YVOD - BACSU - GREMLIN Contacts

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YVOD - Uncharacterized membrane protein YvoD

UniProt:	O34382	Sequences: MKKIFLAGLAAGFQTTWTLGKVIFPVTLLVTLLQHTPVMDWLVRLITPVMGLFGLSGEAAIPLVLGNMLNLYAGIAGILTLDLSVKEVFILAVMLSFCHNLIIESTVAAKVGIRIGVILAVRIGLAAVSAIVINLIWHGGKETAQYGFIAAKSAAPDSWLGMLAEALTKAGLGVLQLAAIVIPLMIIIQFLRDLGWLYRFSRWLSPFTQLLGMNKNTSMTMVTGLTIGLAYGAGVMIKAVEDDGVSKRDMTLAFIFLVACHAVVEDTLVFIPLGIPVWPLLLIRVTTAVLLTMAIAHTWKKWKPSAVGKEAI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	312 (296)
Sequences:	297 (241)
Seq/√Len:	14.0

BACSU - YVOD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
66_G	95_L	5.066	1.00
106_T	109_A	4.939	1.00
92_A	270_F	4.460	1.00
89_F	279_P	4.411	1.00
100_N	230_A	3.594	0.99
277_V	281_L	3.198	0.98
66_G	74_G	3.015	0.97
162_M	166_A	2.822	0.96
222_V	226_T	2.776	0.96
209_Q	247_K	2.750	0.95
132_V	136_I	2.537	0.93
7_A	193_D	2.478	0.92
204_L	217_T	2.471	0.92
74_G	95_L	2.436	0.91
124_G	128_V	2.408	0.91
123_I	127_A	2.321	0.89
94_M	130_A	2.298	0.89
16_T	178_A	2.283	0.88
175_L	179_A	2.274	0.88
213_M	253_A	2.260	0.88
188_I	227_I	2.246	0.88
76_A	222_V	2.217	0.87
94_M	126_A	2.207	0.87
53_F	127_A	2.184	0.86
68_M	102_I	2.157	0.85
289_V	297_H	2.140	0.85
75_I	273_L	2.134	0.85
202_R	205_S	2.047	0.82
191_L	297_H	2.044	0.82
69_L	73_A	1.981	0.80
217_T	253_A	1.966	0.79
195_G	198_Y	1.948	0.79
101_L	123_I	1.946	0.79
208_T	221_M	1.915	0.77
180_I	231_Y	1.903	0.77
285_V	293_M	1.871	0.76
191_L	199_R	1.870	0.76
252_L	296_A	1.869	0.76
53_F	130_A	1.850	0.75
256_F	260_C	1.821	0.74
197_L	236_M	1.797	0.73
107_V	240_V	1.765	0.71
12_G	182_I	1.758	0.71
6_L	61_I	1.731	0.70
297_H	300_K	1.730	0.70
93_V	133_I	1.727	0.69
60_A	63_L	1.712	0.69
162_M	165_E	1.692	0.68
57_G	94_M	1.665	0.67
156_P	161_G	1.653	0.66
23_I	30_V	1.644	0.66
12_G	231_Y	1.626	0.65
161_G	166_A	1.611	0.64
115_I	119_L	1.594	0.63
213_M	217_T	1.580	0.62
8_G	12_G	1.545	0.61
18_T	108_A	1.529	0.60
9_L	68_M	1.526	0.60
195_G	227_I	1.517	0.59
161_G	165_E	1.515	0.59
109_A	114_R	1.500	0.58
263_V	268_L	1.492	0.58
8_G	185_M	1.491	0.58
61_I	81_L	1.486	0.57
105_S	115_I	1.485	0.57
248_R	300_K	1.465	0.56
42_L	45_L	1.423	0.54
103_I	110_K	1.417	0.54
74_G	222_V	1.404	0.53
56_S	132_V	1.399	0.53
72_Y	181_V	1.394	0.52
171_G	175_L	1.376	0.52
