YPIA - BACSU - GREMLIN Contacts

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YPIA - TPR repeat-containing protein YpiA

UniProt:	P54389	Sequences: MNTLIQEAIKLVEAGETEKGLNTLSKAEKQLHDEDKAIAAQLYYEWGDVEKAISLISDLHDLYPNETELTNFYAELLIDIDEEEKALAVLETIPETDPSYPESLLLMADLYQMQGLFEVSEQKLFQAKSILDNEPVIDFALGELYFAQGAYAKAVQYFKTTAEEQSEIGGVNVHQRLAESLSASGEFEDAIPWYEKAVDENPDPNTIFGYGFTALQAGLVKTAIKQLSDLKELDPSYTSLYMPLSKSYEAEGMYEEALKTAKEGIRYDEYNKELFLYAAKMALKIGKSEEGKKLLQEALALDPGFVEALHTLLAVYHKEEDYDQIIDLIQEVRSYGEEDPKYNWYLASAYTELEQYEEAKQSFEAAYLHYREDRDFLYEYASFLLEEGLQKEALPLLKKVLEMDGANEELEETILRIEDEFSR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	423 (355)
Sequences:	9538 (8438)
Seq/√Len:	447.8

ECOLI - PGAA HEMY LPSRP BCSC YPHG
BACSU - YPIA YVCD RAPE RAPB RAPH RAPA
SULSO - Q97VC4 Q97V36 Q97WM3

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
253_M	256_E	5.177	1.00
355_Q	358_E	4.673	1.00
287_K	290_E	4.612	1.00
219_L	222_T	4.596	1.00
321_D	324_Q	4.563	1.00
150_A	153_K	4.191	1.00
186_E	189_D	4.156	1.00
82_E	85_K	3.959	1.00
389_L	392_E	3.826	1.00
116_L	119_V	3.710	1.00
245_S	261_A	3.334	1.00
211_G	227_L	2.900	1.00
279_A	295_L	2.725	1.00
178_A	194_Y	2.512	1.00
275_F	294_L	2.420	1.00
313_L	329_I	2.399	1.00
343_N	362_S	2.397	1.00
194_Y	209_G	2.359	1.00
278_A	294_L	2.314	1.00
381_A	397_L	2.273	1.00
174_H	193_W	2.220	1.00
48_D	51_K	2.205	1.00
347_A	363_F	2.195	1.00
108_A	124_L	2.143	1.00
142_G	158_F	2.119	1.00
380_Y	384_L	2.081	1.00
262_K	278_A	2.078	1.00
309_L	328_L	2.058	1.00
228_S	244_L	2.053	1.00
241_Y	260_T	2.048	1.00
248_Y	256_E	1.972	1.00
107_M	111_Y	1.961	1.00
227_L	243_P	1.959	1.00
295_L	311_T	1.906	1.00
195_E	210_Y	1.899	1.00
210_Y	226_Q	1.894	1.00
292_K	296_Q	1.894	1.00
73_Y	77_L	1.869	1.00
330_Q	346_L	1.857	1.00
282_A	290_E	1.856	1.00
296_Q	312_L	1.855	1.00
329_I	345_Y	1.833	1.00
214_A	222_T	1.809	1.00
312_L	316_Y	1.803	1.00
261_A	277_Y	1.803	1.00
326_I	330_Q	1.802	1.00
248_Y	260_T	1.797	1.00
214_A	226_Q	1.744	1.00
159_K	177_L	1.737	1.00
278_A	282_A	1.732	1.00
207_I	226_Q	1.727	1.00
282_A	294_L	1.700	1.00
138_D	157_Y	1.694	1.00
74_A	90_L	1.687	1.00
258_L	285_I	1.679	1.00
298_A	308_A	1.670	1.00
210_Y	214_A	1.655	1.00
258_L	282_A	1.629	1.00
350_Y	358_E	1.602	1.00
258_L	262_K	1.601	1.00
224_I	228_S	1.599	1.00
