YAAR - BACSU - GREMLIN Contacts

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YAAR - Uncharacterized protein YaaR

UniProt:	P37539	Sequences: MKINKDIRTFIDNKQIPSVKTSEITASFKTSMENQSSKMKLDQLTRLLSDIEAFGKRLTKSRNFKDLARFKGLVKRFVKEAVDSGLSHETSKSFDLYGNSRTLGLVKEIDDKLIQLTEEMMDQEKPAIDLLERIGEIKGLLINLYT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	146 (144)
Sequences:	409 (331)
Seq/√Len:	27.6

BACSU - YAAR

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
75_K	110_D	4.085	1.00
2_K	5_K	3.050	1.00
114_I	118_E	2.925	1.00
85_G	114_I	2.605	0.99
89_E	107_K	2.555	0.99
71_K	117_T	2.374	0.99
131_L	136_E	2.359	0.99
63_N	66_D	2.291	0.98
52_E	56_K	2.263	0.98
119_E	122_D	2.156	0.98
135_G	138_K	2.122	0.97
114_I	143_N	2.063	0.97
110_D	135_G	2.033	0.97
2_K	7_I	2.023	0.96
85_G	143_N	1.881	0.95
66_D	101_R	1.845	0.94
16_I	140_L	1.759	0.92
126_P	129_D	1.741	0.92
54_F	63_N	1.726	0.92
85_G	145_Y	1.698	0.91
53_A	56_K	1.693	0.91
87_S	128_I	1.684	0.91
37_S	50_D	1.682	0.91
105_L	135_G	1.589	0.88
112_K	136_E	1.565	0.87
32_M	143_N	1.540	0.86
44_L	77_F	1.495	0.84
79_K	83_D	1.454	0.83
19_V	23_E	1.439	0.82
111_D	115_Q	1.430	0.82
109_I	144_L	1.424	0.81
55_G	134_I	1.424	0.81
93_S	103_L	1.414	0.81
31_S	135_G	1.410	0.81
124_E	135_G	1.381	0.79
96_L	99_N	1.378	0.79
131_L	135_G	1.362	0.78
61_S	66_D	1.350	0.78
59_T	110_D	1.350	0.78
51_I	103_L	1.345	0.77
55_G	120_M	1.345	0.77
109_I	141_L	1.344	0.77
91_S	107_K	1.343	0.77
47_L	73_L	1.325	0.76
44_L	48_L	1.302	0.75
1_M	141_L	1.298	0.75
69_R	144_L	1.297	0.75
112_K	115_Q	1.283	0.74
119_E	133_R	1.270	0.73
26_A	30_T	1.262	0.73
130_L	142_I	1.260	0.73
49_S	53_A	1.218	0.70
37_S	125_K	1.208	0.69
135_G	143_N	1.202	0.69
12_D	78_V	1.171	0.67
115_Q	128_I	1.162	0.66
74_V	128_I	1.144	0.65
3_I	84_S	1.141	0.65
41_L	45_T	1.141	0.65
86_L	114_I	1.122	0.63
20_K	83_D	1.102	0.62
54_F	64_F	1.100	0.62
73_L	80_E	1.088	0.61
70_F	81_A	1.082	0.61
105_L	109_I	1.081	0.60
63_N	134_I	1.080	0.60
4_N	57_R	1.073	0.60
21_T	134_I	1.067	0.59
27_S	134_I	1.060	0.59
4_N	8_R	1.057	0.59
6_D	16_I	1.049	0.58
20_K	53_A	1.029	0.57
112_K	128_I	1.028	0.57
78_V	102_T	1.022	0.56
138_K	141_L	1.021	0.56
31_S	106_V	1.020	0.56
21_T	46_R	1.016	0.56
124_E	127_A	1.015	0.56
118_E	121_M	1.014	0.56
75_K	120_M	1.010	0.55
6_D	144_L	1.004	0.55
21_T	24_I	0.997	0.54
44_L	137_I	0.984	0.53
51_I	73_L	0.983	0.53
2_K	6_D	0.966	0.52
16_I	59_T	0.962	0.52
4_N	63_N	0.959	0.51
99_N	103_L	0.955	0.51
105_L	115_Q	0.955	0.51
28_F	98_G	0.952	0.51
88_H	104_G	0.951	0.51
108_E	112_K	0.937	0.50
63_N	101_R	0.928	0.49
16_I	21_T	0.923	0.49
43_Q	80_E	0.917	0.48
62_R	136_E	0.903	0.47
122_D	132_E	0.901	0.47
77_F	109_I	0.898	0.47
64_F	121_M	0.895	0.46
75_K	134_I	0.892	0.46
31_S	124_E	0.889	0.46
39_M	47_L	0.884	0.46
106_V	112_K	0.875	0.45
24_I	128_I	0.857	0.44
67_L	90_T	0.856	0.44
113_L	136_E	0.850	0.43
32_M	71_K	0.849	0.43
48_L	87_S	0.841	0.42
71_K	84_S	0.833	0.42
