YHHQ - ECOLI - GREMLIN Contacts

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YHHQ - Inner membrane protein YhhQ

UniProt:	P37619	Sequences: MNVFSQTQRYKALFWLSLFHLLVITSSNYLVQLPVSILGFHTTWGAFSFPFIFLATDLTVRIFGAPLARRIIFAVMIPALLISYVISSLFYMGSWQGFGALAHFNLFVARIATASFMAYALGQILDVHVFNRLRQSRRWWLAPTASTLFGNVSDTLAFFFIAFWRSPDAFMAEHWMEIALVDYCFKVLISIVFFLPMYGVLLNMLLKRLADKSEINALQAS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12217
Length:	221 (195)
Sequences:	1755 (1078)
Seq/√Len:	77.2

ECOLI - YHHQ
BACSU - YPDP
HALSA - Q9HN39

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
125_L	153_S	4.706	1.00
117_M	161_I	4.373	1.00
110_R	165_R	3.444	1.00
140_W	199_G	3.089	1.00
132_R	135_Q	2.824	1.00
114_A	161_I	2.806	1.00
59_T	71_I	2.699	1.00
157_A	161_I	2.687	1.00
100_A	103_H	2.569	1.00
92_M	95_W	2.549	1.00
117_M	157_A	2.356	1.00
171_M	174_H	2.280	1.00
23_V	52_I	2.280	1.00
152_V	183_Y	2.229	1.00
73_F	124_I	2.202	1.00
99_G	102_A	2.147	1.00
57_D	146_S	2.110	1.00
155_T	186_K	2.093	1.00
17_S	71_I	2.093	1.00
49_F	122_G	2.085	1.00
66_P	69_R	1.927	1.00
73_F	77_I	1.878	1.00
98_F	102_A	1.867	1.00
156_L	179_A	1.855	1.00
125_L	149_F	1.831	1.00
75_V	119_Y	1.827	1.00
129_V	133_L	1.741	1.00
60_V	131_N	1.741	1.00
121_L	157_A	1.739	1.00
144_T	194_F	1.696	1.00
158_F	162_A	1.695	1.00
31_V	43_T	1.673	1.00
28_N	115_S	1.652	1.00
152_V	156_L	1.650	1.00
138_R	141_L	1.644	1.00
122_G	150_G	1.627	1.00
90_F	102_A	1.627	1.00
133_L	136_S	1.624	1.00
194_F	199_G	1.622	1.00
25_T	82_I	1.607	1.00
148_L	183_Y	1.605	1.00
110_R	163_F	1.600	1.00
123_Q	127_V	1.597	1.00
125_L	129_V	1.584	0.99
43_T	182_D	1.577	0.99
204_M	208_R	1.500	0.99
121_L	153_S	1.482	0.99
174_H	177_E	1.462	0.99
143_P	194_F	1.451	0.99
126_D	150_G	1.409	0.99
148_L	187_V	1.406	0.99
21_L	25_T	1.367	0.99
18_L	74_A	1.358	0.98
56_T	126_D	1.348	0.98
175_W	179_A	1.342	0.98
155_T	183_Y	1.317	0.98
203_N	207_K	1.302	0.98
43_T	159_F	1.296	0.98
143_P	193_F	1.296	0.98
110_R	166_S	1.260	0.97
83_S	112_A	1.256	0.97
128_H	132_R	1.250	0.97
139_W	198_Y	1.241	0.97
140_W	194_F	1.235	0.97
115_S	154_D	1.230	0.97
46_A	182_D	1.228	0.97
31_V	46_A	1.223	0.97
54_L	198_Y	1.220	0.97
126_D	130_F	1.204	0.97
172_A	176_M	1.191	0.96
66_P	70_R	1.190	0.96
79_A	83_S	1.169	0.96
203_N	206_L	1.160	0.96
111_I	162_A	1.159	0.96
123_Q	130_F	1.150	0.96
31_V	182_D	1.137	0.95
22_L	78_P	1.133	0.95
91_Y	106_L	1.132	0.95
58_L	201_L	1.120	0.95
183_Y	187_V	1.116	0.95
61_R	142_A	1.115	0.95
76_M	116_F	1.113	0.95
80_L	116_F	1.094	0.94
177_E	181_V	1.093	0.94
146_S	190_S	1.074	0.94
193_F	196_P	1.072	0.94
151_N	190_S	1.071	0.94
