YKWD - BACSU - GREMLIN Contacts

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YKWD - Uncharacterized protein YkwD

UniProt:	O31398	Sequences: MKKAFILSAAAAVGLFTFGGVQQASAKELSCQPVVTVKTGNTVQNMSLNDAVKKLHINTNIKTLNAANEKEMKQLLQKHAKQSNVKVQDVQKTETAKPAQKTTEKAAADQNTASKAPATAEKTNTTTSAPSSVSAYEKKVVELTNAERQKQGLKPLQIDETLSKSARAKSQDMKDKNYFDHQSPTYGSPFDMMKSFGISYKTAGENIAKGQKTPEEVVKAWMNSEGHRKNILNPNFTHIGVGYVESGSIWTQQFIGK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	257 (246)
Sequences:	455 (440)
Seq/√Len:	28.1

BACSU - YKWD YLBC

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
170_S	251_T	7.677	1.00
137_E	167_R	4.518	1.00
225_E	229_K	3.780	1.00
136_Y	214_P	3.519	1.00
159_D	238_H	3.287	1.00
144_T	218_V	3.073	1.00
183_S	187_G	2.948	1.00
222_M	231_I	2.871	1.00
186_Y	192_M	2.818	1.00
139_K	215_E	2.806	1.00
169_K	192_M	2.765	1.00
217_V	250_W	2.755	1.00
211_Q	250_W	2.527	0.99
169_K	183_S	2.430	0.99
218_V	221_W	2.423	0.99
139_K	142_E	2.360	0.99
147_E	222_M	2.260	0.98
211_Q	217_V	2.260	0.98
140_V	214_P	2.239	0.98
141_V	239_I	2.210	0.98
172_D	183_S	2.192	0.98
190_F	203_A	2.191	0.98
171_Q	175_D	2.177	0.98
140_V	250_W	2.165	0.98
204_G	236_F	2.159	0.98
186_Y	196_F	2.146	0.98
140_V	221_W	2.134	0.98
178_Y	183_S	2.064	0.97
214_P	221_W	2.026	0.97
217_V	221_W	1.998	0.96
133_V	158_I	1.997	0.96
147_E	150_K	1.937	0.96
183_S	192_M	1.928	0.96
141_V	158_I	1.833	0.94
140_V	217_V	1.807	0.94
192_M	196_F	1.781	0.93
169_K	172_D	1.779	0.93
209_K	249_I	1.763	0.93
229_K	234_P	1.711	0.92
187_G	192_M	1.667	0.91
141_V	241_V	1.655	0.90
228_R	232_L	1.621	0.89
140_V	218_V	1.599	0.89
179_F	207_I	1.576	0.88
169_K	184_P	1.561	0.87
210_G	217_V	1.557	0.87
212_K	216_E	1.552	0.87
214_P	250_W	1.524	0.86
140_V	252_Q	1.516	0.86
165_S	192_M	1.511	0.86
149_Q	155_P	1.494	0.85
172_D	178_Y	1.493	0.85
147_E	231_I	1.481	0.84
165_S	253_Q	1.473	0.84
165_S	196_F	1.466	0.84
174_K	244_V	1.455	0.83
168_A	196_F	1.433	0.82
183_S	186_Y	1.426	0.82
221_W	250_W	1.419	0.82
214_P	217_V	1.416	0.82
171_Q	244_V	1.413	0.81
173_M	183_S	1.382	0.80
137_E	170_S	1.379	0.80
165_S	186_Y	1.349	0.78
172_D	192_M	1.341	0.78
169_K	173_M	1.339	0.78
173_M	178_Y	1.336	0.78
144_T	239_I	1.328	0.77
180_D	253_Q	1.325	0.77
192_M	253_Q	1.318	0.77
169_K	253_Q	1.318	0.77
222_M	228_R	1.281	0.74
243_Y	248_S	1.265	0.74
140_V	211_Q	1.263	0.73
244_V	249_I	1.263	0.73
210_G	250_W	1.261	0.73
172_D	189_P	1.256	0.73
147_E	151_Q	1.251	0.73
