Lamed R, Bayer EA, Hazlewood GP, Gilbert HJ (December 1992). "Identification of the cellulose-binding domain of the cellulosome subunit S1 from Clostridium thermocellum YS". FEMS Microbiol. Lett. 78 (2-3): 181–6. doi:10.1016/0378-1097(92)90022-g. PMID 1490597.
- Tormo J, Lamed R, Chirino AJ, Morag E, Bayer EA, Shoham Y, Steitz TA (November 1996). "Crystal structure of a bacterial family-III cellulose-binding domain: a general mechanism for attachment to cellulose". EMBO J. 15 (21): 5739–51. PMC . PMID 8918451.
- Brun E, Johnson PE, Creagh AL, Tomme P, Webster P, Haynes CA, McIntosh LP (March 2000). "Structure and binding specificity of the second N-terminal cellulose-binding domain from Cellulomonas fimi endoglucanase C". Biochemistry. 39 (10): 2445–58. doi:10.1021/bi992079u. PMID 10704194.
- Johnson PE, Joshi MD, Tomme P, Kilburn DG, McIntosh LP (November 1996). "Structure of the N-terminal cellulose-binding domain of Cellulomonas fimi CenC determined by nuclear magnetic resonance spectroscopy". Biochemistry. 35 (45): 14381–94. doi:10.1021/bi961612s. PMID 8916925.
- Akagi, K. -I.; Watanabe, J.; Hara, M.; Kezuka, Y.; Chikaishi, E.; Yamaguchi, T.; Akutsu, H.; Nonaka, T.; Watanabe, T.; Ikegami, T. (2006). "Identification of the Substrate Interaction Region of the Chitin-Binding Domain of Streptomyces griseus Chitinase C". Journal of Biochemistry. 139 (3): 483–493. doi:10.1093/jb/mvj062. PMID 16567413.
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- Winterhalter, C.; Heinrich, P.; Candussio, A.; Wich, G.; Liebl, W. (1995). "Identification of a novel cellulose-binding domain within the multidomain 120 kDa xylanase XynA of the hyperthermophilic bacterium Thermotoga maritima". Molecular Microbiology. 15 (3): 431–444. doi:10.1111/j.1365-2958.1995.tb02257.x. PMID 7783614.
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- Fanutti C, Ponyi T, Black GW, Hazlewood GP, Gilbert HJ (December 1995). "The conserved noncatalytic 40-residue sequence in cellulases and hemicellulases from anaerobic fungi functions as a protein docking domain". J. Biol. Chem. 270 (49): 29314–22. doi:10.1074/jbc.270.49.29314. PMID 7493964.
- Raghothama S, Eberhardt RY, Simpson P, Wigelsworth D, White P, Hazlewood GP, Nagy T, Gilbert HJ, Williamson MP (September 2001). "Characterization of a cellulosome dockerin domain from the anaerobic fungus Piromyces equi". Nat. Struct. Biol. 8 (9): 775–8. doi:10.1038/nsb0901-775. PMID 11524680.
- Carvalho, A. L.; Goyal, A.; Prates, J. A.; Bolam, D. N.; Gilbert, H. J.; Pires, V. M.; Ferreira, L. M.; Planas, A.; Romão, M. J.; Fontes, C. M. (2004). "The Family 11 Carbohydrate-binding Module of Clostridium thermocellum Lic26A-Cel5E Accommodates -1,4- and -1,3-1,4-Mixed Linked Glucans at a Single Binding Site". Journal of Biological Chemistry. 279 (33): 34785–34793. doi:10.1074/jbc.M405867200. PMID 15192099.
- Shen Z, Jacobs-Lorena M (July 1998). "A type I peritrophic matrix protein from the malaria vector Anopheles gambiae binds to chitin. Cloning, expression, and characterization". J. Biol. Chem. 273 (28): 17665–70. doi:10.1074/jbc.273.28.17665. PMID 9651363.
- Elvin CM, Vuocolo T, Pearson RD, East IJ, Riding GA, Eisemann CH, Tellam RL (April 1996). "Characterization of a major peritrophic membrane protein, peritrophin-44, from the larvae of Lucilia cuprina. cDNA and deduced amino acid sequences". J. Biol. Chem. 271 (15): 8925–35. doi:10.1074/jbc.271.15.8925. PMID 8621536.
- Casu R, Eisemann C, Pearson R, Riding G, East I, Donaldson A, Cadogan L, Tellam R (August 1997). "Antibody-mediated inhibition of the growth of larvae from an insect causing cutaneous myiasis in a mammalian host". Proc. Natl. Acad. Sci. U.S.A. 94 (17): 8939–44. doi:10.1073/pnas.94.17.8939. PMC . PMID 9256413.
- Notenboom V, Boraston AB, Chiu P, Freelove AC, Kilburn DG, Rose DR (December 2001). "Recognition of cello-oligosaccharides by a family 17 carbohydrate-binding module: an X-ray crystallographic, thermodynamic and mutagenic study". J. Mol. Biol. 314 (4): 797–806. doi:10.1006/jmbi.2001.5153. PMID 11733998.
