Summary: Alpha conotoxin precursor

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Conotoxin Edit Wikipedia article

Alpha conotoxin precursor

α-Conotoxin PnIB from C. pennaceus, disulfide bonds shown in yellow. From the University of Michigan's Orientations of Proteins in Membranes database, PDB 1AKG.

Identifiers

Symbol

Toxin_8

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

Omega conotoxin

Schematic diagram of the three-dimensional structure of ω-conotoxin MVIIA (ziconotide). Disulfide bonds are shown in gold. From PDB 1DW5.

Identifiers

Symbol

Conotoxin

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

A conotoxin is one of a group of neurotoxic peptides isolated from the venom of the marine cone snail, genus Conus.

Conotoxins, which are peptides consisting of 10 to 30 amino acid residues, typically have one or more disulfide bonds. Conotoxins have a variety of mechanisms of actions, most of which have not been determined. However, it appears that many of these peptides modulate the activity of ion channels.^[1] Over the last few decades conotoxins have been subject of pharmacological interest.^[2]

[edit] Types and biological activities of conotoxins

The number of conotoxins whose activities have been determined so far is five, and they are called the α(alpha)-, δ(delta)-, κ(kappa)-, μ(mu)-, and ω(omega)- types. Each of the five types of conotoxins attacks a different target:

α-conotoxin inhibits nicotinic acetylcholine receptors at nerves and muscles.^[3]
δ-conotoxin inhibits the inactivation of voltage-dependent sodium channels.^[4]
κ-conotoxin inhibits potassium channels.^[5]
μ-conotoxin inhibits voltage-dependent sodium channels in muscles.^[6]
ω-conotoxin inhibits N-type voltage-dependent calcium channels.^[7] Because N-type voltage-dependent calcium channels are related to algesia (sensitivity to pain) in the nervous system, ω-conotoxin has an analgesic effect: the effect of ω-conotoxin M VII A is 100 to 1000 times that of morphine.^[8] Therefore a synthetic version of ω-conotoxin M VII A has found application as an analgesic drug ziconotide (Prialt).^[9]

[edit] Disulfide connectivities

Types of conotoxins also differ in the number and pattern of disulfide bonds.^[10] The disulfide bonding network, as well as specific amino acids in inter-cysteine loops, provide the specificity of conotoxins.^[11]

[edit] Omega, delta and kappa conotoxins

Omega, delta and kappa families of conotoxins have a knottin or inhibitor cysteine knot scaffold. The knottin scaffold is a very special disulfide-through-disulfide knot, in which the III-VI disulfide bond crosses the macrocycle formed by two other disulfide bonds (I-IV and II-V) and the interconnecting backbone segments, where I-VI indicates the six cysteine residues starting from the N-terminus. The cysteine arrangements are the same for omega, delta and kappa families, even though omega conotoxins are calcium channel blockers, whereas delta conotoxins delay the inactivation of sodium channels, and kappa conotoxins are potassium channel blockers.^[10]

[edit] Mu conotoxins

Mu-conotoxin

nmr solution structure of piiia toxin, nmr, 20 structures

Identifiers

Symbol

Mu-conotoxin

Pfam clan

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

Mu-conotoxins have two types of cysteine arrangements, but the knottin scaffold is not observed.^[12] Mu-conotoxins target the muscle-specific voltage-gated sodium channels,^[10] and are useful probes for investigating voltage-dependent sodium channels of excitable tissues.^[12]^[13] Mu-conotoxins target the voltage-gated sodium channels, preferentially those of skeletal muscle,^[14] and are useful probes for investigating voltage-dependent sodium channels of excitable tissues.^[15]

Different subtypes of voltage-gated sodium channels are found in different tissues in mammals, e.g., in muscle and brain, and studies have been carried out to determine the sensitivity and specificity of the mu-conotoxins for the different isoforms.^[16]

[edit] Alpha conotoxins

Alpha conotoxins have two types of cysteine arrangements,^[17] and are competitive nicotinic acetylcholine receptor antagonists.

