YTXG - BACSU - GREMLIN Contacts

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YTXG - UPF0478 protein YtxG

UniProt:	P40779	Sequences: MIIILYLSVALIAVAFLVLVIYLSKTLKSLQLTLKNVASTLEGLEGQMKGITTETAELLHKTNRLAEDIQEKSEKLNTVVHAVQGVGASVQQFNTSMKQAAGSVSASVRENQDKINQVVTWSQAAMEIWEKWKQKKKSAL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	140 (131)
Sequences:	435 (324)
Seq/√Len:	28.3

BACSU - YTXG

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
9_V	12_I	8.194	1.00
68_D	72_K	3.453	1.00
4_I	10_A	3.109	1.00
11_L	17_L	3.090	1.00
5_L	9_V	2.954	1.00
50_G	54_E	2.326	0.99
38_A	51_I	2.228	0.98
37_V	41_L	2.139	0.98
58_L	61_K	1.862	0.95
33_T	62_T	1.806	0.94
79_V	83_V	1.759	0.93
33_T	38_A	1.756	0.93
118_V	122_S	1.736	0.92
5_L	8_S	1.695	0.91
32_L	35_K	1.669	0.91
5_L	59_L	1.582	0.88
92_Q	98_K	1.575	0.88
27_L	41_L	1.554	0.87
65_L	85_G	1.548	0.87
6_Y	9_V	1.512	0.86
21_I	25_K	1.510	0.86
12_I	16_F	1.500	0.85
8_S	12_I	1.493	0.85
16_F	19_L	1.487	0.85
28_K	32_L	1.451	0.83
82_A	94_N	1.446	0.83
29_S	35_K	1.412	0.82
7_L	102_G	1.407	0.81
75_K	84_Q	1.375	0.80
125_A	129_W	1.373	0.80
16_F	62_T	1.364	0.79
97_M	101_A	1.351	0.79
122_S	126_M	1.349	0.79
8_S	70_Q	1.348	0.79
64_R	98_K	1.327	0.77
35_K	115_I	1.326	0.77
22_Y	93_F	1.252	0.73
54_E	87_G	1.229	0.72
76_L	87_G	1.213	0.71
75_K	81_H	1.203	0.70
104_V	115_I	1.200	0.70
30_L	44_L	1.199	0.70
40_T	44_L	1.196	0.70
14_V	106_A	1.185	0.69
21_I	114_K	1.184	0.69
26_T	29_S	1.183	0.69
39_S	42_E	1.182	0.69
55_T	100_A	1.178	0.68
22_Y	28_K	1.162	0.67
55_T	96_S	1.146	0.66
5_L	12_I	1.142	0.66
49_K	86_V	1.142	0.66
7_L	10_A	1.130	0.65
44_L	51_I	1.129	0.65
44_L	48_M	1.127	0.65
104_V	109_R	1.119	0.64
40_T	96_S	1.117	0.64
14_V	18_V	1.111	0.64
84_Q	87_G	1.101	0.63
18_V	134_Q	1.094	0.63
65_L	73_S	1.084	0.62
25_K	31_Q	1.067	0.61
79_V	89_S	1.066	0.61
30_L	125_A	1.060	0.60
15_A	19_L	1.055	0.60
48_M	51_I	1.044	0.59
54_E	60_H	1.020	0.57
61_K	94_N	1.015	0.57
42_E	75_K	1.008	0.56
12_I	17_L	0.999	0.55
65_L	89_S	0.979	0.54
62_T	66_A	0.979	0.54
62_T	73_S	0.972	0.53
52_T	64_R	0.964	0.53
4_I	8_S	0.961	0.53
95_T	102_G	0.959	0.52
74_E	77_N	0.944	0.51
23_L	108_V	0.931	0.50
34_L	37_V	0.917	0.49
8_S	20_V	0.916	0.49
66_A	94_N	0.915	0.49
21_I	34_L	0.911	0.49
82_A	85_G	0.910	0.49
59_L	62_T	0.908	0.48
18_V	64_R	0.904	0.48
109_R	133_K	0.903	0.48
6_Y	117_Q	0.890	0.47
81_H	103_S	0.887	0.47
58_L	81_H	0.881	0.46
91_Q	125_A	0.871	0.46
5_L	20_V	0.865	0.45
55_T	97_M	0.854	0.44
25_K	29_S	0.838	0.43
12_I	51_I	0.833	0.43
8_S	82_A	0.829	0.42
17_L	101_A	0.829	0.42
111_N	123_Q	0.828	0.42
51_I	93_F	0.825	0.42
8_S	13_A	0.818	0.42
90_V	94_N	0.818	0.42
