YNDF - BACSU - GREMLIN Contacts

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YNDF - Spore germination protein YndF

UniProt:	O31810	Sequences: MKSKLKRQLPAMVIVCLLMICVTGCWSSREIEDLGLTFAIAIDKGKETNTEKELKEEGGSYPKKDNITLTYQFVNEKAAGAGTSGGGGSGQGAQKAYINISETGDSLQQIGSEVALRRDREVFSPHLKVVVMSEDVLHTFPIDEMLDQFFRDNEIRLSCLVLSAKGEARDALQLKENGEIPAFRLIGLGENEHKVSRILPPMTLAKLIGKLHSGSSFLLQNVVAANGAVKYSGAAVINGKSKKMIGTLNEYETEGITWIRGEGKGGVVKSHDKKSQQTLAYDINKIKSRIQPIVKGKDISFHVDIESEGDLVENWNTKEALDTQFIDRLETTIENEVKKIVGQVLKKIQHDYKADVAGFDESFRLTYPHLWKRVKNNWDDTFSKADITYSVNVTITHFGTVKTQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	404 (363)
Sequences:	2203 (1910)
Seq/√Len:	100.3

BACSU - YNDF GERKC YFKR GERBC GERAC

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
302_H	388_T	5.335	1.00
304_D	390_S	4.484	1.00
134_E	138_H	4.228	1.00
44_K	139_T	4.190	1.00
252_E	347_K	4.183	1.00
272_D	316_N	3.618	1.00
68_T	169_R	3.609	1.00
338_K	342_G	3.553	1.00
134_E	165_K	3.515	1.00
131_V	164_A	3.217	1.00
281_Y	333_I	2.985	1.00
167_E	170_D	2.964	1.00
306_E	392_N	2.945	1.00
334_E	393_V	2.856	1.00
141_P	242_K	2.801	1.00
221_N	247_T	2.724	1.00
301_F	359_F	2.621	1.00
66_N	103_T	2.571	1.00
338_K	391_V	2.563	1.00
301_F	385_A	2.535	1.00
169_R	173_Q	2.521	1.00
300_S	386_D	2.470	1.00
349_Q	382_F	2.432	1.00
305_I	341_V	2.420	1.00
348_I	382_F	2.388	1.00
71_Y	114_V	2.364	1.00
244_M	247_T	2.361	1.00
69_L	110_I	2.358	1.00
308_E	396_T	2.344	1.00
235_A	244_M	2.293	1.00
353_K	383_S	2.268	1.00
163_S	235_A	2.196	1.00
300_S	388_T	2.192	1.00
70_T	168_A	2.178	1.00
255_G	344_V	2.160	1.00
207_L	217_F	2.148	1.00
234_A	253_T	2.105	1.00
246_G	352_Y	2.088	1.00
345_L	387_I	2.080	1.00
137_L	163_S	2.067	1.00
348_I	356_V	2.026	1.00
68_T	103_T	1.986	1.00
377_N	380_D	1.946	1.00
132_M	145_M	1.942	1.00
302_H	390_S	1.941	1.00
161_V	207_L	1.940	1.00
147_D	151_R	1.925	1.00
66_N	105_D	1.921	1.00
348_I	357_A	1.913	1.00
43_D	168_A	1.880	1.00
102_E	113_E	1.851	1.00
42_I	136_V	1.833	1.00
234_A	256_I	1.824	1.00
303_V	359_F	1.822	1.00
218_L	256_I	1.789	1.00
37_T	122_V	1.774	1.00
39_A	182_A	1.771	1.00
45_G	103_T	1.767	1.00
293_I	302_H	1.765	1.00
327_D	330_E	1.761	1.00
207_L	219_L	1.720	1.00
370_L	374_V	1.712	1.00
41_A	168_A	1.710	1.00
162_L	222_V	1.706	1.00
43_D	133_S	1.646	1.00
133_S	168_A	1.637	1.00
