Summary: Tyrosine phosphatase family

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Protein tyrosine phosphatase Edit Wikipedia article

Protein-tyrosine-phosphatase

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NCBI	proteins

Protein tyrosine phosphatases (EC 3.1.3.48, PTPs, phosphotyrosine phosphatase, phosphoprotein phosphatase (phosphotyrosine), phosphotyrosine histone phosphatase, protein phosphotyrosine phosphatase, tyrosylprotein phosphatase, phosphotyrosine protein phosphatase, phosphotyrosylprotein phosphatase, tyrosine O-phosphate phosphatase, PPT-phosphatase, PTPase, [phosphotyrosine]protein phosphatase, PTP-phosphatase) are a group of enzymes that remove phosphate groups from phosphorylated tyrosine residues on proteins. Protein tyrosine (pTyr) phosphorylation is a common post-translational modification that can create novel recognition motifs for protein interactions and cellular localisation, affect protein stability, and regulate enzyme activity. As a consequence, maintaining an appropriate level of protein tyrosine phosphorylation is essential for many cellular functions. Tyrosine-specific protein phosphatases (PTPase; EC 3.1.3.48) catalyse the removal of a phosphate group attached to a tyrosine residue, using a cysteinyl-phosphate enzyme intermediate. These enzymes are key regulatory components in signal transduction pathways (such as the MAP kinase pathway) and cell cycle control, and are important in the control of cell growth, proliferation, differentiation and transformation.^[1]^[2]

[edit] Functions

Together with tyrosine kinases, PTPs regulate the phosphorylation state of many important signalling molecules, such as the MAP kinase family. PTPs are increasingly viewed as integral components of signal transduction cascades, despite less study and understanding compared to tyrosine kinases.

PTPs have been implicated in regulation of many cellular processes, including, but not limited to:

[edit] Classification

[edit] By mechanism

The PTP superfamily can be divided into four subfamilies.^[3]^[4]

Links to all 107 members of the protein tyrosine phosphatase family can be found in the template at the bottom of this article.

[edit] Class I

The class I PTPs, are the largest group of PTPs with 99 members, which can be further subdivided into

38 classical PTPs
- 21 receptor tyrosine phosphatase
- 17 nonreceptor-type PTPs
61 VH-1-like or dual-specific phosphatases (DSPs)
- 11 MAPK phosphatases (MPKs)
- 3 Slingshots
- 3 PRLs
- 4 CDC14s
- 19 atypical DSPs
- 5 Phosphatase and tensin homologs (PTENs)
- 16 Myotubularins

Dual-specificity phosphatases (dTyr and dSer/dThr) dual-specificity protein-tyrosine phosphatases. Ser/Thr and Tyr dual-specificity phosphatases are a group of enzymes with both Ser/Thr (EC 3.1.3.16) and tyrosine-specific protein phosphatase (EC 3.1.3.48) activity able to remove the serine/threonine or the tyrosine-bound phosphate group from a wide range of phosphoproteins, including a number of enzymes that have been phosphorylated under the action of a kinase. Dual-specificity protein phosphatases (DSPs) regulate mitogenic signal transduction and control the cell cycle.

LEOPARD syndrome, Noonan syndrome, and Metachondromatosis are associated with PTPN11.

[edit] Class II

LMW (low-molecular-weight) phosphatases, or acid phosphatases act on tyrosine phosphorylated proteins, low-MW aryl phosphates and natural and synthetic acyl phosphates.^[5]^[6]

The class II PTPs contain only one member, low-molecular-weight phosphotyrosine phosphatase (LMPTP).

[edit] Class III

Cdc25 phosphatases (dTyr and/or dThr)

The Class III PTPs contains three members, CDC25 A, B, and C

[edit] Class IV

pTyr-specific phosphatases

The class IV PTPs contains four members, Eya1-4.

This class is believed to have evolved separately from the other three.^[7]

[edit] By location

Based on their cellular localization, PTPases are also classified as:

Receptor-like, which are transmembrane receptors that contain PTPase domains.^[8] In terms of structure, all known receptor PTPases are made up of a variable-length extracellular domain, followed by a transmembrane region and a C-terminal catalytic cytoplasmic domain. Some of the receptor PTPases contain fibronectin type III (FN-III) repeats, immunoglobulin-like domains, MAM domains, or carbonic anhydrase-like domains in their extracellular region. In general, the cytoplasmic region contains two copies of the PTPase domain. The first seems to have enzymatic activity, whereas the second is inactive.
Non-receptor (intracellular) PTPases^[9]

[edit] Common elements

All PTPases carry the highly conserved active site motif C(X)5R (PTP signature motif), employ a common catalytic mechanism, and possess a similar core structure made of a central parallel beta-sheet with flanking alpha-helices containing a beta-loop-alpha-loop that encompasses the PTP signature motif.^[10] Functional diversity between PTPases is endowed by regulatory domains and subunits.

