YJGD - BACSU - GREMLIN Contacts

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YJGD - Uncharacterized protein YjgD

UniProt:	O34681	Sequences: MAKAIKRIQKIEVTEEDQRKRDLREIEDALIDHKEAILETLHMLGHMNERGVLPLLRGLFGQGDKVLDILVKKADTEETANTLKNLLLLFGTLGMLDVKQLEPLILKVNAGVASAVEQKNSEEKTGYFDIIRSLKDPEINKSITLLFSFLKGMGQDTKELERTTQPPEHQKHHQEPREKRGMNKRD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	186 (159)
Sequences:	189 (154)
Seq/√Len:	12.2

BACSU - YJGD YRHD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
59_L	66_V	6.477	1.00
36_A	56_L	3.205	0.97
13_V	21_R	3.131	0.97
26_I	38_L	3.079	0.96
69_I	73_K	3.017	0.96
35_E	127_Y	3.005	0.96
21_R	143_I	2.954	0.95
114_S	155_Q	2.797	0.94
40_T	44_L	2.568	0.91
125_T	144_T	2.489	0.89
29_A	38_L	2.171	0.81
18_Q	22_D	2.026	0.76
62_Q	84_K	2.012	0.76
136_D	151_K	1.989	0.75
26_I	37_I	1.973	0.74
108_V	153_M	1.963	0.74
39_E	48_N	1.880	0.71
142_S	153_M	1.863	0.70
3_K	71_V	1.789	0.67
101_L	151_K	1.749	0.65
149_F	153_M	1.693	0.62
47_M	60_F	1.683	0.62
123_E	127_Y	1.663	0.61
96_L	126_G	1.653	0.60
48_N	130_I	1.652	0.60
85_N	96_L	1.612	0.58
50_R	63_G	1.573	0.56
28_D	35_E	1.570	0.56
4_A	154_G	1.561	0.56
56_L	143_I	1.488	0.52
82_T	153_M	1.464	0.51
43_M	74_A	1.444	0.50
28_D	43_M	1.421	0.49
41_L	52_V	1.413	0.48
64_D	67_L	1.406	0.48
63_G	67_L	1.403	0.48
76_T	79_T	1.400	0.47
31_I	156_D	1.372	0.46
12_E	126_G	1.350	0.45
129_D	139_I	1.342	0.45
37_I	152_G	1.319	0.43
44_L	106_L	1.297	0.42
50_R	133_S	1.283	0.42
2_A	154_G	1.277	0.41
39_E	54_P	1.261	0.41
10_K	28_D	1.256	0.40
60_F	112_V	1.243	0.40
22_D	44_L	1.227	0.39
142_S	145_L	1.221	0.39
81_N	100_Q	1.218	0.38
19_R	28_D	1.213	0.38
15_E	19_R	1.198	0.38
17_D	108_V	1.160	0.36
60_F	74_A	1.157	0.36
83_L	123_E	1.157	0.36
83_L	99_K	1.151	0.35
89_L	94_G	1.144	0.35
137_P	154_G	1.134	0.35
141_K	150_L	1.119	0.34
44_L	83_L	1.114	0.34
73_K	76_T	1.107	0.33
50_R	55_L	1.084	0.32
97_D	104_L	1.081	0.32
84_K	101_L	1.069	0.32
4_A	84_K	1.065	0.31
4_A	32_D	1.063	0.31
65_K	117_E	1.043	0.30
125_T	140_N	1.035	0.30
108_V	131_I	1.023	0.30
90_F	94_G	1.020	0.30
80_A	151_K	1.019	0.29
25_E	34_K	1.011	0.29
32_D	39_E	1.001	0.29
64_D	78_E	1.000	0.29
101_L	143_I	0.999	0.29
47_M	53_L	0.999	0.29
52_V	110_A	0.996	0.29
25_E	108_V	0.988	0.28
27_E	92_T	0.980	0.28
38_L	83_L	0.976	0.28
25_E	146_L	0.971	0.27
14_T	143_I	0.970	0.27
64_D	134_L	0.964	0.27
26_I	36_A	0.959	0.27
8_I	99_K	0.958	0.27
64_D	135_K	0.947	0.27
20_K	23_L	0.944	0.26
51_G	132_R	0.928	0.26
46_H	70_L	0.928	0.26
29_A	105_I	0.927	0.26
37_I	112_V	0.924	0.26
124_K	140_N	0.919	0.25
85_N	94_G	0.919	0.25
10_K	49_E	0.915	0.25
82_T	91_G	0.911	0.25
83_L	97_D	0.906	0.25
12_E	58_G	0.902	0.25
66_V	112_V	0.898	0.25
56_L	144_T	0.898	0.25
61_G	112_V	0.896	0.25
139_I	154_G	0.888	0.24
6_K	141_K	0.888	0.24
3_K	59_L	0.885	0.24
24_R	104_L	0.882	0.24
96_L	110_A	0.876	0.24
1_M	5_I	0.874	0.24
43_M	82_T	0.871	0.24
63_G	150_L	0.868	0.24
41_L	127_Y	0.858	0.23
27_E	67_L	0.856	0.23
44_L	49_E	0.855	0.23
8_I	149_F	0.851	0.23
24_R	147_F	0.848	0.23
27_E	33_H	0.846	0.23
66_V	69_I	0.838	0.22
65_K	122_E	0.835	0.22
25_E	29_A	0.834	0.22
142_S	150_L	0.825	0.22
70_L	135_K	0.823	0.22