224_I	251_E	1.576	1.00
292_K	312_L	1.571	1.00
346_L	350_Y	1.564	1.00
158_F	176_R	1.562	1.00
264_G	274_L	1.554	1.00
350_Y	355_Q	1.554	1.00
224_I	247_S	1.551	1.00
177_L	181_L	1.546	1.00
346_L	362_S	1.538	1.00
292_K	316_Y	1.530	1.00
141_L	145_Y	1.526	1.00
248_Y	253_M	1.519	1.00
244_L	248_Y	1.518	1.00
326_I	350_Y	1.517	1.00
258_L	281_M	1.511	1.00
224_I	244_L	1.497	1.00
292_K	319_E	1.489	1.00
145_Y	157_Y	1.476	1.00
208_F	243_P	1.472	1.00
77_L	85_K	1.451	1.00
363_F	379_E	1.450	1.00
316_Y	321_D	1.421	1.00
224_I	248_Y	1.400	1.00
181_L	189_D	1.392	1.00
326_I	353_L	1.381	1.00
121_E	125_F	1.380	1.00
360_K	364_E	1.380	1.00
255_E	285_I	1.374	1.00
364_E	380_Y	1.364	1.00
377_L	396_L	1.355	1.00
347_A	366_A	1.350	1.00
191_I	217_A	1.344	1.00
244_L	260_T	1.328	1.00
214_A	219_L	1.322	1.00
272_K	298_A	1.318	1.00
299_L	309_L	1.315	1.00
145_Y	153_K	1.311	1.00
350_Y	362_S	1.310	1.00
258_L	278_A	1.309	1.00
312_L	328_L	1.305	1.00
111_Y	123_K	1.301	1.00
384_L	392_E	1.298	1.00
181_L	193_W	1.289	1.00
280_K	295_L	1.288	1.00
241_Y	264_G	1.274	1.00
360_K	384_L	1.267	1.00
344_W	348_S	1.265	1.00
191_I	195_E	1.244	1.00
221_K	251_E	1.230	1.00
191_I	210_Y	1.223	1.00
326_I	349_A	1.222	1.00
292_K	315_V	1.220	1.00
155_V	159_K	1.213	1.00
178_A	190_A	1.207	1.00
316_Y	328_L	1.196	1.00
297_E	300_A	1.190	1.00
155_V	181_L	1.186	1.00
191_I	214_A	1.182	1.00
242_M	277_Y	1.181	1.00
90_L	106_L	1.180	1.00
181_L	186_E	1.176	1.00
275_F	297_E	1.174	1.00
360_K	383_F	1.173	1.00
211_G	223_A	1.168	1.00
299_L	308_A	1.163	1.00
121_E	145_Y	1.159	1.00
316_Y	324_Q	1.158	1.00
279_A	298_A	1.156	1.00
197_A	206_T	1.155	1.00
230_L	240_L	1.151	1.00
241_Y	263_E	1.148	1.00
332_V	342_Y	1.143	1.00
323_D	353_L	1.140	1.00
351_T	363_F	1.139	1.00
378_Y	382_S	1.138	1.00
302_D	305_F	1.137	1.00
333_R	343_N	1.134	1.00
282_A	287_K	1.129	1.00
104_L	123_K	1.126	1.00
53_I	57_S	1.126	1.00
256_E	259_K	1.125	1.00
276_L	311_T	1.123	1.00
343_N	365_A	1.110	1.00
174_H	196_K	1.107	1.00
268_D	271_N	1.105	1.00
188_E	217_A	1.104	1.00
317_H	329_I	1.101	1.00
175_Q	209_G	1.099	1.00
178_A	197_A	1.092	1.00
77_L	89_V	1.084	1.00
313_L	332_V	1.083	1.00
77_L	82_E	1.080	1.00
358_E	361_Q	1.073	1.00
245_S	264_G	1.070	1.00
108_A	127_A	1.069	1.00
211_G	230_L	1.065	1.00
177_L	193_W	1.065	1.00
43_Y	51_K	1.064	1.00