Low-molecular-weight phosphotyrosine protein phosphatase

Structure of a low-molecular-weight phosphotyrosine protein phosphatase.^[11]

Identifiers

Symbol

LMWPc

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

Protein-tyrosine phosphatase

Structure of Yersinia protein tyrosine phosphatase.^[12]

Identifiers

Symbol

Y_phosphatase

Pfam clan

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

Dual-specificity phosphatase, catalytic domain

Structure of the dual-specificity protein phosphatase VHR.^[13]

Identifiers

Symbol

DSPc

Pfam clan

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

Protein-tyrosine phosphatase, SIW14-like

Structure of a putative phosphoprotein phosphatase from Arabidopsis thaliana.^[14]

Identifiers

Symbol

Y_phosphatase2

Pfam clan

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

Protein-tyrosine phosphatase-like, PTPLA

Identifiers

Symbol

PTPLA

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

[edit] Expression pattern

Individual PTPs may be expressed by all cell types, or their expression may be strictly tissue-specific. Most cells express 30% to 60% of all the PTPs, however hematopoietic and neuronal cells express a higher number of PTPs in comparison to other cell types. T cells and B cells of hematopoietic origin express around 60 to 70 different PTPs. The expression of several PTPS is restricted to hematopoietic cells, for example, LYP, SHP1, CD45, and HePTP.^[15]

[edit] References

^ Dixon JE, Denu JM (1998). "Protein tyrosine phosphatases: mechanisms of catalysis and regulation". Curr Opin Chem Biol 2 (5): â. PMID 9818190.
^ Paul S, Lombroso PJ (2003). "Receptor and nonreceptor protein tyrosine phosphatases in the nervous system". Cell. Mol. Life Sci. 60 (11): â. doi:10.1007/s00018-003-3123-7. PMID 14625689.
^ Sun JP, Zhang ZY, Wang WQ (2003). "An overview of the protein tyrosine phosphatase superfamily". Curr Top Med Chem 3 (7): â. PMID 12678841.
^ Alonso A, Sasin J, et al. (2004). "Protein tyrosine phosphatases in the human genome". Cell 117 (6): 699â711. doi:10.1016/j.cell.2004.05.018. PMID 15186772.
^ Wo YY, Shabanowitz J, Hunt DF, Davis JP, Mitchell GL, Van Etten RL, McCormack AL (1992). "Sequencing, cloning, and expression of human red cell-type acid phosphatase, a cytoplasmic phosphotyrosyl protein phosphatase". J. Biol. Chem. 267 (15): 10856â10865. PMID 1587862.
^ Shekels LL, Smith AJ, Bernlohr DA, Van Etten RL (1992). "Identification of the adipocyte acid phosphatase as a PAO-sensitive tyrosyl phosphatase". Protein Sci. 1 (6): 710â721. doi:10.1002/pro.5560010603. PMC 2142247. PMID 1304913.
^ William C. Plaxton; Michael T. McManus (2006). Control of primary metabolism in plants. Wiley-Blackwell. pp. 130â. ISBN 978-1-4051-3096-7. Retrieved 12 December 2010.
^ Knapp S, Longman E, Debreczeni JE, Eswaran J, Barr AJ (2006). "The crystal structure of human receptor protein tyrosine phosphatase kappa phosphatase domain 1". Protein Sci. 15 (6): â. doi:10.1110/ps.062128706. PMC 2242534. PMID 16672235.
^ Perrimon N, Johnson MR, Perkins LA, Melnick MB (1996). "The nonreceptor protein tyrosine phosphatase corkscrew functions in multiple receptor tyrosine kinase pathways in Drosophila". Dev. Biol. 180 (1): â. doi:10.1006/dbio.1996.0285. PMID 8948575.
^ Barford D, Das AK, Egloff MP (1998). "The structure and mechanism of protein phosphatase s: insights into catalysis and regulation". Annu. Rev. Biophys. Biomol. Struct. 27 (1): â. doi:10.1146/annurev.biophys.27.1.133. PMID 9646865.
^ Su XD, Taddei N, Stefani M, Ramponi G, Nordlund P (August 1994). "The crystal structure of a low-molecular-weight phosphotyrosine protein phosphatase". Nature 370 (6490): 575â8. doi:10.1038/370575a0. PMID 8052313.
^ Stuckey JA, Schubert HL, Fauman EB, Zhang ZY, Dixon JE, Saper MA (August 1994). "Crystal structure of Yersinia protein tyrosine phosphatase at 2.5 A and the complex with tungstate". Nature 370 (6490): 571â5. doi:10.1038/370571a0. PMID 8052312.
^ Yuvaniyama J, Denu JM, Dixon JE, Saper MA (May 1996). "Crystal structure of the dual specificity protein phosphatase VHR". Science 272 (5266): 1328â31. doi:10.1126/science.272.5266.1328. PMID 8650541.
^ Aceti DJ, Bitto E, Yakunin AF, et al. (October 2008). "Structural and functional characterization of a novel phosphatase from the Arabidopsis thaliana gene locus At1g05000". Proteins 73 (1): 241â53. doi:10.1002/prot.22041. PMID 18433060.
^ Mustelin T, Vang T and Bottini N. (2005). "Protein tyrosine phosphatases and the immune response". Nat. Rev. Immunol. 5 (1): 43â57. doi:10.1038/nri1530. PMID 15630428.

