CFTR Blasts

BLAST results showing the consensus sequences along the length of the native CFTR protein for S.Aureus, P.Aeruginosa, S.Maltophilia or autoantigen matches: The B cell and T cell epitope immunogenicity index is also provided. Values above the server-set thresholds (0.35 for B cell and 0.5 for T cell ) are shown in red. The topology of the CFTR protein is shown in the final column (EXT = extracellular: IN = intracellular; TM = transmembrane): Extracellular regions are highlighted in red: Autoantigen overlaps are highlighted in blue. The whole protein is not processed and BLAST searches were focussed on auto antigen overlaps in antigenic extracellular regions.

Jens Erik Pontoppidan Larsen, Ole Lund and Morten Nielsen. Improved method for predicting linear B-cell epitopes. Immunome Res. 2006; 2: 2.

M. Nielsen, C. Lundegaard, O. Lund, and C. Kesmir. 2005. The role of the proteasome in generating cytotoxic T cell epitopes: Insights obtained from improved predictions of proteasomal cleavage. Immunogenetics. 57:33-41.

BLAST results of the F508del and 19 other mutants are shown at the bottom of this page

N	Autoantigen coverage in blue	Pathogen or autoantigen alignment	B cell epitopes in red	T cell epitopes in red	Topology (Extracellular= Red)
1	M	S.Malt MQR PL AS	0.64	0.84	IN
2	Q	Q	0.36	0.10	IN
3	R	(mucin) RSP EK S P.Aer R PLEK S and RSPLE KA and RSPL KA S.Malt RSPL+K S.Aur R P LEKA	0.61	0.59	IN
4	S	S	0.65	0.03	IN
5	P	S.Aur and S.Malt PLEKA	0.60	0.02	IN
6	L	L	0.83	0.40	IN
7	E	S.Malt LEKAS	0.63	0.03	IN
8	K	K	0.36	0.30	IN
9	A	A	0.19	0.09	IN
10	S	S	0.07	0.04	IN
11	V	V	-0.17	0.27	IN
12	V	V	-0.75	0.94	IN
13	S	S	-1.19	0.06	IN
14	K	K	-1.17	0.84	IN
15	L	L	-1.48	0.96	IN
16	F	F	-1.14	0.82	IN
17	F	F	-0.90	0.15	IN
18	S	S	-0.89	0.03	IN
19	W	W	-1.07	0.93	IN
20	T	T	-0.94	0.03	IN
21	R	R	-0.60	0.58	IN
22	P	(myelo) PILR P.Aer and S.Aur and S.Malt PILRK S.Malt P+LR GYRQ	-0.20	0.10	IN
23	I	I	-0.15	0.49	IN
24	L	(S.Malt) LRK Y QR	0.07	0.66	IN
25	R	R	-0.06	0.55	IN
26	K	(P.Aer)KGYR	-0.16	0.95	IN
27	G	S.Malt GYRQRL	-0.15	0.07	IN
28	Y	(P.Aer) YRQRL	-0.25	0.92	IN
29	R	(P.Aer) RQRLE-SD	0.03	0.84	IN
30	Q	(S.Malt) QRL LSD	-0.21	0.08	IN
31	R	(P.Aer) RLEL	-0.19	0.57	IN
32	L	L	-0.18	0.98	IN
33	E	E	-0.35	0.02	IN
34	L	L	-0.57	0.71	IN
35	S	S	-0.49	0.04	IN
36	D	(P.Aer) DIYQI	-0.64	0.03	IN