252_L	256_F	1.361	0.51
123_I	167_L	1.357	0.50
188_I	222_V	1.356	0.50
66_G	180_I	1.355	0.50
57_G	90_I	1.334	0.49
200_F	203_W	1.330	0.49
23_I	60_A	1.311	0.48
155_A	294_A	1.300	0.47
128_V	302_W	1.300	0.47
234_G	260_C	1.292	0.47
166_A	234_G	1.285	0.47
22_V	44_R	1.277	0.46
97_F	129_S	1.274	0.46
224_G	257_L	1.259	0.45
46_I	68_M	1.250	0.45
237_I	247_K	1.244	0.44
289_V	294_A	1.231	0.44
32_L	102_I	1.229	0.44
80_T	236_M	1.225	0.43
100_N	107_V	1.223	0.43
60_A	66_G	1.221	0.43
62_P	91_L	1.214	0.43
201_S	236_M	1.212	0.43
31_T	166_A	1.200	0.42
163_L	298_T	1.184	0.41
23_I	77_G	1.182	0.41
138_H	209_Q	1.177	0.41
106_T	213_M	1.163	0.40
98_C	130_A	1.161	0.40
177_L	181_V	1.159	0.40
28_L	136_I	1.159	0.40
43_V	214_N	1.158	0.40
98_C	253_A	1.156	0.40
221_M	253_A	1.148	0.39
41_W	45_L	1.146	0.39
118_I	227_I	1.132	0.38
18_T	257_L	1.132	0.38
93_V	132_V	1.130	0.38
16_T	20_G	1.130	0.38
49_V	198_Y	1.125	0.38
101_L	119_L	1.121	0.38
21_K	207_F	1.117	0.38
136_I	141_K	1.111	0.37
14_Q	226_T	1.106	0.37
198_Y	210_L	1.104	0.37
32_L	145_Q	1.093	0.37
68_M	114_R	1.092	0.36
85_V	145_Q	1.080	0.36
260_C	288_A	1.077	0.36
200_F	204_L	1.073	0.36
20_G	177_L	1.072	0.35
137_W	278_W	1.067	0.35
120_A	128_V	1.062	0.35
26_V	30_V	1.061	0.35
222_V	227_I	1.050	0.34
43_V	219_M	1.050	0.34
236_M	245_V	1.045	0.34
281_L	296_A	1.042	0.34
204_L	219_M	1.041	0.34
77_G	250_M	1.038	0.34
73_A	272_P	1.037	0.34
53_F	94_M	1.028	0.33
126_A	279_P	1.025	0.33
234_G	256_F	1.023	0.33
202_R	286_T	1.017	0.33
9_L	186_I	1.016	0.33
278_W	282_L	1.013	0.33
51_G	128_V	1.004	0.32
285_V	289_V	1.002	0.32
73_A	92_A	1.000	0.32
22_V	114_R	0.996	0.32
11_A	223_T	0.995	0.32
102_I	262_A	0.992	0.32
150_A	243_D	0.991	0.32
130_A	250_M	0.990	0.31
54_G	134_N	0.990	0.31
80_T	215_K	0.987	0.31
74_G	119_L	0.978	0.31
31_T	251_T	0.975	0.31
235_V	254_F	0.972	0.31
200_F	297_H	0.970	0.31
131_I	295_I	0.966	0.30
52_L	136_I	0.964	0.30
189_Q	263_V	0.962	0.30
93_V	102_I	0.960	0.30
256_F	296_A	0.959	0.30
200_F	230_A	0.952	0.30
49_V	138_H	0.952	0.30
121_V	291_L	0.945	0.29
28_L	101_L	0.945	0.29
57_G	236_M	0.944	0.29
254_F	259_A	0.941	0.29
197_L	231_Y	0.939	0.29
74_G	192_R	0.934	0.29
202_R	215_K	0.933	0.29
173_G	288_A	0.930	0.29
67_N	277_V	0.930	0.29
210_L	213_M	0.928	0.29
141_K	241_E	0.928	0.29
9_L	131_I	0.924	0.28