314_A	345_Y	1.060	1.00
207_I	229_D	1.049	1.00
348_S	379_E	1.035	1.00
220_V	247_S	1.032	1.00
111_Y	119_V	1.028	1.00
331_E	334_S	1.022	1.00
74_A	93_I	1.022	1.00
155_V	177_L	1.017	1.00
124_L	140_A	1.014	1.00
191_I	213_T	1.013	1.00
171_V	197_A	1.012	1.00
336_G	339_D	1.011	1.00
222_T	225_K	1.007	1.00
296_Q	316_Y	1.006	1.00
290_E	293_K	1.005	1.00
326_I	346_L	1.001	1.00
145_Y	150_A	0.995	1.00
215_L	247_S	0.991	1.00
394_L	398_K	0.988	1.00
126_Q	130_I	0.987	1.00
138_D	160_T	0.977	1.00
384_L	396_L	0.977	1.00
310_H	345_Y	0.975	1.00
105_L	109_D	0.972	1.00
373_D	376_F	0.972	1.00
108_A	120_S	0.969	1.00
234_D	237_Y	0.966	1.00
231_K	240_L	0.966	1.00
155_V	184_S	0.965	1.00
384_L	389_L	0.965	1.00
279_A	294_L	0.963	1.00
111_Y	116_L	0.963	1.00
125_F	141_L	0.962	1.00
56_I	72_F	0.954	1.00
70_T	89_V	0.949	1.00
313_L	325_I	0.946	1.00
142_G	161_T	0.945	1.00
360_K	380_Y	0.944	1.00
152_A	184_S	0.940	1.00
246_K	277_Y	0.938	1.00
344_W	379_E	0.937	1.00
348_S	363_F	0.933	1.00
87_L	91_E	0.933	1.00
276_L	280_K	0.928	1.00
91_E	107_M	0.925	1.00
322_Y	349_A	0.920	1.00
351_T	383_F	0.920	1.00
380_Y	396_L	0.919	1.00
71_N	74_A	0.918	1.00
343_N	369_H	0.910	1.00
198_V	210_Y	0.907	1.00
360_K	387_E	0.903	1.00
362_S	365_A	0.902	1.00
153_K	156_Q	0.900	1.00
127_A	137_I	0.895	1.00
279_A	291_G	0.890	1.00
180_S	184_S	0.889	1.00
283_L	295_L	0.888	1.00
288_S	315_V	0.887	1.00
331_E	335_Y	0.886	1.00
187_F	213_T	0.881	1.00
238_T	264_G	0.881	1.00
309_L	331_E	0.871	1.00
366_A	376_F	0.865	1.00
142_G	154_A	0.862	1.00
249_E	261_A	0.862	1.00
265_I	274_L	0.854	1.00
208_F	212_F	0.854	1.00
231_K	241_Y	0.851	1.00
365_A	368_L	0.849	1.00
254_Y	281_M	0.847	1.00
190_A	213_T	0.843	1.00
42_L	45_E	0.840	1.00
383_F	387_E	0.839	1.00
349_A	353_L	0.836	1.00
119_V	122_Q	0.834	1.00
348_S	351_T	0.830	1.00
74_A	86_A	0.829	1.00
110_L	114_Q	0.824	1.00
310_H	314_A	0.824	1.00
330_Q	358_E	0.823	1.00
245_S	260_T	0.822	1.00
229_D	232_E	0.820	1.00
175_Q	206_T	0.818	1.00
333_R	346_L	0.815	1.00
283_L	311_T	0.813	1.00
363_F	383_F	0.813	1.00
265_I	275_F	0.812	1.00
57_S	73_Y	0.811	1.00
263_E	266_R	0.803	1.00
106_L	109_D	0.803	1.00
72_F	75_E	0.801	1.00
358_E	362_S	0.799	1.00
324_Q	327_D	0.798	1.00
213_T	217_A	0.798	1.00
207_I	233_L	0.798	1.00
207_I	230_L	0.797	1.00
127_A	131_L	0.791	1.00
128_K	138_D	0.791	1.00