22_D	29_A	0.820	0.22
14_T	141_K	0.819	0.22
36_A	53_L	0.817	0.22
17_D	83_L	0.811	0.22
97_D	111_G	0.802	0.21
78_E	94_G	0.802	0.21
7_R	85_N	0.801	0.21
59_L	148_S	0.798	0.21
26_I	34_K	0.797	0.21
115_A	148_S	0.796	0.21
43_M	60_F	0.791	0.21
42_H	86_L	0.786	0.21
5_I	155_Q	0.782	0.21
36_A	58_G	0.779	0.20
60_F	116_V	0.779	0.20
59_L	132_R	0.767	0.20
21_R	54_P	0.766	0.20
35_E	123_E	0.764	0.20
14_T	17_D	0.762	0.20
71_V	117_E	0.761	0.20
75_D	85_N	0.754	0.20
68_D	143_I	0.744	0.19
63_G	84_K	0.734	0.19
126_G	129_D	0.734	0.19
44_L	118_Q	0.734	0.19
35_E	90_F	0.734	0.19
38_L	127_Y	0.733	0.19
44_L	129_D	0.729	0.19
81_N	149_F	0.720	0.19
3_K	18_Q	0.719	0.19
107_K	157_T	0.710	0.18
138_E	151_K	0.707	0.18
5_I	17_D	0.701	0.18
16_E	26_I	0.701	0.18
2_A	5_I	0.696	0.18
143_I	147_F	0.696	0.18
17_D	90_F	0.695	0.18
34_K	135_K	0.693	0.18
62_Q	155_Q	0.688	0.18
52_V	111_G	0.683	0.17
16_E	124_K	0.676	0.17
138_E	157_T	0.675	0.17
17_D	37_I	0.674	0.17
3_K	113_A	0.674	0.17
26_I	131_I	0.673	0.17
13_V	17_D	0.673	0.17
40_T	129_D	0.670	0.17
70_L	73_K	0.669	0.17
72_K	89_L	0.668	0.17
115_A	157_T	0.668	0.17
34_K	105_I	0.665	0.17
76_T	87_L	0.661	0.17
75_D	94_G	0.648	0.16
1_M	154_G	0.647	0.16
33_H	96_L	0.643	0.16
73_K	92_T	0.635	0.16
133_S	140_N	0.634	0.16
5_I	45_G	0.632	0.16
98_V	157_T	0.631	0.16
52_V	101_L	0.630	0.16
7_R	52_V	0.628	0.16
29_A	94_G	0.622	0.16
109_N	144_T	0.619	0.16
58_G	137_P	0.615	0.16
33_H	135_K	0.614	0.16
70_L	92_T	0.613	0.16
32_D	52_V	0.611	0.15
130_I	133_S	0.604	0.15
41_L	139_I	0.602	0.15
30_L	149_F	0.601	0.15
56_L	135_K	0.595	0.15
34_K	38_L	0.595	0.15
63_G	140_N	0.593	0.15
19_R	70_L	0.593	0.15
71_V	115_A	0.591	0.15
133_S	137_P	0.584	0.15
80_A	101_L	0.584	0.15
33_H	41_L	0.583	0.15
12_E	70_L	0.579	0.15
70_L	76_T	0.576	0.15
111_G	152_G	0.573	0.14
5_I	82_T	0.572	0.14
15_E	134_L	0.568	0.14
85_N	148_S	0.560	0.14
13_V	89_L	0.560	0.14
62_Q	141_K	0.556	0.14
71_V	103_P	0.554	0.14
56_L	148_S	0.554	0.14
5_I	150_L	0.553	0.14
13_V	26_I	0.552	0.14
145_L	157_T	0.544	0.14
16_E	23_L	0.544	0.14
6_K	25_E	0.542	0.14
137_P	150_L	0.542	0.14
104_L	130_I	0.540	0.14
26_I	138_E	0.537	0.14
76_T	80_A	0.534	0.14
95_M	116_V	0.534	0.14
13_V	143_I	0.533	0.13
149_F	154_G	0.532	0.13
3_K	102_E	0.532	0.13
81_N	91_G	0.530	0.13
5_I	8_I	0.530	0.13
55_L	63_G	0.529	0.13
40_T	58_G	0.528	0.13
54_P	61_G	0.528	0.13
84_K	146_L	0.528	0.13
31_I	73_K	0.527	0.13
42_H	130_I	0.522	0.13
53_L	150_L	0.521	0.13
19_R	27_E	0.520	0.13
1_M	8_I	0.519	0.13
32_D	101_L	0.514	0.13
69_I	91_G	0.514	0.13
19_R	23_L	0.509	0.13
32_D	151_K	0.509	0.13
84_K	103_P	0.505	0.13
48_N	82_T	0.501	0.13
26_I	149_F	0.500	0.13

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
1k8kG	1	0.6613	17.2	0.948	Contact Map
2d6fC	1	0.0538	9.6	0.953	Contact Map
1hx1B	1	0.3871	8.9	0.954	Contact Map
1sj7A	2	0.5269	8.9	0.954	Contact Map
1i6zA	1	0.457	7.7	0.955	Contact Map
1r1tA	2	0.4839	6.4	0.957	Contact Map
1pu6A	1	0.7473	6.4	0.957	Contact Map
3p3vA	1	0.5968	6.1	0.957	Contact Map
3bpqA	2	0.2097	5.7	0.958	Contact Map
2jnkA	1	0.6022	5.6	0.958	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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