Summary: DHHC palmitoyltransferase

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DHHC domain Edit Wikipedia article

DHHC domain

A depiction of the topology of DHHC family palmitoyltransferases. Transmembrane alpha helices are represented as black tubes. The DHHC domain is shown as a light orange oval.

Identifiers

Symbol

DHHC

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

In molecular biology the DHHC domain is a protein domain that acts as an enzyme, which adds a palmitoyl chemical group to proteins in order to anchor them to cell membranes. The DHHC domain was discovered in 1999 and named after a conserved sequence motif found in its protein sequence.^[1] Roth and colleagues showed that the yeast Akr1p protein could palmitoylate Yck2p in vitro and inferred that the DHHC domain defined a large family of palmitoyltransferases.^[2] In mammals twenty three members of this family have been identified and their substrate specificities investigated.^[3] Some members of the family such as ZDHHC3 and ZDHHC7 enhance palmitoylation of proteins such as PSD-95, SNAP-25, GAP43, GÎ±s. Others such as ZDHHC9 showed specificity only toward the H-Ras protein.^[3] However, a recent study questions the involvement of classical enzyme-substrate recognition and specificity in the palmitoylation reaction.^[4] Several members of the family have been implicated in human diseases.

[edit] Sequence motifs

Conserved motifs within protein sequences point towards the most important amino acid residues for function. In the DHHC domain there is a tetrapeptide motif composed of aspartate-histidine-histidine-cysteine. However this short sequence is embedded in a larger region of about fifty amino acids in length that shares many more conserved amino acids. The canonical DHHC domain can be described with the following sequence motif:

C-x2-C-x9-HC-x2-C-x4-DHHC-x5-C-x4-N-x3-F (x shows region of unconserved residues)

However many examples of DHHC domains are known that do not contain all these conserved residues. In addition to the central DHHC domain three further sequence motifs have been identified in members of the DHHC family. A DPG (aspartate-proline-glycine) motif has been identified just to the C-terminus of the second transmembrane region.^[5] A TTxE (threonine-threonine-any-glutamate) motif has also been identified after the fourth transmembrane helix.^[5] A third motif towards the C-terminus of many proteins has been identified that contains a conserved aromatic amino acid, a glycine and an asparagine called the PaCCT motif (PAlmitoiltransferase Conserved C-Terminus motif).^[6]

[edit] Chemical inhibitors

In 2006, five chemical classes of small molecules were discovered which were shown to act against palmitoyltransferases.^[7] Further studies in 2009 showed that of the 5 classes studied, 2-(2-hydroxy-5-nitro-benzylidene)-benzo[b]thiophen-3-one was shown to behave similarly to 2-Bromopalmitate and were identified as able to inhibit the palmitoylation reaction of a range of DHHC domain containing proteins. Inhibition with 2-Bromopalmitate was found to be irreversible, the other however was found to be mostly reversible.^[8] Because of the roles of DHHC domain proteins in human diseases it has been suggested that chemical inhibitors of specific DHHC proteins may be a potential route to treatment of disease.^[8]

[edit] In human disease

Several proteins containing DHHC domains have been implicated in human disease. Two missense mutations within the DHHC domain of ZDHHC9 were identified in X-linked mental retardation associated with a Marfanoid Habitus.^[9] A potential link of ZDHHC11 with bladder cancer has been suggested by the discovery that 5 out of 9 high-grade bladder cancer samples surveyed contained a duplication of the 5p15.33 genomic region.^[10] However, this region contains another gene TPPP which may be the causative gene. The HIP14 palmitoyltransferase is responsible for palmitoylating the Huntingtin protein. Expansions of the triplet repeat in the huntington's gene leads to loss of interaction with HIP14 which Yanai and colleagues speculate is involved in the pathology of Huntington's disease.^[11] A gene knockout experiment of the mouse homologue of ZDHHC13 showed hair loss, severe osteoporosis, and systemic amyloidosis, both of AL and AA depositions.^[12]