216_E	220_A	1.250	0.73
211_Q	220_A	1.245	0.72
206_N	230_N	1.237	0.72
151_Q	232_L	1.237	0.72
183_S	189_P	1.199	0.69
189_P	192_M	1.180	0.68
169_K	189_P	1.176	0.68
169_K	187_G	1.167	0.67
172_D	191_D	1.167	0.67
172_D	176_K	1.161	0.67
169_K	178_Y	1.161	0.67
222_M	232_L	1.144	0.66
161_T	164_K	1.132	0.65
170_S	242_G	1.127	0.65
211_Q	221_W	1.127	0.65
169_K	186_Y	1.122	0.64
167_R	244_V	1.120	0.64
215_E	219_K	1.115	0.64
169_K	185_T	1.105	0.63
165_S	169_K	1.103	0.63
14_G	25_S	1.078	0.61
218_V	250_W	1.077	0.61
183_S	191_D	1.077	0.61
167_R	170_S	1.077	0.61
137_E	251_T	1.071	0.60
150_K	231_I	1.065	0.60
200_Y	203_A	1.064	0.60
218_V	231_I	1.063	0.60
230_N	252_Q	1.044	0.58
202_T	235_N	1.040	0.58
189_P	222_M	1.035	0.58
193_M	203_A	1.035	0.58
153_L	234_P	1.021	0.57
140_V	239_I	1.013	0.56
173_M	189_P	1.012	0.56
133_V	167_R	1.007	0.56
167_R	242_G	1.005	0.56
207_I	217_V	1.000	0.55
135_A	159_D	1.000	0.55
188_S	191_D	0.997	0.55
174_K	249_I	0.989	0.54
189_P	203_A	0.988	0.54
190_F	193_M	0.987	0.54
108_A	118_A	0.983	0.54
181_H	227_H	0.981	0.54
183_S	190_F	0.978	0.53
217_V	243_Y	0.971	0.53
62_K	67_A	0.968	0.53
157_Q	238_H	0.963	0.52
158_I	163_S	0.959	0.52
18_F	21_V	0.958	0.52
10_A	13_V	0.953	0.52
198_I	203_A	0.951	0.51
208_A	217_V	0.950	0.51
178_Y	189_P	0.945	0.51
210_G	231_I	0.931	0.50
214_P	218_V	0.922	0.49
211_Q	214_P	0.918	0.49
107_A	113_A	0.915	0.49
105_K	109_D	0.913	0.49
133_V	137_E	0.911	0.48
241_V	249_I	0.905	0.48
173_M	191_D	0.903	0.48
219_K	223_N	0.894	0.47
139_K	176_K	0.891	0.47
97_K	107_A	0.882	0.46
190_F	198_I	0.880	0.46
189_P	231_I	0.877	0.46
222_M	230_N	0.866	0.45
165_S	190_F	0.864	0.45
19_G	24_A	0.863	0.45
178_Y	190_F	0.857	0.44
226_G	233_N	0.852	0.44
189_P	210_G	0.851	0.44
224_S	227_H	0.842	0.43
219_K	235_N	0.839	0.43
173_M	179_F	0.831	0.42
100_Q	105_K	0.830	0.42
173_M	192_M	0.830	0.42
95_T	105_K	0.827	0.42
186_Y	195_S	0.822	0.42
167_R	251_T	0.821	0.42
246_S	249_I	0.820	0.41
187_G	203_A	0.819	0.41
174_K	242_G	0.817	0.41
141_V	157_Q	0.815	0.41
242_G	251_T	0.814	0.41
135_A	139_K	0.811	0.41
184_P	192_M	0.807	0.40
193_M	253_Q	0.805	0.40
170_S	183_S	0.805	0.40
165_S	183_S	0.801	0.40
226_G	230_N	0.801	0.40
169_K	191_D	0.797	0.40
188_S	192_M	0.795	0.40
228_R	231_I	0.794	0.40
100_Q	115_K	0.791	0.39
185_T	192_M	0.790	0.39
21_V	24_A	0.789	0.39
137_E	244_V	0.787	0.39
203_A	217_V	0.781	0.39
99_A	120_A	0.780	0.39
193_M	255_I	0.777	0.38
