YSNF - BACSU - GREMLIN Contacts

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YSNF - Stress response protein YsnF

UniProt:	P94560	Sequences: MKSIVGVYETPQETIAAIEGLLTKGYDSDDISVVTSRRDTDYLESRTGTEVNQAIDAHQDESESFFDKLKDYFTMDDTATHSKALSDLDIKTDEIDKYQEDLDDGKLLVAVDTDADVIAPIDNGNALSGGFSSTNELDYTTKEEKTMPLREEQLKVDKEDVQTGEVEIGKEVKTEKRDMDIPVRHDEIYVERRPVDENKTDAAPVNDSEEIRVPIVEEKLEVTKKPVVTDEVVVGKRTVEENEHISETVKKEEPRLNKEGKVDGLDDDPLNNK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	273 (211)
Sequences:	476 (411)
Seq/√Len:	28.3

BACSU - YSNF

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
185_H	241_E	4.246	1.00
171_E	255_R	3.522	1.00
149_L	254_P	3.483	1.00
168_I	234_V	3.423	1.00
184_R	238_T	3.238	1.00
224_K	247_E	3.083	1.00
66_F	116_D	3.064	1.00
187_E	239_V	2.885	1.00
193_R	233_V	2.657	1.00
170_K	252_E	2.578	0.99
173_K	253_E	2.428	0.99
165_E	212_R	2.346	0.99
151_E	251_K	2.291	0.99
196_D	199_K	2.276	0.98
128_S	131_F	2.194	0.98
158_K	236_K	2.170	0.98
153_Q	225_K	2.154	0.98
153_Q	229_T	2.152	0.98
174_T	250_K	2.113	0.97
199_K	203_A	2.050	0.97
64_S	69_L	2.023	0.97
166_V	256_L	1.976	0.96
162_Q	165_E	1.935	0.96
58_H	109_V	1.919	0.95
232_V	256_L	1.886	0.95
154_L	247_E	1.822	0.94
103_D	106_K	1.781	0.93
159_E	221_E	1.774	0.93
88_L	92_T	1.767	0.93
155_K	225_K	1.758	0.93
114_D	118_I	1.742	0.92
178_D	246_S	1.728	0.92
178_D	244_H	1.722	0.92
178_D	247_E	1.713	0.92
196_D	201_D	1.708	0.92
55_I	68_K	1.680	0.91
65_F	69_L	1.664	0.91
77_D	82_S	1.649	0.90
167_E	257_N	1.644	0.90
160_D	219_K	1.639	0.90
157_D	221_E	1.636	0.90
170_K	182_P	1.584	0.88
67_D	72_Y	1.581	0.88
180_D	242_N	1.513	0.86
183_V	241_E	1.479	0.85
119_A	261_K	1.464	0.84
124_G	222_V	1.438	0.83
184_R	240_E	1.422	0.82
67_D	74_T	1.406	0.81
158_K	212_R	1.397	0.81
190_V	263_D	1.393	0.81
57_A	68_K	1.388	0.80
153_Q	191_E	1.380	0.80
189_Y	237_R	1.376	0.80
124_G	128_S	1.352	0.79
159_E	219_K	1.339	0.78
199_K	202_A	1.339	0.78
131_F	139_Y	1.336	0.78
60_D	72_Y	1.317	0.77
124_G	127_L	1.317	0.77
95_I	113_T	1.312	0.77
186_D	236_K	1.283	0.75
161_V	217_E	1.282	0.75
147_M	165_E	1.255	0.73
162_Q	218_E	1.236	0.72
192_R	230_D	1.219	0.71
60_D	161_V	1.216	0.71
85_L	94_E	1.202	0.70
112_D	115_A	1.186	0.69
218_E	256_L	1.183	0.69
83_K	109_V	1.183	0.69
231_E	236_K	1.182	0.69
228_V	231_E	1.176	0.68
215_I	252_E	1.172	0.68
199_K	211_I	1.164	0.67
56_D	68_K	1.164	0.67
139_Y	143_E	1.158	0.67
74_T	147_M	1.152	0.67
177_R	250_K	1.151	0.66
78_T	255_R	1.142	0.66
75_M	100_E	1.138	0.66
122_D	127_L	1.136	0.65
122_D	126_A	1.127	0.65
209_E	236_K	1.122	0.64
98_Y	236_K	1.118	0.64
157_D	220_L	1.116	0.64
185_H	247_E	1.100	0.63
220_L	233_V	1.097	0.63
89_D	111_V	1.092	0.62
167_E	208_S	1.074	0.61
85_L	92_T	1.056	0.60
212_R	221_E	1.044	0.59
182_P	186_D	1.036	0.58
227_V	252_E	1.027	0.57
189_Y	235_G	1.021	0.57
149_L	253_E	1.013	0.56