[edit] See also

[edit] References

^ Putilina T, Wong P, Gentleman S (May 1999). "The DHHC domain: a new highly conserved cysteine-rich motif". Mol. Cell. Biochem. 195 (1â2): 219â26. doi:10.1023/A:1006932522197. PMID 10395086.
^ Roth AF, Feng Y, Chen L, Davis NG (October 2002). "The yeast DHHC cysteine-rich domain protein Akr1p is a palmitoyl transferase". J. Cell Biol. 159 (1): 23â8. doi:10.1083/jcb.200206120. PMC 2173492. PMID 12370247. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2173492/.
^ ^a ^b Fukata Y, Iwanaga T, Fukata M (October 2006). "Systematic screening for palmitoyl transferase activity of the DHHC protein family in mammalian cells". Methods 40 (2): 177â82. doi:10.1016/j.ymeth.2006.05.015. PMID 17012030.
^ Rocks O, Gerauer M, Vartak N, et al. (April 2010). "The palmitoylation machinery is a spatially organizing system for peripheral membrane proteins". Cell 141 (3): 458â71. doi:10.1016/j.cell.2010.04.007. PMID 20416930.
^ ^a ^b Mitchell DA, Vasudevan A, Linder ME, Deschenes RJ (June 2006). "Protein palmitoylation by a family of DHHC protein S-acyltransferases". J. Lipid Res. 47 (6): 1118â27. doi:10.1194/jlr.R600007-JLR200. PMID 16582420.
^ GonzÃ¡lez Montoro A, Quiroga R, Maccioni HJ, Valdez Taubas J (April 2009). "A novel motif at the C-terminus of palmitoyltransferases is essential for Swf1 and Pfa3 function in vivo". Biochem. J. 419 (2): 301â8. doi:10.1042/BJ20080921. PMID 19138168.
^ Stober R (June 1987). "[Total or subtotal amputation of a long finger with destruction of the metacarpophalangeal joint--regaining function by replantation?]" (in German). Aktuelle Traumatol 17 (3): 100â4. PMID 2888271.
^ ^a ^b Jennings BC, Nadolski MJ, Ling Y, et al. (February 2009). "2-Bromopalmitate and 2-(2-hydroxy-5-nitro-benzylidene)-benzobthiophen-3-one inhibit DHHC-mediated palmitoylation in vitro". J. Lipid Res. 50 (2): 233â42. doi:10.1194/jlr.M800270-JLR200. PMC 2636914. PMID 18827284. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2636914/.
^ Raymond FL, Tarpey PS, Edkins S, et al. (May 2007). "Mutations in ZDHHC9, Which Encodes a Palmitoyltransferase of NRAS and HRAS, Cause X-Linked Mental Retardation Associated with a Marfanoid Habitus". Am. J. Hum. Genet. 80 (5): 982â7. doi:10.1086/513609. PMC 1852737. PMID 17436253. //www.ncbi.nlm.nih.gov/pmc/articles/PMC1852737/.
^ Yamamoto Y, Chochi Y, Matsuyama H, et al. (2007). "Gain of 5p15.33 is associated with progression of bladder cancer". Oncology 72 (1â2): 132â8. doi:10.1159/111132. PMID 18025801.
^ Yanai A, Huang K, Kang R, et al. (June 2006). "Palmitoylation of huntingtin by HIP14 is essential for its trafficking and function". Nat. Neurosci. 9 (6): 824â31. doi:10.1038/nn1702. PMC 2279235. PMID 16699508. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2279235/.
^ Saleem AN, Chen YH, Baek HJ, et al. (2010). MacDonald, Marcy E.. ed. "Mice with Alopecia, Osteoporosis, and Systemic Amyloidosis Due to Mutation in Zdhhc13, a Gene Coding for Palmitoyl Acyltransferase". PLoS Genet. 6 (6): e1000985. doi:10.1371/journal.pgen.1000985. PMC 2883605. PMID 20548961. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2883605/.

