YODR - BACSU - GREMLIN Contacts

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YODR - Probable coenzyme A transferase subunit beta

UniProt:	O34466	Sequences: MGLGVAEREQIAKRAATEIKQGMIVNLGIGIPSLVPNFLKPDMQVMFQAENGVLGIGESPEKGEEDAHLCNAAGYPVRAVKGASYFDTTMSFAMIRKGKIDITILGALQVSQSGDLANWLVPGKKVPGMGGAMELAQKAKKVVVVMSHTDQKGRPKLTERCTLPLTAAGCVDLIITEKAVLEVDSHHFILKELMNGSTIDEVTRLTEAEIKIDMPFS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	217 (208)
Sequences:	3139 (1538)
Seq/√Len:	106.6

ECOLI - ATOA YDIF
BACSU - YODR SCOB
HALSA - Q9HHP2
SULSO - Q97Z51

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
111_S	115_D	4.035	1.00
200_D	204_R	3.505	1.00
150_D	154_R	3.442	1.00
181_L	210_I	3.202	1.00
87_D	90_M	3.151	1.00
184_D	187_H	3.149	1.00
173_L	182_E	3.015	1.00
159_E	207_E	2.941	1.00
193_L	202_V	2.661	1.00
184_D	189_I	2.597	1.00
182_E	191_K	2.546	1.00
193_L	199_I	2.533	1.00
79_A	83_A	2.358	1.00
112_Q	159_E	2.356	1.00
178_K	205_L	2.350	1.00
157_L	188_F	2.318	1.00
14_R	192_E	2.286	1.00
183_V	188_F	2.256	1.00
190_L	212_I	2.231	1.00
20_K	23_M	2.195	1.00
199_I	212_I	2.191	1.00
201_E	205_L	2.177	1.00
79_A	85_Y	2.052	1.00
15_A	145_V	1.996	1.00
59_S	75_Y	1.948	1.00
61_E	64_E	1.934	1.00
189_I	213_D	1.922	1.00
53_V	79_A	1.874	1.00
199_I	203_T	1.770	1.00
198_T	201_E	1.767	1.00
113_S	160_R	1.760	1.00
189_I	211_K	1.756	1.00
112_Q	209_E	1.741	1.00
48_Q	95_I	1.733	1.00
11_I	145_V	1.723	1.00
174_I	183_V	1.717	1.00
15_A	104_I	1.704	1.00
203_T	210_I	1.694	1.00
201_E	204_R	1.681	1.00
178_K	197_S	1.674	1.00
190_L	199_I	1.672	1.00
15_A	175_I	1.666	1.00
35_V	104_I	1.656	1.00
148_H	206_T	1.627	1.00
9_E	38_F	1.625	1.00
96_R	134_E	1.605	1.00
161_C	165_L	1.596	1.00
23_M	102_I	1.595	1.00
191_K	213_D	1.506	1.00
19_I	35_V	1.502	1.00
173_L	191_K	1.500	1.00
194_M	197_S	1.485	1.00
203_T	209_E	1.479	1.00
101_D	140_K	1.410	1.00
107_A	146_M	1.404	1.00
141_K	171_V	1.368	1.00
157_L	174_I	1.344	1.00
154_R	157_L	1.301	0.99
18_E	175_I	1.292	0.99
155_P	207_E	1.287	0.99
49_A	53_V	1.285	0.99
19_I	25_V	1.269	0.99
7_E	10_Q	1.268	0.99
174_I	188_F	1.263	0.99
18_E	173_L	1.252	0.99
206_T	210_I	1.244	0.99
182_E	189_I	1.243	0.99
143_V	175_I	1.226	0.99
179_A	202_V	1.225	0.99
109_Q	162_T	1.217	0.99
159_E	209_E	1.188	0.99
61_E	65_E	1.176	0.99
149_T	205_L	1.169	0.99
53_V	56_I	1.168	0.99
187_H	211_K	1.167	0.99
200_D	203_T	1.151	0.98
107_A	116_L	1.129	0.98
158_T	162_T	1.114	0.98
141_K	173_L	1.108	0.98
186_H	211_K	1.108	0.98
102_I	141_K	1.104	0.98
155_P	163_L	1.101	0.98
31_I	145_V	1.094	0.98
153_G	161_C	1.086	0.98
165_L	168_A	1.083	0.98
8_R	147_S	1.080	0.98
180_V	192_E	1.076	0.98
102_I	143_V	1.053	0.97
193_L	197_S	1.043	0.97
71_N	75_Y	1.040	0.97
8_R	34_L	1.040	0.97
181_L	203_T	1.032	0.97
