YWCB - BACSU - GREMLIN Contacts

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YWCB - Uncharacterized protein YwcB

UniProt:	P39600	Sequences: MYKADYKQIAATPSFQAFLKQKRAFIVPSAIFFFVFYFSLPVLTSYFTFLNAPAIGAVSWAWLFAIAQFAMTWILSTVYSRRAAHFDKYVSALKEDLKGEQT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	102 (94)
Sequences:	682 (411)
Seq/√Len:	42.4

BACSU - YWCB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
14_S	92_A	3.158	1.00
54_A	63_L	3.078	1.00
20_K	24_A	3.037	1.00
14_S	96_D	2.599	1.00
74_I	78_V	2.576	1.00
63_L	67_A	2.424	1.00
23_R	27_V	2.280	1.00
70_A	74_I	2.142	0.99
22_K	26_I	2.074	0.99
9_I	97_L	2.029	0.99
17_A	89_Y	2.018	0.99
89_Y	92_A	1.974	0.99
91_S	95_E	1.968	0.99
54_A	60_W	1.953	0.99
32_F	71_M	1.901	0.99
74_I	77_T	1.878	0.99
82_R	86_F	1.829	0.98
36_F	68_Q	1.546	0.95
76_S	80_S	1.542	0.95
31_I	35_V	1.489	0.94
35_V	39_S	1.427	0.93
58_V	63_L	1.393	0.92
5_D	46_Y	1.377	0.91
43_L	64_F	1.356	0.91
36_F	67_A	1.346	0.90
44_T	61_A	1.341	0.90
45_S	71_M	1.338	0.90
49_F	60_W	1.334	0.90
55_I	58_V	1.333	0.90
53_P	59_S	1.331	0.90
92_A	96_D	1.306	0.89
73_W	90_V	1.275	0.88
61_A	76_S	1.267	0.88
5_D	8_Q	1.260	0.87
9_I	96_D	1.248	0.87
17_A	21_Q	1.185	0.84
39_S	90_V	1.185	0.84
80_S	93_L	1.106	0.79
22_K	82_R	1.104	0.79
13_P	17_A	1.093	0.79
33_F	75_L	1.086	0.78
8_Q	13_P	1.029	0.74
30_A	33_F	1.027	0.74
68_Q	72_T	1.022	0.74
40_L	60_W	1.000	0.72
40_L	76_S	0.998	0.72
9_I	13_P	0.988	0.71
54_A	58_V	0.986	0.71
36_F	40_L	0.983	0.71
29_S	34_F	0.981	0.71
10_A	16_Q	0.966	0.69
19_L	65_A	0.959	0.69
21_Q	24_A	0.929	0.66
26_I	82_R	0.926	0.66
67_A	71_M	0.898	0.64
47_F	50_L	0.898	0.64
32_F	74_I	0.893	0.63
26_I	87_D	0.889	0.63
43_L	47_F	0.882	0.62
42_V	46_Y	0.869	0.61
22_K	45_S	0.862	0.60
36_F	72_T	0.860	0.60
44_T	80_S	0.860	0.60
31_I	34_F	0.859	0.60
33_F	87_D	0.856	0.60
12_T	28_P	0.844	0.59
85_H	88_K	0.841	0.59
33_F	50_L	0.832	0.58
39_S	64_F	0.824	0.57
27_V	31_I	0.810	0.56
53_P	57_A	0.810	0.56
7_K	11_A	0.809	0.56
5_D	97_L	0.809	0.56
13_P	92_A	0.800	0.55
50_L	62_W	0.795	0.54
29_S	78_V	0.790	0.54
17_A	55_I	0.783	0.53
22_K	38_F	0.781	0.53
35_V	38_F	0.781	0.53
33_F	37_Y	0.743	0.49
21_Q	89_Y	0.736	0.49
61_A	80_S	0.716	0.47
29_S	56_G	0.712	0.46
12_T	23_R	0.710	0.46
29_S	75_L	0.703	0.46
77_T	80_S	0.697	0.45
26_I	61_A	0.693	0.45
67_A	70_A	0.691	0.44
61_A	68_Q	0.687	0.44
60_W	64_F	0.681	0.44
34_F	80_S	0.675	0.43
6_Y	95_E	0.665	0.42
11_A	38_F	0.664	0.42
78_V	81_R	0.660	0.42
18_F	89_Y	0.656	0.41
24_A	95_E	0.649	0.41
28_P	31_I	0.648	0.41
28_P	76_S	0.647	0.40
62_W	76_S	0.647	0.40
19_L	23_R	0.636	0.39
81_R	84_A	0.624	0.38
26_I	37_Y	0.616	0.38
72_T	75_L	0.612	0.37
45_S	76_S	0.611	0.37
18_F	88_K	0.605	0.37
21_Q	94_K	0.604	0.37
61_A	84_A	0.604	0.37
35_V	96_D	0.601	0.36
84_A	96_D	0.600	0.36
82_R	85_H	0.590	0.35
91_S	94_K	0.588	0.35
49_F	63_L	0.585	0.35
53_P	90_V	0.580	0.35
52_A	59_S	0.569	0.34
24_A	78_V	0.566	0.33
81_R	85_H	0.563	0.33
44_T	76_S	0.562	0.33
87_D	91_S	0.562	0.33
12_T	93_L	0.561	0.33
30_A	55_I	0.559	0.33
40_L	68_Q	0.558	0.33
6_Y	9_I	0.551	0.32
5_D	55_I	0.545	0.32
38_F	42_V	0.543	0.31
72_T	76_S	0.541	0.31
7_K	46_Y	0.537	0.31
57_A	90_V	0.532	0.31
14_S	88_K	0.529	0.30
19_L	59_S	0.527	0.30
32_F	36_F	0.527	0.30
33_F	90_V	0.523	0.30
35_V	92_A	0.521	0.30
20_K	96_D	0.517	0.29
77_T	81_R	0.516	0.29
65_A	88_K	0.512	0.29
77_T	85_H	0.508	0.29
25_F	78_V	0.508	0.29
12_T	81_R	0.507	0.29
48_T	55_I	0.506	0.28
55_I	93_L	0.502	0.28
19_L	27_V	0.500	0.28

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
4x9eA	4	0.7647	39.1	0.919	Contact Map
2pgsA	4	0.6667	35.6	0.92	Contact Map
3bg2A	4	0.7255	28.4	0.924	Contact Map
4hkrA	3	0.8627	11.9	0.936	Contact Map
3wvfA	1	0.951	8.5	0.94	Contact Map
3rlfF	1	0.7451	8.5	0.94	Contact Map
3d31C	2	0.7745	7.3	0.942	Contact Map
4jrbA	1	0.3922	6.6	0.943	Contact Map
4eogA	2	0.6373	5.9	0.945	Contact Map
4m32A	6	0.4902	5.5	0.945	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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