Summary: Cathelicidin

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Cathelicidin Edit Wikipedia article

Cathelicidin

Crystal Structure Analysis of the Cathelicidin Motif of Protegrins

Identifiers

Symbol

Cathelicidin

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Cathelicidin antimicrobial peptide

Rendering based on PDB 2FBS.

Available structures

PDB

Ortholog search: PDBe, RCSB

List of PDB id codes
2FBS, 2FBU, 2FCG, 2K6O, 2LMF, 4EYC

Identifiers

Symbols

CAMP; CAP-18; CAP18; CRAMP; FALL-39; FALL39; LL37

External IDs

OMIM: 600474 MGI: 108443 HomoloGene: 110678 GeneCards: CAMP Gene

Gene Ontology
Molecular function	â¢ protein binding
Cellular component	â¢ extracellular region â¢ cell wall â¢ cytosol
Biological process	â¢ defense response to bacterium â¢ negative regulation of growth of symbiont on or near host surface â¢ interaction with host â¢ killing by host of symbiont cells â¢ phagosome maturation
Sources: Amigo / QuickGO

RNA expression pattern

More reference expression data

Orthologs

Species

Human

Mouse

RefSeq (mRNA)

RefSeq (protein)

Location (UCSC)

Chr 3:
48.26 â 48.27 Mb

Chr 9:
109.85 â 109.85 Mb

PubMed search

[1]

[2]

Cathelicidin-related antimicrobial peptides are a family of polypeptides found in lysosomes of macrophages and polymorphonuclear leukocytes (PMNs).^[1] Cathelicidins serve a critical role in mammalian innate immune defense against invasive bacterial infection.^[2]

Members of the cathelicidin family of antimicrobial polypeptides are characterized by a highly conserved region (cathelin domain) and a highly variable cathelicidin peptide domain.^[3]

Cathelicidin peptides have been isolated from many different species of mammals. Cathelicidins were originally found in neutrophils but have since been found in many other cells including epithelial cells and macrophages after activation by bacteria, viruses, fungi, or the hormone 1,25-D, which is the hormonally active form of vitamin D.^[4]

The cathelicidin family shares primary sequence homology with the cystatin^[5] family of cysteine proteinase inhibitors, although amino acid residues thought to be important in such protease inhibition are usually lacking.

[edit] Characteristics

Cathelicidins range in size from 12 to 80 amino acid residues and have a wide range of structures.^[6] Most cathelicidins are linear peptides with 23-37 amino acid residues, and fold into amphiphatic Î±-helices. Additionally cathelicidins may also be small-sized molecules (12-18 residues) with beta-hairpin structures, stabilized by one or two disulphide bonds. Even larger cathelicidin peptides (39-80 amino acid residues) are also present. These larger cathelicidins display repetitive proline motifs forming extended polyproline-type structures.^[3]

[edit] Family members

Cathelicidin family components have been found in: humans, monkeys, mice, rats, rabbits, guinea pigs, pandas, pigs, cattle, sheep, goats, and horses.

Currently identified cathelicidins include the following:^[3]

Human:hCAP-18/LL-37
Rhesus Monkey: RL-37
Mice:CRAMP-1/2, (Cathelicidin-related Antimicrobial Peptide^[7]
Rats: rCRAMP
Rabbits: CAP-18
Guinea Pig: CAP-11
Pigs: PR-39, Prophenin, PMAP-23,36,37
Cattle: BMAP-27,28,34 (Bovine Myeloid Antimicrobial Peptides); Bac5, Bac7
Sheep:
Goats:
Horses:
Pandas:

[edit] Clinical significance

Patients with rosacea have elevated levels of cathelicidin and elevated levels of stratum corneum tryptic enzymes (SCTEs). Antibiotics have been used in the past to treat rosacea, but antibiotics may only work because they inhibit some SCTEs.^[8]

Higher levels of human cathelicidin antimicrobial protein (hCAP18), which are regulated by vitamin D, appear to significantly reduce the risk of death from infection in dialysis patients. Patients with a high level of this protein were 3.7 times more likely to survive kidney dialysis for a year without a fatal infection.^[9]