[edit] See also

[edit] References

^ Terlau H, Olivera BM (2004). "Conus venoms: a rich source of novel ion channel-targeted peptides". Physiol. Rev. 84 (1): 41–68. doi:10.1152/physrev.00020.2003. PMID 14715910.
^ Olivera BM, Teichert RW (2007). "Diversity of the neurotoxic Conus peptides: a model for concerted pharmacological discovery.". Mol Interv 7 (5): 251–60. doi:10.1124/mi.7.5.7. PMID 17932414.
^ Nicke A, Wonnacott S, Lewis RJ (2004). "Alpha-conotoxins as tools for the elucidation of structure and function of neuronal nicotinic acetylcholine receptor subtypes". Eur. J. Biochem. 271 (12): 2305–2319. doi:10.1111/j.1432-1033.2004.04145.x. PMID 15182346.
^ Leipold E, Hansel A, Olivera BM, Terlau H, Heinemann SH (2005). "Molecular interaction of delta-conotoxins with voltage-gated sodium channels". FEBS Lett. 579 (18): 3881–3884. doi:10.1016/j.febslet.2005.05.077. PMID 15990094.
^ Shon KJ, Stocker M, Terlau H, Stühmer W, Jacobsen R, Walker C, Grilley M, Watkins M, Hillyard DR, Gray WR, Olivera BM (1998). "kappa-Conotoxin PVIIA is a peptide inhibiting the shaker K+ channel". J. Biol. Chem. 273 (1): 33–38. doi:10.1074/jbc.273.1.33. PMID 9417043.
^ Li RA, Tomaselli GF (2004). "Using the deadly mu-conotoxins as probes of voltage-gated sodium channels". Toxicon 44 (2): 117–122. doi:10.1016/j.toxicon.2004.03.028. PMC 2698010. PMID 15246758.
^ Nielsen KJ, Schroeder T, Lewis R (2000). "Structure-activity relationships of omega-conotoxins at N-type voltage-sensitive calcium channels" (abstract). J. Mol. Recognit. 13 (2): 55–70. doi:10.1002/(SICI)1099-1352(200003/04)13:2<55::AID-JMR488>3.0.CO;2-O. PMID 10822250.
^ Bowersox SS, Luther R (1998). "Pharmacotherapeutic potential of omega-conotoxin MVIIA (SNX-111), an N-type neuronal calcium channel blocker found in the venom of Conus magus". Toxicon 36 (11): 1651–1658. doi:10.1016/S0041-0101(98)00158-5. PMID 9792182.
^ Prommer E (2006). "Ziconotide: a new option for refractory pain". Drugs Today 42 (6): 369–78. doi:10.1358/dot.2006.42.6.973534. PMID 16845440.
^ ^a ^b ^c Jones RM, McIntosh JM (2001). "Cone venom--from accidental stings to deliberate injection". Toxicon 39 (10): 1447–1451. doi:10.1016/S0041-0101(01)00145-3. PMID 11478951.
^ Sato K, Kini RM, Gopalakrishnakone P, Balaji RA, Ohtake A, Seow KT, Bay BH (2000). "lambda-conotoxins, a new family of conotoxins with unique disulfide pattern and protein folding. Isolation and characterization from the venom of Conus marmoreus". J. Biol. Chem. 275 (50): 39516–39522. doi:10.1074/jbc.M006354200. PMID 10988292.
^ ^a ^b Nielsen KJ, Watson M, Adams DJ, HammarstrÃ¶m AK, Gage PW, Hill JM, Craik DJ, Thomas L, Adams D, Alewood PF, Lewis RJ (July 2002). J. Biol. Chem. 277 (30): 27247–55. doi:10.1074/jbc.M201611200. PMID 12006587.
^ Zeikus RD, Gray WR, Cruz LJ, Olivera BM, Kerr L, Moczydlowski E, Yoshikami D (1985). "Conus geographus toxins that discriminate between neuronal and muscle sodium channels". J. Biol. Chem. 260 (16): 9280–8. PMID 2410412.
^ McIntosh JM, Jones RM (October 2001). "Cone venom--from accidental stings to deliberate injection". Toxicon 39 (10): 1447–51. doi:10.1016/S0041-0101(01)00145-3. PMID 11478951.
^ Cruz LJ, Gray WR, Olivera BM, Zeikus RD, Kerr L, Yoshikami D, Moczydlowski E (August 1985). "Conus geographus toxins that discriminate between neuronal and muscle sodium channels". J. Biol. Chem. 260 (16): 9280–8. PMID 2410412.
^ Floresca CZ (2003). "A comparison of the mu-conotoxins by [3H]saxitoxin binding assays in neuronal and skeletal muscle sodium channel.". Toxicol Appl Pharmacol 190 (2): 95–101. PMID 12878039.
^ Gray WR, Olivera BM, Zafaralla GC, Ramilo CA, Yoshikami D, Nadasdi L, Hammerland LG, Kristipati R, Ramachandran J, Miljanich G (1992). "Novel alpha- and omega-conotoxins from Conus striatus venom". Biochemistry 31 (41): 11864–11873. doi:10.1021/bi00162a027. PMID 1390774.

