YVDQ - BACSU - GREMLIN Contacts

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YVDQ - Uncharacterized protein YvdQ

UniProt:	O06998	Sequences: MGILSGNPQDEPMHYGEVFGLWSYVMAGNKMVGNYQMLLNHVGDDDLKKLLRESIEKCQDEIKQVSTILKENGVALPPASPEPPTADLNDIPPGARFLDPDVAASAAAENAAGLVTCSKMMGQSIREDIAMMFGQFHMSKAATGAKYLRLLKNKGWLIPPPLHLQKHHEA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	170 (151)
Sequences:	976 (821)
Seq/√Len:	66.8

BACSU - YVDQ

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
53_E	146_K	4.704	1.00
44_D	154_K	4.239	1.00
46_D	153_N	3.488	1.00
54_S	143_T	3.277	1.00
21_L	65_V	3.259	1.00
50_L	147_Y	2.908	1.00
130_A	145_A	2.599	1.00
61_E	139_S	2.538	1.00
38_L	102_V	2.290	1.00
28_G	61_E	2.228	1.00
60_D	139_S	2.184	1.00
132_M	136_F	2.162	1.00
134_G	145_A	2.028	1.00
64_Q	135_Q	2.027	1.00
28_G	31_M	1.988	1.00
31_M	58_C	1.892	1.00
55_I	73_G	1.860	1.00
34_N	105_S	1.844	1.00
18_V	74_V	1.747	1.00
43_G	95_A	1.717	1.00
29_N	62_I	1.700	0.99
51_L	102_V	1.643	0.99
41_H	95_A	1.626	0.99
21_L	68_I	1.532	0.99
134_G	141_A	1.528	0.99
13_M	21_L	1.520	0.99
103_A	151_L	1.498	0.99
24_Y	133_F	1.483	0.99
13_M	68_I	1.476	0.99
13_M	129_I	1.446	0.98
145_A	149_R	1.443	0.98
47_L	103_A	1.441	0.98
61_E	117_C	1.439	0.98
119_K	123_Q	1.433	0.98
63_K	67_T	1.433	0.98
50_L	150_L	1.431	0.98
98_L	150_L	1.424	0.98
134_G	142_A	1.416	0.98
42_V	47_L	1.404	0.98
103_A	150_L	1.374	0.98
121_M	134_G	1.353	0.97
11_E	159_P	1.333	0.97
20_G	120_M	1.307	0.97
125_I	157_L	1.289	0.97
151_L	156_W	1.288	0.96
115_V	118_S	1.287	0.96
127_E	149_R	1.283	0.96
31_M	113_G	1.276	0.96
144_G	148_L	1.270	0.96
27_A	116_T	1.269	0.96
20_G	123_Q	1.269	0.96
67_T	70_K	1.263	0.96
42_V	51_L	1.258	0.96
72_N	126_R	1.203	0.95
67_T	71_E	1.189	0.94
35_Y	106_A	1.185	0.94
134_G	138_M	1.137	0.93
22_W	44_D	1.130	0.93
100_P	156_W	1.113	0.92
135_Q	139_S	1.101	0.92
127_E	145_A	1.100	0.92
25_V	62_I	1.080	0.91
52_R	56_E	1.063	0.90
47_L	150_L	1.054	0.90
105_S	109_E	1.054	0.90
38_L	97_F	1.053	0.90
32_V	59_Q	1.052	0.90
10_D	71_E	1.048	0.90
41_H	102_V	1.041	0.89
31_M	140_K	1.037	0.89
64_Q	139_S	1.030	0.89
46_D	154_K	1.028	0.89
22_W	50_L	1.020	0.89
13_M	18_V	1.018	0.88
39_L	42_V	1.011	0.88
57_K	143_T	1.007	0.88
115_V	119_K	0.987	0.87
36_Q	59_Q	0.986	0.87
28_G	143_T	0.985	0.87
159_P	162_L	0.983	0.87
45_D	49_K	0.979	0.86
27_A	108_A	0.970	0.86
76_L	80_S	0.966	0.86
64_Q	132_M	0.963	0.85
142_A	146_K	0.960	0.85
40_N	89_N	0.949	0.85
56_E	63_K	0.946	0.84
40_N	88_L	0.945	0.84
54_S	140_K	0.944	0.84
66_S	76_L	0.943	0.84
29_N	66_S	0.941	0.84
24_Y	117_C	0.940	0.84
54_S	57_K	0.928	0.83
26_M	29_N	0.926	0.83
117_C	136_F	0.904	0.82
118_S	137_H	0.903	0.82
28_G	140_K	0.882	0.80
18_V	163_H	0.876	0.80
74_V	163_H	0.875	0.80
32_V	58_C	0.863	0.79
58_C	113_G	0.861	0.78
31_M	54_S	0.859	0.78
28_G	54_S	0.851	0.78
39_L	52_R	0.843	0.77
62_I	73_G	0.839	0.77
32_V	81_P	0.817	0.75
33_G	80_S	0.812	0.74
25_V	66_S	0.808	0.74
106_A	147_Y	0.803	0.73
53_E	64_Q	0.789	0.72
102_V	158_I	0.789	0.72
46_D	146_K	0.785	0.72
13_M	17_E	0.784	0.72
