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Team:Imperial College London/Stomach
From 2009.igem.org
(Difference between revisions)
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<div id='sib_container'> | <div id='sib_container'> | ||
<div id = 'sib_body'> | <div id = 'sib_body'> | ||
| - | <b>PeptideCutter</b> [<A HREF="/tools/peptidecutter/peptidecutter_references.html">references</A> / | + | <b>PeptideCutter</b> [<A HREF="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_references.html">references</A> / |
| - | <A HREF="/tools/peptidecutter/peptidecutter_instructions.html">documentation</A>] | + | <A HREF="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_instructions.html">documentation</A>] |
predicts potential cleavage sites cleaved by proteases or chemicals in a given protein | predicts potential cleavage sites cleaved by proteases or chemicals in a given protein | ||
sequence. | sequence. | ||
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<P> | <P> | ||
| - | <form method=POST action="/cgi-bin/peptidecutter/peptidecutter.pl"> | + | <form method=POST action="http://www.expasy.ch/tools/peptidecutter/cgi-bin/peptidecutter/peptidecutter.pl"> |
Enter a UniProtKB (Swiss-Prot or TrEMBL) protein | Enter a UniProtKB (Swiss-Prot or TrEMBL) protein | ||
identifier, ID (e.g. ALBU_HUMAN), or accession number, AC (e.g. P04406), | identifier, ID (e.g. ALBU_HUMAN), or accession number, AC (e.g. P04406), | ||
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<input type=radio name=enzyme_number value= less_enzymes> only the following selection of<b> | <input type=radio name=enzyme_number value= less_enzymes> only the following selection of<b> | ||
| - | <A HREF="/tools/peptidecutter/peptidecutter_enzymes.html">enzymes and chemicals</A></b> | + | <A HREF="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html">enzymes and chemicals</A></b> |
<dl><dd> | <dl><dd> | ||
<table > | <table > | ||
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<table> | <table> | ||
| - | <tr><td><input type=checkbox name=enzyme value=ArgC> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#ArgC">Arg-C proteinase</a></td> | + | <tr><td><input type=checkbox name=enzyme value=ArgC> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#ArgC">Arg-C proteinase</a></td> |
| - | <td><input type=checkbox name=enzyme value=AspN> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#AspN">Asp-N endopeptidase</a></td> | + | <td><input type=checkbox name=enzyme value=AspN> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#AspN">Asp-N endopeptidase</a></td> |
| - | <td><input type=checkbox name=enzyme value=AspGluN> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#AspGluN">Asp-N endopeptidase + N-terminal Glu</a></td></tr> | + | <td><input type=checkbox name=enzyme value=AspGluN> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#AspGluN">Asp-N endopeptidase + N-terminal Glu</a></td></tr> |
| - | <tr><td><input type=checkbox name=enzyme value=BNPS> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#BNPS">BNPS-Skatole</a></td> | + | <tr><td><input type=checkbox name=enzyme value=BNPS> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#BNPS">BNPS-Skatole</a></td> |
| - | <td><input type=checkbox name=enzyme value=Casp1> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#Casp1">Caspase1</a></td> | + | <td><input type=checkbox name=enzyme value=Casp1> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Casp1">Caspase1</a></td> |
| - | <td><input type=checkbox name=enzyme value=Casp2> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#Casp2">Caspase2</a></td></tr> | + | <td><input type=checkbox name=enzyme value=Casp2> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Casp2">Caspase2</a></td></tr> |
| - | <tr><td><input type=checkbox name=enzyme value=Casp3> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#Casp3">Caspase3</a></td> | + | <tr><td><input type=checkbox name=enzyme value=Casp3> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Casp3">Caspase3</a></td> |
| - | <td><input type=checkbox name=enzyme value=Casp4> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#Casp4">Caspase4</a></td> | + | <td><input type=checkbox name=enzyme value=Casp4> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Casp4">Caspase4</a></td> |
| - | <td><input type=checkbox name=enzyme value=Casp5> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#Casp5">Caspase5</a></td></tr> | + | <td><input type=checkbox name=enzyme value=Casp5> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Casp5">Caspase5</a></td></tr> |
| - | <tr><td><input type=checkbox name=enzyme value=Casp6> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#Casp6">Caspase6</a></td> | + | <tr><td><input type=checkbox name=enzyme value=Casp6> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Casp6">Caspase6</a></td> |