This article incorporates text from the public domain Pfam and InterPro IPR008036

[edit] External links

Conotoxins at the US National Library of Medicine Medical Subject Headings (MeSH)
Baldomero "Toto" Olivera. "iBioSeminar on Conus Peptides". The American Society for Cell Biology.
Kaas Q, Westermann JC, Halai R, Wang CK, Craik DJ. "ConoServer". Institute of Molecular Bioscience, The University of Queensland, Australia. Retrieved 2009-06-02. "A database for conopeptide sequences and structures"

v t e Protein tertiary structure

General	Structural domain Protein folding Structure determination methods

All-α folds:	Helix bundle Globin fold Homeodomain fold Alpha solenoid

All-β folds:	Immunoglobulin domain Beta barrel Beta-propeller

α/β folds:	TIM barrel Leucine-rich repeat Flavodoxin fold Rossmann fold Thioredoxin fold Trefoil knot fold

α+β folds:	DNA clamp Ferredoxin fold Ribonuclease A SH2-like fold

Irregular folds:	Conotoxin

←Secondary structure Quaternary structure→

Toxins (enterotoxin · neurotoxin · hemotoxin · cardiotoxin · phototoxin)

Bacterial toxins

Exotoxin

Gram positive

Bacilli	Clostridium: tetani (Tetanospasmin) · perfringens (Alpha toxin, Enterotoxin) · difficile (A, B) · botulinum (Botox) other: Anthrax toxin · Listeriolysin O

Cocci	Streptolysin · Leukocidin (Panton-Valentine leukocidin) · Staphylococcus (Staphylococcus aureus alpha/beta/delta, Exfoliatin, Toxic shock syndrome toxin, SEB)

Actinobacteria	Cord factor · Diphtheria toxin

Gram negative

Shiga toxin · Verotoxin/shiga-like toxin (E. coli) · E. coli heat-stable enterotoxin/enterotoxin · Cholera toxin · Pertussis toxin · Pseudomonas exotoxin · Extracellular adenylate cyclase

By mechanism

type I (Superantigen) · type II (Pore-forming toxin) · type III (AB toxin/AB5)

Endotoxin

Lipopolysaccharide (Lipid A) · Bacillus thuringiensis delta endotoxin

Virulence factor

Clumping factor A · Fibronectin binding protein A

Mycotoxins

Aflatoxin · Amatoxin (alpha-amanitin, beta-amanitin, gamma-amanitin, epsilon-amanitin) · Citrinin · Cytochalasin · Ergotamine · Fumonisin (Fumonisin B1, Fumonisin B2) · Gliotoxin · Ibotenic acid · Muscimol · Ochratoxin · Patulin · Phalloidin · Sterigmatocystin · Trichothecene · Vomitoxin · Zeranol · Zearalenone

Invertebrates

arthropod: scorpion: Charybdotoxin, Maurotoxin, Agitoxin, Margatoxin, Slotoxin, Scyllatoxin, Hefutoxin, Lq2, Birtoxin, Bestoxin, BmKAEP, Phaiodotoxin · spider: Latrotoxin (Alpha-latrotoxin) · PhTx3 · Stromatoxin · Vanillotoxin · Huwentoxin
mollusca: Conotoxin · Eledoisin · Onchidal · Saxitoxin · Tetrodotoxin

Vertebrates

fish: Ciguatera · Tetrodotoxin

amphibian: (+)-Allopumiliotoxin 267A · Batrachotoxin · Bufotoxins (Arenobufagin, Bufotalin, Bufotenin · Cinobufagin, Marinobufagin) · Epibatidine · Histrionicotoxin · Pumiliotoxin 251D · Samandarin · Samandaridine · Tarichatoxin

reptile/snake venom: Bungarotoxin (Alpha-Bungarotoxin, Beta-Bungarotoxin) · Calciseptine · Taicatoxin · Calcicludine · Cardiotoxin III

note: some toxins are produced by lower species and pass through intermediate species