37	I	I	-0.26	0.10	IN
38	Y	Y	-0.13	0.97	IN
39	Q	Q	0.18	0.05	IN
40	I	I	0.33	0.70	IN
41	P	P	0.40	0.17	IN
42	S	(P.Aer) SVDSA-N	0.70	0.05	IN
43	V	V	1.04	0.82	IN
44	D	D	1.08	0.23	IN
45	S	S	1.02	0.10	IN
46	A	A	1.06	0.13	IN
47	D	D	0.95	0.07	IN
48	N	(P.Aer) +NLSE	1.01	0.10	IN
49	L	(myelo) LSEK +P.Aer and S.Aur and S.Malt LSEKL	0.54	0.68	IN
50	S	S	0.50	0.06	IN
51	E	S.Malt EKLERE	0.43	0.04	IN
52	K	K	0.44	0.85	IN
53	L	L	0.12	0.97	IN
54	E	E	0.56	0.02	IN
55	R	R	0.49	0.26	IN
56	E	E	0.56	0.03	IN
57	W	W	0.22	0.53	IN
58	D	D	0.45	0.02	IN
59	R	(P.Aer) RELAS	0.43	0.75	IN
60	E	E	0.53	0.03	IN
61	L	L	0.56	0.95	IN
62	A	A	1.00	0.16	IN
63	S	S	0.84	0.18	IN
64	K	K	0.89	0.60	IN
65	K	K	0.56	0.31	IN
66	N	N	0.53	0.03	IN
67	P	P	0.51	0.02	IN
68	K	K	0.31	0.28	IN
69	L	L	-0.11	0.80	IN
70	I	I	-0.43	0.19	IN
71	N	(P.Aer) NALR	-0.83	0.03	IN
72	A	A	-1.11	0.15	IN
73	L	L	-1.61	0.82	IN
74	R	(prot) RRC F F F P.Aer RRCFF S.Aur RCFF S.Malt RR FF	-1.81	0.69	IN
75	R	R	-1.92	0.11	IN
76	C	C	-2.00	0.03	IN
77	F	F	-2.28	0.05	IN
78	F	(P.Aer) FWRF+ Y	-2.29	0.06	IN
79	W	(P.Aer) WRFM (rheum) WRF+F	-2.56	0.11	IN
80	R	R	-2.62	0.05	IN
81	F	F	-2.46	0.89	IN
82	M	(P.Aer) MFYG	-2.40	0.09	IN
83	F	(BPI) F+G F L EV K	-2.34	0.11	IN
84	Y	Y	-2.43	0.85	TM
85	G	G	-2.54	0.06	TM
86	I	I	-2.46	0.24	TM
87	F	S.Malt FLYLG	-2.12	0.34	TM
88	L	(P.Aer) LYLG+VT	-1.65	0.63	TM
89	Y	Y	-1.50	0.96	TM
90	L	(myelo)LGEV L L	-1.35	0.97	TM
91	G	G	-0.97	0.13	TM
92	E	E	-0.63	0.02	TM
93	V	(BPI) VT AV P	-0.17	0.86	TM
94	T	T	0.18	0.03	TM
95	K	K	0.46	0.97	TM
96	A	A	0.14	0.80	TM
97	V	V	-0.24	0.92	TM
98	Q	(P.Aer) QPLL-GRI	-0.57	0.03	TM
99	P	P	-0.72	0.04	TM
100	L	L	-0.84	0.94	TM
101	L	S.Malt LLGR+I S	-1.09	0.78	TM
102	L	L	-1.36	0.20	TM
103	G	G	-1.58	0.05	TM
104	R	R	-1.46	0.21	TM
105	I	I	-1.09	0.61	TM
106	I	I	-0.49	0.54	TM
107	A	S.Malt A YDPDN E ERS+ and A YDPD S.Aur ASYD and A YDPD S.Malt ASYDP DN and AS DPDN P.Aer A YDPD and ASYD D and ASYD P EE	0.07	0.72	EXT
108	S	P.Aer SYDPD N E R S.Aur SY DP++KE and SY D DNKE and SYDP EE S.Malt SYDPD	0.49	0.09	EXT
109	Y	(prot) YD +NK (P.Aer) YDPD and YD KEER S.Aur Y PD NKEE and YD +NKE+ and YDPD EE and YD +NKE+ and YDP DNK	0.87	0.98	EXT
110	D	S.Aureus DPDNKE and DP++ EER and +PD KEE and D KEER and DPD NKE and D DNKE S.Malt DPDN ER	1.31	0.02	EXT
111	P	(myelo) PD +ERS S.Malt P+ KEER and PDNK+ R P.Aer PDNKE and P+NK ER S.Aur PD KEER	1.77	0.26	EXT
