Summary: Histidine carboxylase PI chain

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Wikipedia: Histidine decarboxylase
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Histidine decarboxylase Edit Wikipedia article

histidine decarboxylase

Conversion of histidine to histamine by histidine decarboxylase

Identifiers

Databases

PDB structures

AmiGO / EGO

Search
PMC	articles
PubMed	articles
NCBI	proteins

Histidine carboxylase PI chain

structure of the d53,54n mutant of histidine decarboxylase at-170 c

Identifiers

Symbol

HDC

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

Histidine decarboxylase

Available structures

PDB

Ortholog search: PDBe, RCSB

List of PDB id codes
4E1O

Identifiers

Symbols

HDC; MGC163399

External IDs

OMIM: 142704 MGI: 96062 HomoloGene: 20490 GeneCards: HDC Gene

EC number

4.1.1.22

Gene Ontology
Molecular function	â¢ histidine decarboxylase activity â¢ amino acid binding â¢ pyridoxal phosphate binding
Cellular component	â¢ cytosol â¢ dendrite â¢ neuronal cell body
Biological process	â¢ histamine biosynthetic process â¢ histidine metabolic process â¢ histidine catabolic process â¢ cellular nitrogen compound metabolic process â¢ catecholamine biosynthetic process â¢ small molecule metabolic process
Sources: Amigo / QuickGO

Orthologs

Species

Human

Mouse

RefSeq (mRNA)

RefSeq (protein)

Location (UCSC)

Chr 15:
50.53 â 50.56 Mb

Chr 2:
126.59 â 126.62 Mb

PubMed search

[1]

[2]

Histidine decarboxylase (HDC) is the enzyme that catalyzes the reaction that produces histamine from histidine with the help of vitamin B₆ as follows:^[1]^[2]^[3]

Known inhibitors of histidine decarboxylase : catechin, tritoqualine an atypical antihistaminic (HypostaminÂ©).

C₆H₉N₃O₂ â C₅H₉N₃ + CO₂

In humans, the histidine decarboxylase enzyme is encoded by the HDC gene.^[4]^[5]

The biogenic amine histamine is an important modulator of numerous physiologic processes, including neurotransmission, gastric acid secretion, and smooth muscle tone. The biosynthesis of histamine from histidine is catalyzed by the enzyme L-histidine decarboxylase. This homodimeric enzyme is a pyridoxal phosphate (PLP)-dependent decarboxylase and is highly specific for its histidine substrate.^[4]

Some mutations in the gene for this enzyme can cause symptoms of Tourette syndrome; however, these mutations have only been observed in one family and are not thought to account for most cases of Tourette syndrome.^[6]

In bacteria, it is synthesised as a proenzyme, PI. Cleavage of the proenzyme PI chain yields two subunits, alpha and beta, which arrange as a hexamer, (alpha beta)6, by nonhydrolytic self-catalysis.^[7]

[edit] See also

Aromatic L-amino acid decarboxylase

[edit] References

^ Epps HM (1945). "Studies on bacterial amino-acid decarboxylases: 4. l(-)-histidine decarboxylase from Cl. welchii Type A". Biochem. J. 39 (1): 42â6. PMC 1258146. PMID 16747851. //www.ncbi.nlm.nih.gov/pmc/articles/PMC1258146/.
^ Riley WD, Snell EE (October 1968). "Histidine decarboxylase of Lactobacillus 30a. IV. The presence of covalently bound pyruvate as the prosthetic group". Biochemistry 7 (10): 3520â8. doi:10.1021/bi00850a029. PMID 5681461.
^ Rosenthaler J, Guirard BM, Chang GW, Snell EE (July 1965). "Purification and properties of histidine decarboxylase from Lactobacillus 30a". Proc. Natl. Acad. Sci. U.S.A. 54 (1): 152â8. doi:10.1073/pnas.54.1.152. PMC 285813. PMID 5216347. //www.ncbi.nlm.nih.gov/pmc/articles/PMC285813/.
^ ^a ^b "Entrez Gene: histidine decarboxylase". http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=3067.
^ Bruneau G, Nguyen VC, Gros F, Bernheim A, Thibault J (November 1992). "Preparation of a rat brain histidine decarboxylase (HDC) cDNA probe by PCR and assignment of the human HDC gene to chromosome 15". Hum. Genet. 90 (3): 235â8. PMID 1487235.
^ "Online Mendelian Inheritance in Man: histidine decarboxylase". http://www.ncbi.nlm.nih.gov/omim/142704.
^ Coton E, Rollan GC, Lonvaud-Funel A (1998). "Histidine carboxylase of Leuconostoc oenos 9204: purification, kinetic properties, cloning and nucleotide sequence of the hdc gene.". J Appl Microbiol 84 (2): 143â51. PMID 9633629.