[edit] External links

Eukaryotic Linear Motif resource motif class MOD_SPalmitoyl_2

[edit] Further reading

Greaves J, Gorleku OA, Salaun C, Chamberlain LH (August 2010). "Palmitoylation of the SNAP25 Protein Family: SPECIFICITY AND REGULATION BY DHHC PALMITOYL TRANSFERASES". J. Biol. Chem. 285 (32): 24629â38. doi:10.1074/jbc.M110.119289. PMC 2915699. PMID 20519516. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2915699/.
Greaves J, Chamberlain LH (April 2010). "S-acylation by the DHHC protein family". Biochem. Soc. Trans. 38 (2): 522â4. doi:10.1042/BST0380522. PMID 20298214.
Hines RM, Kang R, Goytain A, Quamme GA (February 2010). "Golgi-specific DHHC Zinc Finger Protein GODZ Mediates Membrane Ca2+ Transport". J. Biol. Chem. 285 (7): 4621â8. doi:10.1074/jbc.M109.069849. PMC 2836067. PMID 19955568. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2836067/.
Mizumaru C, Saito Y, Ishikawa T, et al. (December 2009). "Suppression of APP-containing vesicle trafficking and production of beta-amyloid by AID/DHHC-12 protein". J. Neurochem. 111 (5): 1213â24. doi:10.1111/j.1471-4159.2009.06399.x. PMID 19780898.
Noritake J, Fukata Y, Iwanaga T, et al. (July 2009). "Mobile DHHC palmitoylating enzyme mediates activity-sensitive synaptic targeting of PSD-95". J. Cell Biol. 186 (1): 147â60. doi:10.1083/jcb.200903101. PMC 2712995. PMID 19596852. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2712995/.
Hou H, John Peter AT, Meiringer C, Subramanian K, Ungermann C (August 2009). "Analysis of DHHC acyltransferases implies overlapping substrate specificity and a two-step reaction mechanism". Traffic 10 (8): 1061â73. doi:10.1111/j.1600-0854.2009.00925.x. PMID 19453970.
Greaves J, Prescott GR, Fukata Y, Fukata M, Salaun C, Chamberlain LH (March 2009). "The Hydrophobic Cysteine-rich Domain of SNAP25 Couples with Downstream Residues to Mediate Membrane Interactions and Recognition by DHHC Palmitoyl Transferases". Mol. Biol. Cell 20 (6): 1845â54. doi:10.1091/mbc.E08-09-0944. PMC 2655257. PMID 19158383. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2655257/.
Johswich A, Kraft B, Wuhrer M, et al. (January 2009). "Golgi targeting of Drosophila melanogaster Î²4GalNAcTB requires a DHHC protein familyârelated protein as a pilot". J. Cell Biol. 184 (1): 173â83. doi:10.1083/jcb.200801071. PMC 2615082. PMID 19139268. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2615082/.
Matakatsu H, Blair SS (September 2008). "approximated encodes a DHHC palmitoyltransferase that regulates Fat signaling and the subcellular localization and activity of Dachs". Curr. Biol. 18 (18): 1390â5. doi:10.1016/j.cub.2008.07.067. PMC 2597019. PMID 18804377. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2597019/.
Bannan BA, Van Etten J, Kholer JA, et al. (2008). "The Drosophila protein palmitoylome: Characterizing palmitoyl-thioesterases and DHHC palmitoyl-transferases". Fly (Austin) 2 (4): 198â214. PMC 2898910. PMID 18719403. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2898910/.
Dighe SA, Kozminski KG (October 2008). "Swf1p, a Member of the DHHC-CRD Family of Palmitoyltransferases, Regulates the Actin Cytoskeleton and Polarized Secretion Independently of Its DHHC Motif". Mol. Biol. Cell 19 (10): 4454â68. doi:10.1091/mbc.E08-03-0252. PMC 2555925. PMID 18701706. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2555925/.