[edit] External links

PTP Summary and Relevant Publications at Monash University
Protein-Tyrosine-Phosphatase at the US National Library of Medicine Medical Subject Headings (MeSH)
EC 3.1.3.48

Hydrolase: esterases (EC 3.1)

3.1.1: Carboxylic ester hydrolases

Lipase

Phospholipase
- A1
- A2
- B

3.1.2: Thioesterase

3.1.3: Phosphatase

Phosphoprotein phosphatase: Protein tyrosine phosphatase
Protein serine/threonine phosphatase
Dual-specificity phosphatase

3.1.4: Phosphodiesterase

3.1.6: Sulfatase

Nuclease (includes
deoxyribonuclease and
ribonuclease)

3.1.11-16: Exonuclease

Exodeoxyribonuclease	RecBCD

Exoribonuclease	Oligonucleotidase

3.1.21-31: Endonuclease

Endodeoxyribonuclease	Deoxyribonuclease I Deoxyribonuclease II Deoxyribonuclease IV Restriction enzyme UvrABC endonuclease

Endoribonuclease	RNase III RNase H 1 2A 2B 2C RNase P RNase A 1 2 3 4/5 RNase T1 RNA-induced silencing complex

either deoxy- or ribo-	Aspergillus nuclease S1 Micrococcal nuclease

B
enzm
1.1
- 2
- 3
- 4
- 5
- 6
- 7
- 8
- 10
- 11
- 13
- 14
- 15-18
2.1
- 2
- 3
- 4
- 5
- 6
- 7
- 8
2.7.10
2.7.11-12
3.1
- - 3.1.3.48
- 2
- 3
- 4
  - 3.4.21
- 5
- 6
- 7
- 22
- 23
- 24
4.1
- 2
- 3
- 4
- 5
- 6
5.1
- 2
- 3
- 4
- 99
6.1-3
- 4
- 5-6

Esterase: protein tyrosine phosphatases (EC 3.1.3.48)

Class I

Classical PTPs	Receptor type PTPs PTPRA PTPRB PTPRC PTPRD PTPRE PTPRF PTPRG PTPRH PTPRJ PTPRK PTPRM PTPRN PTPRN2 PTPRO PTPRQ PTPRR PTPRS PTPRT PTPRU PTPRZ1 PTPRZ2 Non receptor type PTPs PTPN1 PTPN2 PTPN3 PTPN4 PTPN5 PTPN6 PTPN7 PTPN9 PTPN11 PTPN12 PTPN13 PTPN14 PTPN18 PTPN20 PTPN21 PTPN22 PTPN23

VH1-like or dual specific phosphatases (DSPs)	MAPK phosphatases (MKPs) DUSP1 DUSP2 DUSP4 DUSP5 DUSP6 DUSP7 DUSP8 DUSP9 DUSP10 DUSP16 MK-STYX Slingshots SSH1 SSH2 SSH3 PRLs PTP4A1 PTP4A2 PTP4A3 CDC14s CDC14A CDC14B CDKN3 PTP9Q22 Atypical DSPs DUSP3 DUSP11 DUSP12 DUSP13A DUSP13B DUSP14 DUSP15 DUSP18 DUSP19 DUSP21 DUSP22 DUSP23 DUSP24 DUSP25 DUSP26 DUSP27 EMP2A RNGTT STYX Phosphatase and tensin homologs (PTENs) PTEN TPIP TPTE TNS TENC1 Myotubularins MTM1 MTMR2 MTMR3 MTMR4 MTMR5 MTMR6 MTMR7 MTMR8 MTMR9 MTMR10 MTMR11 MTMR12 MTMR13 MTMR14 MTMR15

