YPPE - BACSU - GREMLIN Contacts

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YPPE - Uncharacterized protein YppE

UniProt:	P50833	Sequences: MLSQTLLEMTEQMIEVAEKGADRYQEGKNSNHSYDFFETIKPAVEENDELAARWAEGALELIKVRRPKYVHKEQIEAVKDNFLELVLQSYVHHIHKKRFKDITESVLYTLHAVKDEIAREDSR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	123 (114)
Sequences:	146 (121)
Seq/√Len:	11.3

BACSU - YPPE

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
78_V	109_T	4.565	1.00
6_L	58_A	3.329	0.97
55_A	75_I	2.911	0.94
33_S	93_H	2.594	0.89
97_K	101_D	2.539	0.88
58_A	113_V	2.238	0.81
86_V	89_S	2.162	0.78
37_F	91_V	2.100	0.76
40_I	91_V	2.069	0.75
24_Y	52_A	1.915	0.69
39_T	61_L	1.866	0.67
42_P	67_P	1.823	0.65
33_S	92_H	1.750	0.61
23_R	89_S	1.744	0.61
81_N	102_I	1.743	0.61
29_N	86_V	1.715	0.60
14_I	107_L	1.715	0.60
5_T	71_H	1.674	0.58
87_L	90_Y	1.658	0.57
48_D	87_L	1.609	0.55
88_Q	99_F	1.568	0.53
70_V	113_V	1.543	0.52
28_K	87_L	1.533	0.51
49_E	53_R	1.508	0.50
83_L	112_A	1.490	0.49
88_Q	91_V	1.451	0.47
72_K	78_V	1.450	0.47
45_E	87_L	1.441	0.47
48_D	52_A	1.403	0.45
101_D	106_V	1.388	0.44
34_Y	91_V	1.374	0.43
8_E	118_A	1.358	0.43
43_A	86_V	1.320	0.41
95_H	106_V	1.265	0.38
42_P	45_E	1.246	0.37
47_N	76_E	1.222	0.36
91_V	95_H	1.201	0.35
56_E	80_D	1.186	0.35
84_E	102_I	1.183	0.35
42_P	110_L	1.175	0.34
72_K	109_T	1.152	0.33
75_I	98_R	1.139	0.33
101_D	104_E	1.136	0.33
20_G	91_V	1.136	0.33
20_G	82_F	1.134	0.32
47_N	110_L	1.128	0.32
108_Y	118_A	1.114	0.32
61_L	99_F	1.096	0.31
84_E	88_Q	1.079	0.30
48_D	82_F	1.075	0.30
55_A	79_K	1.072	0.30
94_I	99_F	1.071	0.30
81_N	105_S	1.069	0.30
89_S	102_I	1.050	0.29
9_M	44_V	1.045	0.29
77_A	96_K	1.037	0.28
38_E	108_Y	1.037	0.28
82_F	85_L	1.036	0.28
10_T	114_K	1.025	0.28
99_F	113_V	1.022	0.28
23_R	96_K	1.015	0.28
41_K	45_E	0.999	0.27
71_H	98_R	0.996	0.27
43_A	90_Y	0.984	0.26
10_T	44_V	0.972	0.26
47_N	107_L	0.960	0.25
19_K	60_E	0.959	0.25
42_P	69_Y	0.934	0.25
28_K	95_H	0.933	0.25
15_E	21_A	0.922	0.24
105_S	110_L	0.922	0.24
25_Q	38_E	0.911	0.24
51_A	83_L	0.906	0.24
77_A	114_K	0.899	0.23
44_V	87_L	0.899	0.23
109_T	113_V	0.895	0.23
28_K	88_Q	0.893	0.23
26_E	30_S	0.872	0.22
30_S	49_E	0.871	0.22
54_W	98_R	0.861	0.22
23_R	47_N	0.853	0.22
70_V	83_L	0.843	0.21
55_A	106_V	0.842	0.21
60_E	64_V	0.834	0.21
7_L	114_K	0.834	0.21
10_T	98_R	0.830	0.21
15_E	75_I	0.829	0.21
