YLBD - BACSU - GREMLIN Contacts

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YLBD - Uncharacterized protein YlbD

UniProt:	O34880	Sequences: MANQHANHSINDFKQFVKKHPKLIKEVRKEQRSWQDVYENWVLFGESDPIWDPYREPEEASEAVPETPQKNDFVSKMVTAVKKMDVNQMNEQINKMSQSISSLQSLLNTFSGSGQKHSQPGSGQHPFSFRKD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	132 (126)
Sequences:	135 (120)
Seq/√Len:	10.7

BACSU - YLBD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
35_Q	39_E	5.082	1.00
19_K	46_E	3.686	0.98
85_D	88_Q	3.091	0.95
41_W	104_Q	2.988	0.94
24_I	34_W	2.944	0.93
28_R	40_N	2.794	0.91
42_V	95_K	2.410	0.83
48_D	109_T	2.318	0.81
15_Q	101_S	2.161	0.76
98_Q	102_S	2.096	0.74
20_H	100_I	2.079	0.73
58_E	67_T	2.012	0.70
28_R	109_T	1.846	0.63
103_L	116_K	1.781	0.60
49_P	52_D	1.755	0.59
14_K	77_M	1.710	0.57
39_E	43_L	1.706	0.57
70_K	93_I	1.701	0.57
35_Q	40_N	1.648	0.54
17_V	33_S	1.625	0.53
35_Q	44_F	1.574	0.51
37_V	50_I	1.521	0.48
126_P	129_F	1.505	0.48
17_V	82_K	1.505	0.48
79_T	100_I	1.503	0.47
34_W	93_I	1.493	0.47
78_V	96_M	1.469	0.46
11_N	128_S	1.456	0.45
85_D	99_S	1.425	0.44
23_L	100_I	1.424	0.44
43_L	50_I	1.379	0.42
44_F	50_I	1.340	0.40
39_E	82_K	1.323	0.39
18_K	87_N	1.323	0.39
27_V	34_W	1.308	0.38
72_D	75_S	1.306	0.38
35_Q	100_I	1.279	0.37
44_F	101_S	1.245	0.36
77_M	99_S	1.237	0.35
6_A	10_I	1.223	0.35
97_S	103_L	1.218	0.34
47_S	85_D	1.204	0.34
32_R	37_V	1.194	0.33
102_S	105_S	1.186	0.33
47_S	119_Q	1.161	0.32
125_H	130_R	1.153	0.32
98_Q	105_S	1.147	0.32
124_Q	128_S	1.143	0.31
95_K	105_S	1.140	0.31
9_S	107_L	1.133	0.31
81_V	94_N	1.107	0.30
109_T	113_S	1.101	0.30
85_D	103_L	1.092	0.29
67_T	122_S	1.087	0.29
6_A	38_Y	1.077	0.29
54_Y	119_Q	1.077	0.29
35_Q	82_K	1.062	0.28
86_V	102_S	1.060	0.28
28_R	48_D	1.056	0.28
19_K	55_R	1.030	0.27
35_Q	96_M	1.016	0.26
4_Q	125_H	1.009	0.26
90_N	111_S	1.008	0.26
96_M	99_S	1.001	0.26
47_S	65_P	0.999	0.26
24_I	28_R	0.998	0.26
83_K	114_G	0.989	0.25
41_W	111_S	0.987	0.25
38_Y	68_P	0.985	0.25
59_E	69_Q	0.962	0.24
66_E	71_N	0.951	0.24
31_Q	52_D	0.943	0.24
32_R	54_Y	0.938	0.24
88_Q	96_M	0.933	0.23
18_K	31_Q	0.921	0.23
85_D	96_M	0.917	0.23
75_S	110_F	0.914	0.23
12_D	75_S	0.909	0.23
14_K	52_D	0.906	0.23
26_E	126_P	0.905	0.23
43_L	55_R	0.902	0.22
23_L	34_W	0.897	0.22
92_Q	102_S	0.895	0.22
42_V	105_S	0.891	0.22
9_S	28_R	0.882	0.22
60_A	121_G	0.877	0.22
27_V	38_Y	0.874	0.22
20_H	55_R	0.870	0.21
16_F	45_G	0.852	0.21
13_F	45_G	0.852	0.21
13_F	16_F	0.852	0.21
38_Y	43_L	0.848	0.21
127_F	132_D	0.841	0.20
41_W	44_F	0.837	0.20
82_K	94_N	0.831	0.20
77_M	100_I	0.809	0.20