154_D	158_F	1.063	0.93
65_A	127_V	1.062	0.93
65_A	69_R	1.054	0.93
16_L	55_A	1.047	0.93
89_L	101_L	1.045	0.93
170_F	178_I	1.042	0.93
33_L	98_F	1.031	0.92
117_M	121_L	1.022	0.92
184_C	188_L	1.006	0.91
57_D	147_T	0.996	0.91
36_S	39_G	0.989	0.91
160_F	175_W	0.984	0.90
76_M	120_A	0.973	0.90
129_V	132_R	0.972	0.90
37_I	42_T	0.970	0.90
164_W	172_A	0.963	0.89
111_I	115_S	0.961	0.89
42_T	185_F	0.949	0.89
129_V	149_F	0.947	0.89
72_I	127_V	0.942	0.88
19_F	81_L	0.942	0.88
170_F	174_H	0.942	0.88
139_W	143_P	0.942	0.88
56_T	190_S	0.937	0.88
86_I	105_N	0.932	0.88
174_H	178_I	0.932	0.88
90_F	105_N	0.931	0.88
15_W	19_F	0.916	0.87
82_I	86_I	0.916	0.87
67_L	70_R	0.915	0.87
111_I	114_A	0.903	0.86
69_R	73_F	0.897	0.86
87_S	91_Y	0.887	0.85
134_R	142_A	0.887	0.85
11_K	15_W	0.877	0.84
173_E	176_M	0.874	0.84
201_L	205_L	0.870	0.84
147_T	190_S	0.866	0.84
156_L	160_F	0.861	0.83
26_S	82_I	0.861	0.83
160_F	164_W	0.859	0.83
20_H	75_V	0.858	0.83
28_N	154_D	0.855	0.83
76_M	161_I	0.851	0.83
30_L	45_G	0.850	0.83
16_L	59_T	0.847	0.82
22_L	25_T	0.847	0.82
96_Q	99_G	0.845	0.82
49_F	193_F	0.838	0.82
29_Y	105_N	0.835	0.81
20_H	24_I	0.832	0.81
62_I	205_L	0.828	0.81
95_W	98_F	0.817	0.80
123_Q	126_D	0.815	0.80
152_V	179_A	0.812	0.80
29_Y	33_L	0.800	0.79
49_F	186_K	0.797	0.78
57_D	162_A	0.794	0.78
61_R	134_R	0.791	0.78
189_I	193_F	0.791	0.78
30_L	86_I	0.785	0.77
180_L	184_C	0.780	0.77
13_L	67_L	0.779	0.77
66_P	135_Q	0.778	0.77
190_S	193_F	0.777	0.76
101_L	104_F	0.774	0.76
118_A	154_D	0.773	0.76
44_W	182_D	0.771	0.76
139_W	194_F	0.758	0.75
111_I	158_F	0.757	0.75
139_W	202_L	0.755	0.74
125_L	133_L	0.755	0.74
54_L	193_F	0.754	0.74
49_F	53_F	0.753	0.74
148_L	191_I	0.751	0.74
206_L	209_L	0.751	0.74
154_D	186_K	0.747	0.74
90_F	101_L	0.739	0.73
65_A	135_Q	0.737	0.73
80_L	84_Y	0.734	0.72
178_I	182_D	0.734	0.72
159_F	182_D	0.734	0.72
126_D	140_W	0.727	0.72
54_L	122_G	0.725	0.71
65_A	131_N	0.724	0.71
49_F	143_P	0.710	0.70
83_S	108_V	0.709	0.70
94_S	187_V	0.709	0.70
188_L	192_V	0.705	0.69
123_Q	155_T	0.703	0.69
121_L	180_L	0.703	0.69
44_W	89_L	0.703	0.69
119_Y	154_D	0.701	0.69
87_S	90_F	0.696	0.68
56_T	127_V	0.689	0.68
131_N	135_Q	0.688	0.67
19_F	85_V	0.687	0.67
84_Y	88_S	0.684	0.67
97_G	103_H	0.679	0.66
118_A	157_A	0.667	0.65
24_I	52_I	0.666	0.65
126_D	190_S	0.662	0.64
34_P	163_F	0.662	0.64
76_M	119_Y	0.656	0.64
114_A	158_F	0.653	0.63
125_L	128_H	0.652	0.63
21_L	127_V	0.650	0.63
89_L	153_S	0.649	0.63
45_G	124_I	0.648	0.63
27_S	49_F	0.647	0.63
46_A	181_V	0.641	0.62
91_Y	102_A	0.641	0.62
23_V	27_S	0.641	0.62
130_F	143_P	0.639	0.62