20_G	40_I	0.809	0.20
36_F	42_P	0.809	0.20
88_Q	93_H	0.801	0.20
25_Q	108_Y	0.799	0.20
13_M	64_V	0.794	0.20
79_K	89_S	0.778	0.19
58_A	62_I	0.774	0.19
67_P	108_Y	0.773	0.19
33_S	97_K	0.770	0.19
34_Y	40_I	0.765	0.19
5_T	104_E	0.763	0.19
50_L	105_S	0.760	0.19
58_A	105_S	0.759	0.19
69_Y	79_K	0.758	0.19
96_K	101_D	0.741	0.18
7_L	118_A	0.739	0.18
22_D	38_E	0.737	0.18
40_I	44_V	0.737	0.18
18_E	107_L	0.733	0.18
18_E	57_G	0.726	0.18
111_H	114_K	0.726	0.18
62_I	67_P	0.721	0.18
28_K	91_V	0.720	0.18
75_I	95_H	0.715	0.18
52_A	60_E	0.707	0.17
76_E	112_A	0.697	0.17
96_K	113_V	0.692	0.17
28_K	106_V	0.687	0.17
94_I	102_I	0.687	0.17
85_L	106_V	0.684	0.17
93_H	99_F	0.681	0.17
15_E	57_G	0.676	0.16
47_N	86_V	0.670	0.16
87_L	103_T	0.669	0.16
63_K	72_K	0.668	0.16
47_N	82_F	0.663	0.16
9_M	53_R	0.660	0.16
21_A	25_Q	0.651	0.16
28_K	67_P	0.650	0.16
11_E	49_E	0.647	0.16
90_Y	94_I	0.641	0.16
40_I	54_W	0.635	0.15
90_Y	99_F	0.629	0.15
28_K	93_H	0.628	0.15
36_F	110_L	0.625	0.15
16_V	47_N	0.624	0.15
73_E	104_E	0.620	0.15
46_E	63_K	0.611	0.15
74_Q	108_Y	0.608	0.15
42_P	90_Y	0.607	0.15
51_A	79_K	0.606	0.15
77_A	101_D	0.605	0.15
49_E	80_D	0.605	0.15
78_V	107_L	0.584	0.14
13_M	82_F	0.583	0.14
31_N	36_F	0.576	0.14
82_F	108_Y	0.570	0.14
77_A	97_K	0.565	0.14
62_I	68_K	0.564	0.14
64_V	118_A	0.561	0.14
44_V	83_L	0.561	0.14
13_M	55_A	0.560	0.14
80_D	110_L	0.559	0.14
36_F	45_E	0.557	0.13
43_A	89_S	0.555	0.13
71_H	106_V	0.553	0.13
76_E	109_T	0.550	0.13
5_T	57_G	0.548	0.13
8_E	80_D	0.545	0.13
58_A	75_I	0.537	0.13
8_E	38_E	0.537	0.13
6_L	10_T	0.534	0.13
78_V	81_N	0.534	0.13
77_A	102_I	0.534	0.13
77_A	80_D	0.525	0.13
49_E	66_R	0.523	0.13
46_E	64_V	0.520	0.13
78_V	106_V	0.520	0.13
97_K	116_E	0.517	0.13
71_H	112_A	0.517	0.13
80_D	118_A	0.513	0.13
8_E	72_K	0.509	0.12
45_E	67_P	0.505	0.12
59_L	80_D	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
2hfiA	1	1	100	0.136	Contact Map
2hujA	1	1	100	0.185	Contact Map
2etsA	3	0.8943	100	0.252	Contact Map
3wurA	2	0.6098	8.8	0.943	Contact Map
3f5fA	3	0.3252	8.6	0.944	Contact Map
4y66A	1	0.6585	7.6	0.945	Contact Map
2yqcA	1	0.9431	7.1	0.946	Contact Map
4ui9I	1	0.9837	6.3	0.947	Contact Map
2o3lA	1	0.4309	5.1	0.949	Contact Map
4uudA	5	0.6829	4.6	0.95	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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