YLQD - BACSU - GREMLIN Contacts

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YLQD - Uncharacterized protein YlqD

UniProt:	O31739	Sequences: MQIIHRVAVMQVLTERSKEKLLASFAEKKQMLERECSQLYFQLRKHEKEQQNPNMIEQFKKAIEKRKDDIKIIDFQIAQVHTLPLGSELKEKEVDALLTIEAGDDWHEKTAANTIVIKDGKVIEIRQR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	128 (124)
Sequences:	289 (210)
Seq/√Len:	18.9

BACSU - YLQD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
118_K	123_I	4.449	1.00
6_R	95_D	3.105	0.99
22_L	77_I	2.993	0.99
16_R	19_E	2.945	0.99
18_K	85_L	2.660	0.98
88_E	126_R	2.490	0.97
114_T	126_R	2.457	0.96
86_G	124_E	2.452	0.96
62_A	66_R	2.379	0.96
79_Q	87_S	2.125	0.92
86_G	118_K	2.081	0.91
9_V	39_L	2.069	0.91
76_Q	104_D	2.029	0.90
4_I	95_D	2.026	0.90
13_L	18_K	1.921	0.87
44_R	122_V	1.915	0.87
11_Q	91_E	1.846	0.85
35_E	66_R	1.833	0.85
12_V	118_K	1.817	0.84
3_I	94_V	1.710	0.80
9_V	92_K	1.610	0.76
2_Q	97_L	1.577	0.75
76_Q	79_Q	1.556	0.74
20_K	120_G	1.547	0.73
70_I	74_D	1.519	0.72
43_L	59_F	1.516	0.71
35_E	62_A	1.502	0.71
10_M	114_T	1.464	0.69
13_L	89_L	1.440	0.67
11_Q	17_S	1.392	0.65
9_V	84_P	1.364	0.63
107_H	122_V	1.335	0.61
75_F	79_Q	1.331	0.61
51_Q	55_M	1.329	0.61
101_E	104_D	1.286	0.58
62_A	65_K	1.243	0.56
56_I	116_V	1.233	0.55
22_L	26_A	1.229	0.55
52_N	60_K	1.227	0.55
13_L	106_W	1.220	0.54
37_S	98_L	1.179	0.52
42_Q	72_I	1.156	0.50
6_R	86_G	1.152	0.50
21_L	39_L	1.149	0.50
28_K	63_I	1.147	0.50
3_I	122_V	1.125	0.48
76_Q	122_V	1.119	0.48
42_Q	114_T	1.100	0.47
20_K	68_D	1.085	0.46
23_A	85_L	1.075	0.45
61_K	100_I	1.058	0.44
42_Q	93_E	1.047	0.43
105_D	108_E	1.046	0.43
45_K	51_Q	1.041	0.43
121_K	125_I	1.021	0.42
102_A	124_E	0.992	0.40
80_V	97_L	0.981	0.39
21_L	83_L	0.979	0.39
38_Q	79_Q	0.976	0.39
3_I	9_V	0.972	0.39
11_Q	59_F	0.955	0.38
25_F	113_N	0.954	0.38
42_Q	126_R	0.949	0.38
19_E	23_A	0.945	0.37
21_L	97_L	0.941	0.37
15_E	99_T	0.940	0.37
30_Q	122_V	0.932	0.37
8_A	90_K	0.931	0.36
45_K	90_K	0.927	0.36
6_R	90_K	0.927	0.36
5_H	96_A	0.919	0.36
35_E	87_S	0.917	0.36
10_M	88_E	0.907	0.35
121_K	124_E	0.900	0.35
79_Q	84_P	0.888	0.34
29_K	32_L	0.888	0.34
25_F	107_H	0.880	0.34
13_L	126_R	0.874	0.33
105_D	121_K	0.871	0.33
55_M	89_L	0.870	0.33
30_Q	77_I	0.866	0.33
12_V	116_V	0.855	0.32
16_R	115_I	0.854	0.32
92_K	110_T	0.854	0.32
66_R	86_G	0.853	0.32
94_V	116_V	0.844	0.32
38_Q	69_D	0.844	0.32
30_Q	116_V	0.822	0.30
79_Q	93_E	0.822	0.30
84_P	93_E	0.819	0.30
12_V	86_G	0.818	0.30
74_D	123_I	0.816	0.30
41_F	115_I	0.803	0.29
33_E	70_I	0.799	0.29
31_M	101_E	0.798	0.29
