Summary: Gamma-glutamyltranspeptidase

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Wikipedia: Gamma-glutamyl transpeptidase
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Gamma-glutamyl transpeptidase Edit Wikipedia article

Not to be confused with GGGT.

Gamma-glutamyltranspeptidase

Identifiers

Symbol

G_glu_transpept

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

gamma-glutamyltransferase

Identifiers

Databases

PDB structures

AmiGO / EGO

Search
PMC	articles
PubMed	articles
NCBI	proteins

gamma-glutamyltransferase 1
Identifiers
Symbol	GGT1
Alt. symbols	GGT
Entrez	2678
HUGO	4250
OMIM	231950
RefSeq	NM_001032364
UniProt	P19440
Other data
EC number	2.3.2.2
Locus	Chr. 22 q11.1-11.2

gamma-glutamyltransferase 2
Identifiers
Symbol	GGT2
Alt. symbols	GGT
Entrez	2679
HUGO	4251
OMIM	137181
RefSeq	NM_002058
UniProt	P36268
Other data
EC number	2.3.2.2
Locus	Chr. 22 q11.1-11.2

Gamma-glutamyltransferase or gamma-glutamyl transpeptidase (also Î³-glutamyltransferase, GGT, GGTP, gamma-GT) (EC 2.3.2.2) is an enzyme that transfers gamma-glutamyl functional groups. It is found in many tissues, the most notable one being the liver, and has significance in medicine as a diagnostic marker.

GGT^[1] catalyzes the transfer of the gamma-glutamyl moiety of glutathione to an acceptor that may be an amino acid, a peptide or water (forming glutamate). GGT plays a key role in the gamma-glutamyl cycle, a pathway for the synthesis and degradation of glutathione and drug and xenobiotic detoxification.^[2] Other lines of evidence indicate that GGT can also exert a prooxidant role, with regulatory effects at various levels in cellular signal transduction and cellular pathophysiology,^[3]

[edit] Function

GGT is present in the cell membranes of many tissues, including the kidneys, bile duct, pancreas, gallbladder, spleen, heart, brain, and seminal vesicles.^[4] It is involved in the transfer of amino acids across the cellular membrane^[5] and leukotriene metabolism.^[6] It is also involved in glutathione metabolism by transferring the glutamyl moiety to a variety of acceptor molecules including water, certain L-amino acids, and peptides, leaving the cysteine product to preserve intracellular homeostasis of oxidative stress.^[7]^[8] This general reaction is:

(5-L-glutamyl)-peptide + an amino acid $\rightleftharpoons$ peptide + 5-L-glutamyl amino acid

[edit] Structural studies

In prokaryotes and eukaryotes, it is an enzyme that consists of two polypeptide chains, a heavy and a light subunit, processed from a single chain precursor by an autocatalytic cleavage. The active site of GGT is known to be located in the light subunit.

[edit] Medical applications

GGT has several uses as a diagnostic marker in medicine.

Blood test results for GGT suggest that the normal value for men is 15-85 IU/L, whereas for women it is 5-55 IU/L.^[9]

Elevated serum GGT activity can be found in diseases of the liver, biliary system, and pancreas. In this respect, it is similar to alkaline phosphatase (ALP) in detecting disease of the biliary tract. Indeed, the two markers correlate well, though there is conflicting data about whether GGT has better sensitivity.^[10]^[11] In general, ALP is still the first test for biliary disease. The main value of GGT over ALP is in verifying that ALP elevations are, in fact, due to biliary disease; ALP can also be increased in certain bone diseases, but GGT is not.^[11] More recently, slightly elevated serum GGT has also been found to correlate with cardiovascular diseases and is under active investigation as a cardiovascular risk marker. GGT in fact accumulates in atherosclerotic plaques,^[12] suggesting a potential role in pathogenesis of cardiovascular diseases,^[13] and circulates in blood in the form of distinct protein aggregates,^[14] some of which appear to be related to specific pathologies such as metabolic syndrome, alcohol addiction and chronic liver disease. High body mass index is associated with type 2 diabetes only in persons with high serum GGT.^[15]

