YJHA - BACSU - GREMLIN Contacts

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YJHA - Uncharacterized lipoprotein YjhA

UniProt:	O34725	Sequences: MKKVLLLLFVLTIGLALSACSQSSDASEKEKPKEKKSQEELEKELDKELKKGGEPKTKKDDQIHKIGETFKAGHTNFTVNKVDRVQKGEYMNVGGAVNEETKTIKDDEERLIIEVTMENIGEDSISYNFIGFDLRDKNDQSVRPVFSIEEKGRILMGGTLVSGKKVTGVLSYVIPKGEQKHYTLVYNPFLADTNSSNTEERVKDDIDYLVKLD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	213 (176)
Sequences:	360 (328)
Seq/√Len:	24.7

BACSU - YJHA
HALSA - Q9HSI6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
109_E	177_G	3.865	1.00
108_E	173_V	3.804	1.00
118_E	165_K	3.777	1.00
80_N	116_T	3.696	1.00
12_T	16_A	3.515	1.00
107_D	173_V	3.465	1.00
133_D	141_S	3.443	1.00
106_D	173_V	2.764	0.99
112_I	169_V	2.689	0.99
78_T	118_E	2.597	0.99
17_L	20_C	2.534	0.99
75_T	125_I	2.482	0.99
80_N	114_E	2.441	0.98
145_V	173_V	2.439	0.98
16_A	20_C	2.264	0.97
136_D	140_Q	2.101	0.96
187_N	192_D	2.034	0.95
107_D	164_K	2.000	0.95
161_V	164_K	1.957	0.94
128_N	156_M	1.950	0.94
14_G	177_G	1.805	0.91
109_E	178_E	1.787	0.91
69_T	76_N	1.775	0.90
3_K	6_L	1.762	0.90
187_N	194_N	1.703	0.88
186_Y	198_T	1.696	0.88
11_L	14_G	1.599	0.85
72_A	187_N	1.558	0.83
50_K	55_P	1.551	0.83
194_N	198_T	1.541	0.83
134_L	181_H	1.523	0.82
188_P	192_D	1.516	0.82
52_G	56_K	1.516	0.82
105_K	176_K	1.503	0.81
136_D	163_G	1.477	0.80
18_S	21_S	1.464	0.79
77_F	187_N	1.461	0.79
51_K	57_T	1.396	0.76
53_G	58_K	1.386	0.75
80_N	115_V	1.377	0.75
72_A	77_F	1.366	0.74
130_I	161_V	1.364	0.74
128_N	131_G	1.364	0.74
183_T	197_N	1.313	0.71
73_G	121_G	1.310	0.71
114_E	169_V	1.301	0.71
77_F	163_G	1.291	0.70
116_T	165_K	1.289	0.70
51_K	56_K	1.286	0.70
74_H	193_T	1.264	0.68
188_P	194_N	1.256	0.68
4_V	7_L	1.231	0.66
126_S	129_F	1.215	0.65
109_E	117_M	1.213	0.65
48_E	53_G	1.197	0.64
130_I	159_T	1.193	0.64
142_V	149_E	1.182	0.63
6_L	10_V	1.173	0.62
23_S	90_Y	1.170	0.62
72_A	194_N	1.162	0.62
77_F	198_T	1.156	0.61
165_K	177_G	1.148	0.61
72_A	189_F	1.138	0.60
128_N	157_G	1.137	0.60
5_L	12_T	1.132	0.60
131_G	186_Y	1.119	0.59
135_R	141_S	1.115	0.58
73_G	76_N	1.109	0.58
104_I	146_F	1.100	0.57
167_T	184_L	1.098	0.57
16_A	21_S	1.084	0.56
24_S	30_E	1.082	0.56
126_S	159_T	1.072	0.55
70_F	196_S	1.069	0.55
131_G	190_L	1.061	0.55
52_G	59_K	1.046	0.53
170_L	193_T	1.043	0.53
82_V	113_I	1.029	0.52