16_F	20_V	0.814	0.41
61_K	64_R	0.812	0.41
89_S	94_N	0.807	0.41
8_S	28_K	0.804	0.41
85_G	91_Q	0.800	0.40
48_M	71_E	0.788	0.39
102_G	110_E	0.784	0.39
48_M	62_T	0.779	0.39
7_L	11_L	0.764	0.38
23_L	35_K	0.760	0.37
68_D	77_N	0.756	0.37
83_V	112_Q	0.754	0.37
67_E	80_V	0.745	0.36
73_S	118_V	0.739	0.36
17_L	21_I	0.730	0.35
17_L	24_S	0.727	0.35
23_L	89_S	0.726	0.35
20_V	27_L	0.725	0.35
58_L	62_T	0.725	0.35
88_A	98_K	0.721	0.35
41_L	44_L	0.715	0.34
70_Q	78_T	0.714	0.34
49_K	99_Q	0.714	0.34
75_K	93_F	0.713	0.34
15_A	20_V	0.702	0.33
57_E	124_A	0.702	0.33
68_D	80_V	0.694	0.33
10_A	62_T	0.684	0.32
24_S	28_K	0.681	0.32
5_L	17_L	0.679	0.32
59_L	89_S	0.679	0.32
21_I	92_Q	0.678	0.32
45_E	93_F	0.677	0.32
26_T	31_Q	0.669	0.31
4_I	24_S	0.665	0.31
42_E	81_H	0.663	0.31
46_G	55_T	0.662	0.31
84_Q	132_W	0.660	0.30
33_T	122_S	0.660	0.30
8_S	18_V	0.651	0.30
41_L	92_Q	0.651	0.30
53_T	76_L	0.651	0.30
29_S	38_A	0.649	0.30
54_E	72_K	0.649	0.30
84_Q	88_A	0.646	0.30
128_I	133_K	0.644	0.29
122_S	128_I	0.643	0.29
48_M	92_Q	0.639	0.29
46_G	58_L	0.635	0.29
46_G	50_G	0.626	0.28
26_T	38_A	0.620	0.28
50_G	104_V	0.617	0.28
17_L	129_W	0.611	0.27
50_G	55_T	0.610	0.27
106_A	110_E	0.608	0.27
15_A	104_V	0.592	0.26
88_A	105_S	0.591	0.26
60_H	76_L	0.586	0.26
61_K	89_S	0.581	0.26
22_Y	58_L	0.580	0.25
98_K	105_S	0.580	0.25
85_G	98_K	0.579	0.25
12_I	56_A	0.578	0.25
53_T	56_A	0.576	0.25
47_Q	91_Q	0.571	0.25
71_E	85_G	0.571	0.25
53_T	125_A	0.568	0.25
25_K	95_T	0.566	0.25
72_K	77_N	0.564	0.25
18_V	24_S	0.564	0.25
11_L	90_V	0.563	0.24
36_N	71_E	0.559	0.24
21_I	24_S	0.548	0.24
14_V	81_H	0.546	0.24
59_L	96_S	0.545	0.23
53_T	60_H	0.544	0.23
14_V	31_Q	0.543	0.23
23_L	95_T	0.541	0.23
44_L	52_T	0.538	0.23
4_I	108_V	0.532	0.23
4_I	124_A	0.532	0.23
26_T	101_A	0.531	0.23
49_K	53_T	0.527	0.22
55_T	77_N	0.527	0.22
81_H	134_Q	0.521	0.22
13_A	58_L	0.518	0.22
53_T	105_S	0.517	0.22
30_L	33_T	0.511	0.22
46_G	85_G	0.510	0.22
116_N	131_K	0.510	0.22
16_F	33_T	0.508	0.21
73_S	76_L	0.506	0.21
105_S	125_A	0.504	0.21
59_L	72_K	0.504	0.21
58_L	96_S	0.504	0.21
30_L	93_F	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
2ch7A	2	0.8357	80.2	0.89	Contact Map
4cq4A	4	0.5643	76.7	0.893	Contact Map
3zx6A	2	0.8214	76.3	0.893	Contact Map
4i3mA	2	0.85	71.2	0.898	Contact Map
2f95B	2	0.1286	70.3	0.898	Contact Map
4q4gX	1	0	69.6	0.899	Contact Map
4cgkA	3	0.6571	63	0.903	Contact Map
4gycB	2	0.1429	54.9	0.908	Contact Map
2mi2A	1	0.7071	46.7	0.912	Contact Map
1qu7A	2	0.9	41.6	0.915	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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