Summary: Fanconi anaemia group C protein

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Wikipedia: Fanconi anemia, complementation group C
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Fanconi anemia, complementation group C Edit Wikipedia article

Fanconi anemia, complementation group C

Identifiers

Symbols

FANCC; FA3; FAC; FACC

External IDs

OMIM: 613899 MGI: 95480 HomoloGene: 109 GeneCards: FANCC Gene

Gene Ontology
Molecular function	• protein binding
Cellular component	• chromatin • nucleus • nucleoplasm • cytoplasm • cytosol • Fanconi anaemia nuclear complex
Biological process	• myeloid cell homeostasis • DNA repair • nucleotide-excision repair • protein complex assembly • germ cell development • removal of superoxide radicals
Sources: Amigo / QuickGO

RNA expression pattern

More reference expression data

Orthologs

Species

Human

Mouse

RefSeq (mRNA)

RefSeq (protein)

Location (UCSC)

Chr 9:
97.86 – 98.08 Mb

Chr 13:
63.41 – 63.6 Mb

PubMed search

[1]

[2]

Fanconi anaemia group C protein

Identifiers

Symbol

Fanconi_C

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

Fanconi anemia group C protein is a protein that in humans is encoded by the FANCC gene.^[1]^[2]

The protein encoded by this gene delays the onset of apoptosis and promotes homologous recombination repair of damaged DNA. Mutations in this gene result in Fanconi anemia.^[2]

[edit] Interactions

Fanconi anemia, complementation group C has been shown to interact with STAT1,^[3]^[4]^[5] ZBTB32,^[4]^[6] GSTP1,^[4]^[7] Cdk1,^[4]^[8] SPTAN1,^[9]^[10] HSPA1A,^[4]^[11] FANCF,^[12]^[13] FANCA^[10]^[13]^[14]^[15]^[16]^[17]^[18]^[19] and FANCE.^[12]^[18]^[20]^[21]^[22]