148_L	157_L	0.781	0.71
48_K	52_R	0.775	0.71
52_R	55_I	0.766	0.70
117_C	140_K	0.766	0.70
32_V	62_I	0.761	0.69
69_L	88_L	0.759	0.69
36_Q	82_E	0.758	0.69
90_D	96_R	0.757	0.69
155_G	159_P	0.755	0.69
114_L	118_S	0.752	0.68
54_S	110_N	0.751	0.68
127_E	163_H	0.749	0.68
29_N	79_A	0.748	0.68
18_V	75_A	0.742	0.67
11_E	152_K	0.742	0.67
67_T	76_L	0.730	0.66
42_V	48_K	0.724	0.65
124_S	130_A	0.723	0.65
130_A	148_L	0.723	0.65
68_I	132_M	0.723	0.65
53_E	57_K	0.716	0.65
21_L	132_M	0.714	0.64
19_F	101_D	0.713	0.64
20_G	115_V	0.709	0.64
44_D	48_K	0.708	0.64
39_L	48_K	0.707	0.64
10_D	87_D	0.707	0.64
29_N	80_S	0.706	0.64
55_I	140_K	0.705	0.63
59_Q	82_E	0.699	0.63
137_H	141_A	0.693	0.62
48_K	99_D	0.692	0.62
60_D	64_Q	0.690	0.62
61_E	104_A	0.690	0.62
103_A	121_M	0.685	0.61
149_R	153_N	0.685	0.61
11_E	74_V	0.684	0.61
55_I	59_Q	0.678	0.60
22_W	77_P	0.677	0.60
28_G	113_G	0.671	0.60
46_D	57_K	0.670	0.59
8_P	125_I	0.668	0.59
16_G	123_Q	0.667	0.59
34_N	110_N	0.666	0.59
42_V	99_D	0.666	0.59
37_M	86_A	0.664	0.59
87_D	90_D	0.662	0.59
32_V	55_I	0.657	0.58
27_A	120_M	0.645	0.57
18_V	123_Q	0.630	0.55
41_H	96_R	0.629	0.55
107_A	148_L	0.624	0.54
121_M	137_H	0.619	0.54
51_L	147_Y	0.616	0.53
95_A	102_V	0.604	0.52
89_N	162_L	0.603	0.52
152_K	159_P	0.602	0.52
22_W	79_A	0.602	0.52
121_M	149_R	0.601	0.51
75_A	120_M	0.601	0.51
33_G	36_Q	0.599	0.51
34_N	109_E	0.599	0.51
16_G	46_D	0.597	0.51
121_M	141_A	0.594	0.51
30_K	34_N	0.592	0.50
28_G	62_I	0.591	0.50
122_G	160_P	0.589	0.50
16_G	22_W	0.586	0.50
27_A	107_A	0.581	0.49
56_E	142_A	0.578	0.49
25_V	77_P	0.578	0.49
85_T	96_R	0.578	0.49
78_P	95_A	0.575	0.48
29_N	163_H	0.575	0.48
138_M	142_A	0.574	0.48
53_E	145_A	0.570	0.48
117_C	132_M	0.569	0.48
111_A	130_A	0.569	0.48
20_G	116_T	0.562	0.47
22_W	36_Q	0.562	0.47
37_M	149_R	0.560	0.47
59_Q	88_L	0.557	0.46
101_D	145_A	0.555	0.46
13_M	38_L	0.553	0.46
15_Y	162_L	0.551	0.46
28_G	38_L	0.550	0.45
19_F	134_G	0.547	0.45
107_A	147_Y	0.546	0.45
112_A	163_H	0.544	0.45
57_K	139_S	0.544	0.45
9_Q	72_N	0.539	0.44
88_L	158_I	0.539	0.44
97_F	104_A	0.539	0.44
64_Q	127_E	0.535	0.44
39_L	51_L	0.533	0.43
13_M	103_A	0.528	0.43
115_V	133_F	0.523	0.42
81_P	104_A	0.521	0.42
103_A	154_K	0.520	0.42
42_V	90_D	0.519	0.42
36_Q	87_D	0.518	0.42
34_N	59_Q	0.517	0.42
30_K	101_D	0.517	0.42
35_Y	109_E	0.514	0.41
14_H	19_F	0.512	0.41
24_Y	120_M	0.511	0.41
38_L	158_I	0.511	0.41
20_G	27_A	0.510	0.41
10_D	67_T	0.504	0.40
21_L	141_A	0.502	0.40
37_M	88_L	0.501	0.40
43_G	129_I	0.501	0.40
134_G	146_K	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
2rbdA	4	0.9353	100	0.314	Contact Map
4etrA	1	0.7118	94.5	0.88	Contact Map
2gyqA	2	0.8882	93.3	0.886	Contact Map
3q4oA	2	0.8824	92.5	0.889	Contact Map
3bt5A	1	0.8176	86.9	0.902	Contact Map
2oh3A	2	0.8059	84.7	0.904	Contact Map
1vjxA	1	0.8471	83.9	0.905	Contact Map
2qf9A	2	0.8824	80	0.909	Contact Map
2fzfA	2	0.8706	79.1	0.91	Contact Map
3oghB	2	0.8118	66.7	0.918	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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