YEDS - ECOLI - GREMLIN Contacts

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YEDS - Putative outer membrane protein YedS

UniProt:	P76335	Sequences: MKRKVLAMLVPALLVAGAANAAEVYNKDGNKLDLYGKVVGLHYFSDDSGSDGDMSYARIGFKGETQIADQFTGYGQWEFNIGANGPESDKGNTATRLAFAGLGFGQNGTFDYGRNYGVVYDVEAWTDMLPEFGGDTYAGADNFMNGRANGVATYRNNGFFGLVDGLNFALQYQGNNESGGPFGQEGSGSGDGRSLSKENGDGFGMSTSYDFDFGLSLGAAYXNSDRSDRQVGVGLNDRNHSNRNAGGETAEAWTVGAKYDANNVYLAAMYAETRNMTPYGGGEFDNGESRSAIANKTQNFEVVAQYQFDFGLRPSIAYLQSKGKDLGGWAHDGNGDPRYTNKDLVKYVDIGATYYFNKNMSTYVDYKINLLDNDDDFYEANGIATDDIVAVGLVYQF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG14042
Length:	397 (327)
Sequences:	5460 (3885)
Seq/√Len:	214.8

ECOLI - YEDS OMPN OMPC PHOE NMPC OMPF

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
35_Y	60_G	3.875	1.00
63_G	75_G	3.513	1.00
318_Y	346_K	3.449	1.00
72_T	103_G	3.422	1.00
76_Q	99_F	3.250	1.00
64_E	72_T	3.201	1.00
74_Y	101_G	3.109	1.00
264_V	306_Y	2.964	1.00
156_N	168_F	2.870	1.00
366_Y	387_D	2.719	1.00
219_A	253_W	2.522	1.00
270_Y	298_Q	2.474	1.00
312_L	352_A	2.471	1.00
121_D	153_T	2.452	1.00
154_Y	157_N	2.449	1.00
40_G	83_A	2.400	1.00
38_V	83_A	2.390	1.00
62_K	76_Q	2.360	1.00
272_E	298_Q	2.320	1.00
74_Y	109_T	2.317	1.00
74_Y	111_D	2.306	1.00
320_Q	346_K	2.304	1.00
313_R	355_Y	2.285	1.00
170_L	205_M	2.270	1.00
217_L	257_A	2.266	1.00
223_N	251_E	2.255	1.00
118_V	171_Q	2.252	1.00
356_F	362_T	2.227	1.00
353_T	361_S	2.208	1.00
34_L	61_F	2.193	1.00
168_F	207_T	2.191	1.00
361_S	394_V	2.141	1.00
308_F	314_P	2.134	1.00
97_L	116_Y	2.055	1.00
16_A	20_N	2.019	1.00
162_L	167_N	2.006	1.00
261_A	266_L	1.967	1.00
118_V	169_A	1.964	1.00
103_G	109_T	1.963	1.00
151_V	171_Q	1.944	1.00
167_N	208_S	1.920	1.00
71_F	102_L	1.914	1.00
35_Y	78_E	1.895	1.00
312_L	354_Y	1.892	1.00
114_R	149_N	1.890	1.00
219_A	255_V	1.882	1.00
71_F	106_Q	1.879	1.00
84_N	176_N	1.868	1.00
35_Y	76_Q	1.810	1.00
37_K	58_R	1.761	1.00
360_M	395_Y	1.723	1.00
362_T	393_L	1.709	1.00
110_F	152_A	1.694	1.00
112_Y	152_A	1.693	1.00
370_L	385_T	1.680	1.00
39_V	363_Y	1.672	1.00
79_F	93_T	1.662	1.00
92_N	149_N	1.630	1.00
314_P	352_A	1.620	1.00
221_Y	253_W	1.598	1.00
305_Q	313_R	1.595	1.00
74_Y	103_G	1.590	1.00
263_N	306_Y	1.580	1.00
35_Y	62_K	1.578	1.00
157_N	163_V	1.574	1.00
257_A	268_A	1.559	1.00
58_R	78_E	1.557	1.00
361_S	396_Q	1.538	1.00
215_L	259_Y	1.536	1.00
58_R	96_R	1.534	1.00
267_A	303_V	1.533	1.00
67_I	73_G	1.531	1.00
80_N	96_R	1.523	1.00
359_N	395_Y	1.518	1.00
223_N	249_T	1.496	1.00
