VATD - HALSA - GREMLIN Contacts

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VATD - V-type ATP synthase subunit D

UniProt:	Q9HNE7	Sequences: MAQDIKPTRKNLMEIEDRIDLSERGHDTLEQKRDGLIMEFMDILDQSQDVRSGLEGDYETAQQKINMARAMEGDVAVSGAAAALEEYPEITVESMNIMGVVVPQIESTKVKKSFDKRGYGILGTSARIDEAADAYEELLESIVLAAEVETAMKKMLTEIETTKRRVNALEFKLLPELHEGKEYIDQKLEEKEREEMFRMKKVKDKKEAQEEAADEAAAAESTGA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	224 (202)
Sequences:	911 (571)
Seq/√Len:	40.2

HALSA - VATD
SULSO - VATD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
46_Q	144_L	6.913	1.00
23_E	178_H	4.999	1.00
49_D	53_G	4.298	1.00
53_G	141_S	3.598	1.00
11_N	14_E	2.824	1.00
40_F	159_I	2.581	1.00
57_D	137_E	2.571	1.00
119_Y	129_D	2.504	1.00
15_I	181_K	2.435	1.00
95_M	104_Q	2.399	1.00
195_E	198_R	2.328	1.00
19_I	181_K	2.259	1.00
18_R	177_L	2.248	1.00
194_E	200_K	2.126	0.99
60_T	134_A	2.112	0.99
18_R	180_G	2.109	0.99
48_Q	52_S	2.071	0.99
62_Q	135_Y	2.028	0.99
190_E	193_R	1.983	0.99
12_L	181_K	1.931	0.99
96_N	100_V	1.923	0.99
169_L	173_L	1.903	0.98
28_T	32_K	1.893	0.98
91_T	106_E	1.862	0.98
25_G	165_R	1.826	0.98
39_E	95_M	1.821	0.98
137_E	140_E	1.806	0.98
26_H	166_V	1.773	0.98
20_D	23_E	1.773	0.98
173_L	197_F	1.769	0.98
25_G	28_T	1.745	0.97
184_I	188_L	1.723	0.97
46_Q	137_E	1.692	0.97
56_G	59_E	1.691	0.97
97_I	102_V	1.682	0.97
106_E	144_L	1.680	0.97
196_M	200_K	1.663	0.96
102_V	151_A	1.642	0.96
92_V	105_I	1.622	0.96
34_D	68_A	1.582	0.95
61_A	135_Y	1.581	0.95
32_K	162_T	1.573	0.95
15_I	177_L	1.551	0.95
57_D	144_L	1.546	0.95
25_G	32_K	1.543	0.94
69_R	74_D	1.541	0.94
57_D	141_S	1.531	0.94
53_G	137_E	1.528	0.94
61_A	65_I	1.524	0.94
33_R	205_K	1.464	0.93
26_H	170_E	1.435	0.92
51_R	149_E	1.431	0.92
5_I	180_G	1.411	0.91
36_L	154_K	1.407	0.91
194_E	198_R	1.379	0.90
34_D	166_V	1.341	0.89
106_E	140_E	1.320	0.88
4_D	180_G	1.317	0.88
39_E	97_I	1.314	0.88
119_Y	124_T	1.304	0.88
19_I	174_L	1.303	0.88
30_E	40_F	1.302	0.88
30_E	97_I	1.301	0.88
9_R	35_G	1.301	0.88
180_G	183_Y	1.296	0.87
43_I	151_A	1.295	0.87
6_K	11_N	1.278	0.87
121_I	172_K	1.264	0.86
68_A	131_A	1.259	0.86
24_R	27_D	1.240	0.85
9_R	163_K	1.216	0.84
72_E	125_S	1.206	0.83
72_E	128_I	1.199	0.83
29_L	32_K	1.171	0.81
91_T	108_T	1.168	0.81
32_K	100_V	1.167	0.81
60_T	137_E	1.117	0.78
126_A	147_E	1.114	0.78
130_E	134_A	1.114	0.78
18_R	24_R	1.095	0.77
202_V	206_K	1.085	0.76
109_K	140_E	1.072	0.75
163_K	200_K	1.067	0.75
89_E	108_T	1.066	0.75
203_K	207_E	1.057	0.74
36_L	162_T	1.055	0.74
61_A	138_L	1.051	0.74
165_R	188_L	1.048	0.73
98_M	149_E	1.042	0.73
32_K	36_L	1.040	0.73
64_K	134_A	1.036	0.73
176_E	180_G	1.031	0.72