[edit] See also

[edit] References

^ "Entrez Gene: CAMP cathelicidin antimicrobial peptide". http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=820.
^ Nizet V, Ohtake T, Lauth X, Trowbridge J, Rudisill J, Dorschner RA, Pestonjamasp V, Piraino J, Huttner K, Gallo RL (November 2001). "Innate antimicrobial peptide protects the skin from invasive bacterial infection". Nature 414 (6862): 454â7. doi:10.1038/35106587. PMID 11719807.
^ ^a ^b ^c Zanetti M (January 2004). "Cathelicidins, multifunctional peptides of the innate immunity". J. Leukoc. Biol. 75 (1): 39â48. doi:10.1189/jlb.0403147. PMID 12960280.
^ Liu PT, Stenger S, Li H, Wenzel L, Tan BH, Krutzik SR, Ochoa MT, Schauber J, Wu K, Meinken C, Kamen DL, Wagner M, Bals R, Steinmeyer A, ZÃ¼gel U, Gallo RL, Eisenberg D, Hewison M, Hollis BW, Adams JS, Bloom BR, Modlin R (March 2006). "Toll-like receptor triggering of a vitamin D-mediated human antimicrobial response". Science 311 (5768): 1770â3. doi:10.1126/science.1123933. PMID 16497887.
^ Zaiou M, Nizet V, Gallo RL. (May 2003). "Antimicrobial and protease inhibitory functions of the human cathelicidin (hCAP18/LL-37) prosequence". J Invest Dermatol. 5 (120): 810â6. doi:10.1046/j.1523-1747.2003.12132.x3. PMID 12713586.
^ Gennaro R, Zanetti M (2000). "Structural features and biological activities of the cathelicidin-derived antimicrobial peptides". Biopolymers 55 (1): 31â49. doi:10.1002/1097-0282(2000)55:1<31::AID-BIP40>3.0.CO;2-9. PMID 10931440.
^ Gallo RL, Kim KJ, Bernfield M, Kozak CA, Zanetti M, Merluzzi L, Gennaro R (May 1997). "Identification of CRAMP, a cathelin-related antimicrobial peptide expressed in the embryonic and adult mouse". J. Biol. Chem. 272 (20): 13088â93. doi:10.1074/jbc.272.20.13088. PMID 9148921.
^ Yamasaki K, Di Nardo A, Bardan A, Murakami M, Ohtake T, Coda A, Dorschner RA, Bonnart C, Descargues P, Hovnanian A, Morhenn VB, Gallo RL (August 2007). "Increased serine protease activity and cathelicidin promotes skin inflammation in rosacea". Nat. Med. 13 (8): 975â80. doi:10.1038/nm1616. PMID 17676051.
^ Gombart AF, Bhan I, Borregaard N, Tamez H, Camargo CA, Koeffler HP, Thadhani R (February 2009). "Low plasma level of cathelicidin antimicrobial peptide (hCAP18) predicts increased infectious disease mortality in patients undergoing hemodialysis". Clin. Infect. Dis. 48 (4): 418â24. doi:10.1086/596314. PMID 19133797.