155_R	169_A	1.459	1.00
59_I	79_F	1.449	1.00
266_L	304_A	1.449	1.00
66_Q	70_Q	1.442	1.00
311_G	352_A	1.423	1.00
217_L	255_V	1.422	1.00
211_F	214_G	1.416	1.00
368_I	385_T	1.416	1.00
34_L	59_I	1.412	1.00
72_T	105_G	1.398	1.00
111_D	153_T	1.365	1.00
82_G	87_E	1.364	1.00
78_E	96_R	1.355	1.00
258_K	267_A	1.352	1.00
318_Y	348_V	1.350	1.00
307_Q	313_R	1.347	1.00
152_A	174_G	1.346	1.00
111_D	155_R	1.344	1.00
107_N	154_Y	1.319	1.00
55_S	394_V	1.307	1.00
122_V	218_G	1.305	1.00
108_G	154_Y	1.303	1.00
126_T	216_S	1.302	1.00
368_I	387_D	1.300	1.00
173_Q	202_G	1.296	1.00
269_M	301_E	1.294	1.00
111_D	115_N	1.293	1.00
76_Q	97_L	1.284	1.00
210_D	216_S	1.283	1.00
115_N	151_V	1.281	1.00
74_Y	99_F	1.278	1.00
92_N	95_T	1.263	1.00
97_L	115_N	1.263	1.00
148_A	202_G	1.260	1.00
41_L	53_D	1.257	1.00
264_V	304_A	1.242	1.00
90_K	95_T	1.227	1.00
214_G	259_Y	1.224	1.00
65_T	357_N	1.224	1.00
317_A	349_D	1.223	1.00
304_A	316_I	1.219	1.00
258_K	265_Y	1.207	1.00
171_Q	204_G	1.203	1.00
260_D	265_Y	1.200	1.00
43_Y	390_A	1.199	1.00
71_F	107_N	1.198	1.00
151_V	173_Q	1.196	1.00
172_Y	203_F	1.182	1.00
107_N	110_F	1.182	1.00
311_G	355_Y	1.182	1.00
272_E	296_K	1.180	1.00
316_I	348_V	1.174	1.00
156_N	165_G	1.174	1.00
215_L	257_A	1.168	1.00
364_V	391_V	1.156	1.00
79_F	88_S	1.153	1.00
260_D	263_N	1.151	1.00
371_L	383_I	1.150	1.00
96_R	147_R	1.142	1.00
119_V	220_A	1.140	1.00
253_W	272_E	1.135	1.00
66_Q	72_T	1.133	1.00
264_V	268_A	1.132	1.00
109_T	153_T	1.127	1.00
309_D	312_L	1.122	1.00
41_L	390_A	1.118	1.00
37_K	396_Q	1.112	1.00
268_A	300_F	1.112	1.00
64_E	74_Y	1.110	1.00
10_V	13_L	1.103	1.00
73_G	100_A	1.103	1.00
32_L	75_G	1.103	1.00
308_F	312_L	1.099	1.00
38_V	81_I	1.098	1.00
320_Q	344_L	1.092	1.00
268_A	302_V	1.087	1.00
221_Y	251_E	1.086	1.00
99_F	111_D	1.079	1.00
363_Y	392_G	1.077	1.00
71_F	105_G	1.075	1.00
216_S	258_K	1.070	1.00
17_G	20_N	1.062	1.00
299_N	321_S	1.060	1.00
166_L	211_F	1.059	1.00
345_V	369_N	1.056	1.00
351_G	365_D	1.045	1.00
148_A	151_V	1.043	1.00
344_L	372_D	1.035	1.00
153_T	171_Q	1.031	1.00
4_K	8_M	1.030	1.00
46_D	387_D	1.029	1.00
315_S	353_T	1.027	1.00
58_R	147_R	1.023	1.00
345_V	371_L	1.023	1.00
364_V	389_V	1.022	1.00
322_K	344_L	1.020	1.00
77_W	94_A	1.013	1.00
170_L	203_F	1.009	1.00
315_S	351_G	1.008	1.00
167_N	210_D	1.006	1.00
206_S	220_A	1.003	1.00
254_T	271_A	1.000	1.00
348_V	368_I	0.999	1.00
70_Q	105_G	0.997	1.00
77_W	98_A	0.996	1.00
7_A	10_V	0.993	1.00
64_E	103_G	0.991	1.00
303_V	317_A	0.991	1.00
166_L	207_T	0.978	1.00