51_R	55_E	1.026	0.72
163_K	187_K	0.985	0.69
191_K	202_V	0.981	0.68
93_E	144_L	0.981	0.68
22_S	103_P	0.979	0.68
56_G	60_T	0.978	0.68
51_R	195_E	0.966	0.67
90_I	105_I	0.965	0.67
197_F	205_K	0.960	0.67
15_I	180_G	0.957	0.66
57_D	134_A	0.952	0.66
33_R	77_V	0.940	0.65
133_D	137_E	0.935	0.65
198_R	201_K	0.931	0.64
30_E	33_R	0.931	0.64
52_S	56_G	0.926	0.64
52_S	90_I	0.924	0.64
30_E	96_N	0.924	0.64
93_E	106_E	0.923	0.64
34_D	171_F	0.922	0.64
22_S	165_R	0.912	0.63
37_I	159_I	0.910	0.63
9_R	40_F	0.906	0.62
67_M	115_D	0.904	0.62
65_I	99_G	0.903	0.62
177_L	180_G	0.901	0.62
37_I	119_Y	0.901	0.62
99_G	155_M	0.897	0.61
169_L	190_E	0.897	0.61
27_D	31_Q	0.897	0.61
201_K	204_D	0.884	0.60
180_G	190_E	0.880	0.60
50_V	77_V	0.879	0.60
130_E	133_D	0.877	0.60
28_T	165_R	0.868	0.59
46_Q	49_D	0.866	0.59
107_S	143_V	0.861	0.58
40_F	97_I	0.853	0.57
73_G	99_G	0.850	0.57
64_K	131_A	0.843	0.57
133_D	141_S	0.843	0.57
113_S	182_E	0.837	0.56
53_G	60_T	0.831	0.55
73_G	200_K	0.829	0.55
18_R	30_E	0.829	0.55
50_V	117_R	0.828	0.55
64_K	138_L	0.817	0.54
73_G	155_M	0.814	0.54
22_S	28_T	0.810	0.54
45_D	48_Q	0.807	0.53
118_G	136_E	0.804	0.53
10_K	25_G	0.803	0.53
158_E	161_T	0.796	0.52
47_S	152_M	0.796	0.52
49_D	115_D	0.795	0.52
5_I	91_T	0.792	0.52
45_D	130_E	0.786	0.51
110_V	114_F	0.781	0.51
143_V	197_F	0.780	0.51
41_M	148_V	0.779	0.51
85_E	189_E	0.777	0.51
93_E	104_Q	0.773	0.50
68_A	72_E	0.771	0.50
54_L	145_A	0.757	0.49
99_G	200_K	0.752	0.48
6_K	9_R	0.751	0.48
152_M	156_L	0.746	0.48
11_N	186_Q	0.745	0.48
150_T	160_E	0.743	0.47
175_P	190_E	0.743	0.47
116_K	202_V	0.737	0.47
19_I	178_H	0.734	0.47
18_R	191_K	0.729	0.46
193_R	200_K	0.726	0.46
97_I	198_R	0.725	0.46
56_G	97_I	0.724	0.46
21_L	73_G	0.710	0.44
176_E	196_M	0.709	0.44
23_E	50_V	0.709	0.44
41_M	152_M	0.709	0.44
141_S	144_L	0.709	0.44
14_E	151_A	0.709	0.44
68_A	75_V	0.707	0.44
64_K	67_M	0.707	0.44
96_N	164_R	0.705	0.44
58_Y	65_I	0.705	0.44
40_F	163_K	0.704	0.44
57_D	138_L	0.703	0.44
80_A	108_T	0.703	0.44
59_E	92_V	0.702	0.44
26_H	191_K	0.701	0.44
19_I	160_E	0.695	0.43
25_G	188_L	0.693	0.43
58_Y	138_L	0.690	0.43
64_K	78_S	0.686	0.42
40_F	164_R	0.686	0.42
100_V	162_T	0.684	0.42
80_A	124_T	0.683	0.42
39_E	154_K	0.677	0.41
30_E	170_E	0.676	0.41
167_N	188_L	0.675	0.41
131_A	185_D	0.673	0.41
30_E	191_K	0.672	0.41
7_P	82_A	0.671	0.41
16_E	26_H	0.669	0.41
174_L	178_H	0.668	0.41
89_E	115_D	0.668	0.41
97_I	146_A	0.667	0.41
131_A	134_A	0.667	0.41
6_K	202_V	0.661	0.40
121_I	124_T	0.659	0.40
6_K	14_E	0.658	0.40
142_I	166_V	0.658	0.40
9_R	191_K	0.658	0.40
33_R	73_G	0.657	0.40
23_E	173_L	0.656	0.40
32_K	188_L	0.653	0.39
