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cleavelookup

Find cleavage rule for enzyme or compound

Syntax

cleavelookup
cleavelookup('Code', CodeValue)
cleavelookup('Name', NameValue)

Arguments

CodeValueCharacter vector specifying a code representing an abbreviation code for an enzyme or compound. For valid codes, see the table Cleave Lookup.
NameValueCharacter vector specifying an enzyme or compound name. For valid names, see the table Cleave Lookup.

Description

cleavelookup displays a table of abbreviation codes, cleavage positions, cleavage patterns, and full names of enzymes and compounds for which cleavage rules are specified by the cleavage rule library. Trysin's exception rules are also listed in the table. For more information, see the ExPASy PeptideCutter tool.

Cleave Lookup

CodePositionPatternFull Name
ARG-C1RARG-C proteinase
ASP-N2DASP-N endopeptidase
BNPS1WBNPS-Skatole
CASP11(?<=[FWYL]\w[HAT])D(?=[^PEDQKR])Caspase 1
CASP21(?<=DVA)D(?=[^PEDQKR]) Caspase 2
CASP31(?<=DMQ)D(?=[^PEDQKR])Caspase 3
CASP41(?<=LEV)D(?=[^PEDQKR])Caspase 4
CASP51(?<=[LW]EH)DCaspase 5
CASP61(?<=VE[HI])D(?=[^PEDQKR])Caspase 6
CASP71(?<=DEV)D(?=[^PEDQKR])Caspase 7
CASP81(?<=[IL]ET)D(?=[^PEDQKR])Caspase 8
CASP91(?<=LEH)DCaspase 9
CASP101(?<=IEA)DCaspase 10
CH-HI1([FY](?=[^P]))|(W(?=[^MP]))Chymotrypsin- high specificity
CH-LO 1([FLY](?=[^P]))|(W(?=[^MP]))| (M(?=[^PY]))|(H(?=[^DMPW]))Chymotrypsin- low specificity
CLOST1RClostripain
CNBR1MCNBR
ELANE1[AV]Neutrophil elastase
ENTKIN1(?<=[DE][DE][DE])KEnterokinase
FACTXA1(?<=[AFGILTVM][DE]G)RFactor XA
FORMIC1DFormic acid
GLUEND1EGlutamyl endopeptidase
GRANB1(?<=IEP)DGranzyme B
HYDROX1N(?=G)Hydroxylamine
IODOB1WIodosobenzoic acid
LYSC1KLysc
NLATEV1(?<=Y\w)Q(?=[GS])NLA in tobacco etch virus
NTCB1CNTCB
PEPS1((?<=[^HKR][^P])[^R](?=[FL][^P]))|((?<=[^HKR][^P])[FL](?=\w[^P]))Pepsin
PH = 1.3
PEPS21((?<=[^HKR][^P])[^R](?=[FLWY][^P]))|((?<=[^HKR][^P])[FLWY](?=\w[^P]))Pepsin
PH > 2
PROEND1(?<=[HKR])P(?=[^P])Proline endopeptidase
PROTK1[AEFILTVWY] Proteinase K
STAPHP1(?<=[^E])EStaphylococcal peptidase I
THERMO1[^DE](?=[AFILMV])Thermolysin
THROMB1((?<=\w\wG)R(?=G))| ((?<=[AFGILTVM][AFGILTVWA]P)R(?=[^DE][^DE]))Thrombin
TRYPS1((?<=\w)[KR](?=[^P]))| ((?<=W)K(?=P))|((?<=M)R(?=P))Trypsin
XTRYPS1((?<=C)K[DHY])|((?<=D)K(?=D))|((?<=R)R(?=[HR]))|((?<=C)R(?=K))Trypsin exceptions

cleavelookup('Code', CodeValue) displays the cleavage position, cleavage pattern, and full name of the enzyme or compound specified by CodeValue, a character vector specifying an abbreviation code.

cleavelookup('Name', NameValue) displays the cleavage position, cleavage pattern, and abbreviation code of the enzyme or compound specified by NameValue, a character vector specifying an enzyme or compound name.

Examples

Using cleavelookup with an Enzyme Name

Display the cleavage position, cleavage pattern, and abbreviation code of the enzyme Caspase 1.

cleavelookup('name', 'CASPASE 1')

ans =

1	(?<=[FWYL]\w[HAT])D(?=[^PEDQKR])	CASP1

Using cleavelookup with an Abbreviation Code

Display the cleavage position, cleavage pattern, and full name of the enzyme with a abbreviation code of CASP1.

cleavelookup('code', 'CASP1')

ans =

1	(?<=[FWYL]\w[HAT])D(?=[^PEDQKR])	CASPASE 1

Introduced in R2008b

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