119_V	252_A	0.973	1.00
129_L	351_G	0.970	1.00
316_I	350_I	0.961	1.00
40_G	84_N	0.959	1.00
31_K	64_E	0.958	1.00
57_A	81_I	0.957	1.00
260_D	307_Q	0.952	1.00
65_T	359_N	0.947	1.00
6_L	10_V	0.944	1.00
128_M	317_A	0.942	1.00
298_Q	324_K	0.939	0.99
117_G	148_A	0.935	0.99
360_M	393_L	0.930	0.99
122_V	206_S	0.928	0.99
119_V	254_T	0.922	0.99
260_D	306_Y	0.920	0.99
355_Y	361_S	0.918	0.99
170_L	207_T	0.914	0.99
54_M	361_S	0.909	0.99
73_G	102_L	0.909	0.99
308_F	352_A	0.900	0.99
157_N	162_L	0.899	0.99
37_K	394_V	0.892	0.99
263_N	307_Q	0.891	0.99
55_S	396_Q	0.890	0.99
128_M	305_Q	0.889	0.99
173_Q	176_N	0.881	0.99
39_V	52_G	0.878	0.99
169_A	206_S	0.877	0.99
65_T	360_M	0.870	0.99
115_N	153_T	0.867	0.99
15_V	18_A	0.867	0.99
80_N	95_T	0.864	0.99
176_N	179_G	0.863	0.99
129_L	315_S	0.862	0.99
128_M	303_V	0.861	0.99
301_E	319_L	0.860	0.99
30_N	65_T	0.857	0.99
11_P	16_A	0.855	0.99
41_L	55_S	0.852	0.99
122_V	208_S	0.851	0.99
86_P	94_A	0.849	0.99
297_T	321_S	0.848	0.99
60_G	78_E	0.847	0.99
265_Y	305_Q	0.847	0.99
356_F	360_M	0.846	0.99
267_A	305_Q	0.843	0.99
55_S	361_S	0.842	0.99
156_N	170_L	0.841	0.99
9_L	12_A	0.840	0.99
218_G	256_G	0.837	0.99
103_G	106_Q	0.825	0.99
118_V	220_A	0.824	0.99
33_D	62_K	0.824	0.99
8_M	11_P	0.823	0.99
82_G	85_G	0.823	0.99
308_F	311_G	0.822	0.99
349_D	367_K	0.821	0.99
366_Y	389_V	0.819	0.99
68_A	357_N	0.815	0.99
250_A	273_T	0.813	0.99
298_Q	322_K	0.811	0.99
47_D	386_D	0.810	0.99
265_Y	307_Q	0.805	0.98
300_F	322_K	0.805	0.98
122_V	155_R	0.804	0.98
99_F	115_N	0.801	0.98
65_T	68_A	0.799	0.98
353_T	394_V	0.796	0.98
118_V	204_G	0.792	0.98
299_N	319_L	0.791	0.98
118_V	206_S	0.787	0.98
88_S	93_T	0.785	0.98
116_Y	120_Y	0.778	0.98
155_R	167_N	0.775	0.98
305_Q	315_S	0.774	0.98
253_W	298_Q	0.774	0.98
313_R	353_T	0.772	0.98
162_L	210_D	0.769	0.98
16_A	19_A	0.769	0.98
132_F	135_D	0.762	0.98
371_L	375_D	0.762	0.98
121_D	155_R	0.762	0.98
203_F	207_T	0.761	0.98
5_V	8_M	0.759	0.98
148_A	171_Q	0.756	0.98
153_T	169_A	0.754	0.98
119_V	204_G	0.753	0.98
273_T	297_T	0.752	0.98
129_L	317_A	0.749	0.98
126_T	256_G	0.746	0.97
7_A	11_P	0.744	0.97
125_W	208_S	0.739	0.97
59_I	93_T	0.738	0.97
66_Q	69_D	0.737	0.97
8_M	12_A	0.737	0.97
128_M	301_E	0.736	0.97
274_R	296_K	0.728	0.97
65_T	395_Y	0.725	0.97
150_G	176_N	0.725	0.97
198_E	225_D	0.712	0.97
5_V	9_L	0.711	0.97
377_F	380_A	0.708	0.97
46_D	383_I	0.705	0.96
270_Y	300_F	0.705	0.96
109_T	155_R	0.704	0.96
84_N	150_G	0.703	0.96
60_G	96_R	0.703	0.96
311_G	354_Y	0.702	0.96
