YKNW - BACSU - GREMLIN Contacts

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YKNW - Membrane protein YknW

UniProt:	O31709	Sequences: METNVEKNSGTATEKPSLFGVITSPSVQFERIRERPAVWGPLLIVAAIIIVGAVLQSLGTDYSELLKSQDTQGLSAEQMETVATITKFGGMAGAIIGGIAALFIAPLIYWLCVKVSGGVTTYKKMLSLSLFVSLISSLGLLVNGIVAFTTDVNPLYSTTSLAGIIPSDGALASVLNTFEIFSIWSFVLLAIGLHKTGGISKKAGWISAIILFGILVVFSLFSGLINSVAGA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	231 (207)
Sequences:	326 (273)
Seq/√Len:	19.0

BACSU - YKNW

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
159_T	179_E	3.580	1.00
103_F	122_Y	3.566	1.00
135_I	188_L	3.160	0.99
47_A	141_L	3.006	0.99
190_A	205_W	2.833	0.99
128_L	192_G	2.776	0.98
51_V	59_G	2.443	0.96
128_L	131_F	2.417	0.96
181_F	192_G	2.358	0.95
103_F	126_L	2.280	0.95
142_V	200_S	2.273	0.94
133_S	138_L	2.271	0.94
32_I	192_G	2.177	0.93
104_I	107_L	2.148	0.93
22_I	38_V	2.053	0.91
181_F	184_W	2.032	0.90
25_P	192_G	2.004	0.90
25_P	184_W	1.989	0.89
141_L	218_F	1.968	0.89
95_I	99_I	1.958	0.89
49_I	96_I	1.939	0.88
55_L	149_T	1.890	0.87
28_Q	212_F	1.863	0.86
151_D	180_I	1.836	0.85
106_P	221_F	1.780	0.83
132_V	189_L	1.744	0.82
16_P	28_Q	1.742	0.82
23_T	206_I	1.712	0.81
94_A	126_L	1.688	0.80
30_E	195_K	1.660	0.78
50_I	91_M	1.644	0.78
96_I	146_V	1.633	0.77
190_A	207_S	1.633	0.77
125_M	196_T	1.613	0.76
53_A	94_A	1.605	0.76
44_I	173_S	1.565	0.74
106_P	122_Y	1.548	0.73
79_M	84_T	1.527	0.72
18_L	39_W	1.472	0.69
19_F	22_I	1.469	0.69
17_S	31_R	1.462	0.69
108_I	128_L	1.426	0.67
22_I	202_K	1.420	0.67
135_I	201_K	1.416	0.66
32_I	210_I	1.416	0.66
104_I	206_I	1.393	0.65
141_L	204_G	1.392	0.65
95_I	209_I	1.384	0.64
39_W	188_L	1.371	0.64
83_A	142_V	1.368	0.64
120_T	124_K	1.359	0.63
116_S	199_I	1.357	0.63
107_L	122_Y	1.345	0.62
184_W	192_G	1.335	0.62
111_L	134_L	1.330	0.61
20_G	28_Q	1.321	0.61
78_Q	108_I	1.318	0.61
153_N	214_I	1.304	0.60
104_I	213_G	1.301	0.60
34_E	188_L	1.291	0.59
16_P	19_F	1.263	0.57
50_I	54_V	1.254	0.57
93_G	97_G	1.236	0.56
141_L	145_I	1.233	0.55
174_V	206_I	1.215	0.54
21_V	162_A	1.208	0.54
79_M	157_S	1.207	0.54
32_I	38_V	1.206	0.54
207_S	217_V	1.206	0.54
35_R	43_L	1.199	0.53
36_P	114_K	1.194	0.53
42_L	167_S	1.190	0.53
30_E	180_I	1.189	0.53
18_L	188_L	1.185	0.52
89_G	142_V	1.181	0.52
63_S	77_E	1.178	0.52
139_G	156_Y	1.175	0.52
81_T	94_A	1.174	0.52
146_V	203_A	1.174	0.52
89_G	93_G	1.174	0.52
96_I	202_K	1.173	0.52
98_G	129_S	1.173	0.52
109_Y	122_Y	1.167	0.51
92_A	96_I	1.162	0.51
120_T	196_T	1.160	0.51
110_W	125_M	1.142	0.50
128_L	132_V	1.138	0.49
31_R	104_I	1.137	0.49
37_A	163_G	1.135	0.49
46_A	137_S	1.133	0.49
159_T	192_G	1.130	0.49
76_A	80_E	1.122	0.48
73_G	82_V	1.111	0.48
45_V	206_I	1.110	0.48
23_T	104_I	1.104	0.47