M: TOX

gen / txn

mAChR	Agonists: 77-LH-28-1 AC-42 AC-260,584 Aceclidine Acetylcholine AF30 AF150(S) AF267B AFDX-384 Alvameline AQRA-741 Arecoline Bethanechol Butyrylcholine Carbachol CDD-0034 CDD-0078 CDD-0097 CDD-0098 CDD-0102 Cevimeline Choline cis-Dioxolane Ethoxysebacylcholine LY-593,039 L-689,660 LY-2,033,298 McNA343 Methacholine Milameline Muscarine NGX-267 Ocvimeline Oxotremorine PD-151,832 Pilocarpine RS86 Sabcomeline SDZ 210-086 Sebacylcholine Suberylcholine Talsaclidine Tazomeline Thiopilocarpine Vedaclidine VU-0029767 VU-0090157 VU-0152099 VU-0152100 VU-0238429 WAY-132,983 Xanomeline YM-796 Antagonists: 3-Quinuclidinyl Benzilate 4-DAMP Aclidinium Bromide Anisodamine Anisodine Atropine Atropine Methonitrate Benactyzine Benzatropine/Benztropine Benzydamine BIBN 99 Biperiden Bornaprine CAR-226,086 CAR-301,060 CAR-302,196 CAR-302,282 CAR-302,368 CAR-302,537 CAR-302,668 CS-27349 Cyclobenzaprine Cyclopentolate Darifenacin DAU-5884 Dimethindene Dexetimide DIBD Dicyclomine/Dicycloverine Ditran EA-3167 EA-3443 EA-3580 EA-3834 Etanautine Etybenzatropine/Ethylbenztropine Flavoxate Himbacine HL-031,120 Ipratropium bromide J-104,129 Hyoscyamine Mamba Toxin 3 Mamba Toxin 7 Mazaticol Mebeverine Methoctramine Metixene N-Ethyl-3-Piperidyl Benzilate N-Methyl-3-Piperidyl Benzilate Orphenadrine Otenzepad Oxybutynin PBID PD-102,807 PD-0298029 Phenglutarimide Phenyltoloxamine Pirenzepine Piroheptine Procyclidine Profenamine RU-47,213 SCH-57,790 SCH-72,788 SCH-217,443 Scopolamine/Hyoscine Solifenacin Telenzepine Tiotropium bromide Tolterodine Trihexyphenidyl Tripitamine Tropatepine Tropicamide WIN-2299 Xanomeline Zamifenacin; Others: 1st Generation Antihistamines (Brompheniramine chlorphenamine cyproheptadine dimenhydrinate diphenhydramine doxylamine mepyramine/pyrilamine phenindamine pheniramine tripelennamine triprolidine, etc) Tricyclic Antidepressants (Amitriptyline doxepin trimipramine, etc) Tetracyclic Antidepressants (Amoxapine maprotiline, etc) Typical Antipsychotics (Chlorpromazine thioridazine, etc) Atypical Antipsychotics (Clozapine olanzapine, etc.)

nAChR	Agonists: 5-HIAA A-84,543 A-366,833 A-582,941 A-867,744 ABT-202 ABT-418 ABT-560 ABT-894 Acetylcholine Altinicline Anabasine Anatoxin-a AR-R17779 Butinoline Butyrylcholine Carbachol Choline Cotinine Cytisine Decamethonium Desformylflustrabromine Dianicline Dimethylphenylpiperazinium Epibatidine Epiboxidine Ethanol Ethoxysebacylcholine EVP-4473 EVP-6124 Galantamine GTS-21 Ispronicline Lobeline MEM-63,908/RG-3487 Nicotine NS-1738 PHA-543,613 PHA-709,829 PNU-120,596 PNU-282,987 Pozanicline Rivanicline RJR-2429 Sazetidine A Sebacylcholine SIB-1508Y SIB-1553A SSR-180,711 Suberylcholine Suxamethonium/Succinylcholine TC-1698 TC-1734 TC-1827 TC-2216 TC-5214 TC-5619 TC-6683 Tebanicline Tropisetron UB-165 Varenicline WAY-317,538 XY-4083 Antagonists: 18-Methoxycoronaridine α-Bungarotoxin α-Conotoxin Alcuronium Amantadine Anatruxonium Atracurium Bupropion Chandonium Chlorisondamine Cisatracurium Coclaurine Coronaridine Dacuronium Decamethonium Dextromethorphan Dextropropoxyphene Dextrorphan Diadonium DHβE Dimethyltubocurarine/Metocurine Dipyrandium Dizocilpine/MK-801 Doxacurium Duador Esketamine Fazadinium Gallamine Hexafluronium Hexamethonium/Benzohexonium Ibogaine Isoflurane Ketamine Kynurenic acid Laudexium/Laudolissin Levacetylmethadol Malouetine Mecamylamine Memantine Methadone (Levomethadone) Methorphan/Racemethorphan Methyllycaconitine Metocurine Mivacurium Morphanol/Racemorphan Neramexane Nitrous Oxide Pancuronium Pempidine Pentamine Pentolinium Phencyclidine Pipecuronium Radafaxine Rapacuronium Rocuronium Surugatoxin Thiocolchicoside Toxiferine Trimethaphan Tropeinium Tubocurarine Vecuronium Xenon