281_Y	309_G	1.634	1.00
360_D	378_W	1.619	1.00
40_I	127_L	1.603	1.00
304_D	392_N	1.593	1.00
112_S	282_D	1.586	1.00
298_D	386_D	1.582	1.00
111_G	124_S	1.582	1.00
249_N	252_E	1.581	1.00
68_T	101_S	1.572	1.00
307_S	393_V	1.556	1.00
308_E	394_T	1.552	1.00
39_A	172_L	1.508	1.00
101_S	169_R	1.499	1.00
255_G	337_V	1.491	1.00
328_R	332_T	1.477	1.00
292_P	299_I	1.474	1.00
133_S	136_V	1.473	1.00
236_V	356_V	1.469	1.00
290_I	301_F	1.462	1.00
345_L	389_Y	1.461	1.00
45_G	68_T	1.447	1.00
68_T	167_E	1.436	1.00
185_L	222_V	1.434	1.00
329_L	395_I	1.426	1.00
132_M	142_I	1.425	1.00
294_V	299_I	1.421	1.00
330_E	334_E	1.420	1.00
214_G	360_D	1.416	1.00
221_N	244_M	1.415	1.00
334_E	338_K	1.411	1.00
336_E	340_I	1.397	1.00
165_K	223_V	1.391	1.00
301_F	363_F	1.384	0.99
170_D	173_Q	1.373	0.99
163_S	237_I	1.373	0.99
137_L	237_I	1.369	0.99
105_D	109_Q	1.367	0.99
15_V	19_M	1.355	0.99
40_I	149_F	1.352	0.99
216_S	354_A	1.348	0.99
344_V	348_I	1.348	0.99
336_E	339_K	1.328	0.99
132_M	137_L	1.307	0.99
162_L	189_G	1.303	0.99
246_G	354_A	1.302	0.99
157_L	205_A	1.295	0.99
331_T	334_E	1.292	0.99
341_V	389_Y	1.286	0.99
104_G	110_I	1.272	0.99
322_D	325_F	1.261	0.99
261_G	288_S	1.259	0.99
223_V	232_S	1.257	0.99
346_K	349_Q	1.253	0.99
259_I	357_A	1.240	0.99
216_S	379_D	1.240	0.99
288_S	305_I	1.213	0.99
37_T	124_S	1.208	0.99
34_L	123_F	1.200	0.99
309_G	333_I	1.199	0.99
295_K	300_S	1.188	0.98
128_K	186_I	1.179	0.98
259_I	303_V	1.169	0.98
67_I	136_V	1.160	0.98
319_E	322_D	1.145	0.98
35_G	73_F	1.142	0.98
363_F	370_L	1.142	0.98
255_G	348_I	1.142	0.98
236_V	352_Y	1.141	0.98
333_I	393_V	1.139	0.98
38_F	74_V	1.136	0.98
42_I	107_L	1.132	0.98
292_P	366_T	1.127	0.98
378_W	382_F	1.124	0.98
108_Q	112_S	1.121	0.98
292_P	367_Y	1.113	0.98
291_Q	302_H	1.110	0.98
104_G	109_Q	1.106	0.98
164_A	171_A	1.102	0.97
307_S	337_V	1.099	0.97
332_T	335_N	1.097	0.97
289_R	304_D	1.095	0.97
104_G	113_E	1.091	0.97
127_L	155_I	1.085	0.97
108_Q	312_V	1.083	0.97
70_T	101_S	1.082	0.97
70_T	99_N	1.081	0.97
108_Q	282_D	1.079	0.97
135_D	168_A	1.071	0.97
97_Y	181_P	1.067	0.97
359_F	387_I	1.063	0.97
279_L	329_L	1.062	0.97
18_L	21_C	1.062	0.97
108_Q	148_Q	1.060	0.97
310_D	397_H	1.055	0.97
22_V	25_C	1.054	0.97
256_I	356_V	1.053	0.97
150_F	208_I	1.048	0.97
363_F	367_Y	1.040	0.96
349_Q	378_W	1.038	0.96
130_V	159_C	1.031	0.96