| - | <td><input type=checkbox name=enzyme value=Casp7> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#Casp7">Caspase7</a></td> | + | <td><input type=checkbox name=enzyme value=Casp7> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Casp7">Caspase7</a></td> |
| - | <td><input type=checkbox name=enzyme value=Casp8> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#Casp8">Caspase8</a></td></tr> | + | <td><input type=checkbox name=enzyme value=Casp8> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Casp8">Caspase8</a></td></tr> |
| - | <tr><td><input type=checkbox name=enzyme value=Casp9> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#Casp9">Caspase9</a></td> | + | <tr><td><input type=checkbox name=enzyme value=Casp9> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Casp9">Caspase9</a></td> |
| - | <td><input type=checkbox name=enzyme value=Casp10> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#Casp10">Caspase10</a></td> | + | <td><input type=checkbox name=enzyme value=Casp10> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Casp10">Caspase10</a></td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| - | <td><input type=checkbox name=enzyme value=Ch_hi> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#Chym">Chymotrypsin-high specificity (C-term to [FYW], not before P)</a></td> | + | <td><input type=checkbox name=enzyme value=Ch_hi> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Chym">Chymotrypsin-high specificity (C-term to [FYW], not before P)</a></td> |
| - | <td><input type=checkbox name=enzyme value=Ch_lo> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#Chym">Chymotrypsin-low specificity (C-term to [FYWML], not before P)</a></td></tr> | + | <td><input type=checkbox name=enzyme value=Ch_lo> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Chym">Chymotrypsin-low specificity (C-term to [FYWML], not before P)</a></td></tr> |
| - | <tr><td><input type=checkbox name=enzyme value=Clost> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#Clost">Clostripain (Clostridiopeptidase B)</a></td> | + | <tr><td><input type=checkbox name=enzyme value=Clost> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Clost">Clostripain (Clostridiopeptidase B)</a></td> |
| - | <td><input type=checkbox name=enzyme value=CNBr> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#CNBr">CNBr</a></td> | + | <td><input type=checkbox name=enzyme value=CNBr> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#CNBr">CNBr</a></td> |
| - | <td><input type=checkbox name=enzyme value=Enter> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#Enter">Enterokinase</a></td></tr> | + | <td><input type=checkbox name=enzyme value=Enter> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Enter">Enterokinase</a></td></tr> |
| - | <tr><td><input type=checkbox name=enzyme value=Xa> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#Xa">Factor Xa</a></td> | + | <tr><td><input type=checkbox name=enzyme value=Xa> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Xa">Factor Xa</a></td> |
| - | <td><input type=checkbox name=enzyme value=HCOOH> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#HCOOH">Formic acid</a></td> | + | <td><input type=checkbox name=enzyme value=HCOOH> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#HCOOH">Formic acid</a></td> |
| - | <td><input type=checkbox name=enzyme value=Glu> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#Glu">Glutamyl endopeptidase</a></td></tr> | + | <td><input type=checkbox name=enzyme value=Glu> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Glu">Glutamyl endopeptidase</a></td></tr> |
| - | <tr><td><input type=checkbox name=enzyme value=GranB> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#GranB">GranzymeB</a></td> | + | <tr><td><input type=checkbox name=enzyme value=GranB> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#GranB">GranzymeB</a></td> |
| - | <td><input type=checkbox name=enzyme value=Hydro> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#Hydro">Hydroxylamine</a></td> | + | <td><input type=checkbox name=enzyme value=Hydro> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Hydro">Hydroxylamine</a></td> |
| - | <td><input type=checkbox name=enzyme value=Iodo> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#Iodo">Iodosobenzoic acid</a></td> | + | <td><input type=checkbox name=enzyme value=Iodo> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Iodo">Iodosobenzoic acid</a></td> |
</tr> | </tr> | ||
| - | <tr><td><input type=checkbox name=enzyme value=LysC> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#LysC">LysC</a></td> | + | <tr><td><input type=checkbox name=enzyme value=LysC> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#LysC">LysC</a></td> |
| - | <td><input type=checkbox name=enzyme value=LysN> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#LysN">LysN</a></td> | + | <td><input type=checkbox name=enzyme value=LysN> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#LysN">LysN</a></td> |
