YHAH - BACSU - GREMLIN Contacts

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YHAH - Uncharacterized membrane protein YhaH

UniProt:	O07516	Sequences: MASGRSLLTGLFVGGIIGGAAVLLTAPSSGKQLREKMKTNYDSFEETIKRLKSDGLALKDQLIKAAKESTDVIKDVGGELQTSIKKWQEEIKPHQQDLQKEIADIEEKIRQLEKTLQN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	118 (111)
Sequences:	176 (142)
Seq/√Len:	13.5

BACSU - YHAH

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
26_A	33_L	4.859	1.00
61_Q	65_A	2.963	0.97
19_G	92_K	2.793	0.95
99_Q	105_I	2.305	0.88
98_L	101_E	2.257	0.87
5_R	79_E	2.193	0.85
32_Q	88_Q	2.112	0.83
21_A	25_T	2.093	0.82
95_Q	113_E	2.055	0.81
28_S	36_K	2.044	0.81
95_Q	112_L	2.040	0.80
65_A	76_V	1.997	0.79
26_A	37_M	1.994	0.79
91_I	94_H	1.800	0.71
34_R	47_T	1.745	0.69
16_I	29_S	1.718	0.67
26_A	110_R	1.704	0.67
65_A	106_E	1.620	0.63
90_E	99_Q	1.611	0.62
5_R	51_L	1.598	0.62
30_G	34_R	1.575	0.60
22_V	69_S	1.574	0.60
50_R	54_D	1.533	0.58
55_G	76_V	1.517	0.58
95_Q	105_I	1.446	0.54
18_G	90_E	1.415	0.52
48_I	52_K	1.414	0.52
9_T	66_A	1.411	0.52
27_P	32_Q	1.398	0.51
4_G	7_L	1.394	0.51
105_I	113_E	1.359	0.49
83_S	95_Q	1.320	0.47
105_I	112_L	1.315	0.47
37_M	44_F	1.286	0.45
84_I	104_D	1.285	0.45
18_G	22_V	1.282	0.45
12_F	80_L	1.268	0.44
45_E	81_Q	1.268	0.44
58_L	75_D	1.202	0.41
42_D	54_D	1.193	0.40
22_V	48_I	1.183	0.40
69_S	108_K	1.146	0.38
84_I	89_E	1.142	0.38
34_R	113_E	1.141	0.38
22_V	94_H	1.130	0.37
47_T	51_L	1.124	0.37
7_L	28_S	1.107	0.36
101_E	109_I	1.077	0.35
99_Q	107_E	1.070	0.34
56_L	67_K	1.065	0.34
32_Q	87_W	1.057	0.34
25_T	38_K	1.048	0.33
52_K	59_K	1.024	0.32
106_E	110_R	1.023	0.32
62_L	95_Q	1.013	0.32
18_G	104_D	1.012	0.32
80_L	100_K	1.010	0.31
68_E	79_E	1.000	0.31
58_L	66_A	0.988	0.30
4_G	61_Q	0.982	0.30
17_I	21_A	0.979	0.30
19_G	41_Y	0.978	0.30
8_L	81_Q	0.965	0.29
7_L	74_K	0.965	0.29
57_A	99_Q	0.953	0.29
34_R	37_M	0.949	0.29
69_S	74_K	0.944	0.29
11_L	20_A	0.943	0.28
28_S	41_Y	0.940	0.28
18_G	92_K	0.926	0.28
50_R	62_L	0.925	0.28
5_R	43_S	0.924	0.28
55_G	61_Q	0.923	0.28
13_V	37_M	0.889	0.26
7_L	78_G	0.876	0.26
11_L	74_K	0.871	0.25
81_Q	84_I	0.870	0.25
58_L	69_S	0.866	0.25
34_R	95_Q	0.862	0.25
87_W	103_A	0.862	0.25
83_S	87_W	0.858	0.25
42_D	49_K	0.856	0.25
7_L	69_S	0.855	0.25
22_V	87_W	0.852	0.25
19_G	90_E	0.848	0.25