148_P	203_A	1.010	0.56
121_I	127_L	1.008	0.56
229_T	251_K	0.997	0.55
54_A	59_Q	0.997	0.55
70_K	73_F	0.994	0.55
67_D	73_F	0.990	0.55
189_Y	232_V	0.987	0.54
250_K	255_R	0.984	0.54
153_Q	219_K	0.982	0.54
125_N	128_S	0.979	0.54
127_L	131_F	0.979	0.54
89_D	95_I	0.978	0.54
130_G	133_S	0.970	0.53
170_K	175_E	0.955	0.52
137_L	140_T	0.952	0.52
96_D	100_E	0.949	0.52
220_L	248_T	0.946	0.51
123_N	129_G	0.945	0.51
57_A	64_S	0.939	0.51
135_N	139_Y	0.935	0.50
182_P	252_E	0.932	0.50
164_G	224_K	0.921	0.49
194_P	198_N	0.921	0.49
125_N	130_G	0.920	0.49
160_D	217_E	0.917	0.49
80_T	242_N	0.917	0.49
177_R	212_R	0.915	0.49
166_V	228_V	0.912	0.49
151_E	172_V	0.907	0.48
136_E	190_V	0.904	0.48
161_V	213_V	0.903	0.48
165_E	209_E	0.901	0.48
111_V	115_A	0.900	0.48
153_Q	205_V	0.899	0.48
158_K	253_E	0.898	0.48
224_K	231_E	0.897	0.48
101_D	237_R	0.897	0.48
126_A	197_E	0.895	0.47
232_V	237_R	0.886	0.47
150_R	170_K	0.878	0.46
169_G	181_I	0.877	0.46
209_E	241_E	0.874	0.46
191_E	235_G	0.871	0.46
119_A	132_S	0.870	0.45
167_E	249_V	0.860	0.45
135_N	190_V	0.860	0.45
127_L	132_S	0.851	0.44
118_I	129_G	0.850	0.44
122_D	125_N	0.850	0.44
140_T	145_K	0.849	0.44
154_L	236_K	0.849	0.44
193_R	231_E	0.846	0.44
128_S	132_S	0.844	0.43
169_G	234_V	0.842	0.43
122_D	133_S	0.838	0.43
148_P	231_E	0.831	0.43
119_A	223_T	0.830	0.42
185_H	217_E	0.825	0.42
190_V	232_V	0.817	0.41
125_N	129_G	0.815	0.41
81_H	149_L	0.811	0.41
123_N	127_L	0.810	0.41
96_D	113_T	0.807	0.41
77_D	186_D	0.806	0.41
89_D	96_D	0.805	0.41
170_K	215_I	0.803	0.40
81_H	95_I	0.801	0.40
213_V	232_V	0.798	0.40
150_R	252_E	0.797	0.40
137_L	190_V	0.795	0.40
55_I	59_Q	0.794	0.40
157_D	169_G	0.792	0.40
209_E	232_V	0.788	0.39
183_V	227_V	0.787	0.39
119_A	131_F	0.786	0.39
114_D	264_G	0.785	0.39
172_V	233_V	0.778	0.39
158_K	255_R	0.776	0.38
66_F	191_E	0.771	0.38
216_V	225_K	0.762	0.37
196_D	249_V	0.754	0.37
162_Q	195_V	0.753	0.37
70_K	190_V	0.748	0.36
225_K	233_V	0.748	0.36
158_K	218_E	0.746	0.36
62_S	69_L	0.744	0.36
195_V	228_V	0.742	0.36
173_K	216_V	0.742	0.36
149_L	252_E	0.739	0.36
161_V	166_V	0.737	0.36
170_K	209_E	0.736	0.36
145_K	258_K	0.733	0.35
176_K	179_M	0.732	0.35
211_I	231_E	0.732	0.35
215_I	227_V	0.726	0.35
191_E	196_D	0.725	0.35
188_I	239_V	0.725	0.35
235_G	255_R	0.725	0.35
194_P	255_R	0.723	0.35
129_G	134_T	0.719	0.34
190_V	251_K	0.718	0.34
68_K	257_N	0.710	0.34
59_Q	249_V	0.706	0.33
146_T	187_E	0.700	0.33
154_L	179_M	0.699	0.33
124_G	130_G	0.698	0.33
183_V	248_T	0.695	0.33
178_D	182_P	0.693	0.33
215_I	230_D	0.692	0.33
205_V	242_N	0.691	0.32
105_G	194_P	0.685	0.32
170_K	217_E	0.684	0.32
85_L	158_K	0.684	0.32
73_F	97_K	0.684	0.32
156_V	240_E	0.684	0.32
185_H	239_V	0.679	0.32
64_S	67_D	0.676	0.31
173_K	189_Y	0.674	0.31
55_I	247_E	0.673	0.31
208_S	261_K	0.670	0.31
63_E	95_I	0.669	0.31