Lam KK, Davey M, Sun B, Roth AF, Davis NG, Conibear E (July 2006). "Palmitoylation by the DHHC protein Pfa4 regulates the ER exit of Chs3". J. Cell Biol. 174 (1): 19â25. doi:10.1083/jcb.200602049. PMC 2064155. PMID 16818716. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2064155/.
Ohno Y, Kihara A, Sano T, Igarashi Y (April 2006). "Intracellular localization and tissue-specific distribution of human and yeast DHHC cysteine-rich domain-containing proteins". Biochim. Biophys. Acta 1761 (4): 474â83. doi:10.1016/j.bbalip.2006.03.010. PMID 16647879.
Mitchell DA, Vasudevan A, Linder ME, Deschenes RJ (June 2006). "Protein palmitoylation by a family of DHHC protein S-acyltransferases". J. Lipid Res. 47 (6): 1118â27. doi:10.1194/jlr.R600007-JLR200. PMID 16582420.
Hou H, Subramanian K, LaGrassa TJ, et al. (November 2005). "The DHHC protein Pfa3 affects vacuole-associated palmitoylation of the fusion factor Vac8". Proc. Natl. Acad. Sci. U.S.A. 102 (48): 17366â71. doi:10.1073/pnas.0508885102. PMC 1297695. PMID 16301533. //www.ncbi.nlm.nih.gov/pmc/articles/PMC1297695/.
Smotrys JE, Schoenfish MJ, Stutz MA, Linder ME (September 2005). "The vacuolar DHHC-CRD protein Pfa3p is a protein acyltransferase for Vac8p". J. Cell Biol. 170 (7): 1091â9. doi:10.1083/jcb.200507048. PMC 2171546. PMID 16186255. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2171546/.
Gleason EJ, Lindsey WC, Kroft TL, Singson AW, L'hernault SW (January 2006). "spe-10 Encodes a DHHCâCRD Zinc-Finger Membrane Protein Required for Endoplasmic Reticulum/Golgi Membrane Morphogenesis During Caenorhabditis elegans Spermatogenesis". Genetics 172 (1): 145â58. doi:10.1534/genetics.105.047340. PMC 1456142. PMID 16143610. //www.ncbi.nlm.nih.gov/pmc/articles/PMC1456142/.
Seydel KB, Gaur D, Aravind L, Subramanian G, Miller LH (August 2005). "Plasmodium falciparum: characterization of a late asexual stage golgi protein containing both ankyrin and DHHC domains". Exp. Parasitol. 110 (4): 389â93. doi:10.1016/j.exppara.2005.03.030. PMID 15882865.
Saitoh F, Tian QB, Okano A, Sakagami H, Kondo H, Suzuki T (July 2004). "NIDD, a novel DHHC-containing protein, targets neuronal nitric-oxide synthase (nNOS) to the synaptic membrane through a PDZ-dependent interaction and regulates nNOS activity". J. Biol. Chem. 279 (28): 29461â8. doi:10.1074/jbc.M401471200. PMID 15105416.
Nagaya M, Inohaya K, Imai Y, Kudo A (December 2002). "Expression of zisp, a DHHC zinc finger gene, in somites and lens during zebrafish embryogenesis". Gene Expr. Patterns 2 (3â4): 355â8. doi:10.1016/S1567-133X(02)00021-2. PMID 12617825.
Uemura T, Mori H, Mishina M (August 2002). "Isolation and characterization of Golgi apparatus-specific GODZ with the DHHC zinc finger domain". Biochem. Biophys. Res. Commun. 296 (2): 492â6. doi:10.1016/S0006-291X(02)00900-2. PMID 12163046.
Li B, Cong F, Tan CP, Wang SX, Goff SP (August 2002). "Aph2, a protein with a zf-DHHC motif, interacts with c-Abl and has pro-apoptotic activity". J. Biol. Chem. 277 (32): 28870â6. doi:10.1074/jbc.M202388200. PMID 12021275.