59_L	63_Y	0.791	1.00
179_E	209_G	0.790	1.00
309_L	332_V	0.788	1.00
159_K	189_D	0.787	1.00
385_L	397_L	0.786	1.00
313_L	345_Y	0.782	1.00
276_L	308_A	0.781	1.00
121_E	148_Q	0.780	1.00
376_F	379_E	0.777	1.00
322_Y	326_I	0.777	1.00
298_A	301_L	0.774	1.00
182_S	194_Y	0.774	1.00
246_K	261_A	0.772	1.00
59_L	69_L	0.771	1.00
139_F	143_E	0.771	1.00
256_E	260_T	0.769	1.00
230_L	233_L	0.769	1.00
292_K	321_D	0.766	1.00
315_V	319_E	0.765	1.00
226_Q	229_D	0.765	1.00
53_I	80_I	0.764	1.00
392_E	395_P	0.763	1.00
361_Q	365_A	0.762	1.00
226_Q	230_L	0.761	1.00
297_E	301_L	0.759	1.00
223_A	247_S	0.759	1.00
224_I	253_M	0.755	1.00
198_V	207_I	0.755	1.00
317_H	345_Y	0.754	1.00
247_S	251_E	0.751	1.00
283_L	315_V	0.750	1.00
228_S	248_Y	0.750	1.00
280_K	311_T	0.748	1.00
275_F	298_A	0.748	1.00
198_V	206_T	0.747	1.00
293_K	297_E	0.746	1.00
87_L	114_Q	0.745	1.00
228_S	256_E	0.744	1.00
245_S	257_A	0.744	1.00
262_K	282_A	0.744	1.00
87_L	107_M	0.744	1.00
294_L	297_E	0.742	1.00
201_N	204_P	0.742	1.00
225_K	229_D	0.741	1.00
317_H	349_A	0.739	1.00
121_E	141_L	0.737	1.00
215_L	227_L	0.734	1.00
85_K	88_A	0.734	1.00
161_T	164_E	0.727	1.00
50_E	53_I	0.724	1.00
179_E	194_Y	0.723	1.00
135_P	161_T	0.722	1.00
78_I	86_A	0.719	1.00
87_L	111_Y	0.719	1.00
310_H	342_Y	0.718	1.00
159_K	163_E	0.717	1.00
306_V	332_V	0.710	1.00
343_N	366_A	0.709	1.00
102_E	106_L	0.708	1.00
83_E	86_A	0.706	1.00
162_A	174_H	0.706	1.00
249_E	281_M	0.705	1.00
155_V	180_S	0.703	1.00
178_A	193_W	0.703	1.00
365_A	369_H	0.702	1.00
311_T	314_A	0.699	1.00
379_E	382_S	0.698	1.00
242_M	264_G	0.698	1.00
211_G	226_Q	0.696	1.00
215_L	250_A	0.696	1.00
238_T	268_D	0.694	1.00
296_Q	324_Q	0.693	1.00
357_E	387_E	0.692	1.00
192_P	196_K	0.692	1.00
55_L	59_L	0.689	1.00
104_L	130_I	0.688	1.00
89_V	92_T	0.688	1.00
322_Y	353_L	0.688	1.00
364_E	392_E	0.688	1.00
332_V	335_Y	0.687	1.00
345_Y	348_S	0.687	1.00
51_K	57_S	0.685	1.00
381_A	393_A	0.685	1.00
146_F	158_F	0.683	1.00
237_Y	240_L	0.683	1.00
112_Q	140_A	0.682	1.00
275_F	301_L	0.681	1.00
157_Y	161_T	0.680	1.00
104_L	126_Q	0.679	1.00
254_Y	258_L	0.678	1.00
89_V	93_I	0.677	1.00
249_E	254_Y	0.676	1.00
162_A	177_L	0.672	1.00
138_D	164_E	0.671	1.00
160_T	164_E	0.666	1.00
179_E	183_A	0.664	1.00
261_A	281_M	0.663	1.00
51_K	54_S	0.662	1.00