[edit] Further reading

Need AC, Keefe RS, Ge D, et al. (2009). "Pharmacogenetics of antipsychotic response in the CATIE trial: a candidate gene analysis.". Eur. J. Hum. Genet. 17 (7): 946â57. doi:10.1038/ejhg.2008.264. PMC 2986499. PMID 19156168. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2986499/.
Masini E, Fabbroni V, Giannini L, et al. (2005). "Histamine and histidine decarboxylase up-regulation in colorectal cancer: correlation with tumor stage.". Inflamm. Res. 54 Suppl 1: S80-1. doi:10.1007/s00011-004-0437-3. PMID 15928846.
Li Z, Liu J, Tang F, et al. (2008). "Expression of non-mast cell histidine decarboxylase in tumor-associated microvessels in human esophageal squamous cell carcinomas.". APMIS 116 (12): 1034â42. doi:10.1111/j.1600-0463.2008.01048.x. PMID 19133005.
Szafranski K, Schindler S, Taudien S, et al. (2007). "Violating the splicing rules: TG dinucleotides function as alternative 3' splice sites in U2-dependent introns.". Genome Biol. 8 (8): R154. doi:10.1186/gb-2007-8-8-r154. PMC 2374985. PMID 17672918. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2374985/.
Ai W, Liu Y, Langlois M, Wang TC (2004). "Kruppel-like factor 4 (KLF4) represses histidine decarboxylase gene expression through an upstream Sp1 site and downstream gastrin responsive elements.". J. Biol. Chem. 279 (10): 8684â93. doi:10.1074/jbc.M308278200. PMID 14670968.
Raychowdhury R, Fleming JV, McLaughlin JT, et al. (2002). "Identification and characterization of a third gastrin response element (GAS-RE3) in the human histidine decarboxylase gene promoter.". Biochem. Biophys. Res. Commun. 297 (5): 1089â95. doi:10.1016/S0006-291X(02)02345-8. PMID 12372397.
Kimura K, Wakamatsu A, Suzuki Y, et al. (2006). "Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes.". Genome Res. 16 (1): 55â65. doi:10.1101/gr.4039406. PMC 1356129. PMID 16344560. //www.ncbi.nlm.nih.gov/pmc/articles/PMC1356129/.
SkÃ¶ldberg F, Portela-Gomes GM, Grimelius L, et al. (2003). "Histidine decarboxylase, a pyridoxal phosphate-dependent enzyme, is an autoantigen of gastric enterochromaffin-like cells.". J. Clin. Endocrinol. Metab. 88 (4): 1445â52. doi:10.1210/jc.2002-021761. PMID 12679420.
Brew O, Lakasing L, Sullivan M. "Differential activity of histidine decarboxylase in normal and pre-eclamptic placentae.". Placenta 28 (5-6): 585â7. doi:10.1016/j.placenta.2006.05.003. PMID 16822545.
Zhang F, Xiong DH, Wang W, et al. (2006). "HDC gene polymorphisms are associated with age at natural menopause in Caucasian women.". Biochem. Biophys. Res. Commun. 348 (4): 1378â82. doi:10.1016/j.bbrc.2006.08.008. PMID 16919600.
Tippens AS, Gruetter CA (2004). "Detection of histidine decarboxylase mRNA in human vascular smooth muscle and endothelial cells.". Inflamm. Res. 53 (6): 215â6. doi:10.1007/s00011-004-1252-6. PMID 15167966.
Siezen CL, Bont L, Hodemaekers HM, et al. (2009). "Genetic susceptibility to respiratory syncytial virus bronchiolitis in preterm children is associated with airway remodeling genes and innate immune genes.". Pediatr. Infect. Dis. J. 28 (4): 333â5. doi:10.1097/INF.0b013e31818e2aa9. PMID 19258923.
Morgan TK, Montgomery K, Mason V, et al. (2006). "Upregulation of histidine decarboxylase expression in superficial cortical nephrons during pregnancy in mice and women.". Kidney Int. 70 (2): 306â14. doi:10.1038/sj.ki.5001553. PMID 16760908.
Papadopoulou N, Kalogeromitros D, Staurianeas NG, et al. (2005). "Corticotropin-releasing hormone receptor-1 and histidine decarboxylase expression in chronic urticaria.". J. Invest. Dermatol. 125 (5): 952â5. doi:10.1111/j.0022-202X.2005.23913.x. PMID 16297195.
Janssen R, Bont L, Siezen CL, et al. (2007). "Genetic susceptibility to respiratory syncytial virus bronchiolitis is predominantly associated with innate immune genes.". J. Infect. Dis. 196 (6): 826â34. doi:10.1086/520886. PMID 17703412.
Strausberg RL, Feingold EA, Grouse LH, et al. (2002). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.". Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16899â903. doi:10.1073/pnas.242603899. PMC 139241. PMID 12477932. //www.ncbi.nlm.nih.gov/pmc/articles/PMC139241/.
Aichberger KJ, Mayerhofer M, Vales A, et al. (2006). "The CML-related oncoprotein BCR/ABL induces expression of histidine decarboxylase (HDC) and the synthesis of histamine in leukemic cells.". Blood 108 (10): 3538â47. doi:10.1182/blood-2005-12-028456. PMID 16849647.
Lee JK, Kim HT, Cho SM, et al. (2003). "Characterization of 458 single nucleotide polymorphisms of disease candidate genes in the Korean population.". J. Hum. Genet. 48 (5): 213â6. doi:10.1007/s10038-003-0011-9. PMID 12768436.
Jeong HJ, Moon PD, Kim SJ, et al. (2009). "Activation of hypoxia-inducible factor-1 regulates human histidine decarboxylase expression.". Cell. Mol. Life Sci. 66 (7): 1309â19. doi:10.1007/s00018-009-9001-1. PMID 19266161.