Reuptake inhibitors

Plasmalemmal

CHT Inhibitors	Hemicholinium-3/Hemicholine Triethylcholine

Vesicular

VAChT Inhibitors	Vesamicol

Enzyme inhibitors

Anabolism

ChAT inhibitors	1-(-Benzoylethyl)pyridinium 2-(α-Naphthoyl)ethyltrimethylammonium 3-Chloro-4-stillbazole 4-(1-Naphthylvinyl)pyridine Acetylseco hemicholinium-3 Acryloylcholine AF64A B115 BETA CM-54,903 N,N-Dimethylaminoethylacrylate N,N-Dimethylaminoethylchloroacetate

Catabolism

AChE inhibitors	Reversible: Carbamates: Aldicarb Bendiocarb Bufencarb Carbaryl Carbendazim Carbetamide Carbofuran Chlorbufam Chloropropham Ethienocarb Ethiofencarb Fenobucarb Fenoxycarb Formetanate Furadan Ladostigil Methiocarb Methomyl Miotine Oxamyl Phenmedipham Pinmicarb Pirimicarb Propamocarb Propham Propoxur; Stigmines: Ganstigmine Neostigmine Phenserine Physostigmine Pyridostigmine Rivastigmine; Others: Acotiamide Ambenonium Donepezil Caffeine Edrophonium Galantamine Huperzine A Minaprine Tacrine Zanapezil Irreversible: Organophosphates: Acephate Azinphos-methyl Bensulide Cadusafos Chlorethoxyfos Chlorfenvinphos Chlorpyrifos Chlorpyrifos-Methyl Coumaphos Cyclosarin Demeton Demeton-S-Methyl Diazinon Dichlorvos Dicrotophos Diisopropyl fluorophosphate Diisopropylphosphate Dimethoate Dioxathion Disulfoton EA-3148 Echothiophate Ethion Ethoprop Fenamiphos Fenitrothion Fenthion Fosthiazate GV Isofluorophate Isoxathion Malaoxon Malathion Methamidophos Methidathion Metrifonate Mevinphos Monocrotophos Naled Novichok agent Omethoate Oxydemeton-Methyl Paraoxon Parathion Parathion-Methyl Phorate Phosalone Phosmet Phoxim Pirimiphos-Methyl Sarin Soman Tabun Tebupirimfos Temefos Terbufos Tetrachlorvinphos Tribufos Trichlorfon VE VG VM VR VX; Others: Demecarium Onchidal (Onchidella binneyi)

BChE inhibitors	Cymserine * Many of the acetylcholinesterase inhibitors listed above act as butyrylcholinesterase inhibitors.

Others

Precursors	Choline (Lecithin) Citicoline Cyprodenate Dimethylethanolamine Glycerophosphocholine Meclofenoxate/Centrophenoxine Phosphatidylcholine Phosphatidylethanolamine Phosphorylcholine Pirisudanol

Cofactors	Acetic acid Acetylcarnitine Acetyl-coA Vitamin B₅ (Pantethine Pantetheine Panthenol)

Others	Acetylcholine releasing agents: α-Latrotoxin β-Bungarotoxin; Acetylcholine release inhibitors: Botulinum toxin (Botox); Acetylcholinesterase reactivators: Asoxime Obidoxime Pralidoxime

This article incorporates text from the public domain Pfam and InterPro IPR004214

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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Alpha conotoxin precursor Provide feedback

This family consists of several alpha conotoxin precursor proteins from a number of Conus species. The alpha-conotoxins are small peptide neurotoxins from the venom of fish-hunting cone snails which block nicotinic acetylcholine receptors (nAChRs) [1].

