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	TM
197	L	L	-1.13	0.79	TM
198	A	A	-1.59	0.72	TM
199	H	H	-1.90	0.03	TM
200	F	F	-1.64	0.27	TM
201	V	V	-1.55	0.13	TM
202	W	(myelo) W+ PLQV S.Malt� WIAPL +AL	-1.40	0.92	TM
203	I	S.Malt IAPLQVA	-1.16	0.14	TM
204	A	A	-1.25	0.06	TM
205	P	(GAD65) PLQ�� L� L+ E� L+Q	-1.07	0.03	TM
206	L	(P.Aer) L+VALL	-1.23	0.97	TM
207	Q	S.Malt� QVALLM� I	-1.24	0.04	TM
208	V	(P.Aer) V LLMG [VALL](S.Malt) VALLM L	-1.38	0.86	TM
209	A	(P.Aer) A-LMGL	-1.46	0.05	TM
210	L	L	-1.84	0.73	TM
211	L	(P.Aer) LMGLI	-1.88	0.85	TM
212	M	(S.Malt) MG I ELLQ	-2.38	0.82	TM
213	G	G	-2.16	0.05	TM
214	L	L	-2.34	0.23	TM
215	I	I	-2.21	0.08	TM
216	W	S.Malt WELLQAS S.Aur W+LLQ P.Aer WELL+	-1.84	0.56	EXT
217	E	S.Malt� ELLQA	-1.53	0.02	EXT
218	L	L	-1.33	0.96	EXT
219	L	L	-1.08	0.91	TM
220	Q	(P.Aer) QAS-AFCG+G [QASAF]	-1.12	0.05	TM
221	A	A	-0.89	0.64	TM
222	S	S	-0.88	0.23	TM
223	A	A	-0.90	0.25	TM
224	F	(prot) FCG G LI	-0.60	0.45	TM
225	C	C	-1.02	0.03	TM
226	G	(myelo) LG L V�� FQ�� GR ++ + +�� R�� I�� L�� SEM E (P.Aer) GLGFLIV [GLGFL VL ]	-1.40	0.03	TM
227	L	L	-1.96	0.26	TM
228	G	G	-2.17	0.03	TM
229	F	(myelo) +L V AL	-2.31	0.08	TM
230	L	(Adren)� LIVLA (mucin) +LI LA	-2.38	0.24	TM
231	I	I	-2.74	0.17	TM
232	V	V	-2.71	0.22	TM
233	L	(P.Aer) LALF+A	-2.66	0.89	TM
234	A	A	-2.31	0.68	TM
235	L	L	-1.80	0.88	TM
236	F	F	-1.55	0.93	TM
237	Q	Q	-1.19	0.03	TM
238	A	A	-0.85	0.20	TM
239	G	G	-0.88	0.03	TM
240	L	S.Malt LGRMM	-0.79	0.64	TM
241	G	G	-0.77	0.02	TM
242	R	R	-0.86	0.16	IN
243	M	M	-0.93	0.50	IN
244	M	M	-0.98	0.11	IN
245	M	M	-0.59	0.77	IN
246	K	(P.Aer) KYRD+	-0.51	0.90	IN
247	Y	Y	-0.30	0.91	IN
248	R	R	-0.01	0.03	IN
249	D	(myelo) +Q A�� I ERL	0.36	0.03	IN
250	Q	(P.Aer) QRAG	0.75	0.03	IN
251	R	R	0.65	0.09	IN
252	A	A	0.85	0.08	IN
253	G	(hspd1)� GK+ E� VI T +� M�� IE� IQ (P.Aer) GKI ERLV	0.82	0.04	IN
254	K	K	0.63	0.28	IN
255	I	I	0.13	0.82	IN
256	S	S	-0.26	0.02	IN
257	E	(P.Aer) ERLV	-0.62	0.03	IN
258	R	R	-0.65	0.43	IN
259	L	(TNF) LV+ SE	-0.70	0.84	IN
260	V	V	-0.47	0.11	IN