63_I	67_K	0.796	0.29
4_I	97_L	0.794	0.29
25_F	40_Y	0.792	0.29
39_L	59_F	0.791	0.29
16_R	119_D	0.780	0.28
27_E	123_I	0.779	0.28
89_L	123_I	0.778	0.28
78_A	85_L	0.776	0.28
90_K	112_A	0.767	0.28
27_E	65_K	0.755	0.27
25_F	29_K	0.752	0.27
41_F	48_K	0.746	0.26
50_Q	55_M	0.741	0.26
10_M	81_H	0.740	0.26
76_Q	84_P	0.735	0.26
19_E	54_N	0.735	0.26
31_M	95_D	0.731	0.26
37_S	44_R	0.731	0.26
38_Q	76_Q	0.729	0.26
26_A	78_A	0.727	0.26
17_S	106_W	0.725	0.25
87_S	102_A	0.723	0.25
75_F	78_A	0.722	0.25
99_T	115_I	0.716	0.25
65_K	123_I	0.716	0.25
46_H	55_M	0.711	0.25
67_K	100_I	0.704	0.24
25_F	36_C	0.698	0.24
32_L	80_V	0.696	0.24
41_F	62_A	0.691	0.24
57_E	102_A	0.690	0.24
8_A	30_Q	0.687	0.24
33_E	54_N	0.683	0.24
55_M	100_I	0.683	0.24
46_H	108_E	0.678	0.23
21_L	62_A	0.676	0.23
7_V	12_V	0.673	0.23
15_E	19_E	0.671	0.23
42_Q	71_K	0.669	0.23
104_D	122_V	0.654	0.22
39_L	62_A	0.654	0.22
12_V	123_I	0.653	0.22
44_R	93_E	0.652	0.22
43_L	58_Q	0.650	0.22
5_H	25_F	0.649	0.22
36_C	65_K	0.648	0.22
18_K	54_N	0.647	0.22
10_M	118_K	0.643	0.22
35_E	47_E	0.633	0.21
36_C	70_I	0.624	0.21
46_H	117_I	0.618	0.21
42_Q	49_E	0.617	0.21
81_H	123_I	0.617	0.21
51_Q	56_I	0.617	0.21
33_E	37_S	0.610	0.20
3_I	73_I	0.607	0.20
49_E	124_E	0.605	0.20
36_C	101_E	0.602	0.20
104_D	126_R	0.600	0.20
55_M	76_Q	0.597	0.20
27_E	105_D	0.595	0.20
26_A	33_E	0.593	0.20
40_Y	74_D	0.592	0.20
21_L	40_Y	0.586	0.19
80_V	96_A	0.580	0.19
62_A	68_D	0.575	0.19
65_K	118_K	0.570	0.19
74_D	96_A	0.569	0.19
97_L	102_A	0.567	0.19
43_L	95_D	0.564	0.19
23_A	26_A	0.563	0.19
9_V	117_I	0.559	0.18
17_S	44_R	0.555	0.18
8_A	89_L	0.553	0.18
22_L	80_V	0.551	0.18
36_C	110_T	0.551	0.18
38_Q	68_D	0.548	0.18
7_V	96_A	0.546	0.18
84_P	87_S	0.545	0.18
52_N	102_A	0.544	0.18
21_L	41_F	0.543	0.18
43_L	48_K	0.535	0.17
6_R	32_L	0.533	0.17
42_Q	78_A	0.532	0.17
33_E	60_K	0.522	0.17
59_F	80_V	0.515	0.17
41_F	45_K	0.513	0.17
99_T	102_A	0.503	0.16
24_S	114_T	0.503	0.16
3_I	109_K	0.502	0.16
82_T	92_K	0.500	0.16

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
4dciA	3	0.9844	100	0.089	Contact Map
3ghgA	2	0.6172	21.1	0.927	Contact Map
4kisA	2	0.9609	12.7	0.934	Contact Map
1gaxA	1	0.6328	9.7	0.937	Contact Map
3kinB	2	0.375	9.5	0.938	Contact Map
2c41A	6	0.8906	9.3	0.938	Contact Map
2yw6A	6	0.875	9.1	0.938	Contact Map
3kwoA	6	0.8594	8.9	0.939	Contact Map
1deqA	1	0.7812	8.4	0.939	Contact Map
2xgwA	6	0.9375	7.6	0.94	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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