LPTC - ECOLI - GREMLIN Contacts

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LPTC - Lipopolysaccharide export system protein LptC

UniProt:	P0ADV9	Sequences: MSKARRWVIIVLSLAVLVMIGINMAEKDDTAQVVVNNNDPTYKSEHTDTLVYNPEGALSYRLIAQHVEYYSDQAVSWFTQPVLTTFDKDKIPTWSVKADKAKLTNDRMLYLYGHVEVNALVPDSQLRRITTDNAQINLVTQDVTSEDLVTLYGTTFNSSGLKMRGNLRSKNAELIEKVRTSYEIQNKQTQP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12806
Length:	191 (178)
Sequences:	1121 (914)
Seq/√Len:	68.5

ECOLI - LPTC

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
99_D	114_H	9.293	1.00
65_Q	80_Q	4.491	1.00
160_G	174_L	3.284	1.00
145_S	162_K	3.142	1.00
133_N	147_D	3.000	1.00
41_T	69_Y	2.949	1.00
132_D	147_D	2.895	1.00
50_L	58_L	2.876	1.00
166_N	169_S	2.782	1.00
153_G	156_F	2.615	1.00
164_R	173_E	2.589	1.00
161_L	176_E	2.500	1.00
162_K	176_E	2.351	1.00
66_H	79_T	2.314	1.00
99_D	113_G	2.305	1.00
53_N	57_A	2.268	1.00
47_T	64_A	2.242	1.00
68_E	79_T	2.197	1.00
98_A	111_L	2.115	1.00
64_A	78_F	2.050	1.00
45_E	66_H	2.036	1.00
158_S	180_T	2.019	1.00
166_N	171_N	2.017	1.00
115_V	131_T	1.853	1.00
131_T	145_S	1.848	1.00
103_L	109_L	1.801	1.00
131_T	134_A	1.726	1.00
137_N	140_T	1.688	1.00
94_W	167_L	1.688	1.00
149_V	163_M	1.646	0.99
151_L	158_S	1.642	0.99
20_I	23_N	1.606	0.99
116_E	128_R	1.596	0.99
75_V	102_K	1.586	0.99
130_T	150_T	1.574	0.99
116_E	130_T	1.519	0.99
144_T	164_R	1.501	0.99
101_A	111_L	1.475	0.99
161_L	177_K	1.474	0.99
145_S	163_M	1.468	0.99
80_Q	99_D	1.450	0.98
162_K	175_I	1.437	0.98
142_D	166_N	1.421	0.98
18_V	22_I	1.410	0.98
143_V	165_G	1.407	0.98
150_T	157_N	1.399	0.98
100_K	112_Y	1.348	0.98
112_Y	133_N	1.325	0.97
110_Y	135_Q	1.306	0.97
118_N	128_R	1.290	0.97
38_N	72_D	1.276	0.97
13_S	55_E	1.236	0.96
145_S	176_E	1.234	0.96
18_V	21_G	1.233	0.96
47_T	67_V	1.225	0.96
52_Y	70_Y	1.216	0.95
17_L	21_G	1.206	0.95
69_Y	76_S	1.185	0.95
94_W	117_V	1.177	0.95
137_N	166_N	1.157	0.94
150_T	159_S	1.147	0.94
8_V	12_L	1.121	0.93
81_P	94_W	1.118	0.93
81_P	101_A	1.110	0.93
120_L	126_L	1.105	0.93
87_D	90_K	1.082	0.92
15_A	25_A	1.075	0.91
98_A	148_L	1.074	0.91
40_P	70_Y	1.051	0.91
161_L	175_I	1.046	0.90
113_G	157_N	1.036	0.90
110_Y	133_N	1.032	0.90
148_L	159_S	1.031	0.90
164_R	175_I	1.024	0.89
52_Y	94_W	1.015	0.89
158_S	178_V	1.012	0.89
141_Q	168_R	1.008	0.89
131_T	162_K	0.999	0.88
74_A	106_D	0.985	0.87
74_A	105_N	0.977	0.87