241_V	250_W	0.762	0.37
164_K	168_A	0.761	0.37
136_Y	213_T	0.757	0.37
163_S	250_W	0.756	0.37
57_I	66_A	0.755	0.37
145_N	227_H	0.754	0.37
202_T	233_N	0.752	0.36
79_H	84_N	0.750	0.36
188_S	203_A	0.750	0.36
190_F	200_Y	0.750	0.36
113_A	121_E	0.744	0.36
143_L	210_G	0.744	0.36
106_A	109_D	0.743	0.36
210_G	220_A	0.738	0.35
60_N	64_L	0.736	0.35
173_M	207_I	0.736	0.35
24_A	28_E	0.731	0.35
183_S	203_A	0.725	0.35
242_G	249_I	0.722	0.34
186_Y	190_F	0.721	0.34
73_K	77_Q	0.720	0.34
15_L	18_F	0.717	0.34
207_I	221_W	0.716	0.34
92_K	103_T	0.715	0.34
172_D	228_R	0.712	0.34
136_Y	241_V	0.709	0.33
174_K	238_H	0.707	0.33
183_S	207_I	0.707	0.33
152_G	254_F	0.706	0.33
184_P	207_I	0.705	0.33
140_V	150_K	0.704	0.33
98_P	103_T	0.704	0.33
165_S	187_G	0.698	0.33
25_S	30_S	0.697	0.33
96_A	113_A	0.697	0.33
231_I	252_Q	0.696	0.33
178_Y	188_S	0.695	0.33
156_L	206_N	0.694	0.32
218_V	248_S	0.688	0.32
218_V	222_M	0.685	0.32
243_Y	250_W	0.684	0.32
10_A	18_F	0.684	0.32
204_G	241_V	0.684	0.32
208_A	230_N	0.672	0.31
193_M	233_N	0.670	0.31
165_S	250_W	0.670	0.31
183_S	253_Q	0.668	0.31
23_Q	27_K	0.667	0.31
140_V	241_V	0.664	0.30
174_K	253_Q	0.661	0.30
14_G	23_Q	0.660	0.30
25_S	28_E	0.659	0.30
26_A	37_V	0.657	0.30
178_Y	187_G	0.654	0.30
206_N	252_Q	0.654	0.30
165_S	189_P	0.654	0.30
21_V	34_V	0.653	0.30
70_K	74_Q	0.651	0.30
221_W	239_I	0.651	0.30
189_P	193_M	0.651	0.30
190_F	210_G	0.649	0.30
173_M	230_N	0.649	0.30
218_V	239_I	0.649	0.30
187_G	190_F	0.647	0.29
143_L	223_N	0.647	0.29
217_V	241_V	0.645	0.29
206_N	226_G	0.643	0.29
27_K	37_V	0.641	0.29
32_Q	38_K	0.640	0.29
178_Y	193_M	0.640	0.29
165_S	193_M	0.639	0.29
23_Q	26_A	0.638	0.29
206_N	232_L	0.638	0.29
101_K	113_A	0.637	0.29
29_L	37_V	0.635	0.29
147_E	250_W	0.635	0.29
138_K	159_D	0.634	0.29
53_K	56_H	0.634	0.29
179_F	184_P	0.631	0.28
179_F	183_S	0.630	0.28
214_P	239_I	0.627	0.28
10_A	19_G	0.626	0.28
80_A	84_N	0.625	0.28
221_W	249_I	0.623	0.28
245_E	248_S	0.622	0.28
147_E	228_R	0.620	0.28
169_K	193_M	0.619	0.28
76_L	87_V	0.615	0.27
218_V	232_L	0.615	0.27
165_S	203_A	0.614	0.27
170_S	245_E	0.612	0.27
118_A	121_E	0.612	0.27
187_G	198_I	0.610	0.27
168_A	171_Q	0.609	0.27
115_K	125_T	0.608	0.27
115_K	123_T	0.608	0.27
14_G	18_F	0.607	0.27
52_V	55_L	0.600	0.26
169_K	190_F	0.599	0.26
173_M	206_N	0.597	0.26
165_S	176_K	0.595	0.26
18_F	25_S	0.593	0.26
10_A	30_S	0.592	0.26
79_H	83_S	0.592	0.26
137_E	178_Y	0.590	0.26
222_M	252_Q	0.590	0.26