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DHHC palmitoyltransferase Provide feedback

This family includes the well known DHHC zinc binding domain as well as three of the four conserved transmembrane regions found in this family of palmitoyltransferase enzymes.

Literature references

Mesilaty-Gross S, Reich A, Motro B, Wides R; , Gene 1999;231:173-186.: The drosophila STAM gene homolog is in a tight gene cluster, and its expression correlates to that of the adjacent gene ial. PUBMED:10231582 EPMC:10231582
Boehm S, Frishman D, Mewes HW; , Nucleic Acids Res 1997;25:2464-2469.: Variations of the C2H2 zinc finger motif in the yeast genome and classification of yeast zinc finger proteins. PUBMED:9171100 EPMC:9171100
Putilina T, Wong P, Gentleman S; , Mol Cell Biochem 1999;195:219-226.: The DHHC domain: a new highly conserved cysteine-rich motif. PUBMED:10395086 EPMC:10395086
Bartels DJ, Mitchell DA, Dong X, Deschenes RJ; , Mol Cell Biol 1999;19:6775-6787.: Erf2, a Novel Gene Product That Affects the Localization and Palmitoylation of Ras2 in Saccharomyces cerevisiae. PUBMED:10490616 EPMC:10490616
Lobo S, Greentree WK, Linder ME, Deschenes RJ; , J Biol Chem 2002;277:41268-41273.: Identification of a Ras palmitoyltransferase in Saccharomyces cerevisiae. PUBMED:12193598 EPMC:12193598

External database links

PANDIT:	PF01529
Pseudofam:	PF01529
SYSTERS:	zf-DHHC

This tab holds annotation information from the InterPro database.

InterPro entry IPR001594

Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [PUBMED:10529348, PUBMED:15963892, PUBMED:15718139, PUBMED:17210253, PUBMED:12665246]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few [PUBMED:11179890]. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.

This entry represents the DHHC-type zinc finger domain, which is also known as NEW1 [PUBMED:10231582]. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif [PUBMED:10231582]. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues [PUBMED:17051234]. This domain is found in the DHHC proteins which are palmitoyl transferases [PUBMED:15603741]; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site.

More information about these proteins can be found at Protein of the Month: Zinc Fingers [PUBMED:].

Gene Ontology

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

Molecular function

zinc ion binding (GO:0008270)

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 Zn_Beta_Ribbon (CL0167), which contains the following 50 members:

A2L_zn_ribbon Auto_anti-p27 Baculo_LEF5_C DNA_RNApol_7kD DUF1610 DUF1936 DUF2116 DUF2180 DUF2387 DZR Elf1 GATA NinF NOB1_Zn_bind Ogr_Delta OrfB_Zn_ribbon PhnA_Zn_Ribbon Prim_Zn_Ribbon Ribosomal_L32p Ribosomal_L37ae Ribosomal_S27 Ribosomal_S27e RNA_POL_M_15KD RRN7 Spt4 TF_Zn_Ribbon TFIIS_C Tnp_zf-ribbon_2 Topo_Zn_Ribbon Toprim_Crpt Trm112p UPF0547 zf-C4_Topoisom zf-CHC2 zf-DHHC zf-dskA_traR zf-FPG_IleRS zf-GRF zf-NADH-PPase zf-RanBP zf-ribbon_3 zf-TFIIB zinc-ribbons_6 zinc_ribbon_2 zinc_ribbon_4 zinc_ribbon_5 Zn-ribbon_8 Zn_ribbon_recom Zn_Tnp_IS1 Zn_Tnp_IS1595

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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Reformatting

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Downloading

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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 (97)	Full (4432)	Representative proteomes				NCBI (4268)	Meta (82)
	Seed (97)	Full (4432)	RP15 (1087)	RP35 (1605)	RP55 (2335)	RP75 (2951)	NCBI (4268)	Meta (82)
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 (97)	Full (4432)	Representative proteomes				NCBI (4268)	Meta (82)
	Seed (97)	Full (4432)	RP15 (1087)	RP35 (1605)	RP55 (2335)	RP75 (2951)	NCBI (4268)	Meta (82)
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 (97)	Full (4432)	Representative proteomes				NCBI (4268)	Meta (82)
	Seed (97)	Full (4432)	RP15 (1087)	RP35 (1605)	RP55 (2335)	RP75 (2951)	NCBI (4268)	Meta (82)
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_945 (release 4.0)

Previous IDs:

none

Type:

Family

Author:

Bateman A

Number in seed:

97

Number in full:

4432

Average length of the domain:

169.10 aa

Average identity of full alignment:

23 %

Average coverage of the sequence by the domain:

40.72 %

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	21.1	21.1
Trusted cut-off	21.1	21.2
Noise cut-off	21.0	21.0

Model length:

174

Family (HMM) version:

15

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.

Loading sunburst data...

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.

Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: zf-DHHC (PF01529)

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