[edit] External links

Histidine Decarboxylase at the US National Library of Medicine Medical Subject Headings (MeSH)

This article incorporates text from the United States National Library of Medicine, which is in the public domain.

Carbon-carbon lyases (EC 4.1)

4.1.1: Carboxy-lyases

4.1.2: Aldehyde-lyases

4.1.3: Oxo-acid-lyases

3-hydroxy-3-methylglutaryl-CoA lyase

4.1.99: Other

Tryptophanase

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· neurotransmitter enzymes

monoamine

histidineâhistamine	anabolism: Histidine decarboxylase catabolism: Histamine N-methyltransferase Â· Amine oxidase

tyrosineâdopamineâepinephrine	anabolism: Tyrosine hydroxylase Â· Aromatic L-amino acid decarboxylase Â· Dopamine beta hydroxylase Â· Phenylethanolamine N-methyltransferase catabolism: Catechol-O-methyl transferase Â· Monoamine oxidase

glutamateâGABA	anabolism: Glutamate decarboxylase catabolism: 4-aminobutyrate transaminase

tryptophanâserotoninâmelatonin	Tryptophan hydroxylase Â· Aromatic L-amino acid decarboxylase Â· Acetylserotonin O-methyltransferase

arginineâNO

Nitric oxide synthase (NOS1, NOS2, NOS3)

cholineâAcetylcholine

anabolism: Choline acetyltransferase
catabolism: Cholinesterase (Acetylcholinesterase, Butyrylcholinesterase)

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)

Histaminergics

Receptor

H₁	Agonists: 2-Pyridylethylamine Betahistine Histamine HTMT UR-AK49 Antagonists: 1st generation: 4-Methyldiphenhydramine Alimemazine Antazoline Azatadine Bamipine Benzatropine/Benztropine Bepotastine Bromazine Brompheniramine Buclizine Captodiame Carbinoxamine Chlorcyclizine Chloropyramine Chlorothen Chlorphenamine Chlorphenoxamine Cinnarizine Clemastine Clobenzepam Clocinizine Cyclizine Cyproheptadine Dacemazine Deptropine Dexbrompheniramine Dexchlorpheniramine Dimenhydrinate Dimetindene Diphenhydramine Diphenylpyraline Doxylamine Embramine Etodroxizine Etybenzatropine/Ethylbenztropine Etymemazine Flunarizine Histapyrrodine Homochlorcyclizine Hydroxyethylpromethazine Hydroxyzine Isopromethazine Isothipendyl Meclozine Mepyramine/Pyrilamine Mequitazine Methafurylene Methapyrilene Methdilazine Moxastine Niaprazine Orphenadrine Oxatomide Oxomemazine Phenindamine Pheniramine Phenyltoloxamine Pimethixene Piperoxan Pipoxizine Promethazine Propiomazine Pyrrobutamine Talastine Thenalidine Thenyldiamine Thiazinamium Thonzylamine Tolpropamine Tripelennamine Triprolidine 2nd generation: Acrivastine Alinastine Astemizole Azelastine Bamirastine Barmastine Bepiastine Bepotastine Bilastine Cabastinen Carebastine Cetirizine Clemastine Clemizole Clobenztropine Dorastine Ebastine Emedastine Epinastine Flezelastine Ketotifen Latrepirdine Levocabastine Linetastine Loratadine Mapinastine Mebhydrolin Mizolastine Moxastine Noberastine Octastine Olopatadine Perastine Piclopastine Rocastine Rupatadine Setastine Talastine Temelastine Terfenadine Zepastine 3rd generation: Desloratadine Fexofenadine Levocetirizine Ungrouped: Belarizine Efletirizine Elbanizine Flotrenizine Medrylamine Napactadine Pibaxizine Tagorizine Trelnarizine Trenizine Vapitadine Miscellaneous: Tricyclic antidepressants (amitriptyline, doxepin, trimipramine, etc) Tetracyclic antidepressants (mianserin, mirtazapine, etc) Typical antipsychotics (chlorpromazine, thioridazine, etc) Atypical antipsychotics (clozapine, olanzapine, quetiapine, etc)