223_V	230_K	1.031	0.96
291_Q	304_D	1.024	0.96
326_I	330_E	1.021	0.96
97_Y	180_I	1.015	0.96
117_R	228_A	1.010	0.96
252_E	343_Q	1.007	0.96
249_N	253_T	0.996	0.95
72_Q	181_P	0.993	0.95
102_E	114_V	0.993	0.95
131_V	162_L	0.991	0.95
165_K	247_T	0.990	0.95
361_E	364_R	0.988	0.95
126_H	156_R	0.988	0.95
372_K	375_K	0.986	0.95
335_N	339_K	0.984	0.95
121_E	154_E	0.972	0.95
45_G	65_D	0.971	0.95
267_V	282_D	0.966	0.95
259_I	341_V	0.958	0.94
135_D	138_H	0.955	0.94
137_L	235_A	0.955	0.94
248_L	252_E	0.952	0.94
346_K	350_H	0.951	0.94
256_I	260_R	0.947	0.94
162_L	220_Q	0.943	0.94
342_G	346_K	0.941	0.94
342_G	389_Y	0.938	0.94
219_L	237_I	0.938	0.94
130_V	149_F	0.938	0.94
349_Q	383_S	0.933	0.93
41_A	167_E	0.931	0.93
292_P	301_F	0.930	0.93
215_S	358_G	0.927	0.93
137_L	141_P	0.925	0.93
133_S	163_S	0.925	0.93
361_E	365_L	0.923	0.93
76_E	178_G	0.918	0.93
143_D	242_K	0.917	0.93
225_A	230_K	0.917	0.93
32_E	157_L	0.917	0.93
106_S	278_T	0.910	0.93
335_N	338_K	0.910	0.93
362_S	365_L	0.904	0.92
133_S	164_A	0.903	0.92
152_D	312_V	0.897	0.92
268_V	340_I	0.887	0.92
207_L	211_L	0.879	0.91
117_R	230_K	0.879	0.91
367_Y	370_L	0.878	0.91
292_P	362_S	0.875	0.91
379_D	382_F	0.875	0.91
105_D	278_T	0.868	0.91
305_I	391_V	0.862	0.90
279_L	314_N	0.861	0.90
214_G	358_G	0.859	0.90
41_A	70_T	0.858	0.90
102_E	110_I	0.853	0.90
363_F	371_W	0.848	0.90
290_I	303_V	0.844	0.90
134_E	247_T	0.841	0.89
42_I	69_L	0.840	0.89
314_N	318_K	0.839	0.89
294_V	367_Y	0.834	0.89
381_T	384_K	0.834	0.89
142_I	207_L	0.831	0.89
339_K	343_Q	0.829	0.89
138_H	237_I	0.828	0.89
299_I	385_A	0.828	0.89
325_F	328_R	0.827	0.89
72_Q	97_Y	0.826	0.88
331_T	335_N	0.824	0.88
362_S	366_T	0.823	0.88
130_V	161_V	0.819	0.88
11_A	22_V	0.815	0.88
40_I	130_V	0.814	0.88
218_L	356_V	0.813	0.88
245_I	354_A	0.810	0.88
29_R	34_L	0.810	0.88
45_G	66_N	0.808	0.87
129_V	162_L	0.807	0.87
258_W	263_G	0.806	0.87
171_A	222_V	0.804	0.87
293_I	300_S	0.800	0.87
40_I	71_Y	0.799	0.87
11_A	15_V	0.798	0.87
294_V	370_L	0.798	0.87
368_P	371_W	0.797	0.87
137_L	244_M	0.796	0.87
271_H	278_T	0.794	0.86
11_A	19_M	0.794	0.86
327_D	331_T	0.791	0.86
370_L	373_R	0.786	0.86
19_M	23_T	0.785	0.86
174_L	224_A	0.784	0.86
338_K	389_Y	0.780	0.85
255_G	341_V	0.779	0.85
216_S	382_F	0.779	0.85
368_P	372_K	0.778	0.85
337_V	341_V	0.777	0.85
224_A	227_G	0.776	0.85