119_Y	185_F	0.637	0.61
26_S	86_I	0.629	0.60
69_R	134_R	0.626	0.60
54_L	201_L	0.625	0.60
159_F	178_I	0.624	0.60
45_G	79_A	0.624	0.60
61_R	139_W	0.623	0.60
68_A	123_Q	0.622	0.60
88_S	121_L	0.619	0.59
144_T	148_L	0.619	0.59
158_F	163_F	0.618	0.59
173_E	177_E	0.615	0.59
22_L	26_S	0.610	0.58
51_F	85_V	0.609	0.58
39_G	177_E	0.608	0.58
24_I	119_Y	0.607	0.58
144_T	193_F	0.604	0.57
75_V	151_N	0.604	0.57
65_A	128_H	0.603	0.57
114_A	172_A	0.601	0.57
126_D	144_T	0.599	0.57
127_V	130_F	0.597	0.57
139_W	199_G	0.596	0.56
34_P	178_I	0.595	0.56
38_L	113_T	0.594	0.56
62_I	202_L	0.592	0.56
20_H	30_L	0.592	0.56
31_V	37_I	0.589	0.56
109_A	112_A	0.587	0.55
32_Q	86_I	0.585	0.55
130_F	134_R	0.585	0.55
48_S	85_V	0.585	0.55
196_P	201_L	0.583	0.55
90_F	98_F	0.582	0.55
49_F	187_V	0.578	0.54
104_F	113_T	0.577	0.54
20_H	147_T	0.572	0.53
147_T	199_G	0.572	0.53
93_G	98_F	0.570	0.53
46_A	159_F	0.570	0.53
37_I	41_H	0.563	0.52
57_D	126_D	0.561	0.52
15_W	74_A	0.558	0.52
133_L	145_A	0.558	0.52
14_F	74_A	0.556	0.51
54_L	196_P	0.555	0.51
59_T	62_I	0.553	0.51
59_T	142_A	0.552	0.51
155_T	189_I	0.551	0.51
150_G	195_L	0.549	0.50
170_F	175_W	0.542	0.50
107_F	157_A	0.541	0.49
30_L	44_W	0.540	0.49
19_F	51_F	0.537	0.49
58_L	198_Y	0.536	0.49
81_L	85_V	0.534	0.49
49_F	115_S	0.534	0.49
49_F	154_D	0.533	0.48
144_T	191_I	0.530	0.48
59_T	68_A	0.529	0.48
94_S	174_H	0.528	0.48
113_T	138_R	0.522	0.47
176_M	180_L	0.522	0.47
84_Y	135_Q	0.522	0.47
16_L	205_L	0.520	0.47
134_R	186_K	0.520	0.47
133_L	141_L	0.519	0.47
80_L	112_A	0.519	0.47
32_Q	104_F	0.518	0.47
109_A	113_T	0.518	0.47
22_L	74_A	0.517	0.46
21_L	161_I	0.517	0.46
97_G	173_E	0.517	0.46
39_G	178_I	0.516	0.46
27_S	45_G	0.515	0.46
18_L	173_E	0.515	0.46
48_S	127_V	0.515	0.46
126_D	146_S	0.514	0.46
66_P	204_M	0.513	0.46
146_S	149_F	0.511	0.46
136_S	206_L	0.510	0.45
108_V	112_A	0.508	0.45
155_T	182_D	0.508	0.45
43_T	86_I	0.508	0.45
57_D	199_G	0.506	0.45
45_G	149_F	0.506	0.45
36_S	93_G	0.506	0.45
56_T	130_F	0.506	0.45
156_L	203_N	0.500	0.44
131_N	193_F	0.500	0.44
93_G	96_Q	0.500	0.44

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
4rfsS	1	0.7919	73.3	0.929	Contact Map
4huqS	1	0.7376	61.7	0.935	Contact Map
4z7fA	2	0.7466	38	0.943	Contact Map
4dveA	3	0.8281	31.2	0.946	Contact Map
4tkrA	2	0.7873	22.7	0.949	Contact Map
2cfqA	1	0.8914	19.1	0.951	Contact Map
3aqpA	1	0.7602	15.1	0.953	Contact Map
3p5nA	2	0.7014	13.1	0.954	Contact Map
3rlbA	1	0.7647	11.8	0.955	Contact Map
4lz6A	1	0.9457	8.9	0.958	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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