52_Y	58_L	0.975	0.87
19_M	22_I	0.964	0.86
108_M	135_Q	0.963	0.86
67_V	116_E	0.961	0.86
43_K	180_T	0.960	0.86
19_M	101_A	0.958	0.86
19_M	23_N	0.945	0.85
60_Y	83_L	0.944	0.85
149_V	174_L	0.939	0.85
7_W	10_I	0.939	0.85
137_N	142_D	0.922	0.84
174_L	180_T	0.921	0.84
63_I	82_V	0.920	0.84
137_N	144_T	0.917	0.83
107_R	139_V	0.912	0.83
94_W	182_Y	0.912	0.83
97_K	118_N	0.909	0.83
68_E	77_W	0.905	0.83
8_V	14_L	0.903	0.82
108_M	137_N	0.902	0.82
96_V	115_V	0.896	0.82
114_H	132_D	0.893	0.82
82_V	160_G	0.889	0.81
165_G	172_A	0.888	0.81
33_V	37_N	0.884	0.81
9_I	14_L	0.871	0.80
111_L	136_I	0.870	0.80
12_L	15_A	0.856	0.79
156_F	160_G	0.856	0.79
56_G	111_L	0.846	0.78
179_R	182_Y	0.842	0.78
82_V	95_S	0.842	0.78
17_L	22_I	0.841	0.78
44_S	78_F	0.835	0.77
43_K	101_A	0.831	0.77
117_V	129_I	0.830	0.77
102_K	112_Y	0.824	0.76
7_W	15_A	0.810	0.75
174_L	178_V	0.802	0.74
78_F	103_L	0.801	0.74
61_R	84_T	0.788	0.73
30_T	33_V	0.784	0.73
118_N	126_L	0.784	0.73
16_V	30_T	0.777	0.72
10_I	14_L	0.777	0.72
26_E	64_A	0.775	0.72
144_T	163_M	0.773	0.72
154_T	182_Y	0.772	0.71
114_H	150_T	0.771	0.71
55_E	98_A	0.765	0.71
52_Y	158_S	0.761	0.70
160_G	163_M	0.761	0.70
104_T	108_M	0.753	0.70
16_V	24_M	0.746	0.69
92_P	119_A	0.745	0.69
131_T	169_S	0.744	0.69
77_W	102_K	0.741	0.68
60_Y	69_Y	0.740	0.68
18_V	24_M	0.738	0.68
84_T	95_S	0.735	0.68
165_G	182_Y	0.733	0.67
90_K	129_I	0.730	0.67
46_H	65_Q	0.727	0.67
58_L	86_F	0.722	0.66
70_Y	123_D	0.716	0.66
14_L	25_A	0.711	0.65
6_R	12_L	0.710	0.65
46_H	80_Q	0.707	0.65
17_L	20_I	0.699	0.64
40_P	43_K	0.698	0.64
76_S	101_A	0.698	0.64
98_A	163_M	0.695	0.63
53_N	59_S	0.686	0.62
13_S	77_W	0.684	0.62
83_L	96_V	0.684	0.62
139_V	159_S	0.683	0.62
36_N	39_D	0.683	0.62
15_A	29_D	0.678	0.61
115_V	149_V	0.676	0.61
117_V	143_V	0.674	0.61
45_E	55_E	0.674	0.61
11_V	29_D	0.669	0.60
108_M	165_G	0.664	0.60
64_A	88_K	0.663	0.60
60_Y	136_I	0.660	0.59
24_M	28_D	0.659	0.59
100_K	113_G	0.658	0.59
151_L	172_A	0.653	0.59
74_A	177_K	0.653	0.59
20_I	24_M	0.643	0.57
108_M	160_G	0.642	0.57
11_V	20_I	0.641	0.57
60_Y	103_L	0.640	0.57
109_L	166_N	0.640	0.57
64_A	81_P	0.639	0.57
6_R	14_L	0.639	0.57
134_A	176_E	0.634	0.56
152_Y	157_N	0.630	0.56
45_E	140_T	0.629	0.56
63_I	84_T	0.628	0.56
109_L	140_T	0.627	0.55
48_D	63_I	0.623	0.55
134_A	145_S	0.623	0.55
51_V	168_R	0.623	0.55
50_L	61_R	0.622	0.55
44_S	47_T	0.620	0.55