6_L	9_F	1.026	0.52
77_F	115_V	1.025	0.52
8_L	30_E	1.022	0.52
64_H	69_T	1.020	0.52
116_T	167_T	1.012	0.51
54_E	58_K	1.010	0.51
12_T	20_C	1.009	0.51
124_S	159_T	1.004	0.50
76_N	118_E	1.002	0.50
188_P	193_T	0.998	0.50
189_F	193_T	0.996	0.50
163_G	177_G	0.993	0.50
187_N	193_T	0.985	0.49
81_K	114_E	0.974	0.48
117_M	160_L	0.964	0.48
5_L	8_L	0.955	0.47
135_R	140_Q	0.944	0.46
81_K	170_L	0.937	0.46
161_V	173_V	0.932	0.45
79_V	115_V	0.932	0.45
30_E	51_K	0.922	0.45
107_D	161_V	0.922	0.45
5_L	11_L	0.915	0.44
131_G	188_P	0.910	0.44
123_D	184_L	0.907	0.44
185_V	188_P	0.903	0.43
154_I	158_G	0.892	0.42
75_T	188_P	0.892	0.42
13_I	20_C	0.889	0.42
128_N	159_T	0.882	0.42
57_T	60_D	0.881	0.42
79_V	200_E	0.879	0.42
127_Y	132_F	0.877	0.41
74_H	190_L	0.875	0.41
132_F	186_Y	0.873	0.41
73_G	186_Y	0.872	0.41
15_L	19_A	0.871	0.41
21_S	55_P	0.870	0.41
55_P	58_K	0.863	0.40
70_F	139_D	0.850	0.40
88_G	116_T	0.848	0.39
79_V	82_V	0.840	0.39
3_K	191_A	0.825	0.38
157_G	166_V	0.820	0.37
112_I	148_I	0.818	0.37
104_I	173_V	0.812	0.37
13_I	79_V	0.810	0.37
11_L	19_A	0.800	0.36
87_K	110_R	0.797	0.36
70_F	111_L	0.797	0.36
134_L	173_V	0.794	0.36
75_T	132_F	0.792	0.36
158_G	168_G	0.785	0.35
24_S	53_G	0.784	0.35
6_L	11_L	0.783	0.35
89_E	152_G	0.783	0.35
108_E	161_V	0.783	0.35
7_L	11_L	0.781	0.35
183_T	199_E	0.781	0.35
70_F	76_N	0.781	0.35
23_S	30_E	0.775	0.34
120_I	189_F	0.762	0.34
65_K	81_K	0.757	0.33
20_C	124_S	0.752	0.33
72_A	132_F	0.751	0.33
141_S	172_Y	0.746	0.33
3_K	9_F	0.746	0.33
162_S	173_V	0.744	0.32
108_E	164_K	0.740	0.32
120_I	125_I	0.740	0.32
23_S	32_P	0.740	0.32
6_L	21_S	0.738	0.32
103_T	158_G	0.735	0.32
87_K	106_D	0.729	0.32
69_T	78_T	0.727	0.31
10_V	13_I	0.725	0.31
118_E	142_V	0.721	0.31
124_S	161_V	0.720	0.31
56_K	60_D	0.719	0.31
85_V	147_S	0.718	0.31
113_I	139_D	0.716	0.31
108_E	145_V	0.713	0.31
127_Y	158_G	0.710	0.30
46_D	50_K	0.707	0.30
27_S	30_E	0.704	0.30
82_V	140_Q	0.704	0.30
25_D	31_K	0.699	0.30
73_G	108_E	0.697	0.30
72_A	186_Y	0.693	0.29
72_A	173_V	0.690	0.29
79_V	198_T	0.685	0.29
10_V	18_S	0.677	0.28
156_M	189_F	0.677	0.28
142_V	161_V	0.677	0.28
112_I	170_L	0.677	0.28
16_A	25_D	0.677	0.28
55_P	59_K	0.675	0.28
189_F	198_T	0.674	0.28
72_A	192_D	0.673	0.28
20_C	23_S	0.670	0.28
13_I	31_K	0.670	0.28
30_E	78_T	0.669	0.28
125_I	194_N	0.667	0.28
77_F	127_Y	0.663	0.28
125_I	189_F	0.661	0.27
