YGAC - BACSU - GREMLIN Contacts

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YGAC - UPF0374 protein YgaC

UniProt:	Q796Z1	Sequences: MGYPKEGETIQIHSYKHNGLIHRIWNETTILKSTEMCVIGANDRTMVTESDGRTWITREPAICYFHARQWFNVIGMLREDGVHYYCNISSPFAYDGEAIKYIDYDLDVKVFPDMTYNILDEDEYDDHRKAMNYPKEIDSILRDYLNTLLHWIHQRQGPFAPEFVDMWYERYLRYTK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	176 (165)
Sequences:	456 (305)
Seq/√Len:	23.7

BACSU - YGAC

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
124_Y	138_D	5.597	1.00
128_R	138_D	4.199	1.00
118_I	145_L	3.192	1.00
17_H	104_Y	3.026	1.00
39_I	167_W	2.639	0.99
114_M	155_R	2.356	0.98
88_I	141_L	2.309	0.97
151_W	156_Q	2.195	0.97
95_D	99_I	2.069	0.95
65_F	101_Y	1.960	0.93
128_R	135_K	1.956	0.93
21_I	48_T	1.942	0.93
70_W	91_P	1.934	0.93
108_V	149_L	1.886	0.92
86_C	148_L	1.880	0.92
45_T	56_I	1.817	0.91
23_R	49_E	1.811	0.90
33_S	67_A	1.810	0.90
70_W	86_C	1.807	0.90
47_V	55_W	1.724	0.88
22_H	158_P	1.706	0.87
157_G	167_W	1.686	0.87
71_F	151_W	1.669	0.86
46_M	118_I	1.649	0.86
37_C	66_H	1.643	0.85
88_I	156_Q	1.591	0.83
22_H	63_C	1.590	0.83
118_I	121_E	1.587	0.83
40_G	127_H	1.572	0.83
142_R	146_N	1.553	0.82
15_Y	93_A	1.541	0.81
68_R	121_E	1.540	0.81
95_D	100_K	1.536	0.81
125_D	128_R	1.512	0.80
12_I	65_F	1.510	0.80
124_Y	142_R	1.500	0.80
42_N	101_Y	1.487	0.79
25_W	47_V	1.475	0.78
125_D	161_P	1.475	0.78
141_L	144_Y	1.427	0.76
144_Y	147_T	1.415	0.75
65_F	70_W	1.403	0.75
7_G	61_A	1.395	0.74
138_D	142_R	1.389	0.74
73_V	84_Y	1.385	0.74
146_N	153_H	1.385	0.74
15_Y	100_K	1.378	0.73
33_S	38_V	1.361	0.72
22_H	29_T	1.354	0.72
135_K	139_S	1.348	0.72
150_H	154_Q	1.347	0.72
103_D	107_D	1.344	0.71
17_H	86_C	1.343	0.71
139_S	153_H	1.342	0.71
105_D	133_Y	1.335	0.71
13_H	21_I	1.322	0.70
93_A	137_I	1.320	0.70
49_E	55_W	1.311	0.70
108_V	152_I	1.299	0.69
121_E	142_R	1.290	0.68
23_R	55_W	1.286	0.68
105_D	127_H	1.284	0.68
18_N	130_A	1.279	0.68
160_A	166_M	1.244	0.65
157_G	161_P	1.229	0.64
67_A	89_S	1.208	0.63
40_G	122_D	1.201	0.63
49_E	76_M	1.181	0.61
64_Y	167_W	1.178	0.61
23_R	76_M	1.140	0.58
131_M	137_I	1.135	0.58
104_Y	141_L	1.130	0.58
23_R	45_T	1.129	0.58
10_I	30_I	1.128	0.58
72_N	86_C	1.127	0.58
116_Y	153_H	1.116	0.57
127_H	158_P	1.106	0.56
99_I	102_I	1.097	0.55
114_M	126_D	1.084	0.55
118_I	146_N	1.078	0.54
95_D	152_I	1.069	0.54
25_W	55_W	1.059	0.53
94_Y	99_I	1.055	0.53
63_C	127_H	1.043	0.52
8_E	143_D	1.037	0.51
120_D	123_E	1.032	0.51
32_K	134_P	1.021	0.50
14_S	101_Y	1.012	0.49
107_D	120_D	0.998	0.49
49_E	52_G	0.991	0.48
81_G	84_Y	0.990	0.48
102_I	131_M	0.979	0.47
67_A	121_E	0.975	0.47
16_K	103_D	0.971	0.47
103_D	120_D	0.964	0.46
122_D	152_I	0.963	0.46
77_L	97_E	0.952	0.45
45_T	89_S	0.950	0.45
13_H	100_K	0.941	0.45
23_R	51_D	0.922	0.43
10_I	99_I	0.920	0.43
95_D	98_A	0.918	0.43
8_E	139_S	0.916	0.43
85_Y	120_D	0.893	0.41
55_W	76_M	0.887	0.41
111_F	137_I	0.885	0.41
61_A	76_M	0.879	0.40
18_N	131_M	0.878	0.40
21_I	24_I	0.872	0.40
84_Y	87_N	0.871	0.40
61_A	74_I	0.857	0.39
18_N	34_T	0.851	0.38
62_I	127_H	0.848	0.38
108_V	145_L	0.848	0.38
33_S	170_R	0.841	0.38
59_E	78_R	0.834	0.37
113_D	154_Q	0.826	0.37
61_A	81_G	0.816	0.36
106_L	152_I	0.800	0.35
115_T	156_Q	0.789	0.34
35_E	108_V	0.781	0.34
23_R	50_S	0.781	0.34
118_I	122_D	0.777	0.34
33_S	122_D	0.777	0.34