236_V	248_L	0.774	0.85
47_E	66_N	0.773	0.85
281_Y	395_I	0.766	0.84
141_P	237_I	0.763	0.84
108_Q	313_E	0.759	0.84
255_G	258_W	0.758	0.84
109_Q	269_K	0.756	0.84
347_K	352_Y	0.753	0.83
8_Q	21_C	0.752	0.83
210_K	215_S	0.752	0.83
151_R	399_G	0.752	0.83
79_A	96_A	0.749	0.83
100_I	114_V	0.748	0.83
41_A	133_S	0.742	0.83
39_A	129_V	0.741	0.82
73_F	118_R	0.738	0.82
207_L	237_I	0.736	0.82
345_L	349_Q	0.736	0.82
164_A	168_A	0.731	0.82
28_S	36_L	0.731	0.82
163_S	244_M	0.728	0.81
14_I	17_L	0.723	0.81
213_S	361_E	0.722	0.81
115_A	153_N	0.721	0.81
106_S	280_A	0.719	0.80
240_K	379_D	0.719	0.80
102_E	117_R	0.717	0.80
106_S	313_E	0.716	0.80
23_T	26_W	0.715	0.80
257_T	262_E	0.715	0.80
282_D	312_V	0.710	0.80
165_K	221_N	0.709	0.80
237_I	244_M	0.706	0.79
292_P	359_F	0.703	0.79
71_Y	111_G	0.703	0.79
44_K	135_D	0.699	0.79
39_A	72_Q	0.699	0.79
374_V	381_T	0.698	0.79
41_A	169_R	0.697	0.78
206_K	210_K	0.694	0.78
108_Q	152_D	0.692	0.78
160_L	186_I	0.690	0.78
203_T	206_K	0.684	0.77
103_T	107_L	0.684	0.77
308_E	397_H	0.684	0.77
197_R	254_E	0.682	0.77
255_G	340_I	0.680	0.77
132_M	163_S	0.680	0.77
168_A	172_L	0.680	0.77
40_I	69_L	0.680	0.77
259_I	288_S	0.680	0.77
149_F	204_L	0.679	0.77
71_Y	124_S	0.677	0.76
33_D	187_G	0.673	0.76
142_I	237_I	0.672	0.76
30_E	126_H	0.671	0.76
142_I	242_K	0.670	0.76
221_N	235_A	0.669	0.76
113_E	116_L	0.668	0.75
75_N	78_A	0.667	0.75
30_E	120_R	0.666	0.75
341_V	344_V	0.666	0.75
311_L	320_A	0.664	0.75
8_Q	19_M	0.664	0.75
184_R	188_L	0.663	0.75
124_S	130_V	0.662	0.75
353_K	380_D	0.659	0.74
345_L	357_A	0.657	0.74
42_I	67_I	0.656	0.74
36_L	123_F	0.655	0.74
258_W	337_V	0.655	0.74
205_A	209_G	0.653	0.74
119_D	176_E	0.652	0.74
307_S	332_T	0.651	0.74
100_I	118_R	0.650	0.73
273_K	332_T	0.648	0.73
165_K	244_M	0.647	0.73
187_G	191_N	0.647	0.73
240_K	245_I	0.645	0.73
258_W	307_S	0.645	0.73
289_R	296_G	0.642	0.73
188_L	231_Y	0.641	0.72
161_V	219_L	0.640	0.72
134_E	221_N	0.640	0.72
19_M	22_V	0.640	0.72
42_I	130_V	0.640	0.72
318_K	325_F	0.639	0.72
295_K	298_D	0.636	0.72
183_F	186_I	0.631	0.71
38_F	205_A	0.630	0.71
83_T	373_R	0.629	0.71
319_E	323_T	0.627	0.71
127_L	159_C	0.627	0.71
11_A	18_L	0.626	0.71
236_V	354_A	0.626	0.71
133_S	244_M	0.626	0.71
132_M	146_L	0.625	0.71
348_I	352_Y	0.624	0.70
283_I	307_S	0.624	0.70
19_M	343_Q	0.624	0.70