261	I	I	-0.71	0.14	IN
262	T	T	-1.00	0.04	IN
263	S	S	-0.97	0.04	IN
264	E	E	-0.54	0.06	IN
265	M	M	-0.47	0.95	IN
266	I	S.Malt +IENIQ	-0.11	0.46	IN
267	E	E	-0.10	0.02	IN
268	N	N	-0.25	0.02	IN
269	I	I	-0.27	0.14	IN
270	Q	Q	-0.23	0.02	IN
271	S	S	-0.14	0.03	IN
272	V	V	-0.21	0.94	IN
273	K	K	-0.54	0.94	IN
274	A	A	-0.25	0.80	IN
275	Y	GAD65 Y WE� +� + + E L�� QT LK�� K�� RYFN	-0.17	0.51	IN
276	C	C	-0.20	0.02	IN
277	W	W	-0.21	0.90	IN
278	E	E	-0.21	0.02	IN
279	E	E	-0.14	0.03	IN
280	A	A	-0.17	0.04	IN
281	M	M	-0.36	0.19	IN
282	E	Calgran EK IE�� +	-0.09	0.02	IN
283	K	K	-0.18	0.53	IN
284	M	M	-0.56	0.21	IN
285	I	Adren ++NL Q E	-0.55	0.06	IN
286	E	E	-0.37	0.02	IN
287	N	N	-0.37	0.03	IN
288	L	(myelo) LR�� LKL RK	-0.19	0.68	IN
289	R	R	-0.32	0.45	IN
290	Q	Q	-0.06	0.03	IN
291	T	(P.Aer) TELKL	-0.40	0.09	IN
292	E	E	-0.40	0.03	IN
293	L	(myelo) LKL RK	-0.13	0.97	IN
294	K	K	-0.05	0.35	IN
295	L	L	-0.13	0.83	IN
296	T	(prot) TR A YV	-0.24	0.03	IN
297	R	R	-0.49	0.35	IN
298	K	K	-0.37	0.46	IN
299	A	(P.Aer) AAYV-Y	-0.46	0.09	IN
300	A	Adren A� RYF�� F	-0.29	0.06	IN
301	Y	Y	-0.60	0.57	IN
302	V	V	-0.52	0.72	IN
303	R	(P.Aer) R+FNSS (GAD65) RYFN	-0.52	0.15	IN
304	Y	Y	-0.39	0.96	TM
305	F	(mucin) FNSS	-0.42	0.23	TM
306	N	Adren N SAF	-0.65	0.02	TM
307	S	S	-0.81	0.03	TM
308	S	S	-1.05	0.17	TM
309	A	A	-0.87	0.29	TM
310	F	F	-0.60	0.96	TM
311	F	S.Malt FFSGF	-1.00	0.53	TM
312	F	F	-1.47	0.08	TM
313	S	S	-1.92	0.02	TM
314	G	(P.Aer) GFFVVFL	-2.20	0.05	TM
315	F	F	-2.24	0.45	TM
316	F	F	-2.29	0.44	TM
317	V	V	-2.06	0.29	TM
318	V	V	-2.21	0.95	TM
319	F	F	-2.43	0.92	TM
320	L	(mucin) LSV P	-2.11	0.61	TM
321	S	S	-1.85	0.04	TM
322	V	(P.Aer)� V-PYAL	-1.54	0.85	TM
323	L	L	-1.54	0.83	TM
324	P	P	-1.41	0.03	TM
325	Y	Y	-1.05	0.93	TM
326	A	(P.Aer) A-IKGI [ALIK I]	-0.99	0.11	TM
327	L	L	-1.15	0.44	EXT
328	I	I	-1.26	0.25	EXT
329	K	K	-1.66	0.46	EXT
330	G	G	-1.68	0.03	EXT
331	I	I	-1.74	0.62	EXT
332	I	I	-1.69	0.17	EXT
333	L	L	-1.72	0.32	EXT
334	R	R	-1.73	0.62	EXT
335	K	(P.Aer)� KIFTTIS	-1.68	0.92	EXT
336	I	I	-1.61	0.10	EXT
337	F	F	-1.33	0.06	EXT