261_A	264_V	0.701	0.96
114_R	147_R	0.699	0.96
310_F	354_Y	0.699	0.96
301_E	317_A	0.699	0.96
3_R	6_L	0.698	0.96
4_K	7_A	0.697	0.96
179_G	196_S	0.694	0.96
30_N	66_Q	0.690	0.96
9_L	13_L	0.690	0.96
58_R	80_N	0.685	0.96
365_D	390_A	0.684	0.96
15_V	20_N	0.680	0.96
123_E	254_T	0.678	0.96
350_I	366_Y	0.677	0.96
133_G	136_T	0.671	0.95
117_G	204_G	0.671	0.95
204_G	222_X	0.671	0.95
105_G	154_Y	0.670	0.95
370_L	384_A	0.670	0.95
168_F	205_M	0.668	0.95
116_Y	147_R	0.664	0.95
323_G	343_D	0.663	0.95
178_S	196_S	0.661	0.95
391_V	395_Y	0.659	0.95
100_A	357_N	0.653	0.95
122_V	169_A	0.653	0.95
70_Q	106_Q	0.651	0.94
208_S	218_G	0.650	0.94
4_K	15_V	0.650	0.94
59_I	81_I	0.649	0.94
45_S	388_I	0.648	0.94
352_A	364_V	0.648	0.94
154_Y	163_V	0.647	0.94
214_G	261_A	0.647	0.94
91_G	95_T	0.647	0.94
344_L	370_L	0.647	0.94
82_G	89_D	0.645	0.94
80_N	94_A	0.644	0.94
137_Y	140_A	0.643	0.94
43_Y	388_I	0.640	0.94
35_Y	96_R	0.634	0.94
67_I	70_Q	0.633	0.94
32_L	63_G	0.633	0.94
250_A	275_N	0.629	0.93
228_D	231_V	0.629	0.93
80_N	147_R	0.626	0.93
347_Y	369_N	0.621	0.93
105_G	110_F	0.621	0.93
4_K	9_L	0.621	0.93
212_D	259_Y	0.619	0.93
296_K	322_K	0.618	0.93
201_D	225_D	0.617	0.93
349_D	365_D	0.616	0.93
65_T	73_G	0.615	0.93
9_L	15_V	0.611	0.92
44_F	387_D	0.610	0.92
29_G	33_D	0.609	0.92
90_K	93_T	0.607	0.92
56_Y	116_Y	0.606	0.92
172_Y	201_D	0.603	0.92
6_L	11_P	0.603	0.92
129_L	135_D	0.603	0.92
101_G	111_D	0.601	0.92
53_D	390_A	0.599	0.92
10_V	106_Q	0.598	0.92
157_N	165_G	0.598	0.92
202_G	224_S	0.596	0.91
41_L	363_Y	0.593	0.91
319_L	347_Y	0.593	0.91
6_L	13_L	0.592	0.91
44_F	389_V	0.590	0.91
107_N	157_N	0.589	0.91
348_V	370_L	0.587	0.91
126_T	267_A	0.587	0.91
156_N	163_V	0.587	0.91
178_S	198_E	0.585	0.91
296_K	324_K	0.585	0.91
79_F	94_A	0.583	0.91
348_V	385_T	0.581	0.90
375_D	383_I	0.580	0.90
5_V	13_L	0.580	0.90
12_A	20_N	0.579	0.90
321_S	345_V	0.579	0.90
2_K	5_V	0.579	0.90
4_K	11_P	0.577	0.90
127_D	133_G	0.577	0.90
300_F	304_A	0.575	0.90
131_E	135_D	0.575	0.90
112_Y	115_N	0.573	0.90
43_Y	367_K	0.573	0.90
307_Q	311_G	0.573	0.90
136_T	146_G	0.572	0.90
29_G	66_Q	0.571	0.90
51_D	83_A	0.571	0.90
127_D	132_F	0.571	0.90
40_G	43_Y	0.569	0.89
57_A	83_A	0.566	0.89
328_G	343_D	0.564	0.89
253_W	270_Y	0.562	0.89
148_A	173_Q	0.562	0.89
165_G	209_Y	0.561	0.89
357_N	360_M	0.560	0.89
204_G	251_E	0.560	0.89
6_L	9_L	0.559	0.89
44_F	368_I	0.558	0.89
85_G	94_A	0.558	0.89
53_D	56_Y	0.558	0.89
353_T	396_Q	0.557	0.88
32_L	65_T	0.555	0.88
56_Y	95_T	0.553	0.88
67_I	360_M	0.553	0.88