164_R	170_E	0.647	0.39
146_A	203_K	0.646	0.39
85_E	114_F	0.645	0.39
67_M	90_I	0.642	0.38
59_E	187_K	0.638	0.38
35_G	39_E	0.637	0.38
37_I	41_M	0.637	0.38
122_L	185_D	0.635	0.38
29_L	36_L	0.635	0.38
89_E	110_V	0.633	0.38
68_A	103_P	0.632	0.37
117_R	136_E	0.631	0.37
29_L	154_K	0.631	0.37
10_K	28_T	0.626	0.37
162_T	168_A	0.626	0.37
13_M	99_G	0.613	0.36
152_M	201_K	0.607	0.35
164_R	199_M	0.605	0.35
173_L	177_L	0.603	0.35
7_P	34_D	0.601	0.35
7_P	183_Y	0.601	0.35
18_R	139_L	0.599	0.35
60_T	185_D	0.596	0.34
20_D	113_S	0.594	0.34
34_D	169_L	0.594	0.34
59_E	88_P	0.592	0.34
192_E	207_E	0.590	0.34
26_H	171_F	0.585	0.34
9_R	30_E	0.583	0.33
204_D	207_E	0.580	0.33
76_A	79_G	0.577	0.33
16_E	181_K	0.575	0.33
59_E	157_T	0.572	0.32
8_T	12_L	0.571	0.32
17_D	120_G	0.570	0.32
35_G	135_Y	0.570	0.32
172_K	196_M	0.569	0.32
51_R	156_L	0.565	0.32
5_I	63_Q	0.565	0.32
125_S	169_L	0.564	0.32
24_R	171_F	0.559	0.31
96_N	99_G	0.557	0.31
83_A	197_F	0.554	0.31
144_L	148_V	0.553	0.31
7_P	168_A	0.553	0.31
68_A	97_I	0.552	0.31
6_K	171_F	0.552	0.31
61_A	142_I	0.550	0.31
59_E	63_Q	0.550	0.31
10_K	164_R	0.549	0.31
163_K	170_E	0.547	0.31
44_L	47_S	0.546	0.30
122_L	172_K	0.545	0.30
80_A	87_Y	0.542	0.30
12_L	131_A	0.541	0.30
134_A	137_E	0.539	0.30
98_M	192_E	0.536	0.30
43_I	152_M	0.536	0.30
107_S	139_L	0.535	0.30
17_D	110_V	0.535	0.30
10_K	195_E	0.534	0.29
165_R	168_A	0.533	0.29
189_E	195_E	0.533	0.29
29_L	59_E	0.532	0.29
93_E	137_E	0.529	0.29
12_L	109_K	0.528	0.29
95_M	137_E	0.524	0.29
31_Q	206_K	0.522	0.29
140_E	197_F	0.521	0.29
23_E	60_T	0.519	0.28
30_E	166_V	0.518	0.28
117_R	189_E	0.517	0.28
41_M	173_L	0.516	0.28
49_D	141_S	0.514	0.28
117_R	132_A	0.514	0.28
81_A	105_I	0.513	0.28
72_E	184_I	0.513	0.28
57_D	62_Q	0.511	0.28
29_L	164_R	0.511	0.28
144_L	178_H	0.510	0.28
34_D	66_N	0.510	0.28
32_K	159_I	0.509	0.28
15_I	169_L	0.508	0.28
71_M	152_M	0.507	0.27
8_T	73_G	0.507	0.27
63_Q	66_N	0.506	0.27
32_K	165_R	0.506	0.27
100_V	120_G	0.504	0.27
150_T	200_K	0.504	0.27
10_K	13_M	0.503	0.27
108_T	182_E	0.502	0.27
100_V	189_E	0.502	0.27
69_R	159_I	0.501	0.27
173_L	191_K	0.500	0.27

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
4rndA	2	0.7902	100	0.121	Contact Map
3aonA	1	0.8348	100	0.126	Contact Map
3w3aG	1	0.9375	100	0.138	Contact Map
4iloA	3	0.4107	27.3	0.948	Contact Map
4cg4A	2	0.4107	14.1	0.955	Contact Map
3na7A	1	0.4062	13.8	0.955	Contact Map
3wuqA	1	0.2946	11.8	0.956	Contact Map
1yz7A	1	0.5759	9.6	0.958	Contact Map
4cgkA	3	0.7277	8.2	0.959	Contact Map
2wujA	2	0.2232	8.2	0.959	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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