337_V	393_V	0.623	0.70
116_L	250_E	0.621	0.70
35_G	118_R	0.616	0.69
306_E	394_T	0.616	0.69
309_G	330_E	0.615	0.69
284_N	310_D	0.614	0.69
12_M	16_C	0.614	0.69
257_T	261_G	0.613	0.69
12_M	332_T	0.612	0.69
67_I	303_V	0.611	0.69
290_I	385_A	0.609	0.69
21_C	331_T	0.608	0.68
183_F	187_G	0.607	0.68
118_R	122_V	0.606	0.68
248_L	256_I	0.605	0.68
70_T	169_R	0.605	0.68
217_F	358_G	0.605	0.68
359_F	382_F	0.604	0.68
142_I	270_S	0.600	0.67
72_Q	156_R	0.600	0.67
202_M	210_K	0.599	0.67
299_I	374_V	0.599	0.67
295_K	324_Q	0.597	0.67
10_P	22_V	0.595	0.67
114_V	212_H	0.594	0.67
163_S	219_L	0.592	0.66
10_P	324_Q	0.592	0.66
129_V	185_L	0.591	0.66
344_V	347_K	0.591	0.66
44_K	67_I	0.591	0.66
117_R	225_A	0.591	0.66
108_Q	153_N	0.590	0.66
16_C	331_T	0.590	0.66
39_A	183_F	0.589	0.66
71_Y	155_I	0.588	0.66
164_A	233_G	0.588	0.66
254_E	340_I	0.588	0.66
283_I	286_I	0.587	0.66
31_I	189_G	0.587	0.66
70_T	164_A	0.586	0.66
14_I	21_C	0.586	0.66
138_H	324_Q	0.586	0.66
318_K	321_L	0.585	0.65
136_V	145_M	0.585	0.65
263_G	266_G	0.585	0.65
298_D	384_K	0.584	0.65
73_F	100_I	0.584	0.65
276_Q	289_R	0.581	0.65
95_K	175_K	0.581	0.65
290_I	362_S	0.580	0.65
256_I	344_V	0.579	0.65
72_Q	99_N	0.579	0.65
257_T	400_T	0.579	0.65
31_I	96_A	0.578	0.65
197_R	263_G	0.578	0.65
134_E	166_G	0.578	0.65
19_M	69_L	0.578	0.65
36_L	97_Y	0.578	0.65
218_L	234_A	0.577	0.64
376_N	380_D	0.577	0.64
309_G	393_V	0.576	0.64
19_M	342_G	0.575	0.64
129_V	182_A	0.574	0.64
282_D	310_D	0.572	0.64
216_S	356_V	0.572	0.64
270_S	332_T	0.570	0.63
269_K	280_A	0.569	0.63
20_I	138_H	0.568	0.63
248_L	344_V	0.567	0.63
299_I	363_F	0.566	0.63
245_I	352_Y	0.565	0.63
166_G	233_G	0.564	0.63
232_S	250_E	0.563	0.63
349_Q	385_A	0.563	0.63
27_S	33_D	0.562	0.62
23_T	27_S	0.562	0.62
9_L	21_C	0.561	0.62
11_A	139_T	0.561	0.62
8_Q	22_V	0.561	0.62
32_E	184_R	0.559	0.62
72_Q	182_A	0.558	0.62
147_D	313_E	0.557	0.62
13_V	21_C	0.556	0.62
8_Q	335_N	0.556	0.62
193_H	201_P	0.555	0.61
67_I	145_M	0.555	0.61
251_Y	340_I	0.554	0.61
120_R	178_G	0.554	0.61
279_L	309_G	0.553	0.61
19_M	271_H	0.553	0.61
125_P	217_F	0.552	0.61
9_L	12_M	0.551	0.61
131_V	168_A	0.551	0.61
138_H	247_T	0.551	0.61
210_K	270_S	0.550	0.61
137_L	142_I	0.548	0.60
123_F	128_K	0.547	0.60
13_V	297_K	0.547	0.60
206_K	251_Y	0.547	0.60
42_I	132_M	0.547	0.60
363_F	368_P	0.547	0.60