167_L	294_A	0.920	0.28
221_M	251_T	0.917	0.28
116_G	205_S	0.916	0.28
45_L	271_I	0.916	0.28
234_G	279_P	0.914	0.28
257_L	292_T	0.909	0.28
184_L	229_L	0.905	0.28
176_Q	288_A	0.901	0.27
33_L	233_A	0.899	0.27
188_I	235_V	0.899	0.27
262_A	292_T	0.897	0.27
79_L	173_G	0.896	0.27
209_Q	245_V	0.896	0.27
196_W	289_V	0.889	0.27
121_V	255_I	0.887	0.27
73_A	220_T	0.883	0.27
26_V	102_I	0.882	0.27
204_L	222_V	0.882	0.27
213_M	234_G	0.880	0.27
231_Y	257_L	0.880	0.27
27_T	33_L	0.880	0.27
78_I	87_E	0.878	0.26
90_I	94_M	0.877	0.26
27_T	197_L	0.875	0.26
153_S	160_L	0.873	0.26
129_S	283_I	0.872	0.26
85_V	88_V	0.868	0.26
195_G	226_T	0.865	0.26
83_L	188_I	0.861	0.26
76_A	204_L	0.856	0.26
52_L	290_L	0.855	0.26
94_M	125_L	0.854	0.25
143_T	184_L	0.853	0.25
192_R	197_L	0.845	0.25
20_G	107_V	0.844	0.25
273_L	277_V	0.842	0.25
263_V	281_L	0.840	0.25
110_K	114_R	0.839	0.25
58_E	191_L	0.832	0.25
98_C	197_L	0.828	0.24
141_K	209_Q	0.826	0.24
98_C	199_R	0.826	0.24
97_F	173_G	0.823	0.24
109_A	115_I	0.815	0.24
204_L	227_I	0.815	0.24
197_L	257_L	0.812	0.24
154_A	167_L	0.812	0.24
12_G	218_S	0.811	0.24
223_T	298_T	0.808	0.24
180_I	246_S	0.808	0.24
188_I	285_V	0.808	0.24
8_G	101_L	0.806	0.24
199_R	203_W	0.805	0.24
6_L	10_A	0.803	0.23
93_V	200_F	0.802	0.23
113_I	250_M	0.801	0.23
233_A	288_A	0.801	0.23
209_Q	290_L	0.795	0.23
75_I	100_N	0.789	0.23
92_A	177_L	0.788	0.23
128_V	290_L	0.787	0.23
160_L	167_L	0.786	0.23
110_K	262_A	0.785	0.23
40_D	52_L	0.777	0.22
290_L	294_A	0.776	0.22
132_V	168_T	0.776	0.22
31_T	70_N	0.770	0.22
68_M	127_A	0.769	0.22
239_A	243_D	0.769	0.22
100_N	262_A	0.767	0.22
167_L	174_V	0.767	0.22
289_V	300_K	0.766	0.22
108_A	249_D	0.766	0.22
20_G	114_R	0.765	0.22
84_S	289_V	0.763	0.22
180_I	263_V	0.761	0.22
74_G	227_I	0.759	0.22
121_V	166_A	0.757	0.22
107_V	209_Q	0.756	0.22
211_L	249_D	0.755	0.22
113_I	257_L	0.753	0.22
10_A	101_L	0.753	0.22
254_F	279_P	0.753	0.22
133_I	262_A	0.752	0.22
20_G	256_F	0.751	0.21
29_L	200_F	0.750	0.21
127_A	301_K	0.750	0.21
12_G	197_L	0.747	0.21
145_Q	207_F	0.741	0.21
165_E	175_L	0.735	0.21
43_V	213_M	0.729	0.21
26_V	197_L	0.729	0.21
56_S	213_M	0.724	0.21
289_V	295_I	0.720	0.20
130_A	278_W	0.716	0.20
192_R	226_T	0.715	0.20
205_S	276_P	0.711	0.20
298_T	302_W	0.708	0.20
27_T	75_I	0.707	0.20
