YNER - BACSU - GREMLIN Contacts

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YNER - Uncharacterized protein YneR

UniProt:	Q45063	Sequences: MNMTINEDALNWYKEELDLESGDQVRFFVRYGGCSNVQKGFSLGVAKDAPQEAGVTAEADGITFFIEESDLWYFDNHDLLVSYSEDADEPVFEYQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	95 (94)
Sequences:	323 (270)
Seq/√Len:	27.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
54_G	71_L	2.734	1.00
14_K	60_D	2.583	0.99
27_F	81_V	2.547	0.99
7_E	59_A	2.371	0.99
13_Y	92_F	2.289	0.98
14_K	64_F	2.194	0.98
38_Q	92_F	2.135	0.98
34_C	37_V	2.123	0.97
58_E	61_G	2.087	0.97
83_Y	88_D	2.047	0.97
29_V	32_G	2.023	0.97
10_L	13_Y	1.968	0.96
66_I	74_F	1.942	0.96
28_F	44_G	1.928	0.95
4_T	80_L	1.883	0.95
8_D	85_E	1.881	0.95
43_L	94_Y	1.842	0.94
6_N	80_L	1.801	0.93
56_T	63_T	1.736	0.92
38_Q	73_Y	1.706	0.91
8_D	82_S	1.673	0.90
55_V	74_F	1.670	0.90
84_S	91_V	1.642	0.90
32_G	73_Y	1.578	0.88
38_Q	75_D	1.476	0.84
10_L	60_D	1.441	0.82
13_Y	90_P	1.425	0.82
67_E	77_H	1.420	0.81
29_V	38_Q	1.416	0.81
6_N	82_S	1.377	0.79
68_E	71_L	1.340	0.77
50_P	67_E	1.340	0.77
52_E	68_E	1.328	0.77
39_K	92_F	1.328	0.77
77_H	94_Y	1.301	0.75
74_F	89_E	1.166	0.67
34_C	39_K	1.142	0.65
11_N	14_K	1.116	0.63
27_F	79_L	1.100	0.62
29_V	42_S	1.091	0.62
64_F	67_E	1.056	0.59
20_E	23_D	1.038	0.58
35_S	43_L	1.015	0.56
11_N	15_E	1.008	0.55
62_I	65_F	1.003	0.55
36_N	94_Y	0.987	0.54
69_S	83_Y	0.970	0.53
17_L	92_F	0.956	0.51
11_N	65_F	0.951	0.51
36_N	48_D	0.951	0.51
30_R	73_Y	0.945	0.51
8_D	84_S	0.931	0.50
65_F	69_S	0.929	0.49
81_V	92_F	0.928	0.49
53_A	56_T	0.926	0.49
15_E	88_D	0.913	0.48
4_T	7_E	0.883	0.46
34_C	38_Q	0.869	0.45
10_L	64_F	0.867	0.45
5_I	80_L	0.865	0.45
19_L	22_G	0.857	0.44
45_V	53_A	0.849	0.43
30_R	71_L	0.842	0.43
34_C	44_G	0.837	0.42
11_N	28_F	0.835	0.42
26_R	48_D	0.830	0.42
46_A	57_A	0.827	0.42
47_K	75_D	0.824	0.41
10_L	62_I	0.822	0.41
3_M	22_G	0.821	0.41
22_G	44_G	0.815	0.41
42_S	73_Y	0.814	0.41
31_Y	70_D	0.807	0.40
7_E	84_S	0.776	0.38
53_A	67_E	0.775	0.38
3_M	93_E	0.771	0.38
29_V	73_Y	0.765	0.37
24_Q	65_F	0.760	0.37
23_D	47_K	0.751	0.36
34_C	77_H	0.742	0.36
16_E	62_I	0.736	0.35
35_S	77_H	0.732	0.35
35_S	78_D	0.732	0.35
20_E	52_E	0.728	0.35
74_F	78_D	0.728	0.35
57_A	83_Y	0.722	0.34
17_L	25_V	0.715	0.34
8_D	86_D	0.713	0.34
13_Y	83_Y	0.707	0.33
10_L	14_K	0.705	0.33
52_E	82_S	0.703	0.33
63_T	75_D	0.702	0.33
64_F	83_Y	0.680	0.31
33_G	89_E	0.674	0.31
39_K	60_D	0.655	0.30
31_Y	73_Y	0.654	0.30
16_E	19_L	0.647	0.29
31_Y	37_V	0.645	0.29
31_Y	42_S	0.643	0.29
55_V	78_D	0.640	0.29
22_G	81_V	0.630	0.28
7_E	60_D	0.629	0.28
51_Q	60_D	0.627	0.28
6_N	41_F	0.619	0.27
18_D	88_D	0.618	0.27
70_D	74_F	0.616	0.27
86_D	91_V	0.608	0.27
66_I	94_Y	0.606	0.27
37_V	77_H	0.592	0.26
40_G	64_F	0.591	0.26
5_I	58_E	0.591	0.26
21_S	73_Y	0.589	0.26
3_M	82_S	0.571	0.25
5_I	64_F	0.568	0.24
24_Q	50_P	0.566	0.24
24_Q	63_T	0.565	0.24
38_Q	77_H	0.560	0.24
60_D	64_F	0.559	0.24
74_F	90_P	0.559	0.24
36_N	43_L	0.549	0.23
20_E	36_N	0.548	0.23
62_I	81_V	0.547	0.23
27_F	92_F	0.547	0.23
58_E	78_D	0.544	0.23
6_N	91_V	0.539	0.23
30_R	54_G	0.535	0.23
11_N	20_E	0.534	0.23
36_N	55_V	0.533	0.23
57_A	68_E	0.530	0.22
32_G	89_E	0.527	0.22
79_L	92_F	0.525	0.22
42_S	50_P	0.524	0.22
84_S	87_A	0.524	0.22
29_V	75_D	0.517	0.22
7_E	11_N	0.517	0.22
26_R	50_P	0.515	0.22
25_V	29_V	0.512	0.21
30_R	48_D	0.508	0.21
26_R	40_G	0.502	0.21
52_E	73_Y	0.501	0.21
56_T	81_V	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
1r94A	3	0.9368	99.6	0.589	Contact Map
2d2aA	2	0.9368	99.6	0.593	Contact Map
2k4zA	1	0.9368	99.6	0.602	Contact Map
1nwbA	1	0.9368	99.6	0.607	Contact Map
2apnA	1	0.9368	99.5	0.608	Contact Map
1x0gA	4	0.9263	99.5	0.627	Contact Map
2qgoA	1	0.8421	99.1	0.694	Contact Map
2p2eA	1	0.9263	99	0.696	Contact Map
2wtpA	2	0.6632	31.2	0.919	Contact Map
4xwxA	1	0.7158	17.7	0.928	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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