226_N	331_T	0.546	0.60
8_Q	20_I	0.545	0.60
274_K	347_K	0.545	0.60
263_G	286_I	0.543	0.60
254_E	357_A	0.542	0.60
45_G	135_D	0.542	0.60
37_T	71_Y	0.539	0.59
37_T	114_V	0.539	0.59
204_L	207_L	0.539	0.59
74_V	179_E	0.539	0.59
309_G	395_I	0.538	0.59
178_G	187_G	0.538	0.59
25_C	151_R	0.538	0.59
138_H	244_M	0.537	0.59
112_S	115_A	0.537	0.59
299_I	370_L	0.536	0.59
144_E	333_I	0.536	0.59
41_A	131_V	0.536	0.59
390_S	393_V	0.536	0.59
267_V	280_A	0.535	0.59
304_D	307_S	0.534	0.58
296_G	306_E	0.533	0.58
28_S	178_G	0.532	0.58
334_E	392_N	0.531	0.58
70_T	172_L	0.531	0.58
246_G	382_F	0.531	0.58
83_T	322_D	0.531	0.58
237_I	242_K	0.530	0.58
243_K	335_N	0.530	0.58
215_S	361_E	0.530	0.58
236_V	348_I	0.528	0.58
105_D	269_K	0.528	0.58
41_A	173_Q	0.528	0.58
134_E	244_M	0.528	0.58
31_I	120_R	0.527	0.58
120_R	365_L	0.527	0.58
152_D	282_D	0.527	0.58
220_Q	231_Y	0.527	0.58
165_K	353_K	0.526	0.57
133_S	167_E	0.525	0.57
211_L	242_K	0.523	0.57
159_C	205_A	0.523	0.57
96_A	181_P	0.522	0.57
214_G	217_F	0.521	0.57
115_A	122_V	0.521	0.57
27_S	220_Q	0.519	0.56
356_V	382_F	0.519	0.56
10_P	21_C	0.518	0.56
10_P	23_T	0.518	0.56
272_D	279_L	0.517	0.56
143_D	181_P	0.517	0.56
42_I	110_I	0.516	0.56
283_I	309_G	0.514	0.56
292_P	368_P	0.513	0.56
216_S	358_G	0.513	0.56
270_S	333_I	0.513	0.56
106_S	269_K	0.512	0.55
309_G	334_E	0.512	0.55
273_K	277_Q	0.512	0.55
46_K	65_D	0.511	0.55
38_F	128_K	0.510	0.55
125_P	257_T	0.510	0.55
378_W	383_S	0.510	0.55
8_Q	11_A	0.510	0.55
146_L	251_Y	0.510	0.55
76_E	120_R	0.509	0.55
39_A	107_L	0.509	0.55
39_A	168_A	0.509	0.55
200_P	204_L	0.508	0.55
34_L	125_P	0.507	0.55
190_E	279_L	0.505	0.54
215_S	364_R	0.502	0.54
367_Y	376_N	0.502	0.54
293_I	390_S	0.501	0.54
377_N	381_T	0.501	0.54
174_L	183_F	0.500	0.54
11_A	394_T	0.500	0.54

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
3n54B	5	0.7624	100	0.238	Contact Map
3wfdC	1	0.3267	38.6	0.963	Contact Map
3utkA	1	0.2203	16.7	0.969	Contact Map
1xt8A	1	0.5644	11.5	0.971	Contact Map
4fybB	1	0.354	9.3	0.972	Contact Map
4n6kA	1	0.6535	9.1	0.972	Contact Map
3zbiC	1	0.0668	7.9	0.973	Contact Map
4uslA	2	0.3985	7	0.974	Contact Map
4inwA	1	0.1559	6.4	0.974	Contact Map
3hd7A	1	0.0767	5.8	0.975	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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