[edit] References

^ Strathdee CA, Duncan AM, Buchwald M (June 1993). "Evidence for at least four Fanconi anaemia genes including FACC on chromosome 9". Nat Genet 1 (3): 196–8. DOI:10.1038/ng0692-196. PMID 1303234.
^ ^a ^b "Entrez Gene: FANCC Fanconi anemia, complementation group C". http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=2176.
^ Pang, Q; Fagerlie S, Christianson T A, Keeble W, Faulkner G, Diaz J, Rathbun R K, Bagby G C (July 2000). "The Fanconi Anemia Protein FANCC Binds to and Facilitates the Activation of STAT1 by Gamma Interferon and Hematopoietic Growth Factors". Mol. Cell. Biol. (UNITED STATES) 20 (13): 4724–35. DOI:10.1128/MCB.20.13.4724-4735.2000. ISSN 0270-7306. PMC 85895. PMID 10848598. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=85895.
^ ^a ^b ^c ^d ^e Reuter, Tanja Y; Medhurst Annette L, Waisfisz Quinten, Zhi Yu, Herterich Sabine, Hoehn Holger, Gross Hans J, Joenje Hans, Hoatlin Maureen E, Mathew Christopher G, Huber Pia A J (October 2003). "Yeast two-hybrid screens imply involvement of Fanconi anemia proteins in transcription regulation, cell signaling, oxidative metabolism, and cellular transport". Exp. Cell Res. (United States) 289 (2): 211–21. DOI:10.1016/S0014-4827(03)00261-1. ISSN 0014-4827. PMID 14499622.
^ Pang, Q; Christianson T A, Keeble W, Diaz J, Faulkner G R, Reifsteck C, Olson S, Bagby G C (September 2001). "The Fanconi anemia complementation group C gene product: structural evidence of multifunctionality". Blood (United States) 98 (5): 1392–401. DOI:10.1182/blood.V98.5.1392. ISSN 0006-4971. PMID 11520787.
^ Hoatlin, M E; Zhi Y, Ball H, Silvey K, Melnick A, Stone S, Arai S, Hawe N, Owen G, Zelent A, Licht J D (December 1999). "A novel BTB/POZ transcriptional repressor protein interacts with the Fanconi anemia group C protein and PLZF". Blood (UNITED STATES) 94 (11): 3737–47. ISSN 0006-4971. PMID 10572087.
^ Cumming, R C; Lightfoot J, Beard K, Youssoufian H, O'Brien P J, Buchwald M (July 2001). "Fanconi anemia group C protein prevents apoptosis in hematopoietic cells through redox regulation of GSTP1". Nat. Med. (United States) 7 (7): 814–20. DOI:10.1038/89937. ISSN 1078-8956. PMID 11433346.
^ Kupfer, G M; Yamashita T, Naf D, Suliman A, Asano S, D'Andrea A D (August 1997). "The Fanconi anemia polypeptide, FAC, binds to the cyclin-dependent kinase, cdc2". Blood (UNITED STATES) 90 (3): 1047–54. ISSN 0006-4971. PMID 9242535.
^ McMahon, L W; Sangerman J, Goodman S R, Kumaresan K, Lambert M W (June 2001). "Human alpha spectrin II and the FANCA, FANCC, and FANCG proteins bind to DNA containing psoralen interstrand cross-links". Biochemistry (United States) 40 (24): 7025–34. DOI:10.1021/bi002917g. ISSN 0006-2960. PMID 11401546.
^ ^a ^b McMahon, L W; Walsh C E, Lambert M W (November 1999). "Human alpha spectrin II and the Fanconi anemia proteins FANCA and FANCC interact to form a nuclear complex". J. Biol. Chem. (UNITED STATES) 274 (46): 32904–8. DOI:10.1074/jbc.274.46.32904. ISSN 0021-9258. PMID 10551855.
^ Pang, Qishen; Christianson Tracy A, Keeble Winifred, Koretsky Tara, Bagby Grover C (December 2002). "The anti-apoptotic function of Hsp70 in the interferon-inducible double-stranded RNA-dependent protein kinase-mediated death signaling pathway requires the Fanconi anemia protein, FANCC". J. Biol. Chem. (United States) 277 (51): 49638–43. DOI:10.1074/jbc.M209386200. ISSN 0021-9258. PMID 12397061.