GGT is elevated by large quantities of alcohol ingestion. Determination of total serum GGT activity is however not specific to alcohol intoxication,^[16] and the measurement of selected serum forms of the enzyme offer more specific information.^[14] Isolated elevation or disproportionate elevation compared to other liver enzymes (such as ALP or ALT) may indicate alcohol abuse or alcoholic liver disease.^[17] It may indicate excess alcohol consumption up to 3 or 4 weeks prior to the test. The mechanism for this elevation is unclear. Alcohol may increase GGT production by inducing hepatic microsomal production, or it may cause the leakage of GGT from hepatocytes.^[18]

Numerous drugs can raise GGT levels, including barbiturates and phenytoin.^[19] GGT elevation has also been occasionally reported following NSAIDs, St. John's wort, and aspirin. Elevated levels of GGT may also be due to congestive heart failure.^[20]

[edit] Human proteins

GGT1; GGT2; GGT6; GGTL3; GGTL4; GGTLA1; GGTLA4;

[edit] References

^ Tate SS, Meister A (1985). "gamma-Glutamyl transpeptidase from kidney". Meth. Enzymol. Methods in Enzymology 113: 400â419. doi:10.1016/S0076-6879(85)13053-3. ISBN 978-0-12-182013-8. PMID 2868390.
^ Siest G, Courtay C, Oster T, Michelet F, Visvikis A, Diederich M, Wellman M (1992). "Gamma-glutamyltransferase: nucleotide sequence of the human pancreatic cDNA. Evidence for a ubiquitous gamma-glutamyltransferase polypeptide in human tissues". Biochem. Pharmacol. 43 (12): 2527â2533. doi:10.1016/0006-2952(92)90140-E. PMID 1378736.
^ Dominici S, Paolicchi A, Corti A, Maellaro E, Pompella A (2005). "Prooxidant reactions promoted by soluble and cell-bound Î³-glutamyltransferase activity". Meth. Enzymol. 401: 483â500. doi:10.1016/S0076-6879(05)01029-3. PMID 16399404.
^ Goldberg, DM (1980). "Structural, functional, and clinical aspects of gamma-glutamyltransferase". Crit Rev Clin Lab Sci 12 (1): 1â58. doi:10.3109/10408368009108725. PMID 6104563.
^ Meister A (August 1974). "The gamma-glutamyl cycle. Diseases associated with specific enzyme deficiencies". Ann. Intern. Med. 81 (2): 247â53. PMID 4152527.
^ Raulf M, StÃ¼ning M, KÃ¶nig W (May 1985). "Metabolism of leukotrienes by L-gamma-glutamyl-transpeptidase and dipeptidase from human polymorphonuclear granulocytes". Immunology 55 (1): 135â47. PMC 1453575. PMID 2860060.
^ Schulman JD, Goodman SI, Mace JW, Patrick AD, Tietze F, Butler EJ (July 1975). "Glutathionuria: inborn error of metabolism due to tissue deficiency of gamma-glutamyl transpeptidase". Biochem. Biophys. Res. Commun. 65 (1): 68â74. doi:10.1016/S0006-291X(75)80062-3. PMID 238530.
^ Yokoyama H (June 2007). "[Gamma glutamyl transpeptidase (gammaGTP) in the era of metabolic syndrome]". Nihon Arukoru Yakubutsu Igakkai Zasshi (in Japanese) 42 (3): 110â24. PMID 17665541.
^ General Laboratory Manual. Department of Pathology, Hackensack University Medical Centre. 2010. p. 117. Retrieved 20 November 2011.
^ Betro MG, Oon RC, Edwards JB (November 1973). "Gamma-glutamyl transpeptidase in diseases of the liver and bone". Am. J. Clin. Pathol. 60 (5): 672â8. PMID 4148049.