31_R	147_A	1.098	0.47
132_V	207_S	1.085	0.46
166_P	175_L	1.073	0.45
98_G	122_Y	1.068	0.45
113_V	118_G	1.066	0.45
20_G	135_I	1.060	0.44
120_T	197_G	1.056	0.44
35_R	126_L	1.055	0.44
52_G	164_I	1.052	0.44
84_T	157_S	1.047	0.44
102_L	189_L	1.033	0.43
24_S	122_Y	1.030	0.43
164_I	184_W	1.015	0.42
98_G	144_G	1.004	0.41
28_Q	38_V	1.003	0.41
85_I	206_I	1.001	0.41
171_L	196_T	0.999	0.41
104_I	129_S	0.996	0.41
144_G	217_V	0.983	0.40
63_S	111_L	0.973	0.39
81_T	223_G	0.972	0.39
96_I	215_L	0.971	0.39
107_L	110_W	0.970	0.39
132_V	185_S	0.969	0.39
63_S	79_M	0.964	0.39
162_A	166_P	0.958	0.38
102_L	188_L	0.957	0.38
23_T	92_A	0.956	0.38
30_E	33_R	0.955	0.38
60_T	104_I	0.954	0.38
39_W	44_I	0.953	0.38
35_R	92_A	0.947	0.38
45_V	176_N	0.947	0.38
196_T	211_L	0.943	0.37
27_V	31_R	0.940	0.37
44_I	100_A	0.939	0.37
194_H	212_F	0.932	0.37
161_L	203_A	0.929	0.37
113_V	197_G	0.925	0.36
127_S	130_L	0.924	0.36
172_A	213_G	0.914	0.36
38_V	187_V	0.914	0.36
148_F	213_G	0.910	0.35
171_L	189_L	0.910	0.35
120_T	125_M	0.908	0.35
51_V	215_L	0.907	0.35
122_Y	126_L	0.898	0.35
74_L	136_S	0.897	0.35
107_L	131_F	0.894	0.34
74_L	99_I	0.894	0.34
29_F	188_L	0.893	0.34
41_P	109_Y	0.889	0.34
100_A	219_S	0.887	0.34
197_G	212_F	0.883	0.34
181_F	187_V	0.883	0.34
103_F	107_L	0.870	0.33
110_W	120_T	0.868	0.33
195_K	211_L	0.867	0.33
22_I	162_A	0.866	0.33
21_V	134_L	0.866	0.33
25_P	106_P	0.866	0.33
128_L	212_F	0.856	0.32
72_Q	214_I	0.850	0.32
135_I	211_L	0.845	0.32
114_K	146_V	0.841	0.32
128_L	211_L	0.841	0.32
190_A	201_K	0.841	0.32
108_I	131_F	0.839	0.31
53_A	90_G	0.837	0.31
32_I	165_I	0.836	0.31
50_I	58_L	0.834	0.31
16_P	31_R	0.833	0.31
88_F	209_I	0.828	0.31
44_I	176_N	0.828	0.31
108_I	171_L	0.826	0.31
24_S	193_L	0.822	0.30
38_V	183_I	0.820	0.30
45_V	198_G	0.816	0.30
95_I	214_I	0.814	0.30
25_P	41_P	0.814	0.30
76_A	104_I	0.809	0.30
115_V	148_F	0.807	0.30
119_V	166_P	0.802	0.29
127_S	196_T	0.799	0.29
50_I	140_L	0.783	0.28
102_L	132_V	0.783	0.28
158_T	163_G	0.783	0.28
42_L	130_L	0.781	0.28
207_S	211_L	0.781	0.28
111_L	217_V	0.781	0.28
110_W	179_E	0.780	0.28
42_L	62_Y	0.760	0.27
96_I	148_F	0.754	0.27
114_K	183_I	0.754	0.27
51_V	198_G	0.747	0.27
101_A	218_F	0.746	0.27
217_V	222_S	0.733	0.26
93_G	214_I	0.727	0.26
141_L	186_F	0.723	0.25
38_V	130_L	0.723	0.25
194_H	199_I	0.723	0.25
63_S	173_S	0.719	0.25
17_S	134_L	0.718	0.25
54_V	100_A	0.716	0.25
76_A	94_A	0.714	0.25
39_W	42_L	0.710	0.25
134_L	188_L	0.707	0.25
43_L	106_P	0.704	0.25
142_V	188_L	0.704	0.25
199_I	210_I	0.704	0.25
36_P	128_L	0.700	0.24
64_E	127_S	0.699	0.24
113_V	199_I	0.693	0.24
144_G	174_V	0.691	0.24
109_Y	166_P	0.690	0.24
85_I	214_I	0.680	0.23
146_V	193_L	0.678	0.23
57_S	117_G	0.678	0.23
197_G	211_L	0.677	0.23