^ ^a ^b Léveillé, France; Blom Eric, Medhurst Annette L, Bier Patrick, Laghmani El Houari, Johnson Mark, Rooimans Martin A, Sobeck Alexandra, Waisfisz Quinten, Arwert Fré, Patel K J, Hoatlin Maureen E, Joenje Hans, de Winter Johan P (September 2004). "The Fanconi anemia gene product FANCF is a flexible adaptor protein". J. Biol. Chem. (United States) 279 (38): 39421–30. DOI:10.1074/jbc.M407034200. ISSN 0021-9258. PMID 15262960.
^ ^a ^b de Winter, J P; van der Weel L, de Groot J, Stone S, Waisfisz Q, Arwert F, Scheper R J, Kruyt F A, Hoatlin M E, Joenje H (November 2000). "The Fanconi anemia protein FANCF forms a nuclear complex with FANCA, FANCC and FANCG". Hum. Mol. Genet. (ENGLAND) 9 (18): 2665–74. DOI:10.1093/hmg/9.18.2665. ISSN 0964-6906. PMID 11063725.
^ Garcia-Higuera, I; Kuang Y, Näf D, Wasik J, D'Andrea A D (July 1999). "Fanconi Anemia Proteins FANCA, FANCC, and FANCG/XRCC9 Interact in a Functional Nuclear Complex". Mol. Cell. Biol. (UNITED STATES) 19 (7): 4866–73. ISSN 0270-7306. PMC 84285. PMID 10373536. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=84285.
^ Reuter, T; Herterich S, Bernhard O, Hoehn H, Gross H J (January 2000). "Strong FANCA/FANCG but weak FANCA/FANCC interaction in the yeast 2-hybrid system". Blood (UNITED STATES) 95 (2): 719–20. ISSN 0006-4971. PMID 10627486.
^ Thomashevski, Andrei; High Anthony A, Drozd Mary, Shabanowitz Jeffrey, Hunt Donald F, Grant Patrick A, Kupfer Gary M (June 2004). "The Fanconi anemia core complex forms four complexes of different sizes in different subcellular compartments". J. Biol. Chem. (United States) 279 (25): 26201–9. DOI:10.1074/jbc.M400091200. ISSN 0021-9258. PMID 15082718.
^ Meetei, Amom Ruhikanta; de Winter Johan P, Medhurst Annette L, Wallisch Michael, Waisfisz Quinten, van de Vrugt Henri J, Oostra Anneke B, Yan Zhijiang, Ling Chen, Bishop Colin E, Hoatlin Maureen E, Joenje Hans, Wang Weidong (October 2003). "A novel ubiquitin ligase is deficient in Fanconi anemia". Nat. Genet. (United States) 35 (2): 165–70. DOI:10.1038/ng1241. ISSN 1061-4036. PMID 12973351.
^ ^a ^b Taniguchi, Toshiyasu; D'Andrea Alan D (October 2002). "The Fanconi anemia protein, FANCE, promotes the nuclear accumulation of FANCC". Blood (United States) 100 (7): 2457–62. DOI:10.1182/blood-2002-03-0860. ISSN 0006-4971. PMID 12239156.
^ Otsuki, Tetsuya; Young David B, Sasaki Dennis T, Pando Matthew P, Li Jianwu, Manning Anthony, Hoekstra Merl, Hoatlin Maureen E, Mercurio Frank, Liu Johnson M (2002). "Fanconi anemia protein complex is a novel target of the IKK signalsome". J. Cell. Biochem. (United States) 86 (4): 613–23. DOI:10.1002/jcb.10270. ISSN 0730-2312. PMID 12210728.
^ Gordon, Susan M; Buchwald Manuel (July 2003). "Fanconi anemia protein complex: mapping protein interactions in the yeast 2- and 3-hybrid systems". Blood (United States) 102 (1): 136–41. DOI:10.1182/blood-2002-11-3517. ISSN 0006-4971. PMID 12649160.
^ Medhurst, A L; Huber P A, Waisfisz Q, de Winter J P, Mathew C G (February 2001). "Direct interactions of the five known Fanconi anaemia proteins suggest a common functional pathway". Hum. Mol. Genet. (England) 10 (4): 423–9. DOI:10.1093/hmg/10.4.423. ISSN 0964-6906. PMID 11157805.
^ Pace, Paul; Johnson Mark, Tan Wu Meng, Mosedale Georgina, Sng Chelvin, Hoatlin Maureen, de Winter Johan, Joenje Hans, Gergely Fanni, Patel K J (July 2002). "FANCE: the link between Fanconi anaemia complex assembly and activity". EMBO J. (England) 21 (13): 3414–23. DOI:10.1093/emboj/cdf355. ISSN 0261-4189. PMC 125396. PMID 12093742. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=125396.