Literature references

Zafaralla GC, Ramilo C, Gray WR, Karlstrom R, Olivera BM, Cruz LJ; , Biochemistry 1988;27:7102-7105.: Phylogenetic specificity of cholinergic ligands: alpha-conotoxin SI. PUBMED:3196703 EPMC:3196703

External database links

PANDIT:	PF07365
Pseudofam:	PF07365
SCOP:	1mii
SYSTERS:	Toxin_8

This tab holds annotation information from the InterPro database.

InterPro entry IPR009958

This family consists of several alpha conotoxin precursor proteins from a number of Conus species. Cone snail toxins, conotoxins, are small peptides with disulphide connectivity, that target ion-channels or G-protein coupled receptors. Based on the number and pattern of disulphide bonds and biological activities, conotoxins can be classified into several families [PUBMED:11478951]. Alpha-conotoxins are neurotoxins from the venom of fish-hunting cone snails that block nicotinic acetylcholine receptors (nAChRs) [PUBMED:3196703]. Omega, delta and kappa families of conotoxins have a knottin or inhibitor cystine knot scaffold. The knottin scaffold is a very special disulphide through disulphide knot, in which the III-VI disulphide bond crosses the macrocycle formed by two other disulphide bonds (I-IV and II-V) and the interconnecting backbone segments, where I-VI indicates the six cysteine residues starting from the N terminus.

The disulphide bonding network as well as specific amino acids in inter-cysteine loops provide the specificity of conotoxin [PUBMED:10988292]. The cysteine arrangement is the same for omega, delta and kappa families, but omega conotoxins are calcium channel blockers, whereas delta conotoxins delay the inactivation of sodium channels and kappa conotoxins are potassium channel blockers [PUBMED:11478951]. Mu conotoxins have two types of cysteine arrangement, but the knottin scaffold is not observed. Mu conotoxins target the voltage-gated sodium channels [PUBMED:11478951] and are useful probes for investigating voltage-dependent sodium channels of excitable tissues [PUBMED:2410412]. Alpha conotoxins have two types of cysteine arrangement [PUBMED:1390774] and are competitive nicotinic acetylcholine receptor antagonists.

Gene Ontology

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

Cellular component	extracellular region (GO:0005576)
Molecular function	acetylcholine receptor inhibitor activity (GO:0030550)
Biological process	pathogenesis (GO:0009405)

Domain organisation

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Alignments

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	Seed (22)	Full (253)	Representative proteomes				NCBI (244)	Meta (0)
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	Seed (22)	Full (253)	Representative proteomes				NCBI (244)	Meta (0)
	Seed (22)	Full (253)	RP15 (0)	RP35 (0)	RP55 (0)	RP75 (0)	NCBI (244)	Meta (0)
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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_20562 (release 10.0)

Previous IDs:

none

Type:

Family

Author:

Moxon SJ

Number in seed:

22

Number in full:

253

Average length of the domain:

41.20 aa

Average identity of full alignment:

39 %

Average coverage of the sequence by the domain:

81.76 %

HMM information

HMM build commands:

build method: hmmbuild --amino -o /dev/null HMM SEED

search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	21.6	21.6
Trusted cut-off	21.6	22.8
Noise cut-off	21.5	21.5

Model length:

50

Family (HMM) version:

7

Download:

download the raw HMM for this family

Species distribution

Sunburst
Tree

Sunburst controls

Show

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

This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.

How the sunburst is generated

The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:

superkingdom
kingdom
phylum
class
order
family
genus
species

Colouring and labels

Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.

As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.

Anomalies in the taxonomy tree

There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.

Missing taxonomic levels

Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.

Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".

Sub-species

Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.

Too many species/sequences

For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.

Loading sunburst data...

Tree controls

Hide

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

Loading...

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 Toxin_8 domain has been found. There are 19 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.

Loading structure mapping...

Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: Toxin_8 (PF07365)

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Summary: Alpha conotoxin precursor

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Conotoxin Edit Wikipedia article

Contents

[edit] Types and biological activities of conotoxins

[edit] Disulfide connectivities

[edit] Omega, delta and kappa conotoxins

[edit] Mu conotoxins

[edit] Alpha conotoxins

[edit] See also

[edit] References

[edit] External links

Alpha conotoxin precursor Provide feedback

Literature references

External database links

InterPro entry IPR009958

Gene Ontology

Domain organisation

Alignments

Alignment types

Viewing

Reformatting

Downloading

View options

Format an alignment

Download options

External links

HMM logo

Trees

Curation and family details

Curation

HMM information

Species distribution

Sunburst controls

Weight segments by...

Change the size of the sunburst

Colour assignments

Selections

Currently selected:

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