171_E	233_V	0.660	0.30
92_T	256_L	0.659	0.30
190_V	246_S	0.653	0.30
171_E	235_G	0.652	0.30
89_D	109_V	0.651	0.30
147_M	176_K	0.650	0.30
71_D	75_M	0.649	0.30
167_E	212_R	0.647	0.30
66_F	72_Y	0.646	0.29
88_L	93_D	0.644	0.29
69_L	72_Y	0.644	0.29
159_E	206_N	0.643	0.29
209_E	252_E	0.641	0.29
133_S	136_E	0.636	0.29
175_E	217_E	0.636	0.29
132_S	256_L	0.635	0.29
167_E	206_N	0.626	0.28
105_G	177_R	0.623	0.28
79_A	117_V	0.620	0.28
159_E	167_E	0.620	0.28
105_G	108_L	0.620	0.28
88_L	94_E	0.617	0.28
162_Q	214_P	0.616	0.28
182_P	185_H	0.615	0.28
163_T	172_V	0.613	0.27
136_E	139_Y	0.610	0.27
185_H	215_I	0.609	0.27
143_E	148_P	0.608	0.27
179_M	252_E	0.608	0.27
132_S	138_D	0.607	0.27
137_L	194_P	0.607	0.27
168_I	233_V	0.603	0.27
101_D	236_K	0.602	0.27
113_T	117_V	0.595	0.26
107_L	238_T	0.594	0.26
114_D	117_V	0.594	0.26
149_L	153_Q	0.592	0.26
119_A	190_V	0.591	0.26
223_T	226_P	0.591	0.26
205_V	212_R	0.588	0.26
193_R	234_V	0.586	0.26
126_A	132_S	0.584	0.26
167_E	250_K	0.584	0.26
219_K	245_I	0.582	0.26
88_L	96_D	0.582	0.26
196_D	203_A	0.578	0.25
201_D	226_P	0.575	0.25
150_R	216_V	0.574	0.25
127_L	138_D	0.573	0.25
65_F	73_F	0.571	0.25
65_F	72_Y	0.563	0.24
71_D	92_T	0.562	0.24
247_E	260_G	0.561	0.24
66_F	78_T	0.561	0.24
178_D	224_K	0.559	0.24
149_L	251_K	0.555	0.24
136_E	141_T	0.555	0.24
177_R	188_I	0.555	0.24
78_T	96_D	0.555	0.24
178_D	186_D	0.554	0.24
157_D	177_R	0.554	0.24
179_M	213_V	0.553	0.24
66_F	193_R	0.552	0.24
170_K	187_E	0.551	0.24
149_L	170_K	0.549	0.24
71_D	166_V	0.544	0.23
185_H	252_E	0.543	0.23
64_S	194_P	0.543	0.23
160_D	184_R	0.542	0.23
146_T	168_I	0.541	0.23
124_G	129_G	0.540	0.23
149_L	228_V	0.534	0.23
77_D	103_D	0.533	0.23
132_S	201_D	0.530	0.23
62_S	263_D	0.528	0.23
112_D	240_E	0.528	0.23
208_S	257_N	0.528	0.23
192_R	224_K	0.528	0.23
72_Y	153_Q	0.526	0.22
69_L	75_M	0.525	0.22
54_A	57_A	0.523	0.22
93_D	111_V	0.523	0.22
171_E	234_V	0.523	0.22
182_P	187_E	0.519	0.22
158_K	231_E	0.517	0.22
125_N	131_F	0.514	0.22
179_M	226_P	0.513	0.22
62_S	66_F	0.511	0.22
189_Y	251_K	0.508	0.21
59_Q	64_S	0.508	0.21
158_K	224_K	0.505	0.21
126_A	133_S	0.504	0.21
131_F	255_R	0.503	0.21
83_K	94_E	0.503	0.21
63_E	147_M	0.502	0.21
135_N	143_E	0.502	0.21
184_R	209_E	0.502	0.21
173_K	234_V	0.500	0.21
98_Y	102_L	0.500	0.21

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
2wjnH	1	0.5128	87.7	0.931	Contact Map
1rzhH	1	0.5018	83.1	0.935	Contact Map
3htrA	2	0.3297	81.6	0.936	Contact Map
1eysH	1	0.5385	71.8	0.941	Contact Map
1x60A	1	0.1245	46	0.95	Contact Map
1utaA	1	0.1319	40.1	0.952	Contact Map
1t1vA	2	0.3114	18.5	0.959	Contact Map
2lfvA	1	0.1575	12.8	0.962	Contact Map
4oi3A	2	0.1355	10.2	0.964	Contact Map
1gudA	1	0.3333	9.7	0.964	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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