[edit] Further reading

Strathdee CA, Gavish H, Shannon WR, Buchwald M (1992). "Cloning of cDNAs for Fanconi's anaemia by functional complementation". Nature 356 (6372): 763–7. DOI:10.1038/356763a0. PMID 1574115.
Strathdee CA, Gavish H, Shannon WR, Buchwald M (1992). "Cloning of cDNAs for Fanconi's anaemia by functional complementation". Nature 358 (6385): 434. DOI:10.1038/358434a0. PMID 1641028.
Verlander PC, Kaporis A, Liu Q et al. (1996). "Carrier frequency of the IVS4 + 4 A-->T mutation of the Fanconi anemia gene FAC in the Ashkenazi Jewish population". Blood 86 (11): 4034–8. PMID 7492758.
Yamashita T, Barber DL, Zhu Y et al. (1994). "The Fanconi anemia polypeptide FACC is localized to the cytoplasm". Proc. Natl. Acad. Sci. U.S.A. 91 (14): 6712–6. DOI:10.1073/pnas.91.14.6712. PMC 44273. PMID 7517562. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=44273.
Segal GM, Magenis RE, Brown M et al. (1994). "Repression of Fanconi anemia gene (FACC) expression inhibits growth of hematopoietic progenitor cells". J. Clin. Invest. 94 (2): 846–52. DOI:10.1172/JCI117405. PMC 296166. PMID 7518843. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=296166.
Youssoufian H (1994). "Localization of Fanconi anemia C protein to the cytoplasm of mammalian cells". Proc. Natl. Acad. Sci. U.S.A. 91 (17): 7975–9. DOI:10.1073/pnas.91.17.7975. PMC 44527. PMID 8058745. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=44527.
Whitney MA, Jakobs P, Kaback M et al. (1994). "The Ashkenazi Jewish Fanconi anemia mutation: incidence among patients and carrier frequency in the at-risk population". Hum. Mutat. 3 (4): 339–41. DOI:10.1002/humu.1380030402. PMID 8081385.
Murer-Orlando M, Llerena JC, Birjandi F et al. (1993). "FACC gene mutations and early prenatal diagnosis of Fanconi's anaemia". Lancet 342 (8872): 686. DOI:10.1016/0140-6736(93)91800-2. PMID 8103176.
Maruyama K, Sugano S (1994). "Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides". Gene 138 (1–2): 171–4. DOI:10.1016/0378-1119(94)90802-8. PMID 8125298.
Verlander PC, Lin JD, Udono MU et al. (1994). "Mutation analysis of the Fanconi anemia gene FACC". Am. J. Hum. Genet. 54 (4): 595–601. PMC 1918103. PMID 8128956. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1918103.
Whitney MA, Saito H, Jakobs PM et al. (1993). "A common mutation in the FACC gene causes Fanconi anaemia in Ashkenazi Jews". Nat. Genet. 4 (2): 202–5. DOI:10.1038/ng0693-202. PMID 8348157.
Gibson RA, Buchwald M, Roberts RG, Mathew CG (1993). "Characterisation of the exon structure of the Fanconi anaemia group C gene by vectorette PCR". Hum. Mol. Genet. 2 (1): 35–8. DOI:10.1093/hmg/2.1.35. PMID 8490620.
Gavish H, dos Santos CC, Buchwald M (1993). "A Leu554-to-Pro substitution completely abolishes the functional complementing activity of the Fanconi anemia (FACC) protein". Hum. Mol. Genet. 2 (2): 123–6. DOI:10.1093/hmg/2.2.123. PMID 8499901.
Youssoufian H, Li Y, Martin ME, Buchwald M (1996). "Induction of Fanconi anemia cellular phenotype in human 293 cells by overexpression of a mutant FAC allele". J. Clin. Invest. 97 (4): 957–62. DOI:10.1172/JCI118519. PMC 507141. PMID 8613549. //www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=507141.
Yamashita T, Wu N, Kupfer G et al. (1996). "Clinical variability of Fanconi anemia (type C) results from expression of an amino terminal truncated Fanconi anemia complementation group C polypeptide with partial activity". Blood 87 (10): 4424–32. PMID 8639804.
Lo Ten Foe JR, Rooimans MA, Joenje H, Arwert F (1996). "Novel frameshift mutation (1806insA) in exon 14 of the Fanconi anemia C gene, FAC". Hum. Mutat. 7 (3): 264–5. DOI:10.1002/(SICI)1098-1004(1996)7:3<264::AID-HUMU11>3.0.CO;2-0. PMID 8829660.
Gibson RA, Morgan NV, Goldstein LH et al. (1996). "Novel mutations and polymorphisms in the Fanconi anemia group C gene". Hum. Mutat. 8 (2): 140–8. DOI:10.1002/(SICI)1098-1004(1996)8:2<140::AID-HUMU6>3.0.CO;2-F. PMID 8844212.
Kupfer GM, Yamashita T, Naf D et al. (1997). "The Fanconi anemia polypeptide, FAC, binds to the cyclin-dependent kinase, cdc2". Blood 90 (3): 1047–54. PMID 9242535.
Suzuki Y, Yoshitomo-Nakagawa K, Maruyama K et al. (1997). "Construction and characterization of a full length-enriched and a 5'-end-enriched cDNA library". Gene 200 (1–2): 149–56. DOI:10.1016/S0378-1119(97)00411-3. PMID 9373149.