^ ^a ^b Lum G, Gambino SR (April 1972). "Serum gamma-glutamyl transpeptidase activity as an indicator of disease of liver, pancreas, or bone". Clin. Chem. 18 (4): 358â62. PMID 5012259.
^ Emdin M, Pompella A, Paolicchi A (2005). "Editorial - Gamma-glutamyltransferase, atherosclerosis, and cardiovascular disease: triggering oxidative stress within the plaque". Circulation 112 (14): 2078â80. doi:10.1161/CIRCULATIONAHA.105.571919. PMID 16203922.
^ Pompella A, Emdin M, Passino C, Paolicchi A (2004). "The significance of serum gamma-glutamyltransferase in cardiovascular diseases". Clin. Chem. Lab. Med. 42 (10): 1085â91. doi:10.1515/CCLM.2004.224. PMID 15552264.
^ ^a ^b Franzini M, Bramanti E, Ottaviano V, Ghiri E, Scatena F, Pompella A, Donato L, Emdin M, Paolicchi A (2006). "A high performance gel filtration chromatography method for gamma-glutamyltransferase fraction analysis". Anal. Biochem. 374: 1â8. doi:10.1016/j.ab.2007.10.025. PMID 18023410.
^ Lim JS, Lee DH, Park JY, Jin SH, Jacobs DR Jr (2007). "A strong interaction between serum gamma-glutamyltransferase and obesity on the risk of prevalent type 2 diabetes: results from the Third National Health and Nutrition Examination Survey". CLINICAL CHEMISTRY 53 (6): 1092â1098. doi:10.1016/j.jacl.2011.05.004. PMID 17478563.
^ Lamy J, Baglin MC, Ferrant JP, Weill J (1974). "Determination de la gamma-glutamyl transpeptidase senque des ethyliques a la suite du sevrage". Clin Chim Acta 56: 169.
^ Kaplan MM, et al. (1985). "Biochemical basis for serum enzyme abnormalities in alcoholic liver disease". In Chang NC, Chan NM. Research Monograph No. 17 (in Early identification of alcohol abuse) (NIAAA). p. 186.
^ Barouki R, Chobert MN, Finidori J, Aggerbeck M, Nalpas B, Hanoune J (1983). "Ethanol effects in a rat hepatoma cell line: induction of gamma-glutamyltransferase". Hepatology 3 (3): 323â9. doi:10.1002/hep.1840030308. PMID 6132864.
^ Rosalki SB, Tarlow D, Rau D (August 1971). "Plasma gamma-glutamyl transpeptidase elevation in patients receiving enzyme-inducing drugs". Lancet 2 (7720): 376â7. PMID 4105075.
^ Ruttmann E, Brant LJ, Concin H, Diem G, Rapp K, Ulmer H (October 2005). "Gamma-glutamyltransferase as a risk factor for cardiovascular disease mortality: an epidemiological investigation in a cohort of 163,944 Austrian adults". Circulation 112 (14): 2130â7. doi:10.1161/CIRCULATIONAHA.105.552547. PMID 16186419.

[edit] External links

MedlinePlus Encyclopedia 003458
gamma-Glutamyltransferase at the US National Library of Medicine Medical Subject Headings (MeSH)

Transferases: acyltransferases (EC 2.3)

2.3.1: other than amino-acyl groups

2.3.2: Aminoacyltransferases

2.3.3: converted into alkyl on transfer

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

Metabolism: amino acid metabolism Â· synthesis and catabolism enzymes (essential in CAPS)

Kâacetyl-CoA

LYSINEâ	Saccharopine dehydrogenase Glutaryl-CoA dehydrogenase

LEUCINEâ	Branched chain aminotransferase Branched-chain alpha-keto acid dehydrogenase complex Isovaleryl coenzyme A dehydrogenase Methylcrotonyl-CoA carboxylase Methylglutaconyl-CoA hydratase 3-hydroxy-3-methylglutaryl-CoA lyase

