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cleavelookup

Find cleavage rule for enzyme or compound

Syntax

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

Arguments

CodeValue Character vector specifying a code representing an abbreviation code for an enzyme or compound. For valid codes, see the table Cleave Lookup.
NameValue Character 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-C 1R ARG-C proteinase
ASP-N 2D ASP-N endopeptidase
BNPS 1W BNPS-Skatole
CASP1 1(?<=[FWYL]\w[HAT])D(?=[^PEDQKR]) Caspase 1
CASP2 1(?<=DVA)D(?=[^PEDQKR]) Caspase 2
CASP3 1(?<=DMQ)D(?=[^PEDQKR]) Caspase 3
CASP4 1(?<=LEV)D(?=[^PEDQKR]) Caspase 4
CASP5 1(?<=[LW]EH)D Caspase 5
CASP6 1(?<=VE[HI])D(?=[^PEDQKR]) Caspase 6
CASP7 1(?<=DEV)D(?=[^PEDQKR]) Caspase 7
CASP8 1(?<=[IL]ET)D(?=[^PEDQKR]) Caspase 8
CASP9 1(?<=LEH)D Caspase 9
CASP10 1(?<=IEA)D Caspase 10
CH-HI 1([FY](?=[^P]))|(W(?=[^MP])) Chymotrypsin- high specificity
CH-LO 1([FLY](?=[^P]))|(W(?=[^MP]))| (M(?=[^PY]))|(H(?=[^DMPW])) Chymotrypsin- low specificity
CLOST 1R Clostripain
CNBR 1M CNBR
ELANE1[AV]Neutrophil elastase
ENTKIN 1 (?<=[DE][DE][DE])KEnterokinase
FACTXA 1(?<=[AFGILTVM][DE]G)R Factor XA
FORMIC 1D Formic acid
GLUEND 1E Glutamyl endopeptidase
GRANB 1(?<=IEP)D Granzyme B
HYDROX 1N(?=G) Hydroxylamine
IODOB 1W Iodosobenzoic acid
LYSC 1K Lysc
NLATEV1(?<=Y\w)Q(?=[GS])NLA in tobacco etch virus
NTCB 1C NTCB
PEPS 1 ((?<=[^HKR][^P])[^R](?=[FL][^P]))|((?<=[^HKR][^P])[FL](?=\w[^P]))Pepsin
PH = 1.3
PEPS2 1 ((?<=[^HKR][^P])[^R](?=[FLWY][^P]))|((?<=[^HKR][^P])[FLWY](?=\w[^P]))Pepsin
PH > 2
PROEND 1(?<=[HKR])P(?=[^P]) Proline endopeptidase
PROTK 1[AEFILTVWY] Proteinase K
STAPHP 1(?<=[^E])E Staphylococcal peptidase I
THERMO 1[^DE](?=[AFILMV]) Thermolysin
THROMB 1((?<=\w\wG)R(?=G))| ((?<=[AFGILTVM][AFGILTVWA]P)R(?=[^DE][^DE])) Thrombin
TRYPS 1((?<=\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

Example 8. 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
Example 9. 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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