7_L	19_A	0.660	0.27
64_H	77_F	0.658	0.27
31_K	55_P	0.656	0.27
75_T	131_G	0.656	0.27
44_E	48_E	0.656	0.27
6_L	12_T	0.652	0.27
43_K	48_E	0.649	0.27
13_I	25_D	0.648	0.27
30_E	66_I	0.641	0.26
52_G	58_K	0.640	0.26
20_C	25_D	0.639	0.26
33_K	58_K	0.633	0.26
12_T	165_K	0.628	0.26
163_G	175_P	0.625	0.25
68_E	176_K	0.621	0.25
3_K	162_S	0.619	0.25
133_D	171_S	0.613	0.25
59_K	68_E	0.612	0.25
86_Q	145_V	0.609	0.25
71_K	74_H	0.607	0.24
127_Y	175_P	0.605	0.24
4_V	17_L	0.604	0.24
51_K	66_I	0.595	0.24
16_A	26_A	0.595	0.24
128_N	161_V	0.594	0.24
79_V	139_D	0.594	0.24
24_S	112_I	0.593	0.24
17_L	154_I	0.592	0.24
171_S	200_E	0.592	0.24
112_I	162_S	0.590	0.24
82_V	153_R	0.589	0.24
87_K	171_S	0.589	0.24
132_F	187_N	0.587	0.23
50_K	59_K	0.587	0.23
75_T	127_Y	0.586	0.23
26_A	29_K	0.584	0.23
75_T	189_F	0.584	0.23
85_V	88_G	0.582	0.23
127_Y	164_K	0.579	0.23
106_D	162_S	0.578	0.23
131_G	192_D	0.577	0.23
26_A	31_K	0.576	0.23
189_F	192_D	0.571	0.23
104_I	107_D	0.568	0.22
125_I	196_S	0.566	0.22
125_I	187_N	0.563	0.22
29_K	55_P	0.562	0.22
122_E	150_E	0.560	0.22
10_V	50_K	0.559	0.22
23_S	28_E	0.558	0.22
43_K	46_D	0.557	0.22
77_F	196_S	0.557	0.22
144_P	172_Y	0.556	0.22
141_S	157_G	0.548	0.21
84_R	113_I	0.546	0.21
28_E	32_P	0.546	0.21
49_L	71_K	0.545	0.21
189_F	194_N	0.540	0.21
9_F	118_E	0.538	0.21
111_L	174_I	0.533	0.21
5_L	172_Y	0.531	0.21
57_T	62_Q	0.530	0.21
132_F	181_H	0.527	0.20
25_D	56_K	0.526	0.20
32_P	53_G	0.524	0.20
4_V	11_L	0.523	0.20
146_F	157_G	0.522	0.20
71_K	140_Q	0.519	0.20
120_I	194_N	0.518	0.20
64_H	68_E	0.517	0.20
66_I	158_G	0.516	0.20
103_T	152_G	0.516	0.20
117_M	200_E	0.515	0.20
74_H	120_I	0.515	0.20
82_V	111_L	0.514	0.20
48_E	51_K	0.512	0.20
47_K	180_K	0.511	0.20
7_L	43_K	0.508	0.20
28_E	46_D	0.506	0.20
10_V	17_L	0.500	0.19
90_Y	152_G	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
3cfuA	1	0.6854	100	0.421	Contact Map
4lesA	1	0.5962	99.9	0.519	Contact Map
4r4gA	1	0.6338	99.9	0.559	Contact Map
5bxgA	1	0.6761	99.4	0.717	Contact Map
2llgA	1	0.6103	96.9	0.862	Contact Map
1lmiA	1	0.5775	96.8	0.865	Contact Map
3qfgA	2	0.6244	95.6	0.878	Contact Map
3pmqA	1	0.5023	95.1	0.883	Contact Map
3nrfA	3	0.4883	90.8	0.899	Contact Map
4kysA	1	0.6056	85.1	0.909	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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