193_W	197_A	0.660	1.00
340_P	366_A	0.660	1.00
262_K	290_E	0.655	1.00
351_T	356_Y	0.655	1.00
328_L	331_E	0.653	1.00
360_K	363_F	0.653	1.00
328_L	332_V	0.651	1.00
193_W	196_K	0.651	1.00
347_A	362_S	0.650	1.00
333_R	342_Y	0.646	0.99
277_Y	311_T	0.646	0.99
123_K	127_A	0.645	0.99
347_A	359_A	0.645	0.99
189_D	192_P	0.642	0.99
347_A	383_F	0.642	0.99
282_A	285_I	0.642	0.99
241_Y	275_F	0.641	0.99
212_F	243_P	0.640	0.99
70_T	93_I	0.639	0.99
283_L	288_S	0.635	0.99
330_Q	350_Y	0.635	0.99
309_L	335_Y	0.633	0.99
367_Y	376_F	0.630	0.99
195_E	214_A	0.629	0.99
71_N	75_E	0.627	0.99
174_H	197_A	0.620	0.99
43_Y	48_D	0.619	0.99
392_E	396_L	0.619	0.99
317_H	352_E	0.619	0.99
78_I	83_E	0.618	0.99
125_F	129_S	0.617	0.99
42_L	46_W	0.616	0.99
144_L	148_Q	0.615	0.99
360_K	389_L	0.615	0.99
326_I	355_Q	0.614	0.99
260_T	263_E	0.614	0.99
143_E	147_A	0.614	0.99
105_L	108_A	0.614	0.99
229_D	233_L	0.612	0.99
262_K	266_R	0.608	0.99
201_N	206_T	0.606	0.99
305_F	308_A	0.606	0.99
351_T	379_E	0.606	0.99
212_F	215_L	0.605	0.99
87_L	110_L	0.605	0.99
156_Q	160_T	0.604	0.99
196_K	199_D	0.602	0.99
288_S	319_E	0.600	0.99
366_A	369_H	0.600	0.99
363_F	380_Y	0.599	0.99
53_I	76_L	0.598	0.99
220_V	251_E	0.597	0.99
195_E	222_T	0.596	0.99
44_Y	49_V	0.596	0.99
227_L	244_L	0.596	0.99
152_A	156_Q	0.595	0.99
126_Q	129_S	0.593	0.99
364_E	384_L	0.593	0.99
197_A	200_E	0.592	0.99
348_S	352_E	0.591	0.99
367_Y	371_R	0.590	0.99
246_K	249_E	0.590	0.99
329_I	346_L	0.590	0.99
385_L	390_Q	0.589	0.99
131_L	134_E	0.589	0.99
364_E	368_L	0.587	0.99
53_I	73_Y	0.586	0.99
374_R	381_A	0.586	0.99
182_S	213_T	0.586	0.99
281_M	285_I	0.585	0.99
299_L	312_L	0.585	0.99
308_A	311_T	0.585	0.99
191_I	219_L	0.584	0.99
276_L	298_A	0.584	0.99
376_F	380_Y	0.583	0.99
139_F	176_R	0.583	0.99
128_K	131_L	0.580	0.99
140_A	143_E	0.578	0.99
70_T	73_Y	0.577	0.99
296_Q	300_A	0.577	0.99
104_L	111_Y	0.576	0.99
380_Y	383_F	0.574	0.99
295_L	315_V	0.572	0.99
313_L	346_L	0.571	0.99
97_D	100_Y	0.571	0.99
57_S	61_D	0.571	0.99
220_V	224_I	0.570	0.99
76_L	80_I	0.570	0.99
317_H	322_Y	0.570	0.99
242_M	246_K	0.568	0.99
263_E	267_Y	0.567	0.99
77_L	80_I	0.565	0.99
101_P	127_A	0.565	0.99
94_P	98_P	0.565	0.99
67_T	74_A	0.564	0.99
289_E	319_E	0.563	0.99
75_E	79_D	0.561	0.99
56_I	60_H	0.560	0.99
215_L	220_V	0.558	0.99