83_K	122_S	0.807	0.19
20_H	77_M	0.806	0.19
44_F	76_K	0.801	0.19
102_S	111_S	0.798	0.19
73_F	79_T	0.798	0.19
37_V	95_K	0.792	0.19
22_K	55_R	0.786	0.19
59_E	94_N	0.786	0.19
76_K	101_S	0.772	0.18
31_Q	54_Y	0.761	0.18
33_S	40_N	0.752	0.18
84_M	128_S	0.748	0.18
33_S	78_V	0.736	0.17
33_S	94_N	0.733	0.17
25_K	122_S	0.728	0.17
9_S	38_Y	0.722	0.17
27_V	30_E	0.717	0.17
101_S	106_L	0.716	0.17
63_A	120_P	0.715	0.17
57_P	66_E	0.713	0.17
79_T	96_M	0.711	0.17
49_P	108_N	0.710	0.17
48_D	96_M	0.702	0.17
63_A	121_G	0.702	0.17
127_F	131_K	0.700	0.16
111_S	116_K	0.698	0.16
22_K	57_P	0.689	0.16
70_K	125_H	0.688	0.16
22_K	43_L	0.680	0.16
39_E	83_K	0.676	0.16
115_Q	124_Q	0.672	0.16
39_E	100_I	0.668	0.16
84_M	89_M	0.665	0.16
44_F	48_D	0.664	0.16
60_A	117_H	0.662	0.16
32_R	44_F	0.661	0.15
90_N	104_Q	0.660	0.15
15_Q	103_L	0.653	0.15
67_T	121_G	0.646	0.15
88_Q	95_K	0.643	0.15
57_P	67_T	0.641	0.15
8_H	42_V	0.636	0.15
31_Q	37_V	0.628	0.15
32_R	105_S	0.619	0.14
17_V	42_V	0.619	0.14
76_K	97_S	0.613	0.14
80_A	101_S	0.610	0.14
23_L	29_K	0.610	0.14
5_H	63_A	0.607	0.14
4_Q	103_L	0.606	0.14
65_P	77_M	0.600	0.14
29_K	92_Q	0.599	0.14
104_Q	127_F	0.599	0.14
40_N	95_K	0.595	0.14
106_L	123_G	0.594	0.14
50_I	54_Y	0.588	0.14
46_E	73_F	0.584	0.14
12_D	57_P	0.581	0.14
47_S	99_S	0.576	0.13
69_Q	91_E	0.570	0.13
68_P	106_L	0.570	0.13
74_V	103_L	0.569	0.13
103_L	111_S	0.564	0.13
36_D	87_N	0.561	0.13
119_Q	124_Q	0.560	0.13
14_K	130_R	0.549	0.13
30_E	130_R	0.547	0.13
32_R	50_I	0.544	0.13
20_H	128_S	0.541	0.13
37_V	97_S	0.541	0.13
16_F	21_P	0.536	0.13
21_P	45_G	0.536	0.13
13_F	21_P	0.536	0.13
49_P	53_P	0.536	0.13
112_G	115_Q	0.533	0.13
30_E	129_F	0.530	0.13
37_V	42_V	0.529	0.12
17_V	34_W	0.524	0.12
43_L	112_G	0.524	0.12
69_Q	87_N	0.523	0.12
67_T	117_H	0.522	0.12
76_K	105_S	0.520	0.12
53_P	69_Q	0.518	0.12
10_I	103_L	0.516	0.12
52_D	60_A	0.516	0.12
77_M	119_Q	0.509	0.12
114_G	120_P	0.508	0.12
79_T	106_L	0.506	0.12
48_D	88_Q	0.505	0.12
19_K	77_M	0.505	0.12
48_D	73_F	0.504	0.12
91_E	122_S	0.504	0.12
75_S	112_G	0.500	0.12

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
4pz1A	2	0.5455	39.2	0.932	Contact Map
2beqA	1	0.2727	13	0.946	Contact Map
2jrbA	1	0.2045	11.2	0.948	Contact Map
3sooA	2	0.2121	10.8	0.948	Contact Map
3hr1A	1	0.2955	8.3	0.951	Contact Map
1vlrA	2	0.4167	6.5	0.953	Contact Map
3l6gA	1	0.4242	6.5	0.953	Contact Map
4n17A	1	0.3258	6.3	0.953	Contact Map
3mpkA	1	0.3182	6.2	0.953	Contact Map
4wfcB	1	0.3485	6.2	0.953	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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