TRYPTOPHANâ	Indoleamine 2,3-dioxygenase/Tryptophan 2,3-dioxygenase Arylformamidase Kynureninase 3-hydroxyanthranilate oxidase Aminocarboxymuconate-semialdehyde decarboxylase Aminomuconate-semialdehyde dehydrogenase

PHENYLALANINEâtyrosineâ	(see below)

G

Gâpyruvate
âcitrate

glycineâserineâ	Serine hydroxymethyltransferase Serine dehydratase glycineâcreatine: Guanidinoacetate N-methyltransferase Creatine kinase

alanineâ	Alanine transaminase

cysteineâ	D-cysteine desulfhydrase

threonineâ	L-threonine dehydrogenase

Gâglutamateâ
Î±-ketoglutarate

HISTIDINEâ	Histidine ammonia-lyase Urocanate hydratase Formiminotransferase cyclodeaminase

prolineâ	Proline oxidase Pyrroline-5-carboxylate reductase 1-Pyrroline-5-carboxylate dehydrogenase/ALDH4A1 PYCR1

arginineâ	Ornithine aminotransferase Ornithine decarboxylase Agmatinase

âalpha-ketoglutarateâTCA	Glutamate dehydrogenase

Other	cysteine+glutamateâglutathione: Gamma-glutamylcysteine synthetase Glutathione synthetase Gamma-glutamyl transpeptidase glutamateâglutamine: Glutamine synthetase Glutaminase

Gâpropionyl-CoAâ
succinyl-CoA

VALINEâ	Branched chain aminotransferase Branched-chain alpha-keto acid dehydrogenase complex Enoyl-CoA hydratase 3-hydroxyisobutyryl-CoA hydrolase 3-hydroxyisobutyrate dehydrogenase Methylmalonate semialdehyde dehydrogenase

ISOLEUCINEâ	Branched chain aminotransferase Branched-chain alpha-keto acid dehydrogenase complex 3-hydroxy-2-methylbutyryl-CoA dehydrogenase

METHIONINEâ	generation of homocysteine: Methionine adenosyltransferase Adenosylhomocysteinase regeneration of methionine: Methionine synthase/Homocysteine methyltransferase Betaine-homocysteine methyltransferase conversion to cysteine: Cystathionine beta synthase Cystathionine gamma-lyase

THREONINEâ	Threonine aldolase

âsuccinyl-CoAâTCA	Propionyl-CoA carboxylase Methylmalonyl CoA epimerase Methylmalonyl-CoA mutase

Gâfumarate

PHENYLALANINEâtyrosineâ	Phenylalanine hydroxylase Tyrosine aminotransferase 4-Hydroxyphenylpyruvate dioxygenase Homogentisate 1,2-dioxygenase Fumarylacetoacetate hydrolase tyrosineâmelanin: Tyrosinase

Gâoxaloacetate

asparagineâaspartateâ	Asparaginase/Asparagine synthetase Aspartate transaminase

M: MET

mt, k, c/g/r/p/y/i, f/h/s/l/o/e, a/u, n, m

k, cgrp/y/i, f/h/s/l/o/e, au, n, m, epon

m (A16/C10), i (k, c/g/r/p/y/i, f/h/s/o/e, a/u, n, m)

Metabolism: lipid metabolism - eicosanoid metabolism enzymes

Precursor

Phospholipase A2

Prostanoids

Cyclooxygenase
- PTGS1
- PTGS2

PGD2 synthase

PGI2 synthase

TXA synthase

Leukotrienes

5-Lipoxygenase activating protein/Arachidonate 5-lipoxygenase

LTA4 hydrolase (B4 synthesis)

LTC4 synthase
Gamma-glutamyl transpeptidase
DPEP2

Ungrouped

HPGD

M: MET

mt, k, c/g/r/p/y/i, f/h/s/l/o/e, a/u, n, m

k, cgrp/y/i, f/h/s/l/o/e, au, n, m, epon

m (A16/C10), i (k, c/g/r/p/y/i, f/h/s/o/e, a/u, n, m)

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.