65_T	75_G	0.553	0.88
93_T	98_A	0.553	0.88
197_K	201_D	0.550	0.88
157_N	164_D	0.549	0.88
156_N	166_L	0.549	0.88
211_F	257_A	0.548	0.88
357_N	395_Y	0.546	0.88
271_A	297_T	0.546	0.88
269_M	303_V	0.544	0.87
255_V	270_Y	0.543	0.87
54_M	351_G	0.543	0.87
211_F	215_L	0.542	0.87
74_Y	153_T	0.542	0.87
66_Q	358_K	0.541	0.87
145_N	222_X	0.538	0.87
142_N	220_A	0.538	0.87
139_G	142_N	0.537	0.87
41_L	392_G	0.535	0.86
40_G	44_F	0.535	0.86
56_Y	80_N	0.535	0.86
275_N	297_T	0.534	0.86
346_K	372_D	0.534	0.86
171_Q	202_G	0.534	0.86
392_G	397_F	0.532	0.86
3_R	10_V	0.532	0.86
306_Y	312_L	0.532	0.86
350_I	364_V	0.531	0.86
95_T	98_A	0.531	0.86
123_E	269_M	0.531	0.86
129_L	136_T	0.530	0.86
138_A	141_D	0.529	0.86
156_N	167_N	0.529	0.86
177_E	199_N	0.528	0.86
58_R	97_L	0.528	0.86
307_Q	355_Y	0.527	0.86
216_S	219_A	0.527	0.86
157_N	167_N	0.526	0.86
117_G	222_X	0.526	0.86
154_Y	168_F	0.526	0.86
216_S	260_D	0.526	0.86
176_N	196_S	0.525	0.85
275_N	278_P	0.524	0.85
264_V	308_F	0.523	0.85
295_N	325_D	0.522	0.85
40_G	390_A	0.522	0.85
54_M	353_T	0.521	0.85
300_F	320_Q	0.519	0.85
10_V	15_V	0.518	0.85
75_G	94_A	0.517	0.85
211_F	217_L	0.516	0.84
102_L	105_G	0.516	0.84
175_N	179_G	0.515	0.84
199_N	226_R	0.514	0.84
132_F	136_T	0.514	0.84
52_G	83_A	0.514	0.84
79_F	98_A	0.513	0.84
56_Y	130_P	0.513	0.84
7_A	13_L	0.512	0.84
108_G	157_N	0.512	0.84
12_A	15_V	0.512	0.84
5_V	17_G	0.512	0.84
346_K	370_L	0.512	0.84
31_K	34_L	0.512	0.84
232_G	246_G	0.511	0.84
385_T	388_I	0.511	0.84
31_K	63_G	0.510	0.84
6_L	12_A	0.510	0.84
325_D	372_D	0.508	0.84
134_G	365_D	0.508	0.84
89_D	95_T	0.507	0.83
271_A	299_N	0.507	0.83
73_G	360_M	0.507	0.83
319_L	349_D	0.506	0.83
214_G	219_A	0.505	0.83
54_M	394_V	0.504	0.83
367_K	388_I	0.504	0.83
271_A	301_E	0.504	0.83
178_S	197_K	0.504	0.83
4_K	16_A	0.503	0.83
165_G	211_F	0.502	0.83
88_S	92_N	0.502	0.83
211_F	219_A	0.501	0.83
68_A	395_Y	0.501	0.83
101_G	109_T	0.500	0.83
52_G	57_A	0.500	0.83
297_T	323_G	0.500	0.83

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
2j1nA	3	0.8615	100	0.313	Contact Map
1phoA	3	0.8186	100	0.316	Contact Map
3nsgA	3	0.8388	100	0.316	Contact Map
2zfgA	3	0.8262	100	0.334	Contact Map
2fgqX	3	0.7683	100	0.347	Contact Map
3vy8X	3	0.8111	100	0.369	Contact Map
3wi5A	3	0.7506	100	0.403	Contact Map
2porA	3	0.733	100	0.44	Contact Map
3prnA	3	0.6826	100	0.455	Contact Map
2o4vA	3	0.8539	99.3	0.802	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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