43_Y	55_L	0.557	0.99
237_Y	271_N	0.556	0.99
367_Y	380_Y	0.555	0.98
63_Y	66_E	0.553	0.98
317_H	348_S	0.552	0.98
60_H	63_Y	0.551	0.98
160_T	163_E	0.551	0.98
46_W	50_E	0.550	0.98
92_T	95_E	0.550	0.98
122_Q	126_Q	0.550	0.98
118_E	148_Q	0.549	0.98
189_D	193_W	0.549	0.98
175_Q	179_E	0.548	0.98
151_Y	184_S	0.547	0.98
370_Y	373_D	0.547	0.98
261_A	265_I	0.546	0.98
70_T	92_T	0.545	0.98
257_A	281_M	0.544	0.98
146_F	151_Y	0.543	0.98
322_Y	352_E	0.542	0.98
182_S	209_G	0.540	0.98
377_L	381_A	0.538	0.98
330_Q	334_S	0.537	0.98
182_S	187_F	0.537	0.98
290_E	294_L	0.536	0.98
271_N	274_L	0.535	0.98
291_G	295_L	0.534	0.98
314_A	348_S	0.533	0.98
58_D	62_L	0.532	0.98
265_I	278_A	0.531	0.98
109_D	140_A	0.531	0.98
181_L	184_S	0.530	0.98
260_T	264_G	0.530	0.98
309_L	316_Y	0.530	0.98
59_L	62_L	0.529	0.98
154_A	180_S	0.528	0.98
161_T	173_V	0.527	0.98
102_E	105_L	0.527	0.98
310_H	329_I	0.525	0.98
53_I	56_I	0.524	0.98
344_W	376_F	0.523	0.98
88_A	91_E	0.523	0.98
87_L	90_L	0.523	0.98
170_G	174_H	0.523	0.98
326_I	329_I	0.522	0.98
356_Y	360_K	0.522	0.98
176_R	179_E	0.521	0.98
139_F	173_V	0.521	0.98
55_L	58_D	0.521	0.98
382_S	386_E	0.520	0.98
277_Y	281_M	0.520	0.98
243_P	277_Y	0.519	0.98
378_Y	381_A	0.519	0.98
167_E	170_G	0.517	0.98
302_D	308_A	0.516	0.98
192_P	195_E	0.516	0.98
249_E	277_Y	0.516	0.98
222_T	226_Q	0.516	0.98
196_K	200_E	0.516	0.98
194_Y	210_Y	0.515	0.98
272_K	305_F	0.513	0.97
50_E	57_S	0.512	0.97
314_A	318_K	0.510	0.97
351_T	386_E	0.510	0.97
91_E	94_P	0.509	0.97
227_L	247_S	0.509	0.97
381_A	396_L	0.509	0.97
271_N	275_F	0.507	0.97
107_M	110_L	0.506	0.97
157_Y	160_T	0.505	0.97
194_Y	206_T	0.505	0.97
390_Q	393_A	0.505	0.97
329_I	349_A	0.502	0.97
241_Y	267_Y	0.502	0.97
143_E	176_R	0.501	0.97
359_A	363_F	0.500	0.97
52_A	56_I	0.500	0.97

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
1w3bA	2	0.9149	100	0.143	Contact Map
4ui9J	2	0.9882	100	0.168	Contact Map
4ui9C	2	0.9858	100	0.184	Contact Map
2xpiA	2	0.9811	100	0.19	Contact Map
4ui9X	2	0.9764	100	0.195	Contact Map
4rg9A	2	0.8534	100	0.201	Contact Map
4kvmA	3	1	100	0.23	Contact Map
4bujB	1	0.9929	100	0.242	Contact Map
2gw1A	2	0.9858	100	0.256	Contact Map
3fp2A	1	0.9149	100	0.257	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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