160_R	163_L	1.027	0.97
154_R	163_L	1.024	0.97
149_T	177_E	1.014	0.97
152_K	155_P	1.011	0.96
21_Q	43_M	1.000	0.96
143_V	173_L	1.000	0.96
58_E	80_V	0.996	0.96
153_G	164_P	0.995	0.96
145_V	175_I	0.995	0.96
6_A	10_Q	0.991	0.96
21_Q	44_Q	0.988	0.96
8_R	31_I	0.981	0.96
109_Q	155_P	0.979	0.96
154_R	162_T	0.978	0.96
159_E	208_A	0.971	0.96
104_I	145_V	0.969	0.95
36_P	39_L	0.966	0.95
178_K	201_E	0.959	0.95
94_M	100_I	0.946	0.95
186_H	189_I	0.944	0.95
153_G	163_L	0.938	0.95
10_Q	13_K	0.936	0.95
39_L	47_F	0.936	0.95
32_P	106_G	0.934	0.94
113_S	169_G	0.921	0.94
197_S	201_E	0.917	0.94
66_D	69_L	0.913	0.94
190_L	202_V	0.911	0.94
12_A	35_V	0.899	0.93
57_G	78_R	0.898	0.93
29_I	51_N	0.897	0.93
54_L	86_F	0.897	0.93
160_R	164_P	0.885	0.93
109_Q	163_L	0.880	0.93
136_A	167_A	0.877	0.92
188_F	208_A	0.872	0.92
19_I	45_V	0.862	0.92
156_K	163_L	0.859	0.92
19_I	104_I	0.857	0.92
18_E	141_K	0.856	0.91
159_E	162_T	0.854	0.91
110_V	116_L	0.846	0.91
6_A	11_I	0.841	0.91
107_A	110_V	0.839	0.91
60_P	78_R	0.837	0.91
14_R	180_V	0.834	0.90
161_C	164_P	0.834	0.90
15_A	35_V	0.829	0.90
9_E	42_D	0.829	0.90
148_H	178_K	0.829	0.90
158_T	161_C	0.826	0.90
109_Q	158_T	0.826	0.90
24_I	94_M	0.825	0.90
184_D	211_K	0.822	0.90
53_V	85_Y	0.820	0.90
154_R	161_C	0.820	0.90
86_F	91_S	0.812	0.89
190_L	210_I	0.806	0.89
155_P	160_R	0.805	0.89
62_K	65_E	0.801	0.89
57_G	60_P	0.796	0.88
36_P	59_S	0.795	0.88
10_Q	195_N	0.795	0.88
9_E	34_L	0.791	0.88
197_S	202_V	0.790	0.88
109_Q	150_D	0.789	0.88
153_G	160_R	0.785	0.88
184_D	213_D	0.784	0.87
108_L	122_P	0.779	0.87
157_L	160_R	0.768	0.86
199_I	210_I	0.766	0.86
67_A	71_N	0.762	0.86
31_I	34_L	0.760	0.86
31_I	147_S	0.759	0.86
120_L	126_V	0.758	0.86
32_P	51_N	0.749	0.85
13_K	38_F	0.747	0.85
53_V	77_V	0.744	0.85
153_G	162_T	0.736	0.84
104_I	175_I	0.735	0.84
76_P	127_P	0.734	0.84
181_L	212_I	0.734	0.84
21_Q	42_D	0.731	0.84
162_T	207_E	0.731	0.84
14_R	18_E	0.721	0.83
188_F	210_I	0.718	0.82
157_L	164_P	0.718	0.82
167_A	170_C	0.717	0.82
171_V	182_E	0.712	0.82
112_Q	208_A	0.710	0.82
13_K	17_T	0.705	0.81
174_I	181_L	0.705	0.81
29_I	33_S	0.704	0.81
154_R	164_P	0.703	0.81
56_I	79_A	0.703	0.81
9_E	13_K	0.700	0.81
67_A	76_P	0.694	0.80
200_D	209_E	0.690	0.80
178_K	202_V	0.690	0.80
40_K	43_M	0.689	0.80
15_A	143_V	0.689	0.80
11_I	15_A	0.686	0.80
24_I	54_L	0.678	0.79
141_K	172_D	0.676	0.79
203_T	211_K	0.674	0.78
116_L	171_V	0.672	0.78
136_A	170_C	0.671	0.78
129_M	133_M	0.667	0.78
203_T	212_I	0.660	0.77
75_Y	137_Q	0.660	0.77
151_Q	161_C	0.659	0.77
178_K	194_M	0.657	0.77
193_L	198_T	0.657	0.77
193_L	196_G	0.652	0.76
6_A	194_M	0.649	0.76
152_K	157_L	0.649	0.76
29_I	106_G	0.647	0.75
119_W	122_P	0.647	0.75
151_Q	163_L	0.645	0.75
19_I	102_I	0.642	0.75
59_S	76_P	0.640	0.75
14_R	17_T	0.638	0.74