208_A	252_Q	0.588	0.26
213_T	250_W	0.588	0.26
101_K	106_A	0.585	0.26
191_D	223_N	0.584	0.26
102_T	107_A	0.583	0.25
59_T	63_T	0.582	0.25
212_K	250_W	0.582	0.25
184_P	187_G	0.581	0.25
174_K	209_K	0.580	0.25
172_D	187_G	0.579	0.25
217_V	220_A	0.578	0.25
23_Q	31_C	0.577	0.25
185_T	196_F	0.576	0.25
200_Y	255_I	0.575	0.25
144_T	231_I	0.574	0.25
203_A	210_G	0.574	0.25
170_S	192_M	0.573	0.25
197_G	200_Y	0.572	0.25
31_C	44_Q	0.568	0.25
36_T	45_N	0.563	0.24
85_V	88_Q	0.560	0.24
172_D	184_P	0.559	0.24
144_T	147_E	0.559	0.24
238_H	255_I	0.559	0.24
186_Y	253_Q	0.558	0.24
50_D	63_T	0.557	0.24
213_T	243_Y	0.556	0.24
137_E	163_S	0.555	0.24
190_F	255_I	0.552	0.24
93_T	98_P	0.552	0.24
92_K	99_A	0.551	0.24
217_V	239_I	0.551	0.24
193_M	200_Y	0.548	0.23
169_K	203_A	0.547	0.23
186_Y	198_I	0.546	0.23
228_R	251_T	0.545	0.23
145_N	206_N	0.545	0.23
145_N	148_R	0.544	0.23
169_K	200_Y	0.543	0.23
204_G	223_N	0.542	0.23
136_Y	211_Q	0.539	0.23
59_T	66_A	0.539	0.23
136_Y	250_W	0.537	0.23
185_T	203_A	0.537	0.23
23_Q	28_E	0.534	0.23
148_R	205_E	0.533	0.23
29_L	40_G	0.533	0.23
100_Q	103_T	0.533	0.23
178_Y	207_I	0.533	0.23
211_Q	243_Y	0.532	0.23
162_L	193_M	0.530	0.23
165_S	185_T	0.530	0.23
61_I	90_V	0.529	0.22
169_K	177_N	0.528	0.22
14_G	24_A	0.527	0.22
179_F	200_Y	0.527	0.22
176_K	185_T	0.526	0.22
196_F	216_E	0.520	0.22
174_K	246_S	0.518	0.22
171_Q	174_K	0.518	0.22
172_D	197_G	0.516	0.22
169_K	176_K	0.516	0.22
54_K	57_I	0.515	0.22
145_N	181_H	0.514	0.22
243_Y	255_I	0.513	0.22
144_T	250_W	0.513	0.22
92_K	106_A	0.513	0.22
75_L	83_S	0.512	0.22
20_G	23_Q	0.512	0.22
74_Q	82_Q	0.509	0.21
172_D	253_Q	0.506	0.21
154_K	157_Q	0.505	0.21
134_S	214_P	0.505	0.21
181_H	205_E	0.505	0.21
156_L	230_N	0.504	0.21
159_D	215_E	0.504	0.21
101_K	120_A	0.504	0.21
69_E	81_K	0.501	0.21
250_W	255_I	0.501	0.21
169_K	196_F	0.500	0.21
203_A	208_A	0.500	0.21
211_Q	216_E	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
4ifaA	1	0.9066	100	0.48	Contact Map
4h0aA	1	0.8988	100	0.511	Contact Map
4aiwA	1	0.4436	99.9	0.638	Contact Map
1cfeA	1	0.4086	99.9	0.668	Contact Map
4p27A	1	0.4358	99.7	0.743	Contact Map
3q2uA	1	0.4825	99.7	0.743	Contact Map
2ddbA	2	0.4397	99.6	0.762	Contact Map
1xtaA	2	0.4708	99.5	0.77	Contact Map
4tpvA	2	0.4397	99.3	0.8	Contact Map
1u53A	1	0.4553	99.2	0.809	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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