H₂	Agonists: Amthamine Betazole Dimaprit Histamine HTMT Impromidine UR-AK49 Antagonists: Bisfentidine Burimamide Cimetidine Dalcotidine Donetidine Ebrotidine Etintidine Famotidine Lafutidine Lamtidine Lavoltidine/Loxtidine Lupitidine Metiamide Mifentidine Niperotidine Nizatidine Osutidine Oxmetidine Pibutidine Quisultazine/Quisultidine Ramixotidine Ranitidine Roxatidine Sufotidine Tiotidine Tuvatidine Venritidine Xaltidine

H₃	Agonists: Î±-Methylhistamine Cipralisant Histamine Imetit Immepip Immethridine Methimepip Proxyfan Antagonists: A-349,821 A-423,579 ABT-239 Betahistine Burimamide Ciproxifan Clobenpropit Conessine GSK-189,254 Impentamine Iodophenpropit JNJ-5,207,852 MK-0249 NNC-38-1,049 PF-03654746 Pitolisant SCH-79,687 Thioperamide VUF-5,681

H₄	Agonists: 4-Methylhistamine Histamine VUF-8,430 Antagonists: JNJ-7,777,120 Thioperamide VUF-6,002

Transporter

VMAT	Inhibitors: Ibogaine Reserpine Tetrabenazine

Enzyme

HDC	Inhibitors: Catechin Meciadanol Naringenin Tritoqualine

DAO	Inhibitors: Aminoguanidine

Others

Endogenous	Histamine; Precursors: L-Histidine; Cofactors: Vitamin B6

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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.

Histidine carboxylase PI chain Provide feedback

Histidine carboxylase catalyses the formation of histamine from histidine. Cleavage of the proenzyme PI chain yields two subunits, alpha and beta, which arrange as a hexamer (alpha beta)6.

Literature references

Coton E, Rollan GC, Lonvaud-Funel A; , J Appl Microbiol 1998;84:143-151.: Histidine carboxylase of Leuconostoc oenos 9204: purification, kinetic properties, cloning and nucleotide sequence of the hdc gene. PUBMED:9633629 EPMC:9633629

External database links

PANDIT:	PF02329
Pseudofam:	PF02329
SCOP:	1pya
SYSTERS:	HDC

This tab holds annotation information from the InterPro database.

InterPro entry IPR003427

Histidine decarboxylase (EC) catalyses the formation of histamine from histidine [PUBMED:11243783]. It requires a pyruvoyl group for its activity. Cleavage of the proenzyme PI chain yields two subunits, alpha and beta, which arrange as a hexamer (alpha beta) 6 by nonhydrolytic self-catalysis.

Gene Ontology

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

Molecular function	histidine decarboxylase activity (GO:0004398)
Biological process	histidine metabolic process (GO:0006547)

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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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

Viewing

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

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

Reformatting

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

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Downloading

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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 (4)	Full (71)	Representative proteomes				NCBI (58)	Meta (3)
	Seed (4)	Full (71)	RP15 (4)	RP35 (7)	RP55 (8)	RP75 (9)	NCBI (58)	Meta (3)
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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 (4)	Full (71)	Representative proteomes				NCBI (58)	Meta (3)
	Seed (4)	Full (71)	RP15 (4)	RP35 (7)	RP55 (8)	RP75 (9)	NCBI (58)	Meta (3)
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 (4)	Full (71)	Representative proteomes				NCBI (58)	Meta (3)
	Seed (4)	Full (71)	RP15 (4)	RP35 (7)	RP55 (8)	RP75 (9)	NCBI (58)	Meta (3)
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_19599 (release 5.2)

Previous IDs:

none

Type:

Domain

Author:

Mian N, Bateman A

Number in seed:

4

Number in full:

71

Average length of the domain:

262.60 aa

Average identity of full alignment:

46 %

Average coverage of the sequence by the domain:

94.92 %

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	28.3	28.0
Noise cut-off	15.8	15.1

Model length:

306

Family (HMM) version:

11

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.

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 HDC domain has been found. There are 34 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: HDC (PF02329)

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Summary: Histidine carboxylase PI chain

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Histidine decarboxylase Edit Wikipedia article

Contents

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Histidine carboxylase PI chain Provide feedback

Literature references

External database links

InterPro entry IPR003427

Gene Ontology

Domain organisation

Alignments

Alignment types

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Trees

Curation and family details

Curation

HMM information

Species distribution

Sunburst controls

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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

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Selected sequences

Species trees

Interactive tree

Structures