[edit] Further reading

DÃ¼rr UH, Sudheendra US, Ramamoorthy A (September 2006). "LL-37, the only human member of the cathelicidin family of antimicrobial peptides". Biochim. Biophys. Acta 1758 (9): 1408â25. doi:10.1016/j.bbamem.2006.03.030. PMID 16716248.
Chromek M, SlamovÃ¡ Z, Bergman P, KovÃ¡cs L, PodrackÃ¡ L, EhrÃ©n I, HÃ¶kfelt T, Gudmundsson GH, Gallo RL, Agerberth B, Brauner A (June 2006). "The antimicrobial peptide cathelicidin protects the urinary tract against invasive bacterial infection". Nat. Med. 12 (6): 636â41. doi:10.1038/nm1407. PMID 16751768.
Gombart AF, Borregaard N, Koeffler HP (July 2005). "Human cathelicidin antimicrobial peptide (CAMP) gene is a direct target of the vitamin D receptor and is strongly up-regulated in myeloid cells by 1,25-dihydroxyvitamin D3". FASEB J. 19 (9): 1067â77. doi:10.1096/fj.04-3284com. PMID 15985530.
LÃ³pez-GarcÃa B, Lee PH, Gallo RL (May 2006). "Expression and potential function of cathelicidin antimicrobial peptides in dermatophytosis and tinea versicolor". J. Antimicrob. Chemother. 57 (5): 877â82. doi:10.1093/jac/dkl078. PMID 16556635.
Lehrer RI, Ganz T (2002). "Cathelicidins: a family of endogenous antimicrobial peptides.". Curr. Opin. Hematol. 9 (1): 18â22. doi:10.1097/00062752-200201000-00004. PMID 11753073.
Niyonsaba F, Hirata M, Ogawa H, Nagaoka I (2003). "Epithelial cell-derived antibacterial peptides human beta-defensins and cathelicidin: multifunctional activities on mast cells.". Current drug targets. Inflammation and allergy 2 (3): 224â31. doi:10.2174/1568010033484115. PMID 14561157.
van Wetering S, Tjabringa GS, Hiemstra PS (2005). "Interactions between neutrophil-derived antimicrobial peptides and airway epithelial cells.". J. Leukoc. Biol. 77 (4): 444â50. doi:10.1189/jlb.0604367. PMID 15591123.
Agerberth B, Gunne H, Odeberg J, et al. (1995). "FALL-39, a putative human peptide antibiotic, is cysteine-free and expressed in bone marrow and testis.". Proc. Natl. Acad. Sci. U.S.A. 92 (1): 195â9. doi:10.1073/pnas.92.1.195. PMC 42844. PMID 7529412. //www.ncbi.nlm.nih.gov/pmc/articles/PMC42844/.
Cowland JB, Johnsen AH, Borregaard N (1995). "hCAP-18, a cathelin/pro-bactenecin-like protein of human neutrophil specific granules.". FEBS Lett. 368 (1): 173â6. doi:10.1016/0014-5793(95)00634-L. PMID 7615076.
Gudmundsson GH, Magnusson KP, Chowdhary BP, et al. (1995). "Structure of the gene for porcine peptide antibiotic PR-39, a cathelin gene family member: comparative mapping of the locus for the human peptide antibiotic FALL-39.". Proc. Natl. Acad. Sci. U.S.A. 92 (15): 7085â9. doi:10.1073/pnas.92.15.7085. PMC 41476. PMID 7624374. //www.ncbi.nlm.nih.gov/pmc/articles/PMC41476/.
Larrick JW, Hirata M, Balint RF, et al. (1995). "Human CAP18: a novel antimicrobial lipopolysaccharide-binding protein.". Infect. Immun. 63 (4): 1291â7. PMC 173149. PMID 7890387. //www.ncbi.nlm.nih.gov/pmc/articles/PMC173149/.
Gudmundsson GH, Agerberth B, Odeberg J, et al. (1996). "The human gene FALL39 and processing of the cathelin precursor to the antibacterial peptide LL-37 in granulocytes.". Eur. J. Biochem. 238 (2): 325â32. doi:10.1111/j.1432-1033.1996.0325z.x. PMID 8681941.
Larrick JW, Lee J, Ma S, et al. (1997). "Structural, functional analysis and localization of the human CAP18 gene.". FEBS Lett. 398 (1): 74â80. doi:10.1016/S0014-5793(96)01199-4. PMID 8946956.
Frohm M, Agerberth B, Ahangari G, et al. (1997). "The expression of the gene coding for the antibacterial peptide LL-37 is induced in human keratinocytes during inflammatory disorders.". J. Biol. Chem. 272 (24): 15258â63. doi:10.1074/jbc.272.24.15258. PMID 9182550.
Bals R, Wang X, Zasloff M, Wilson JM (1998). "The peptide antibiotic LL-37/hCAP-18 is expressed in epithelia of the human lung where it has broad antimicrobial activity at the airway surface.". Proc. Natl. Acad. Sci. U.S.A. 95 (16): 9541â6. doi:10.1073/pnas.95.16.9541. PMC 21374. PMID 9689116. //www.ncbi.nlm.nih.gov/pmc/articles/PMC21374/.
De Yang , Chen Q, Schmidt AP, et al. (2000). "LL-37, the neutrophil granule- and epithelial cell-derived cathelicidin, utilizes formyl peptide receptor-like 1 (FPRL1) as a receptor to chemoattract human peripheral blood neutrophils, monocytes, and T cells.". J. Exp. Med. 192 (7): 1069â74. doi:10.1084/jem.192.7.1069. PMC 2193321. PMID 11015447. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2193321/.
Agerberth B, Charo J, Werr J, et al. (2000). "The human antimicrobial and chemotactic peptides LL-37 and alpha-defensins are expressed by specific lymphocyte and monocyte populations.". Blood 96 (9): 3086â93. PMID 11049988.
Bals R, Lang C, Weiner DJ, et al. (2001). "Rhesus monkey (Macaca mulatta) mucosal antimicrobial peptides are close homologues of human molecules.". Clin. Diagn. Lab. Immunol. 8 (2): 370â5. doi:10.1128/CDLI.8.2.370-375.2001. PMC 96065. PMID 11238224. //www.ncbi.nlm.nih.gov/pmc/articles/PMC96065/.
Nagaoka I, Hirota S, Niyonsaba F, et al. (2001). "Cathelicidin family of antibacterial peptides CAP18 and CAP11 inhibit the expression of TNF-alpha by blocking the binding of LPS to CD14(+) cells.". J. Immunol. 167 (6): 3329â38. PMID 11544322.
Hase K, Eckmann L, Leopard JD, et al. (2002). "Cell differentiation is a key determinant of cathelicidin LL-37/human cationic antimicrobial protein 18 expression by human colon epithelium.". Infect. Immun. 70 (2): 953â63. doi:10.1128/IAI.70.2.953-963.2002. PMC 127717. PMID 11796631. //www.ncbi.nlm.nih.gov/pmc/articles/PMC127717/.
Giuliani A, Pirri G, Nicoletto S (2007). "Antimicrobial peptides: an overview of a promising class of therapeutics .". Cent. Eur. J. Biol. 2 (1): 1â33. doi:10.2478/s11535-007-0010-5.
Burton MF, Steel PG (2009). "Chemistry and Biology of LL-37". Natural Product Reports, 26 (12): 1572â1584. doi:10.1039/b912533g.