121_V	124_K	0.638	0.74
165_L	172_D	0.637	0.74
199_I	202_V	0.636	0.74
49_A	91_S	0.632	0.74
110_V	188_F	0.630	0.73
156_K	161_C	0.629	0.73
154_R	160_R	0.629	0.73
25_V	45_V	0.628	0.73
155_P	208_A	0.628	0.73
60_P	65_E	0.626	0.73
24_I	46_M	0.626	0.73
153_G	158_T	0.621	0.72
18_E	143_V	0.619	0.72
6_A	9_E	0.618	0.72
10_Q	194_M	0.616	0.72
150_D	155_P	0.616	0.72
70_C	73_A	0.613	0.71
181_L	188_F	0.612	0.71
194_M	202_V	0.609	0.71
70_C	74_G	0.607	0.71
33_S	70_C	0.606	0.71
108_L	121_V	0.605	0.70
155_P	161_C	0.604	0.70
15_A	137_Q	0.603	0.70
111_S	160_R	0.602	0.70
153_G	156_K	0.600	0.70
7_E	177_E	0.598	0.70
18_E	180_V	0.596	0.69
114_G	187_H	0.591	0.69
202_V	205_L	0.590	0.69
24_I	100_I	0.589	0.68
6_A	179_A	0.588	0.68
98_G	105_L	0.587	0.68
109_Q	159_E	0.584	0.68
179_A	191_K	0.580	0.67
50_E	92_F	0.577	0.67
128_G	175_I	0.576	0.67
32_P	145_V	0.575	0.67
149_T	155_P	0.572	0.66
9_E	41_P	0.569	0.66
209_E	212_I	0.567	0.66
178_K	206_T	0.563	0.65
53_V	83_A	0.561	0.65
97_K	138_K	0.561	0.65
116_L	144_V	0.560	0.65
100_I	105_L	0.559	0.64
128_G	143_V	0.558	0.64
116_L	136_A	0.558	0.64
154_R	158_T	0.551	0.63
12_A	31_I	0.550	0.63
12_A	34_L	0.548	0.63
12_A	38_F	0.548	0.63
122_P	128_G	0.546	0.63
16_A	38_F	0.546	0.63
23_M	101_D	0.546	0.63
151_Q	156_K	0.544	0.62
65_E	69_L	0.544	0.62
17_T	203_T	0.542	0.62
30_G	50_E	0.542	0.62
133_M	138_K	0.542	0.62
179_A	210_I	0.540	0.62
66_D	71_N	0.540	0.62
102_I	137_Q	0.539	0.62
54_L	84_S	0.536	0.61
20_K	43_M	0.536	0.61
166_T	169_G	0.534	0.61
15_A	146_M	0.533	0.61
137_Q	167_A	0.532	0.61
39_L	45_V	0.532	0.61
33_S	73_A	0.532	0.61
186_H	213_D	0.528	0.60
35_V	39_L	0.527	0.60
181_L	211_K	0.526	0.60
115_D	169_G	0.525	0.60
25_V	51_N	0.524	0.60
179_A	193_L	0.524	0.60
17_T	20_K	0.524	0.60
48_Q	100_I	0.521	0.59
21_Q	40_K	0.519	0.59
159_E	185_S	0.515	0.58
23_M	141_K	0.513	0.58
155_P	164_P	0.513	0.58
103_T	139_A	0.513	0.58
29_I	71_N	0.512	0.58
125_K	129_M	0.510	0.57
157_L	161_C	0.509	0.57
80_V	83_A	0.509	0.57
66_D	70_C	0.508	0.57
197_S	205_L	0.507	0.57
53_V	82_G	0.507	0.57
29_I	88_T	0.507	0.57
103_T	135_L	0.504	0.57
121_V	125_K	0.504	0.57
33_S	36_P	0.503	0.56
116_L	129_M	0.503	0.56
59_S	127_P	0.503	0.56
134_E	138_K	0.503	0.56
11_I	177_E	0.500	0.56

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
1poiB	1	0.9493	100	0.294	Contact Map
3k6mA	2	0.977	100	0.324	Contact Map
4kgbA	2	0.9724	100	0.329	Contact Map
2ahuA	3	0.9078	100	0.36	Contact Map
1xr4A	2	0.9862	100	0.458	Contact Map
2hj0A	2	0.9862	100	0.475	Contact Map
3gk7A	2	1	100	0.499	Contact Map
3rrlB	1	0.9539	100	0.504	Contact Map
3d3uA	1	0.8756	100	0.52	Contact Map
2oasA	3	0.9355	100	0.527	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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