- Jamal, S.; Nurizzo, D.; Boraston, A. B.; Davies, G. J. (2004). "X-ray Crystal Structure of a Non-crystalline Cellulose-specific Carbohydrate-binding Module: CBM28". Journal of Molecular Biology. 339 (2): 253–258. doi:10.1016/j.jmb.2004.03.069. PMID 15136030.
- Wright HT, Sandrasegaram G, Wright CS (September 1991). "Evolution of a family of N-acetylglucosamine binding proteins containing the disulfide-rich domain of wheat germ agglutinin". J. Mol. Evol. 33 (3): 283–94. doi:10.1007/bf02100680. PMID 1757999.
- Butler AR, O'Donnell RW, Martin VJ, Gooday GW, Stark MJ (July 1991). "Kluyveromyces lactis toxin has an essential chitinase activity". Eur. J. Biochem. 199 (2): 483–8. doi:10.1111/j.1432-1033.1991.tb16147.x. PMID 2070799.
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- Penninga, D.; Van Der Veen, B. A.; Knegtel, R. M.; Van Hijum, S. A.; Rozeboom, H. J.; Kalk, K. H.; Dijkstra, B. W.; Dijkhuizen, L. (1996). "The raw starch binding domain of cyclodextrin glycosyltransferase from Bacillus circulans strain 251". The Journal of Biological Chemistry. 271 (51): 32777–32784. doi:10.1074/jbc.271.51.32777. PMID 8955113.
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- Boraston, A. B.; Healey, M.; Klassen, J.; Ficko-Blean, E.; Lammerts Van Bueren, A.; Law, V. (2005). "A Structural and Functional Analysis of -Glucan Recognition by Family 25 and 26 Carbohydrate-binding Modules Reveals a Conserved Mode of Starch Recognition". Journal of Biological Chemistry. 281 (1): 587–598. doi:10.1074/jbc.M509958200. PMID 16230347.
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- Polekhina, G.; Gupta, A.; Michell, B. J.; Van Denderen, B.; Murthy, S.; Feil, S. C.; Jennings, I. G.; Campbell, D. J.; Witters, L. A.; Parker, M. W.; Kemp, B. E.; Stapleton, D. (2003). "AMPK beta subunit targets metabolic stress sensing to glycogen". Current Biology. 13 (10): 867–871. doi:10.1016/S0960-9822(03)00292-6. PMID 12747837.
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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.
Cellulose binding domain Provide feedback
Two tryptophan residues are involved in cellulose binding. Cellulose binding domain found in bacteria.
Xu GY, Ong E, Gilkes NR, Kilburn DG, Muhandiram DR, Harris-Brandts M, Carver JP, Kay LE, Harvey TS; , Biochemistry 1995;34:6993-7009.: Solution structure of a cellulose-binding domain from Cellulomonas fimi by nuclear magnetic resonance spectroscopy. PUBMED:7766609 EPMC:7766609
Internal database links
|Similarity to PfamA using HHSearch:||CBM49|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR001919
The microbial degradation of cellulose and xylans requires several types of enzyme such as endoglucanases (EC 22.214.171.124), cellobiohydrolases (EC 126.96.36.199) (exoglucanases), or xylanases (EC 188.8.131.52) [PUBMED:1886523]. Structurally, cellulases and xylanases generally consist of a catalytic domain and a conserved region of ~100 amino acid residues, the carbohydrate-binding module 2 (CBM2) [PUBMED:1812490]. It is found either at the N-terminal or at the C-terminal extremity of these enzymes.
CBM2 can be classified in 2 subfamilies according to substrate specificities: CBM2a which binds cellulose and CBM2b which interacts specifically with xylan. Like other CBM domains CBM2 is a beta-sheet domain containing a planar face which interacts with its ligand via a hydrophobic strip of aromatic residues [PUBMED:7766609]. In family 2a this hydrophobic surface consists of three tryptophan residues, which are all required for binding soluble and insoluble forms of cellulose [PUBMED:9662439]. In family 2b only 2 surface-exposed tryptophans are conserved and the first one is oriented differently. It is therefore not well oriented to interact with cellulose but is ideal for binding xylan [PUBMED:10425686].
This domain recognises both CBM2 subfamilies.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||carbohydrate binding (GO:0030246)|
|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|
|Biological process||carbohydrate metabolic process (GO:0005975)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
- 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
- a link to the page in the Pfam site showing information about the sequence that the graphic describes
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Note that you can see the family page for a particular domain by clicking on the graphic. You can also choose to see all sequences which have a given architecture by clicking on the Show link in each row.
Finally, because some families can be found in a very large number of architectures, we load only the first fifty architectures by default. If you want to see more architectures, click the button at the bottom of the page to load the next set.
Loading domain graphics...
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
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 UniProtKB sequence database using the family HMM
- 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:
- a Java applet developed at the University of Dundee. You will need Java installed before running jalview
- an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
- an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.
You can download (or view in your browser) a text representation of a Pfam alignment in various formats:
You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.
You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.
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.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
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.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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...
If you find these logos useful in your own work, please consider citing the following article:
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.
|Previous IDs:||CBD_1; CBD_2;|
|Number in seed:||14|
|Number in full:||2331|
|Average length of the domain:||97.90 aa|
|Average identity of full alignment:||33 %|
|Average coverage of the sequence by the domain:||17.64 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||18|
|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
This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
There are 3 interactions 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 CBM_2 domain has been found. There are 16 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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