112	D	S.Aur DNKE+R and DNKEE P.Aer D KEER	2.06	0.03	EXT
113	N	S.Aur and S.Malt NKEER P.Aer NK+ER	2.02	0.03	EXT
114	K	K	2.03	0.27	EXT
115	E	E	1.42	0.08	EXT
116	E	E	1.14	0.03	EXT
117	R	R	0.41	0.38	EXT
118	S	S	-0.05	0.04	EXT
119	I	(S.Aur) IAI LG G S.Malt IAI LGIG	-0.61	0.11	EXT
120	A	(GAD65) A LGIG	-0.77	0.03	EXT
121	I	I	-1.24	0.32	TM
122	Y	Y	-1.31	0.69	TM
123	L	(GAD65) LGIG (S.Malt) LGIGL	-1.83	0.76	TM
124	G	G	-1.76	0.06	TM
125	I	I	-2.19	0.40	TM
126	G	G	-2.35	0.03	TM
127	L	S.Malt LCLLF	-2.68	0.17	TM
128	C	C	-2.71	0.03	TM
129	L	L	-2.98	0.76	TM
130	L	(myelo) L TLLL	-2.78	0.81	TM
131	F	F	-2.85	0.12	TM
132	I	S.Malt IVRTLL	-2.82	0.15	TM
133	V	V	-3.02	0.40	TM
134	R	R	-2.81	0.57	TM
135	T	T	-2.30	0.07	TM
136	L	(P.Aer) LLLH-A	-1.82	0.91	TM
137	L	L	-1.43	0.97	TM
138	L	L	-1.33	0.79	TM
139	H	H	-1.58	0.03	TM
140	P	P	-1.56	0.05	TM
141	A	A	-1.48	0.38	TM
142	I	I	-1.15	0.39	TM
143	F	F	-0.93	0.89	TM
144	G	G	-1.22	0.03	IN
145	L	L	-1.19	0.96	IN
146	H	H	-1.39	0.15	IN
147	H	(P.Aer) HIGM	-1.21	0.18	IN
148	I	I	-1.14	0.58	IN
149	G	G	-1.13	0.05	IN
150	M	M	-1.16	0.35	IN
151	Q	Q	-1.23	0.03	IN
152	M	M	-1.37	0.96	IN
153	R	R	-1.43	0.04	IN
154	I	I	-1.55	0.23	IN
155	A	A	-1.72	0.03	IN
156	M	(mucin) MF L IYK	-2.06	0.05	IN
157	F	F	-1.98	0.39	IN
158	S	S	-1.90	0.02	IN
159	L	L	-1.52	0.57	IN
160	I	I	-1.31	0.32	IN
161	Y	Y	-1.38	0.95	IN
162	K	K	-1.02	0.69	IN
163	K	(P.Aer) KT KLSS	-1.23	0.97	IN
164	T	T	-0.77	0.04	IN
165	L	(rheum) LKLSS S.Aur amd P.Aer LKLSS S.Malt LKLS	-0.44	0.92	IN
166	K	(P.Aer) KLSS (rheum) KLSS	-0.28	0.67	IN
167	L	L	-0.48	0.97	IN
168	S	S	-0.80	0.09	IN
169	S	S	-0.79	0.03	IN
170	R	R	-0.44	0.65	IN
171	V	V	-0.69	0.44	IN
172	L	L	-0.33	0.90	IN
173	D	D	-0.62	0.03	IN
174	K	K	-0.61	0.55	IN
175	I	I	-0.59	0.39	IN
176	S	(P.Aer) SIG LVS	-0.67	0.02	IN
177	I	I	-0.60	0.46	IN
178	G	G	-0.77	0.22	IN
179	Q	Q	-1.14	0.32	IN
180	L	(P.Aer) +LVSLLS	-1.19	0.61	IN
181	V	VSLL	-1.22	0.42	IN
182	S	S.Malt SLLSN+	-0.95	0.08	IN
183	L	L	-0.88	0.83	IN
184	L	(P.Aer) LSNNL	-1.12	0.84	IN
185	S	(rheum) SNNL	-0.83	0.03	IN
186	N	N	-0.57	0.04	IN
187	N	N	-0.67	0.03	IN
188	L	L	-0.11	0.95	IN
189	N	N	0.31	0.04	IN
190	K	K	0.41	0.76	IN
191	F	(P.Aer) FDE-LA [FDEG]	0.09	0.96	IN
192	D	(P.Aer) DEGL	-0.09	0.02	IN
193	E	(P.Aer) +GLALAH	-0.19	0.03	IN
194	G	G	-0.35	0.02	IN
195	L	(P.Aer) LALAHF	-0.52	0.81	IN
196	A	A	-0.64	0.04