This immunology article is a stub. You can help Wikipedia by expanding it.

Antimicrobial peptides: Granulocyte granule contents

Azurophilic granules (1Â°)

Myeloperoxidase Â· Defensins Â· neutral serine proteases (Proteinase 3) Â· Lysozyme Â· Bactericidal/permeability increasing protein Â· Collagenase

Specific granules (2Â°)

Neutrophil	Alkaline phosphatase Â· Lactoferrin Â· Lysozyme Â· NADPH oxidase Â· Collagenase Â· Cathelicidin

Eosinophil	Cathepsin Â· Major basic protein Â· Eosinophil cationic protein Â· Eosinophil peroxidase Â· Eosinophil-derived neurotoxin

Basophil	Heparin Â· Histamine

M: MYL

cell/phys (coag, heme, immu, gran), csfs

rbmg/mogr/tumr/hist, sysi/epon, btst

drug (B1/2/3+5+6), btst, trns

v t e Pore-forming toxins (TC 1C)

Antimicrobial cationic peptides	Cathelicidin Defensin Dermcidin Histatin (HTN1, HTN3)

Other, human	Perforin

Other, nonhuman	Cecropin Diphtheria toxin Dermaseptin Magainin Melittin Nisin Pneumolysin

B memb: cead, trns (1A, 1C, 1F, 2A, 3A1, 3A2-3, 3D), othr

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.

Cathelicidin Provide feedback

A novel protein family, showing a conserved proregion and a variable carboxyl-terminal antimicrobial domain. This region shows similarity to cystatins.