Gamma-glutamyltranspeptidase Provide feedback

No Pfam abstract.

External database links

MEROPS:	T3
PANDIT:	PF01019
PROSITE:	PDOC00404
Pseudofam:	PF01019
SYSTERS:	G_glu_transpept

This tab holds annotation information from the InterPro database.

InterPro entry IPR000101

Gamma-glutamyltranspeptidase (EC) (GGT) [PUBMED:2868390] catalyzes the transfer of the gamma-glutamyl moiety of glutathione to an acceptor that may be an amino acid, a peptide or water (forming glutamate). GGT plays a key role in the gamma-glutamyl cycle, a pathway for the synthesis and degradation of glutathione and drug and xenobiotic detoxification [PUBMED:1378736]. In prokaryotes and eukaryotes, it is an enzyme that consists of two polypeptide chains, a heavy and a light subunit, processed from a single chain precursor by an autocatalytic cleavage. The active site of GGT is known to be located in the light subunit. The sequences of mammalian and bacterial GGT show a number of regions of high similarity [PUBMED:2570061]. Pseudomonas cephalosporin acylases (EC) that convert 7-beta-(4-carboxybutanamido)-cephalosporanic acid (GL-7ACA) into 7-aminocephalosporanic acid (7ACA) and glutaric acid are evolutionary related to GGT and also show some GGT activity [PUBMED:1358202]. Like GGT, these GL-7ACA acylases, are also composed of two subunits.

As an autocatalytic peptidase GGT belongs to MEROPS peptidase family T3 (gamma-glutamyltransferase family, clan PB(T)). The active site residue for members of this family and family T1 is C-terminal to the autolytic cleavage site. The type example is gamma-glutamyltransferase 1 from Escherichia coli.

Gene Ontology

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

Molecular function

gamma-glutamyltransferase activity (GO:0003840)

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 NTN (CL0052), which contains the following 14 members:

AAT Asparaginase_2 CBAH DUF1933 DUF3700 G_glu_transpept GATase_2 GATase_4 GATase_6 GATase_7 Penicil_amidase Peptidase_C69 Phospholip_B Proteasome

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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HTML: an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
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
Stockholm
FASTA
MSF

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 (52)	Full (5126)	Representative proteomes				NCBI (4680)	Meta (4706)
	Seed (52)	Full (5126)	RP15 (561)	RP35 (1043)	RP55 (1459)	RP75 (1814)	NCBI (4680)	Meta (4706)
Jalview	View	View	View	View	View	View	View	View
HTML	View		View	View	View	View
PP/heatmap	₁		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 (52)	Full (5126)	Representative proteomes				NCBI (4680)	Meta (4706)
	Seed (52)	Full (5126)	RP15 (561)	RP35 (1043)	RP55 (1459)	RP75 (1814)	NCBI (4680)	Meta (4706)
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 (52)	Full (5126)	Representative proteomes				NCBI (4680)	Meta (4706)
	Seed (52)	Full (5126)	RP15 (561)	RP35 (1043)	RP55 (1459)	RP75 (1814)	NCBI (4680)	Meta (4706)
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_878 (release 3.0)

Previous IDs:

none

Type:

Family

Author:

Bateman A

Number in seed:

52

Number in full:

5126

Average length of the domain:

454.30 aa

Average identity of full alignment:

29 %

Average coverage of the sequence by the domain:

87.76 %

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	19.1	19.1
Trusted cut-off	19.3	19.3
Noise cut-off	18.9	19.0

Model length:

510

Family (HMM) version:

16

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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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

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G_glu_transpept

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 G_glu_transpept domain has been found. There are 76 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: G_glu_transpept (PF01019)

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Summary: Gamma-glutamyltranspeptidase

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Gamma-glutamyl transpeptidase Edit Wikipedia article

Contents

[edit] Function

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[edit] Human proteins

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External database links

InterPro entry IPR000101

Gene Ontology

Domain organisation

Pfam Clan

Alignments

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Curation and family details

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Interactions

Structures