60_A	245_V	0.707	0.20
58_E	149_I	0.707	0.20
12_G	73_A	0.705	0.20
106_T	115_I	0.702	0.20
131_I	134_N	0.701	0.20
158_S	161_G	0.699	0.20
210_L	247_K	0.697	0.20
220_T	272_P	0.697	0.20
143_T	212_G	0.691	0.19
51_G	155_A	0.688	0.19
156_P	190_F	0.687	0.19
100_N	245_V	0.687	0.19
63_L	98_C	0.686	0.19
46_I	61_I	0.685	0.19
200_F	250_M	0.683	0.19
31_T	35_H	0.683	0.19
56_S	138_H	0.682	0.19
128_V	199_R	0.682	0.19
73_A	258_V	0.681	0.19
115_I	134_N	0.681	0.19
157_D	286_T	0.680	0.19
61_I	294_A	0.678	0.19
240_V	250_M	0.676	0.19
49_V	133_I	0.675	0.19
40_D	179_A	0.675	0.19
262_A	299_W	0.672	0.19
15_T	71_L	0.667	0.19
92_A	147_G	0.661	0.18
56_S	91_L	0.659	0.18
27_T	170_A	0.658	0.18
24_F	31_T	0.657	0.18
154_A	157_D	0.656	0.18
236_M	257_L	0.653	0.18
192_R	236_M	0.652	0.18
119_L	123_I	0.652	0.18
188_I	296_A	0.651	0.18
127_A	157_D	0.651	0.18
295_I	302_W	0.651	0.18
71_L	285_V	0.650	0.18
42_L	82_D	0.646	0.18
276_P	279_P	0.644	0.18
67_N	242_D	0.644	0.18
15_T	81_L	0.643	0.18
68_M	269_V	0.642	0.18
92_A	262_A	0.639	0.18
28_L	93_V	0.636	0.18
59_A	170_A	0.636	0.18
155_A	290_L	0.635	0.18
50_M	264_V	0.634	0.18
47_T	282_L	0.633	0.17
112_G	206_P	0.631	0.17
38_V	47_T	0.630	0.17
128_V	167_L	0.628	0.17
134_N	138_H	0.627	0.17
227_I	262_A	0.626	0.17
93_V	129_S	0.624	0.17
33_L	78_I	0.624	0.17
43_V	46_I	0.620	0.17
223_T	231_Y	0.618	0.17
192_R	198_Y	0.616	0.17
214_N	253_A	0.615	0.17
66_G	69_L	0.614	0.17
126_A	254_F	0.612	0.17
246_S	289_V	0.612	0.17
20_G	234_G	0.612	0.17
129_S	137_W	0.608	0.17
83_L	91_L	0.603	0.17
191_L	259_A	0.602	0.17
169_K	251_T	0.601	0.17
118_I	262_A	0.600	0.16
125_L	287_T	0.599	0.16
33_L	83_L	0.594	0.16
161_G	164_A	0.593	0.16
137_W	282_L	0.590	0.16
209_Q	215_K	0.589	0.16
121_V	252_L	0.589	0.16
6_L	148_F	0.589	0.16
219_M	250_M	0.589	0.16
47_T	149_I	0.588	0.16
31_T	170_A	0.587	0.16
171_G	301_K	0.586	0.16
6_L	247_K	0.585	0.16
141_K	174_V	0.583	0.16
53_F	56_S	0.583	0.16
160_L	164_A	0.580	0.16
82_D	154_A	0.578	0.16
184_L	237_I	0.577	0.16
218_S	286_T	0.576	0.16
76_A	219_M	0.575	0.16
17_W	79_L	0.575	0.16
106_T	253_A	0.574	0.16
11_A	195_G	0.573	0.16
82_D	190_F	0.573	0.16
132_V	164_A	0.572	0.16
186_I	203_W	0.572	0.16
16_T	26_V	0.572	0.16
85_V	140_G	0.569	0.16
225_L	271_I	0.569	0.16
161_G	190_F	0.568	0.16
166_A	300_K	0.568	0.16
10_A	56_S	0.567	0.16