Literature references

Zanetti M, Gennaro R, Romeo D; , FEBS Lett 1995;374:1-5.: Cathelicidins: a novel protein family with a common proregion and a variable C-terminal antimicrobial domain. PUBMED:7589491 EPMC:7589491

Internal database links

SCOOP:	HPS3_N Spp-24
Similarity to PfamA using HHSearch:	Cystatin

External database links

PANDIT:	PF00666
PROSITE:	PDOC00729
Pseudofam:	PF00666
SCOP:	1lyp
SYSTERS:	Cathelicidins
Transporter classification:	1.C.33

This tab holds annotation information from the InterPro database.

InterPro entry IPR001894

The precursor sequences of a number of antimicrobial peptides secreted by neutrophils (polymorphonuclear leukocytes) upon activation have been found to be evolutionarily related and are collectively known as cathelicidins [PUBMED:7589491].

Structurally, these proteins consist of three domains: a signal sequence, a conserved region of about 100 residues that contains four cysteines involved in two disulphide bonds, and a highly divergent C-terminal section of variable size. It is in this C-terminal section that the antibacterial peptides are found; they are proteolytically processed from their precursor by enzymes such as elastase. This structure is shown in the following schematic representation:

   +---+--------------------------------+--------------------+
   |Sig| Propeptide     C  C  C  C      | Antibacterial pep. |
   +---+----------------|--|--|--|------+--------------------+
                        |  |  |  |
                        +--+  +--+
'C': conserved cysteine involved in a disulphide bond.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Cellular component	extracellular region (GO:0005576)
Biological process	defense response (GO:0006952)

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 Cystatin (CL0121), which contains the following 4 members:

Cathelicidins Cystatin PP1 Spp-24

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...

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.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
NCBI: alignment generated by searching the NCBI sequence database using the family HMM
meta: alignment generated by searching the metagenomics sequence database using the family HMM

Viewing

You can see the alignments as HTML or in three different sequence viewers:

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PP/Heatmap: 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.
Pfam viewer: an HTML-based viewer that uses DAS to retrieve alignment fragments on request

Reformatting

You can download (or view in your browser) a text representation of a Pfam alignment in various formats:

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Stockholm
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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.

Downloading

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.

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 (8)	Full (193)	Representative proteomes				NCBI (189)	Meta (1)
	Seed (8)	Full (193)	RP15 (1)	RP35 (1)	RP55 (18)	RP75 (87)	NCBI (189)	Meta (1)
Jalview	View	View	View	View	View	View	View	View
HTML	View	View	View	View	View	View
PP/heatmap	₁	View	View	View	View	View
Pfam viewer	View	View

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

Key: available, not generated, — not available.

Format an alignment

	Seed (8)	Full (193)	Representative proteomes				NCBI (189)	Meta (1)
	Seed (8)	Full (193)	RP15 (1)	RP35 (1)	RP55 (18)	RP75 (87)	NCBI (189)	Meta (1)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	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 (8)	Full (193)	Representative proteomes				NCBI (189)	Meta (1)
	Seed (8)	Full (193)	RP15 (1)	RP35 (1)	RP55 (18)	RP75 (87)	NCBI (189)	Meta (1)
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

Seed source:

Pfam-B_276 (release 2.1)

Previous IDs:

none

Type:

Family

Author:

Bateman A

Number in seed:

8

Number in full:

193

Average length of the domain:

65.00 aa

Average identity of full alignment:

50 %

Average coverage of the sequence by the domain:

41.10 %

HMM information

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	20.7	20.7
Trusted cut-off	20.8	20.7
Noise cut-off	20.6	20.4

Model length:

67

Family (HMM) version:

12

Download:

download the raw HMM for this family

Species distribution

Sunburst
Tree

Sunburst controls

Show

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...

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:

superkingdom
kingdom
phylum
class
order
family
genus
species

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".

Sub-species

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.

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Tree controls

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The tree shows the occurrence of this domain across different species. More...

Species trees

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.

Interactive tree

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

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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.

Interactions

There is 1 interaction for this family. More...

Cathelicidins

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 Cathelicidins domain has been found. There are 5 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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Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: Cathelicidins (PF00666)

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