64_K	114_K	0.838	0.24
65_A	70_T	0.825	0.24
73_I	86_K	0.819	0.23
22_V	91_I	0.817	0.23
66_A	105_I	0.803	0.23
38_K	51_L	0.794	0.22
15_G	24_L	0.791	0.22
61_Q	98_L	0.791	0.22
17_I	31_K	0.784	0.22
25_T	80_L	0.774	0.22
66_A	81_Q	0.769	0.22
19_G	104_D	0.763	0.21
31_K	74_K	0.757	0.21
24_L	42_D	0.754	0.21
36_K	62_L	0.742	0.21
7_L	87_W	0.734	0.20
77_G	82_T	0.733	0.20
37_M	63_I	0.705	0.19
10_G	14_G	0.704	0.19
59_K	62_L	0.700	0.19
47_T	84_I	0.698	0.19
24_L	106_E	0.697	0.19
31_K	88_Q	0.695	0.19
38_K	110_R	0.691	0.19
54_D	65_A	0.685	0.19
9_T	56_L	0.680	0.19
79_E	102_I	0.673	0.18
65_A	88_Q	0.669	0.18
70_T	106_E	0.666	0.18
106_E	113_E	0.663	0.18
109_I	113_E	0.661	0.18
66_A	90_E	0.657	0.18
28_S	32_Q	0.655	0.18
18_G	88_Q	0.647	0.17
10_G	30_G	0.646	0.17
21_A	33_L	0.646	0.17
11_L	46_E	0.642	0.17
49_K	73_I	0.635	0.17
21_A	68_E	0.630	0.17
56_L	82_T	0.628	0.17
66_A	70_T	0.617	0.17
22_V	33_L	0.608	0.16
14_G	30_G	0.605	0.16
45_E	78_G	0.604	0.16
105_I	108_K	0.591	0.16
28_S	102_I	0.586	0.16
15_G	79_E	0.581	0.16
96_Q	114_K	0.564	0.15
25_T	104_D	0.564	0.15
18_G	65_A	0.562	0.15
76_V	98_L	0.562	0.15
50_R	111_Q	0.562	0.15
54_D	77_G	0.561	0.15
83_S	101_E	0.560	0.15
24_L	79_E	0.557	0.15
51_L	75_D	0.553	0.15
94_H	102_I	0.552	0.15
83_S	108_K	0.549	0.15
9_T	54_D	0.548	0.15
68_E	89_E	0.546	0.15
35_E	79_E	0.538	0.14
103_A	108_K	0.534	0.14
66_A	83_S	0.533	0.14
11_L	97_D	0.533	0.14
15_G	34_R	0.533	0.14
85_K	114_K	0.531	0.14
34_R	40_N	0.529	0.14
55_G	62_L	0.524	0.14
83_S	90_E	0.522	0.14
60_D	96_Q	0.521	0.14
7_L	54_D	0.520	0.14
17_I	42_D	0.519	0.14
98_L	105_I	0.518	0.14
12_F	105_I	0.516	0.14
8_L	105_I	0.516	0.14
58_L	101_E	0.515	0.14
90_E	104_D	0.515	0.14
32_Q	48_I	0.508	0.14
35_E	80_L	0.505	0.14
16_I	111_Q	0.505	0.14
26_A	64_K	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
4q4gX	1	0	94.9	0.831	Contact Map
4cgkA	3	0.5508	93.1	0.844	Contact Map
4aurA	1	0.8644	82.3	0.872	Contact Map
3qprA	8	0.0085	78.4	0.877	Contact Map
3s84A	2	0.8814	75.3	0.88	Contact Map
4rsiB	1	0.9068	70.5	0.884	Contact Map
3ghgB	3	0.8983	68.4	0.886	Contact Map
2nrjA	1	0.8814	60.3	0.892	Contact Map
3r2pA	2	0.7542	57.2	0.894	Contact Map
1i5pA	1	0.9153	56.5	0.894	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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