53_R	60_P	0.777	0.34
12_I	21_I	0.776	0.33
20_L	142_R	0.774	0.33
41_A	89_S	0.772	0.33
85_Y	107_D	0.771	0.33
87_N	107_D	0.769	0.33
53_R	119_L	0.768	0.33
18_N	96_G	0.765	0.33
57_T	76_M	0.764	0.33
48_T	162_E	0.760	0.32
47_V	83_H	0.757	0.32
78_R	109_K	0.756	0.32
39_I	144_Y	0.754	0.32
109_K	119_L	0.754	0.32
41_A	71_F	0.752	0.32
126_D	130_A	0.738	0.31
55_W	60_P	0.738	0.31
139_S	143_D	0.738	0.31
22_H	45_T	0.726	0.30
36_M	66_H	0.726	0.30
21_I	27_E	0.725	0.30
10_I	143_D	0.721	0.30
59_E	74_I	0.720	0.30
11_Q	89_S	0.716	0.30
39_I	102_I	0.708	0.29
49_E	104_Y	0.708	0.29
127_H	168_Y	0.705	0.29
163_F	167_W	0.704	0.29
16_K	107_D	0.697	0.29
142_R	153_H	0.687	0.28
8_E	46_M	0.684	0.28
34_T	94_Y	0.681	0.28
14_S	22_H	0.680	0.28
86_C	104_Y	0.680	0.28
61_A	104_Y	0.680	0.28
48_T	84_Y	0.678	0.28
135_K	166_M	0.677	0.28
23_R	119_L	0.676	0.27
39_I	57_T	0.675	0.27
138_D	141_L	0.669	0.27
66_H	151_W	0.663	0.27
66_H	167_W	0.662	0.27
85_Y	123_E	0.658	0.26
150_H	169_E	0.654	0.26
167_W	170_R	0.650	0.26
18_N	79_E	0.649	0.26
65_F	100_K	0.649	0.26
123_E	158_P	0.647	0.26
55_W	82_V	0.645	0.26
31_L	149_L	0.644	0.26
91_P	101_Y	0.644	0.26
42_N	45_T	0.641	0.26
41_A	134_P	0.638	0.25
126_D	135_K	0.637	0.25
76_M	119_L	0.632	0.25
115_T	154_Q	0.631	0.25
134_P	158_P	0.628	0.25
57_T	86_C	0.626	0.25
21_I	72_N	0.624	0.25
70_W	101_Y	0.624	0.25
44_R	83_H	0.624	0.25
123_E	127_H	0.622	0.25
150_H	165_D	0.620	0.24
116_Y	154_Q	0.619	0.24
44_R	111_F	0.617	0.24
30_I	73_V	0.614	0.24
57_T	91_P	0.612	0.24
55_W	72_N	0.609	0.24
96_G	130_A	0.607	0.24
86_C	91_P	0.607	0.24
52_G	57_T	0.605	0.24
19_G	105_D	0.605	0.24
92_F	148_L	0.604	0.24
157_G	163_F	0.601	0.23
126_D	169_E	0.598	0.23
64_Y	145_L	0.596	0.23
17_H	70_W	0.592	0.23
14_S	127_H	0.585	0.23
13_H	54_T	0.585	0.23
6_E	170_R	0.583	0.23
33_S	62_I	0.581	0.22
69_Q	147_T	0.580	0.22
124_Y	141_L	0.578	0.22
57_T	119_L	0.578	0.22
132_N	169_E	0.577	0.22
18_N	136_E	0.577	0.22
33_S	36_M	0.577	0.22
62_I	169_E	0.573	0.22
56_I	126_D	0.571	0.22
10_I	112_P	0.569	0.22
110_V	148_L	0.569	0.22
25_W	81_G	0.565	0.22
25_W	123_E	0.565	0.22
6_E	64_Y	0.563	0.22
56_I	165_D	0.557	0.21
17_H	57_T	0.557	0.21
20_L	119_L	0.557	0.21
130_A	154_Q	0.555	0.21
69_Q	160_A	0.554	0.21
10_I	38_V	0.552	0.21
72_N	104_Y	0.550	0.21
63_C	100_K	0.550	0.21
122_D	129_K	0.546	0.21
64_Y	163_F	0.546	0.21
12_I	102_I	0.543	0.21
94_Y	134_P	0.541	0.21
14_S	63_C	0.540	0.21
35_E	87_N	0.535	0.20
69_Q	144_Y	0.535	0.20
136_E	143_D	0.535	0.20
44_R	79_E	0.534	0.20
83_H	145_L	0.529	0.20
60_P	72_N	0.527	0.20
25_W	76_M	0.524	0.20
45_T	90_S	0.524	0.20
27_E	124_Y	0.520	0.20
25_W	120_D	0.518	0.20
77_L	87_N	0.516	0.19
134_P	165_D	0.507	0.19
52_G	91_P	0.505	0.19
17_H	124_Y	0.503	0.19
38_V	94_Y	0.503	0.19
28_T	42_N	0.501	0.19
147_T	150_H	0.500	0.19

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
3exmA	1	0.9773	100	0.435	Contact Map
2p12A	2	0.9034	99.9	0.602	Contact Map
3l2hA	3	0.6648	21.4	0.95	Contact Map
1mrzA	2	0.75	20.8	0.95	Contact Map
3op1A	4	0.8182	20.2	0.951	Contact Map
3wg3A	2	0.7045	19.9	0.951	Contact Map
3kv5D	2	0.8807	16.6	0.953	Contact Map
2vb2X	1	0.1648	10.9	0.956	Contact Map
2kjgA	1	0.3295	10.1	0.957	Contact Map
3kxeA	2	0.233	8.6	0.958	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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