YQAA - ECOLI - GREMLIN Contacts

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YQAA - Inner membrane protein YqaA

UniProt:	P0ADR0	Sequences: MSEALSLFSLFASSFLSATLLPGNSEVVLVAMLLSGISHPWVLVLTATMGNSLGGLTNVILGRFFPLRKTSRWQEKATGWLKRYGAVTLLLSWMPVVGDLLCLLAGWMRISWGPVIFFLCLGKALRYVAVAAATVQGMMWWH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13529
Length:	142 (129)
Sequences:	1016 (720)
Seq/√Len:	63.4

ECOLI - YQAA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
48_T	124_A	7.197	1.00
15_F	57_T	5.557	1.00
52_S	120_C	4.504	1.00
44_V	131_A	3.404	1.00
115_V	119_L	2.966	1.00
44_V	128_V	2.446	1.00
92_S	122_G	2.443	1.00
86_A	114_P	2.324	1.00
11_F	50_G	2.280	1.00
30_V	134_T	2.155	1.00
58_N	102_C	2.096	1.00
17_S	23_G	1.953	1.00
13_S	28_V	1.939	1.00
56_L	112_W	1.935	1.00
55_G	119_L	1.867	1.00
33_L	131_A	1.865	1.00
59_V	112_W	1.821	1.00
57_T	61_L	1.788	1.00
30_V	130_V	1.718	0.99
33_L	40_P	1.661	0.99
111_S	114_P	1.646	0.99
97_V	100_L	1.532	0.99
32_M	43_L	1.484	0.98
20_L	103_L	1.452	0.98
128_V	132_A	1.441	0.98
89_L	105_A	1.421	0.98
48_T	52_S	1.376	0.97
37_I	40_P	1.372	0.97
11_F	53_L	1.316	0.96
60_I	64_F	1.312	0.96
91_L	94_M	1.305	0.96
90_L	118_F	1.295	0.96
117_F	121_L	1.258	0.95
75_E	78_T	1.250	0.95
44_V	124_A	1.241	0.95
58_N	103_L	1.231	0.95
18_A	99_D	1.227	0.95
30_V	34_L	1.225	0.95
130_V	134_T	1.221	0.94
29_L	43_L	1.197	0.94
81_L	110_I	1.196	0.94
56_L	116_I	1.163	0.93
90_L	93_W	1.158	0.93
112_W	116_I	1.138	0.92
16_L	94_M	1.125	0.92
13_S	23_G	1.119	0.91
125_L	128_V	1.095	0.91
6_S	9_S	1.093	0.90
76_K	80_W	1.086	0.90
131_A	135_V	1.081	0.90
66_P	69_K	1.066	0.89
74_Q	107_W	1.058	0.89
122_G	125_L	1.053	0.89
116_I	120_C	1.051	0.89
78_T	108_M	1.045	0.88
86_A	118_F	1.035	0.88
10_L	29_L	1.030	0.88
16_L	23_G	1.022	0.87
52_S	124_A	1.007	0.86
81_L	92_S	1.000	0.86
27_V	30_V	1.000	0.86
10_L	32_M	0.982	0.85
81_L	88_T	0.979	0.85
34_L	134_T	0.979	0.85
90_L	121_L	0.979	0.85
45_L	49_M	0.977	0.85
113_G	117_F	0.971	0.84
55_G	92_S	0.954	0.83
46_T	49_M	0.951	0.83
68_R	71_S	0.926	0.81
18_A	58_N	0.921	0.81
81_L	115_V	0.908	0.80
33_L	134_T	0.903	0.80
60_I	63_R	0.901	0.80
75_E	79_G	0.899	0.80
67_L	109_R	0.893	0.79
67_L	72_R	0.881	0.78
31_A	35_S	0.875	0.78
86_A	110_I	0.859	0.76
9_S	13_S	0.858	0.76
70_T	73_W	0.851	0.76
16_L	21_L	0.844	0.75
15_F	53_L	0.844	0.75
96_V	100_L	0.841	0.75
49_M	120_C	0.839	0.75
54_G	123_K	0.838	0.75
94_M	97_V	0.834	0.74
87_V	118_F	0.822	0.73
56_L	119_L	0.821	0.73
92_S	102_C	0.820	0.73
93_W	105_A	0.811	0.72
67_L	71_S	0.810	0.72
20_L	100_L	0.807	0.72
131_A	134_T	0.789	0.70
112_W	115_V	0.785	0.70
20_L	99_D	0.783	0.69
94_M	129_A	0.772	0.68
12_A	132_A	0.769	0.68