41_P	122_Y	0.673	0.23
158_T	164_I	0.672	0.23
16_P	38_V	0.671	0.23
50_I	167_S	0.669	0.23
50_I	191_I	0.665	0.23
45_V	138_L	0.661	0.23
51_V	97_G	0.660	0.23
45_V	153_N	0.657	0.22
186_F	216_V	0.657	0.22
167_S	175_L	0.654	0.22
47_A	147_A	0.649	0.22
26_S	197_G	0.648	0.22
124_K	198_G	0.647	0.22
39_W	197_G	0.642	0.22
35_R	127_S	0.642	0.22
131_F	134_L	0.639	0.22
81_T	213_G	0.636	0.22
178_F	194_H	0.634	0.21
100_A	142_V	0.633	0.21
138_L	174_V	0.632	0.21
52_G	117_G	0.630	0.21
167_S	172_A	0.628	0.21
25_P	122_Y	0.628	0.21
35_R	145_I	0.627	0.21
48_I	223_G	0.627	0.21
113_V	196_T	0.625	0.21
137_S	156_Y	0.624	0.21
18_L	37_A	0.623	0.21
43_L	214_I	0.623	0.21
178_F	183_I	0.622	0.21
112_C	180_I	0.620	0.21
16_P	20_G	0.620	0.21
48_I	207_S	0.612	0.21
92_A	111_L	0.611	0.20
73_G	106_P	0.610	0.20
36_P	107_L	0.609	0.20
117_G	198_G	0.602	0.20
129_S	187_V	0.601	0.20
92_A	112_C	0.599	0.20
22_I	104_I	0.598	0.20
45_V	106_P	0.596	0.20
27_V	44_I	0.591	0.20
108_I	156_Y	0.587	0.20
109_Y	152_V	0.586	0.19
107_L	216_V	0.586	0.19
118_G	217_V	0.585	0.19
36_P	127_S	0.585	0.19
122_Y	184_W	0.582	0.19
42_L	144_G	0.578	0.19
100_A	192_G	0.578	0.19
141_L	203_A	0.577	0.19
93_G	99_I	0.575	0.19
104_I	155_L	0.575	0.19
129_S	133_S	0.572	0.19
177_T	180_I	0.568	0.19
173_S	179_E	0.566	0.19
171_L	208_A	0.566	0.19
108_I	215_L	0.565	0.19
56_Q	96_I	0.557	0.18
107_L	218_F	0.553	0.18
102_L	133_S	0.552	0.18
22_I	115_V	0.551	0.18
109_Y	149_T	0.551	0.18
51_V	55_L	0.549	0.18
82_V	86_T	0.549	0.18
91_M	144_G	0.547	0.18
143_N	183_I	0.544	0.18
199_I	224_L	0.541	0.18
47_A	178_F	0.541	0.18
97_G	200_S	0.539	0.18
98_G	140_L	0.538	0.18
40_G	147_A	0.529	0.17
95_I	108_I	0.528	0.17
78_Q	101_A	0.528	0.17
30_E	183_I	0.528	0.17
103_F	170_A	0.528	0.17
31_R	110_W	0.526	0.17
32_I	149_T	0.523	0.17
159_T	193_L	0.523	0.17
180_I	217_V	0.523	0.17
190_A	195_K	0.520	0.17
80_E	142_V	0.520	0.17
25_P	135_I	0.519	0.17
126_L	172_A	0.518	0.17
53_A	93_G	0.517	0.17
139_G	181_F	0.515	0.17
39_W	163_G	0.514	0.17
121_T	130_L	0.513	0.17
124_K	213_G	0.512	0.17
16_P	205_W	0.509	0.17
102_L	197_G	0.508	0.17
41_P	127_S	0.507	0.17
78_Q	188_L	0.504	0.16
82_V	96_I	0.503	0.16
121_T	137_S	0.502	0.16
47_A	77_E	0.500	0.16

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
2ww9A	1	0.6623	8.5	0.953	Contact Map
2kogA	1	0.2597	5.6	0.956	Contact Map
4zrlB	1	0.2381	5	0.957	Contact Map
3pjzA	2	0.4156	4.5	0.958	Contact Map
2jwaA	2	0.1905	4.5	0.958	Contact Map
3mp7B	1	0.2294	3.9	0.96	Contact Map
3fymA	1	0.0649	3.7	0.96	Contact Map
1dofA	4	0.381	3.7	0.96	Contact Map
1pfiA	7	0.1991	3.5	0.961	Contact Map
2l2tA	2	0.1905	3.4	0.961	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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