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

Code	Position	Pattern	Full Name
ARG-C	1	R	ARG-C proteinase
ASP-N	2	D	ASP-N endopeptidase
BNPS	1	W	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	1	R	Clostripain
CNBR	1	M	CNBR
ELANE	1	[AV]	Neutrophil elastase
ENTKIN	1	(?<=[DE][DE][DE])K	Enterokinase
FACTXA	1	(?<=[AFGILTVM][DE]G)R	Factor XA
FORMIC	1	D	Formic acid
GLUEND	1	E	Glutamyl endopeptidase
GRANB	1	(?<=IEP)D	Granzyme B
HYDROX	1	N(?=G)	Hydroxylamine
IODOB	1	W	Iodosobenzoic acid
LYSC	1	K	Lysc
NLATEV	1	(?<=Y\w)Q(?=[GS])	NLA in tobacco etch virus
NTCB	1	C	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
XTRYPS	1	((?<=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 1. 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 2. Using cleavelookup with an Abbreviation Code

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

cleavelookup('code', 'CASP1')

ans =

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

Version History

Introduced in R2008b