| - | <td><input type=checkbox name=enzyme value=NTCB> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#NTCB">NTCB (2-nitro-5-thiocyanobenzoic acid)</a></td></tr> | + | <td><input type=checkbox name=enzyme value=NTCB> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#NTCB">NTCB (2-nitro-5-thiocyanobenzoic acid)</a></td></tr> |
| - | <tr><td><input type=checkbox name=enzyme value=Pn1.3> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#Peps">Pepsin (pH1.3)</a></td> | + | <tr><td><input type=checkbox name=enzyme value=Pn1.3> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Peps">Pepsin (pH1.3)</a></td> |
| - | <td><input type=checkbox name=enzyme value=Pn2> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#Peps">Pepsin (pH>2)</a></td> | + | <td><input type=checkbox name=enzyme value=Pn2> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Peps">Pepsin (pH>2)</a></td> |
| - | <td><input type=checkbox name=enzyme value=Pro> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#Pro">Proline-endopeptidase</a></td> | + | <td><input type=checkbox name=enzyme value=Pro> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Pro">Proline-endopeptidase</a></td> |
</tr> | </tr> | ||
| - | <tr><td><input type=checkbox name=enzyme value=ProtK> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#ProtK">Proteinase K</a></td> | + | <tr><td><input type=checkbox name=enzyme value=ProtK> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#ProtK">Proteinase K</a></td> |
| - | <td><input type=checkbox name=enzyme value=Staph> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#Staph">Staphylococcal peptidase I</a></td> | + | <td><input type=checkbox name=enzyme value=Staph> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Staph">Staphylococcal peptidase I</a></td> |
| - | <td><input type=checkbox name=enzyme value=TEV> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#TEV">Tobacco etch virus protease</a></td> | + | <td><input type=checkbox name=enzyme value=TEV> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#TEV">Tobacco etch virus protease</a></td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| - | <td><input type=checkbox name=enzyme value=Therm> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#Therm">Thermolysin</a></td> | + | <td><input type=checkbox name=enzyme value=Therm> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Therm">Thermolysin</a></td> |
| - | <td><input type=checkbox name=enzyme value=Throm> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#Throm">Thrombin</a></td> | + | <td><input type=checkbox name=enzyme value=Throm> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Throm">Thrombin</a></td> |
| - | <td><input type=checkbox name=enzyme value=Tryps> <a href="/tools/peptidecutter/peptidecutter_enzymes.html#Tryps">Trypsin</a></td> | + | <td><input type=checkbox name=enzyme value=Tryps> <a href="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_enzymes.html#Tryps">Trypsin</a></td> |
</tr> | </tr> | ||
</table> | </table> | ||
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</table> | </table> | ||
</dd></dl> | </dd></dl> | ||
| - | <input type=radio tabIndex=4 name=enzyme_number value= special_enzymes> for the following enzymes an additional, more <b><A HREF="/tools/peptidecutter/peptidecutter_special_enzymes.html">sophisticated model</A> </b>can be applied that attributes a probability of cleavage to each site : | + | <input type=radio tabIndex=4 name=enzyme_number value= special_enzymes> for the following enzymes an additional, more <b><A HREF="http://www.expasy.ch/tools/peptidecutter/tools/peptidecutter/peptidecutter_special_enzymes.html">sophisticated model</A> </b>can be applied that attributes a probability of cleavage to each site : |
</b><p><dl><dd><select name="special_enzyme" size=2> | </b><p><dl><dd><select name="special_enzyme" size=2> | ||
Revision as of 14:49, 29 September 2009
Contents |
Human Digestive Proteases:
- Pepsin = stomach
- Trypsin = duodenum
- Chymotrypsin
- Carboxypeptidase
Stomach
Pepsin
- Released by chief cells in the stomach.
- Expressed as a zymogen pepsinogen.
- Pepsinogen is converted to pepsin by HCl which is released by parietal cells of the stomach.
- Cleaves at the N-terminus after aromatic amino acids such as phenylalanine, tryptophan, and tyrosine.
- Optimum pH of 1.5 to 2. Pepsin denatures when the pH is more than 5.0.
Duodenum
Endopeptidases (trypsin, chymotryopsin, elastase)
Exopeptidases (carboxypeptidases A & B)
Enteropeptidase
Trypsin
Chymotryopsin
Elastase
Enterokinase
Carboxypeptidases A & B
Small Intestine = Aminopeptidase N
Dipeptidyl aminopeptidase IV
Aminopeptidase P
Carboxypeptidase P
Angotensin-converting enzyme
Glutamyl aminopeptidase
Peptide cutter
PeptideCutter [references /
documentation]
predicts potential cleavage sites cleaved by proteases or chemicals in a given protein
sequence.
PeptideCutter returns the query sequence with the
possible cleavage sites mapped on it and /or a table of cleavage site positions.