111_S	116_I	0.760	0.67
17_S	78_T	0.759	0.67
7_L	23_G	0.758	0.67
17_S	24_N	0.756	0.67
81_L	102_C	0.753	0.66
74_Q	78_T	0.750	0.66
77_A	100_L	0.746	0.66
14_S	55_G	0.740	0.65
81_L	119_L	0.739	0.65
26_E	127_Y	0.738	0.65
54_G	122_G	0.735	0.65
120_C	124_A	0.735	0.65
75_E	132_A	0.731	0.64
29_L	59_V	0.723	0.63
59_V	114_P	0.723	0.63
14_S	60_I	0.720	0.63
55_G	115_V	0.710	0.62
110_I	122_G	0.703	0.61
68_R	72_R	0.702	0.61
94_M	122_G	0.688	0.59
20_L	57_T	0.683	0.59
124_A	128_V	0.683	0.59
48_T	120_C	0.680	0.59
56_L	111_S	0.676	0.58
17_S	31_A	0.673	0.58
68_R	73_W	0.669	0.57
59_V	110_I	0.666	0.57
25_S	127_Y	0.664	0.57
55_G	105_A	0.659	0.56
14_S	61_L	0.658	0.56
92_S	101_L	0.647	0.55
7_L	39_H	0.641	0.54
107_W	110_I	0.640	0.54
6_S	12_A	0.637	0.54
66_P	78_T	0.637	0.54
33_L	97_V	0.634	0.53
33_L	135_V	0.628	0.53
39_H	42_V	0.626	0.52
76_K	82_K	0.623	0.52
113_G	116_I	0.614	0.51
102_C	119_L	0.614	0.51
13_S	17_S	0.606	0.50
14_S	28_V	0.606	0.50
6_S	42_V	0.604	0.50
24_N	122_G	0.598	0.49
57_T	102_C	0.593	0.49
24_N	27_V	0.590	0.48
59_V	111_S	0.589	0.48
51_N	126_R	0.588	0.48
69_K	73_W	0.585	0.48
69_K	75_E	0.578	0.47
74_Q	86_A	0.578	0.47
58_N	61_L	0.572	0.46
29_L	130_V	0.567	0.46
28_V	44_V	0.564	0.45
18_A	29_L	0.563	0.45
6_S	48_T	0.563	0.45
100_L	104_L	0.562	0.45
100_L	115_V	0.562	0.45
23_G	66_P	0.560	0.45
25_S	123_K	0.558	0.45
23_G	33_L	0.556	0.44
41_W	128_V	0.555	0.44
89_L	115_V	0.550	0.44
50_G	53_L	0.550	0.44
57_T	100_L	0.544	0.43
118_F	122_G	0.543	0.43
53_L	56_L	0.543	0.43
30_V	33_L	0.542	0.43
64_F	109_R	0.540	0.43
12_A	42_V	0.535	0.42
130_V	135_V	0.534	0.42
17_S	76_K	0.534	0.42
91_L	122_G	0.533	0.42
23_G	96_V	0.533	0.42
10_L	43_L	0.532	0.42
11_F	46_T	0.531	0.41
31_A	42_V	0.531	0.41
72_R	75_E	0.529	0.41
27_V	31_A	0.528	0.41
14_S	47_A	0.527	0.41
20_L	92_S	0.527	0.41
82_K	94_M	0.524	0.41
80_W	97_V	0.524	0.41
37_I	121_L	0.522	0.40
129_A	133_A	0.519	0.40
56_L	118_F	0.515	0.40
86_A	103_L	0.515	0.40
39_H	131_A	0.514	0.40
45_L	124_A	0.513	0.39
59_V	115_V	0.511	0.39
70_T	91_L	0.509	0.39
32_M	89_L	0.506	0.39
42_V	49_M	0.503	0.38
23_G	63_R	0.503	0.38
40_P	131_A	0.500	0.38

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
3kcuA	3	0.4718	24.6	0.94	Contact Map
3klyA	3	0.4789	19.6	0.943	Contact Map
4fc4A	3	0.3873	18.8	0.944	Contact Map
3tdsE	3	0.4859	11.7	0.949	Contact Map
2jlnA	1	0.9507	9.2	0.951	Contact Map
2kncA	1	0.3521	3	0.961	Contact Map
1cp2A	2	0.5211	2.7	0.962	Contact Map
2m20A	2	0.338	2.6	0.962	Contact Map
4huqS	1	0.5423	2.6	0.962	Contact Map
2kv5A	1	0.2324	2.4	0.963	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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