14_K	43_Q	0.833	0.42
49_S	144_L	0.832	0.42
59_T	94_F	0.822	0.41
66_D	120_M	0.816	0.41
54_F	66_D	0.815	0.41
72_G	76_R	0.807	0.40
35_Q	43_Q	0.806	0.40
86_L	145_Y	0.806	0.40
104_G	135_G	0.800	0.39
11_I	27_S	0.800	0.39
9_T	14_K	0.799	0.39
45_T	70_F	0.795	0.39
58_L	126_P	0.781	0.38
38_K	45_T	0.778	0.38
67_L	123_Q	0.774	0.38
35_Q	57_R	0.774	0.38
37_S	49_S	0.771	0.37
70_F	78_V	0.751	0.36
55_G	74_V	0.748	0.36
77_F	138_K	0.746	0.36
20_K	32_M	0.745	0.35
54_F	73_L	0.744	0.35
93_S	102_T	0.737	0.35
108_E	143_N	0.736	0.35
48_L	74_V	0.730	0.34
78_V	145_Y	0.723	0.34
3_I	22_S	0.710	0.33
43_Q	109_I	0.710	0.33
56_K	60_K	0.706	0.33
93_S	99_N	0.703	0.33
47_L	80_E	0.702	0.33
40_K	86_L	0.700	0.32
97_Y	103_L	0.699	0.32
60_K	65_K	0.696	0.32
64_F	103_L	0.693	0.32
94_F	100_S	0.689	0.32
74_V	109_I	0.686	0.31
32_M	80_E	0.685	0.31
62_R	127_A	0.681	0.31
93_S	101_R	0.680	0.31
60_K	144_L	0.677	0.31
58_L	90_T	0.677	0.31
33_E	37_S	0.676	0.31
117_T	120_M	0.673	0.31
63_N	88_H	0.669	0.30
33_E	38_K	0.665	0.30
34_N	41_L	0.664	0.30
64_F	131_L	0.663	0.30
54_F	67_L	0.652	0.29
70_F	103_L	0.650	0.29
100_S	133_R	0.640	0.29
93_S	96_L	0.640	0.29
3_I	20_K	0.636	0.28
50_D	69_R	0.630	0.28
58_L	101_R	0.626	0.28
70_F	128_I	0.624	0.28
45_T	49_S	0.623	0.28
57_R	66_D	0.616	0.27
133_R	142_I	0.615	0.27
19_V	33_E	0.614	0.27
77_F	98_G	0.611	0.27
36_S	128_I	0.608	0.27
53_A	72_G	0.607	0.27
88_H	94_F	0.595	0.26
59_T	80_E	0.594	0.26
112_K	117_T	0.594	0.26
118_E	143_N	0.586	0.25
48_L	63_N	0.583	0.25
90_T	94_F	0.581	0.25
118_E	125_K	0.576	0.25
67_L	120_M	0.560	0.24
34_N	121_M	0.557	0.24
37_S	84_S	0.557	0.24
94_F	112_K	0.557	0.24
13_N	23_E	0.556	0.24
11_I	14_K	0.555	0.24
122_D	128_I	0.555	0.24
105_L	130_L	0.554	0.24
82_V	106_V	0.553	0.23
82_V	141_L	0.551	0.23
17_P	109_I	0.548	0.23
50_D	73_L	0.546	0.23
122_D	125_K	0.546	0.23
7_I	19_V	0.545	0.23
112_K	140_L	0.545	0.23
50_D	76_R	0.539	0.23
11_I	128_I	0.536	0.23
86_L	94_F	0.535	0.22
68_A	111_D	0.535	0.22
62_R	82_V	0.533	0.22
95_D	99_N	0.531	0.22
92_K	95_D	0.529	0.22
29_K	34_N	0.526	0.22
13_N	115_Q	0.526	0.22
77_F	101_R	0.524	0.22
10_F	45_T	0.524	0.22
67_L	101_R	0.521	0.22
18_S	122_D	0.520	0.22
6_D	9_T	0.519	0.22
3_I	69_R	0.518	0.22
21_T	48_L	0.505	0.21
23_E	26_A	0.503	0.21
14_K	121_M	0.503	0.21
85_G	135_G	0.502	0.21
62_R	134_I	0.501	0.21
44_L	74_V	0.501	0.21
101_R	124_E	0.500	0.21

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
2qupA	1	0.8151	100	0.113	Contact Map
2p61A	1	0.774	100	0.156	Contact Map
2hc5A	1	0.7466	66.2	0.908	Contact Map
3d5aX	1	0.7329	14.4	0.937	Contact Map
3ns4A	2	0.2945	11.2	0.94	Contact Map
3wdgB	1	0.3767	9.4	0.942	Contact Map
2kw6A	2	0.3836	8.3	0.943	Contact Map
4e0gA	2	0.9315	7.7	0.944	Contact Map
3bghA	4	0.3836	6	0.947	Contact Map
4yubA	2	0.7055	5.3	0.948	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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