Sequence-based prediction of permissive stretches for internal protein tagging and knockdown

Table 1 Overview of internally tagged protein variants

	Stretch	Span	Insertion site	Original sequence^a	Sequence after insertion^b
Plasmid insertions
Adk	PSI	I72-R78	D76	QEDCRNGFLLD	1-QEDENLYFQGLLD
	PSII	D94-A95	A93	PQADAMKE	PQAENLYFQGMKE
			K97	AMKEAG	AMKENLYFQGEAG
			A99	KEAGIN	1-KEAENLYFQGMKEAGIN
			A99	KEAGIN	2-KEAENLYFQGDAMKEAGIN
	PSIII	V142-G150	P140	NPPKVEGKDDVTGE	NPPENLYFQGTGE
	PSIV	T191-P201	A186	KEAEAGNTK	KEAENLYFQGNTK
GpsA	PSI	P55-V57	C49	DRCNAAFLPDVPFPD	DRCENLYFQGFPD
	PSI	P55-V57	P60	PFPDTL	PFPENLYFQGVPFPDTL
	PSII	P97-D102	M99	PLMRPD	PLMPTTENLYFQGCLGRPD
	PSIII	L128-Q131	I132	DQIPLA	DQIPTTENLYFQGCLGPLA
	PSV	D272-V273	Q269	LGQGMD	LGQPTTENLYFQGGTVGMD
TpiA	PSIII	E53-I59	E55	EAEGSH	1-EAEGGSGENLYFQ G SGGSGSH
					2-EAEGCLGESENLYFQGDERKNKGSH
					3-EAEGCLPTTENLYFQSGTVKNKGSH
	PSIV	D67-N69	N69	DLNLSG	DLNENLYFQGLSG
	PSVI	E133-A156	T130	GETEAENEAGKTE	1-GETENLYFQGGSGKTE
			T130	GETEAENEAGKTE	2-GETGGSENLYFQGGSGKTE
			T153	LKTQGA	LKTDYDIPTTENLYFQSGTVDAGADQGA
Chromosomal insertions
Adk	PSI	I72-R78	D76	QEDCRN	3-QEDENLYFQGESLFKCRN
TpiA	PSIV	D67-N69	L70	LNLSGA	LNLPPKNENLYFQGESLFKGPSGA
AtpA	PSIII	H123-F126	H123	LDHDGE	LDHENLYFQGDGE
AtpD	PSIII	E101-E105	E101	KGEIGE	KGEENLYFQGIGE
Extended TEV-tag
Adk	PSI	I72-R78	D76	QEDCRN	2-QEDENLYFQGCRN
Adk					4-QEDENLYFQGESLFKGGCRN
GpsA	PSI	P55-V57	D56	LPDVPS	1-LPD ENLYFQG VPS
GpsA					2-LPD PPKNENLYFQGESLFKGPVPS

^aResidues deleted during the insertion process are shown in boldface. If no residues were deleted, a 6-residue stretch of the protein sequence is shown, and the insert was placed in the middle
^bMinimal TEV-tag and extended derivatives used for insertion are shown in boldface

ISSN: 1741-7007