Class II

ACP1

Class III

Cdc25
- CDC25A
- CDC25B
- CDC25C

Class IV

Eyes absent homolog
- EYA1
- EYA2
- EYA3
- EYA4

B
enzm
1.1
- 2
- 3
- 4
- 5
- 6
- 7
- 8
- 10
- 11
- 13
- 14
- 15-18
2.1
- 2
- 3
- 4
- 5
- 6
- 7
- 8
2.7.10
2.7.11-12
3.1
- - 3.1.3.48
- 2
- 3
- 4
  - 3.4.21
- 5
- 6
- 7
- 22
- 23
- 24
4.1
- 2
- 3
- 4
- 5
- 6
5.1
- 2
- 3
- 4
- 99
6.1-3
- 4
- 5-6

Intracellular signaling peptides and proteins

MAP

see MAP kinase pathway

Calcium

Intracellular calcium-sensing proteins â¢ Calcineurin â¢ Calcium-calmodulin-dependent protein kinase

G protein

Heterotrimeric	cAMP: Heterotrimeric G protein (Gs/Gi) â¢ Adenylate cyclase â¢ cAMP â¢ 3',5'-cyclic-AMP phosphodiesterase â¢ Protein kinase A cGMP: Guanylate cyclase â¢ cGMP â¢ 3',5'-cyclic-GMP phosphodiesterase â¢ Protein kinase G G beta-gamma complex G_Î² (GNB1, GNB2, GNB3, GNB4, GNB5) â¢ G_Î³ (GNGT1, GNGT2, GNG2, GNG3, GNG4, GNG5, GNG7, GNG8, GNG10, GNG11, GNG12, GNG13, BSCL2) G protein-coupled receptor kinase â¢ AMP-activated protein kinase

Monomeric	ARFs Â· Rabs Â· Ras (HRAS, KRAS, NRAS)

Cyclin

Cyclin-dependent kinase inhibitor protein â¢ Cyclin-dependent kinase â¢ Cyclin

Lipid

Phosphoinositide phospholipase C â¢ Phospholipase c gamma

Other protein kinase

Serine/threonine: Casein kinase (1, 2) â¢ eIF-2 kinase (EIF2AK3) â¢ Glycogen synthase kinase (GSK1, GSK2, GSK-3, GSK3A, GSK3B) â¢ IÎºB kinase (CHUK, IKK2, IKBKG) â¢ Interleukin-1 receptor-associated kinase (IRAK1, IRAK2, IRAK3, IRAK4) â¢ Lim kinase (LIMK1, LIMK2) â¢ p21 activated kinases (PAK1, PAK2, PAK3, PAK4) â¢ Rho-associated protein kinase (ROCK1, ROCK2) â¢ Ribosomal s6 kinase (RPS6KA1)

Tyrosine: ZAP70 â¢ Focal adhesion protein-tyrosine kinase (PTK2, PTK2B) â¢ BTK

both: Dual-specificity kinase

Other phosphoprotein phosphatase

Serine/threonine: Protein phosphatase 2

Tyrosine: protein tyrosine phosphatase: Receptor-like protein tyrosine phosphatase â¢ Sh2 domain-containing protein tyrosine phosphatase

both: Dual-specificity phosphatase

Apoptosis

see apoptosis signaling pathway

GTP-binding protein regulators

see GTP-binding protein regulators

Other

Activating transcription factor 6 â¢ Signal transducing adaptor protein â¢ I-kappa B protein â¢ Mucin-4 â¢ Olfactory marker protein â¢ Phosphatidylethanolamine binding protein â¢ EDARADD â¢ PRKCSH

This article incorporates text from the public domain Pfam and InterPro IPR000106

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.

Tyrosine phosphatase family Provide feedback

This family is closely related to the PF00102 and PF00782 families.

Internal database links

Similarity to PfamA using HHSearch:

DSPc Y_phosphatase3

External database links

PANDIT:	PF03162
Pseudofam:	PF03162
SYSTERS:	Y_phosphatase2

This tab holds annotation information from the InterPro database.