49_T	76_S	0.619	0.55
131_T	143_V	0.616	0.54
134_A	162_K	0.615	0.54
105_N	139_V	0.608	0.53
17_L	25_A	0.601	0.52
36_N	154_T	0.597	0.52
20_I	26_E	0.597	0.52
84_T	92_P	0.596	0.52
103_L	141_Q	0.595	0.52
121_V	124_S	0.593	0.51
96_V	184_I	0.592	0.51
145_S	148_L	0.592	0.51
40_P	71_S	0.591	0.51
141_Q	157_N	0.588	0.51
38_N	68_E	0.587	0.51
129_I	180_T	0.581	0.50
69_Y	117_V	0.578	0.50
9_I	24_M	0.577	0.49
65_Q	81_P	0.577	0.49
62_L	170_K	0.576	0.49
131_T	148_L	0.572	0.49
117_V	151_L	0.570	0.49
131_T	146_E	0.569	0.49
103_L	138_L	0.567	0.48
51_V	138_L	0.567	0.48
160_G	172_A	0.566	0.48
145_S	161_L	0.563	0.48
62_L	119_A	0.562	0.48
6_R	20_I	0.561	0.48
18_V	55_E	0.560	0.47
130_T	152_Y	0.558	0.47
10_I	181_S	0.556	0.47
16_V	37_N	0.555	0.47
39_D	66_H	0.554	0.47
42_Y	143_V	0.554	0.47
62_L	83_L	0.553	0.47
105_N	109_L	0.551	0.46
25_A	28_D	0.548	0.46
96_V	117_V	0.543	0.45
94_W	165_G	0.543	0.45
45_E	102_K	0.542	0.45
52_Y	174_L	0.541	0.45
163_M	174_L	0.540	0.45
35_V	160_G	0.540	0.45
125_Q	154_T	0.540	0.45
42_Y	69_Y	0.538	0.45
97_K	114_H	0.537	0.45
125_Q	153_G	0.536	0.45
147_D	177_K	0.536	0.45
107_R	137_N	0.534	0.44
12_L	23_N	0.533	0.44
57_A	121_V	0.531	0.44
106_D	129_I	0.530	0.44
123_D	126_L	0.530	0.44
98_A	133_N	0.530	0.44
116_E	140_T	0.524	0.43
76_S	170_K	0.523	0.43
91_I	128_R	0.523	0.43
158_S	172_A	0.522	0.43
151_L	179_R	0.522	0.43
165_G	176_E	0.522	0.43
127_R	153_G	0.520	0.43
41_T	145_S	0.518	0.42
114_H	128_R	0.517	0.42
19_M	96_V	0.516	0.42
101_A	104_T	0.516	0.42
10_I	21_G	0.513	0.42
57_A	95_S	0.512	0.42
149_V	162_K	0.511	0.42
46_H	98_A	0.509	0.41
15_A	19_M	0.508	0.41
100_K	159_S	0.507	0.41
153_G	167_L	0.506	0.41
18_V	27_K	0.506	0.41
163_M	172_A	0.506	0.41
121_V	178_V	0.505	0.41
60_Y	67_V	0.504	0.41
82_V	97_K	0.502	0.41
10_I	15_A	0.502	0.41
17_L	27_K	0.502	0.41
149_V	166_N	0.500	0.40

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
3my2A	2	0.6545	100	0.32	Contact Map
4uu4A	1	0.6649	99.3	0.666	Contact Map
2r19A	3	0.7016	99.1	0.695	Contact Map
4q35A	1	0.6283	98.6	0.74	Contact Map
1v54G	1	0.377	7.3	0.94	Contact Map
2y69G	1	0.377	6.9	0.94	Contact Map
4um9B	2	0	5.1	0.944	Contact Map
3ne5B	3	0.5183	4.9	0.944	Contact Map
3wvfA	1	0.6073	4.9	0.944	Contact Map
1y0gA	2	0.7801	4.7	0.945	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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