[edit] External links

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Fanconi anaemia group C protein Provide feedback

No Pfam abstract.

External database links

PANDIT:	PF02106
PRINTS:	PR00494
Pseudofam:	PF02106
SYSTERS:	Fanconi_C

This tab holds annotation information from the InterPro database.

InterPro entry IPR000686

Fanconi anaemia (FA) [PUBMED:8490620, PUBMED:7929819, PUBMED:1574115] is a recessive inherited disease characterised by defective DNA repair. FA cells are sensitive to DNA cross-linking agents that cause chromosomal instability and cell death. The disease is manifested clinically by progressive pancytopenia, variable physical anomalies, and predisposition to malignancy. Four complementation groups have been identified, designated A to D. The gene for group C (FACC) has been cloned. Expression of the FACC cDNA corrects the phenotypic defect of FA(C) cells, resulting in normalized cell growth in the presence of DNA cross-linking agents such as mitomycin C (MMC). Gene transfer of the FACC gene should provide a survival advantage to transduced hematopoietic cells, suggesting that FA might be an ideal candidate for gene therapy [PUBMED:7929819]. The function of the FACC gene is not known. Immunofluorescence and sub-cellular fractionation studies of human cell lines, and COS-7 cells transiently expressing human FACC, showed the protein to be located primarily in the cytoplasm. Yet, placement of a nuclear localisation signal at the N terminus of FACC directed the hybrid protein to the nuclei of transfected COS-7 cells. Such findings suggest an indirect role for FACC in regulating DNA repair in this group of Fanconi anaemia [PUBMED:8058745].

Gene Ontology

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

Biological process

DNA repair (GO:0006281)

Domain organisation

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database 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

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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 (5)	Full (88)	Representative proteomes				NCBI (71)	Meta (0)
	Seed (5)	Full (88)	RP15 (5)	RP35 (6)	RP55 (11)	RP75 (35)	NCBI (71)	Meta (0)
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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 (5)	Full (88)	Representative proteomes				NCBI (71)	Meta (0)
	Seed (5)	Full (88)	RP15 (5)	RP35 (6)	RP55 (11)	RP75 (35)	NCBI (71)	Meta (0)
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 (5)	Full (88)	Representative proteomes				NCBI (71)	Meta (0)
	Seed (5)	Full (88)	RP15 (5)	RP35 (6)	RP55 (11)	RP75 (35)	NCBI (71)	Meta (0)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download
Gzipped	Download	Download	Download	Download	Download	Download	Download

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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.

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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:

IPR000686

Previous IDs:

Fanconi;

Type:

Family

Author:

Mian N, Bateman A

Number in seed:

5

Number in full:

88

Average length of the domain:

385.40 aa

Average identity of full alignment:

44 %

Average coverage of the sequence by the domain:

98.24 %

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	25.0	25.0
Trusted cut-off	26.3	26.1
Noise cut-off	19.8	22.6

Model length:

559

Family (HMM) version:

10

Download:

download the raw HMM for this family

Species distribution

Sunburst
Tree

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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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.

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superkingdom
kingdom
phylum
class
order
family
genus
species

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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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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: Fanconi_C (PF02106)

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