43_V	164_A	0.567	0.16
73_A	201_S	0.567	0.16
68_M	231_Y	0.566	0.15
15_T	18_T	0.566	0.15
120_A	160_L	0.565	0.15
22_V	138_H	0.563	0.15
81_L	250_M	0.562	0.15
57_G	276_P	0.562	0.15
22_V	93_V	0.562	0.15
116_G	124_G	0.562	0.15
73_A	105_S	0.561	0.15
56_S	204_L	0.561	0.15
123_I	207_F	0.560	0.15
250_M	254_F	0.559	0.15
20_G	24_F	0.559	0.15
103_I	204_L	0.559	0.15
171_G	300_K	0.559	0.15
170_A	211_L	0.556	0.15
275_I	280_L	0.555	0.15
62_P	78_I	0.554	0.15
77_G	223_T	0.553	0.15
59_A	62_P	0.553	0.15
19_L	267_T	0.552	0.15
204_L	226_T	0.552	0.15
131_I	300_K	0.552	0.15
21_K	238_K	0.551	0.15
254_F	281_L	0.549	0.15
21_K	150_A	0.548	0.15
46_I	200_F	0.548	0.15
233_A	256_F	0.546	0.15
210_L	217_T	0.545	0.15
129_S	262_A	0.544	0.15
9_L	290_L	0.544	0.15
173_G	256_F	0.544	0.15
98_C	233_A	0.543	0.15
170_A	257_L	0.543	0.15
217_T	243_D	0.543	0.15
144_A	280_L	0.542	0.15
157_D	298_T	0.541	0.15
6_L	134_N	0.541	0.15
124_G	295_I	0.538	0.15
138_H	264_V	0.537	0.15
205_S	214_N	0.535	0.15
19_L	180_I	0.535	0.15
78_I	88_V	0.534	0.15
75_I	88_V	0.534	0.15
235_V	250_M	0.532	0.15
180_I	287_T	0.529	0.14
68_M	229_L	0.527	0.14
37_P	262_A	0.525	0.14
30_V	226_T	0.524	0.14
68_M	120_A	0.524	0.14
71_L	95_L	0.524	0.14
165_E	294_A	0.522	0.14
32_L	289_V	0.521	0.14
68_M	187_I	0.521	0.14
67_N	181_V	0.519	0.14
46_I	56_S	0.518	0.14
167_L	175_L	0.516	0.14
141_K	150_A	0.516	0.14
128_V	286_T	0.516	0.14
93_V	100_N	0.514	0.14
123_I	264_V	0.511	0.14
111_V	227_I	0.510	0.14
279_P	283_I	0.510	0.14
150_A	155_A	0.509	0.14
57_G	197_L	0.509	0.14
130_A	292_T	0.507	0.14
7_A	52_L	0.505	0.14
29_L	102_I	0.505	0.14
34_Q	191_L	0.504	0.14
201_S	218_S	0.500	0.14

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
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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
4pd6A	3	0.8558	96.6	0.936	Contact Map
4r1iA	2	0.6506	15.9	0.974	Contact Map
4r0cA	3	0.6122	14.6	0.974	Contact Map
3w9iA	3	0.4551	4.9	0.979	Contact Map
2gfpA	2	0.391	4.8	0.979	Contact Map
2nwlA	3	0.5288	3.4	0.981	Contact Map
1jb0K	1	0.1314	3.4	0.981	Contact Map
2m20A	2	0.1218	3.2	0.981	Contact Map
4kt0K	1	0.1538	2.8	0.982	Contact Map
4gxbB	1	0.0032	2.6	0.982	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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