YWPE - BACSU - GREMLIN Contacts

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YWPE - Putative cysteine protease YwpE

UniProt:	P94587	Sequences: MRRDQKMGEGNYPLAGHHLKQKNLLFGPLENIKTGAQIVITDFKKDYIYSVTSKDIISEMDADVVEETNKKEITLITCDKAVKTEGRLVVKGELVDSFGHTN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	102 (95)
Sequences:	337 (251)
Seq/√Len:	25.7

BACSU - YWPE YHCS

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
73_I	92_G	5.831	1.00
40_I	73_I	3.116	1.00
2_R	67_E	2.748	0.99
94_L	97_S	2.676	0.99
57_I	89_V	2.502	0.99
76_I	89_V	2.345	0.98
6_K	9_E	2.237	0.98
68_T	72_E	2.186	0.97
2_R	65_V	2.164	0.97
32_I	36_A	2.103	0.96
2_R	13_P	1.987	0.95
32_I	51_V	1.964	0.95
72_E	91_K	1.897	0.94
79_D	86_G	1.878	0.93
50_S	95_V	1.785	0.92
38_I	90_V	1.689	0.89
80_K	84_T	1.621	0.87
57_I	76_I	1.605	0.86
59_E	84_T	1.562	0.85
18_H	27_G	1.551	0.84
16_G	19_L	1.544	0.84
29_L	32_I	1.509	0.83
64_V	76_I	1.496	0.82
52_T	72_E	1.479	0.81
45_K	97_S	1.409	0.78
70_K	93_E	1.363	0.76
9_E	71_K	1.330	0.74
53_S	91_K	1.317	0.73
74_T	89_V	1.317	0.73
50_S	93_E	1.310	0.73
62_A	66_E	1.306	0.72
37_Q	48_I	1.264	0.70
37_Q	50_S	1.255	0.69
79_D	84_T	1.254	0.69
38_I	73_I	1.240	0.68
2_R	68_T	1.212	0.67
18_H	79_D	1.183	0.65
13_P	65_V	1.169	0.64
53_S	64_V	1.131	0.61
39_V	46_D	1.098	0.59
51_V	90_V	1.079	0.57
36_A	51_V	1.079	0.57
7_M	42_D	1.076	0.57
14_L	75_L	1.064	0.56
7_M	12_Y	1.058	0.56
38_I	51_V	1.055	0.56
39_V	42_D	1.007	0.52
6_K	34_T	1.002	0.52
71_K	94_L	0.977	0.50
2_R	43_F	0.971	0.50
54_K	88_L	0.946	0.48
8_G	12_Y	0.941	0.47
5_Q	12_Y	0.940	0.47
12_Y	42_D	0.935	0.47
10_G	15_A	0.928	0.46
55_D	61_D	0.903	0.45
56_I	70_K	0.851	0.41
20_K	84_T	0.846	0.41
22_K	93_E	0.828	0.39
81_A	86_G	0.822	0.39
64_V	89_V	0.821	0.39
30_E	59_E	0.820	0.39
7_M	92_G	0.804	0.38
7_M	73_I	0.801	0.37
37_Q	62_A	0.774	0.36
15_A	84_T	0.761	0.35
34_T	56_I	0.756	0.34
19_L	84_T	0.755	0.34
16_G	54_K	0.752	0.34
8_G	42_D	0.745	0.34
5_Q	8_G	0.740	0.33
12_Y	28_P	0.740	0.33
41_T	46_D	0.739	0.33
30_E	80_K	0.738	0.33
59_E	62_A	0.737	0.33
67_E	71_K	0.736	0.33
9_E	35_G	0.732	0.33
16_G	27_G	0.731	0.33
48_I	98_F	0.724	0.32
33_K	45_K	0.724	0.32
4_D	13_P	0.702	0.31
29_L	65_V	0.701	0.31
37_Q	58_S	0.690	0.30
79_D	85_E	0.690	0.30
34_T	95_V	0.677	0.29
48_I	95_V	0.676	0.29
50_S	96_D	0.673	0.29
56_I	86_G	0.662	0.28
25_L	39_V	0.657	0.28
13_P	71_K	0.642	0.27
2_R	69_N	0.638	0.27
28_P	42_D	0.633	0.27
27_G	80_K	0.632	0.27
42_D	47_Y	0.628	0.26
30_E	54_K	0.627	0.26
64_V	84_T	0.625	0.26
26_F	77_T	0.618	0.26
44_K	69_N	0.617	0.26
81_A	84_T	0.617	0.26
18_H	48_I	0.611	0.25
7_M	15_A	0.611	0.25
29_L	88_L	0.607	0.25
8_G	41_T	0.595	0.25
80_K	85_E	0.594	0.24
51_V	98_F	0.589	0.24
34_T	54_K	0.585	0.24
18_H	30_E	0.579	0.24
84_T	90_V	0.575	0.23
18_H	84_T	0.571	0.23
2_R	72_E	0.570	0.23
54_K	90_V	0.570	0.23
3_R	50_S	0.568	0.23
10_G	35_G	0.564	0.23
31_N	37_Q	0.558	0.23
38_I	58_S	0.558	0.23
29_L	77_T	0.557	0.23
45_K	51_V	0.556	0.22
52_T	93_E	0.547	0.22
44_K	52_T	0.543	0.22
52_T	60_M	0.541	0.22
52_T	76_I	0.540	0.22
9_E	21_Q	0.540	0.22
8_G	15_A	0.538	0.22
30_E	33_K	0.538	0.22
58_S	61_D	0.537	0.22
19_L	24_L	0.536	0.21
54_K	79_D	0.527	0.21
24_L	36_A	0.527	0.21
31_N	96_D	0.525	0.21
20_K	23_N	0.525	0.21
33_K	71_K	0.522	0.21
18_H	25_L	0.521	0.21
23_N	57_I	0.520	0.21
33_K	69_N	0.518	0.21
7_M	16_G	0.513	0.20
7_M	41_T	0.513	0.20
44_K	58_S	0.513	0.20
18_H	59_E	0.511	0.20
18_H	24_L	0.505	0.20
5_Q	40_I	0.503	0.20
37_Q	97_S	0.500	0.20
14_L	42_D	0.500	0.20

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
4tqxA	1	0.9902	99.9	0.42	Contact Map
2kw8A	1	0.9902	99.9	0.439	Contact Map
4o8tA	2	0.9902	99.9	0.442	Contact Map
3fn5A	1	0.9902	99.9	0.443	Contact Map
3rccA	5	0.9314	99.9	0.452	Contact Map
1t2wA	2	0.9412	99.9	0.465	Contact Map
4d70A	1	0.9216	99.9	0.47	Contact Map
2xwgA	1	0.9706	99.9	0.473	Contact Map
3o0pA	1	0.9706	99.8	0.487	Contact Map
2w1jA	1	0.9706	99.8	0.487	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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