InterPro entry IPR004861

Protein tyrosine (pTyr) phosphorylation is a common post-translational modification which can create novel recognition motifs for protein interactions and cellular localisation, affect protein stability, and regulate enzyme activity. Consequently, maintaining an appropriate level of protein tyrosine phosphorylation is essential for many cellular functions. Tyrosine-specific protein phosphatases (PTPase; EC) catalyse the removal of a phosphate group attached to a tyrosine residue, using a cysteinyl-phosphate enzyme intermediate. These enzymes are key regulatory components in signal transduction pathways (such as the MAP kinase pathway) and cell cycle control, and are important in the control of cell growth, proliferation, differentiation and transformation [PUBMED:9818190, PUBMED:14625689]. The PTP superfamily can be divided into four subfamilies [PUBMED:12678841]:

(1) pTyr-specific phosphatases
(2) dual specificity phosphatases (dTyr and dSer/dThr)
(3) Cdc25 phosphatases (dTyr and/or dThr)
(4) LMW (low molecular weight) phosphatases

Based on their cellular localisation, PTPases are also classified as:

Receptor-like, which are transmembrane receptors that contain PTPase domains [PUBMED:16672235]
Non-receptor (intracellular) PTPases [PUBMED:8948575]

All PTPases carry the highly conserved active site motif C(X)5R (PTP signature motif), employ a common catalytic mechanism, and share a similar core structure made of a central parallel beta-sheet with flanking alpha-helices containing a beta-loop-alpha-loop that encompasses the PTP signature motif [PUBMED:9646865]. Functional diversity between PTPases is endowed by regulatory domains and subunits.

This entry represents protein-tyrosine phosphatases predominantly from fungi, plants and bacteria, several of which are putative enzymes. These proteins are closely related to the Y-phosphatase and DSPc families. This entry includes the PTPase SIW14 from Saccharomyces cerevisiae (Baker's yeast), which plays a role in actin filament organisation and endocytosis.

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 Phosphatase (CL0031), which contains the following 9 members:

CDKN3 DSPc DUF442 Init_tRNA_PT Myotub-related PTPlike_phytase Y_phosphatase Y_phosphatase2 Y_phosphatase3

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:

Selex
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MSF

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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 (714)	Representative proteomes				NCBI (1012)	Meta (121)
	Seed (8)	Full (714)	RP15 (143)	RP35 (269)	RP55 (372)	RP75 (416)	NCBI (1012)	Meta (121)
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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 (8)	Full (714)	Representative proteomes				NCBI (1012)	Meta (121)
	Seed (8)	Full (714)	RP15 (143)	RP35 (269)	RP55 (372)	RP75 (416)	NCBI (1012)	Meta (121)
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 (714)	Representative proteomes				NCBI (1012)	Meta (121)
	Seed (8)	Full (714)	RP15 (143)	RP35 (269)	RP55 (372)	RP75 (416)	NCBI (1012)	Meta (121)
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_3756 (release 6.5)

Previous IDs:

DUF252;

Type:

Family

Author:

Mifsud W, Yeats C

Number in seed:

8

Number in full:

714

Average length of the domain:

149.50 aa

Average identity of full alignment:

27 %

Average coverage of the sequence by the domain:

62.75 %

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	20.7	20.7
Noise cut-off	20.6	20.6

Model length:

165

Family (HMM) version:

8

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.

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 Y_phosphatase2 domain has been found. There are 4 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: Y_phosphatase2 (PF03162)

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Summary: Tyrosine phosphatase family

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Protein tyrosine phosphatase Edit Wikipedia article

Contents

[edit] Functions

[edit] Classification

[edit] By mechanism

[edit] Class I

[edit] Class II

[edit] Class III

[edit] Class IV

[edit] By location

[edit] Common elements

[edit] Expression pattern

[edit] References

[edit] External links

Tyrosine phosphatase family Provide feedback

Internal database links

External database links

InterPro entry IPR004861

Domain organisation

Pfam Clan

Alignments

Alignment types

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Format an alignment

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External links

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Trees

Curation and family details

Curation

HMM information

Species distribution

Sunburst controls

Weight segments by...

Change the size of the sunburst

Colour assignments

Selections

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How the sunburst is generated

Colouring and labels

Anomalies in the taxonomy tree

Missing taxonomic levels

Unmapped species names

Sub-species

Too many species/sequences

Tree controls

Annotation

Download tree

Selected sequences

Species trees

Interactive tree

Structures