338	T	T	-1.36	0.02	EXT
339	T	T	-1.45	0.06	EXT
340	I	I	-1.83	0.96	EXT
341	S	S	-1.89	0.07	EXT
342	F	F	-2.04	0.92	EXT
343	C	(S.Aur) CIVL	-2.09	0.03	EXT
344	I	I	-2.38	0.50	EXT
345	V	V	-2.22	0.13	EXT
346	L	L	-2.36	0.75	EXT
347	R	R	-1.86	0.47	EXT
348	M	M	-1.67	0.89	EXT
349	A	A	-1.05	0.08	EXT
350	V	V	-0.87	0.07	EXT
351	T	(prot) TR FP S.Malt TRQFP S.Aurand P.Aer� TR+FP	-0.34	0.03	EXT
352	R	P.Aer RQFP	-0.44	0.39	EXT
353	Q	Q	-0.09	0.03	EXT
354	F	F	-0.11	0.42	EXT
355	P	P	0.18	0.02	EXT
356	W	W	0.17	0.72	EXT
357	A	(P.Aer) AVQTW	0.00	0.05	EXT
358	V	V	-0.18	0.93	EXT
359	Q	Q	0.12	0.12	EXT
360	T	T	0.14	0.38	EXT
361	W	W	0.15	0.97	EXT
362	Y	Y	0.11	0.97	EXT
363	D	(HSPD1) DSL�� N� Q�� TL (TNF)� D L A IN�� D+L	0.16	0.04	EXT
364	S	S	-0.11	0.02	EXT
365	L	L	-0.13	0.38	EXT
366	G	(Mucin) G IN ++D�� F Q�� YKT E�� YNLT� +V	0.06	0.05	EXT
367	A	A	-0.09	0.07	EXT
368	I	I	-0.19	0.27	EXT
369	N	N	-0.23	0.03	EXT
370	K	K	-0.32	0.28	EXT
371	I	I	-0.65	0.88	EXT
372	Q	Calgran� Q+FL K E K�� N�� E +ME+	-0.57	0.10	EXT
373	D	D	-0.32	0.03	EXT
374	F	(GAD65) FLQ�� L+Y	-0.22	0.77	EXT
375	L	L	-0.07	0.38	EXT
376	Q	Q	0.08	0.03	EXT
377	K	K	0.08	0.77	EXT
378	Q	Q	0.06	0.29	EXT
379	E	E	0.08	0.03	EXT
380	Y	(mucin) YKT E�� YNLT� +V	0.47	0.80	EXT
381	K	K	0.28	0.42	EXT
382	T	T	0.27	0.04	EXT
383	L	L	-0.13	0.88	EXT
384	E	E	-0.21	0.03	EXT
385	Y	(mucin)YNLT� +V P.Aer� YN LTTT�� +V M S.Aur Y LT T+VV S.Malt YN T� EVV	-0.10	0.97	EXT
386	N	P.Aer NL TTE� VV S.Aur NLTTTE S.Malt NLTTT and NLTT E++	-0.03	0.03	EXT
387	L	(hspd1) LTT EVV P.Aer� L TT+VV S.Aur LTTT+	0.04	0.71	EXT
388	T	P.Aer and S.Malt TTTEV S.Aur TT� VVM S.Malt +TTTEV	0.09	0.03	EXT
389	T	P.Aer and S.Aur and S.Malt TTEVV	-0.20	0.08	EXT
390	T	P.Aer TEVVM S.Aur TEV+M S.Malt TE� VV M	-0.23	0.08	EXT
391	E	P.Aer and S.Aur EVVM S.Malt EV+M	-0.27	0.04	EXT
392	V	V	0.06	0.82	EXT
393	V	V	-0.10	0.16	EXT
394	M	M	-0.16	0.70	EXT
395	E	E	-0.33	0.02	EXT
396	N	N	-0.66	0.08	EXT
397	V	V	-0.68	0.15	EXT
398	T	T	-0.33	0.06	EXT
399	A	A	0.03	0.20	EXT
400	F	F	0.15	0.84	EXT
401	W	W	-0.07