YBGL - ECOLI - GREMLIN Contacts

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YBGL - UPF0271 protein YbgL

UniProt:	P75746	Sequences: MKIDLNADLGEGCASDAELLTLVSSANIACGFHAGDAQIMQACVREAIKNGVAIGAHPSFPDRENFGRSAMQLPPETVYAQTLYQIGALATIARAQGGVMRHVKPHGMLYNQAAKEAQLADAIARAVYACDPALILVGLAGSELIRAGKQYGLTTREEVFADRGYQADGSLVPRSQSGALIENEEQALAQTLEMVQHGRVKSITGEWATVAAQTVCLHGDGEHALAFARRLRSAFAEKGIVVAA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13308
Length:	244 (240)
Sequences:	2298 (1594)
Seq/√Len:	102.9

ECOLI - YBGL
BACSU - YCSF

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
48_I	98_G	3.348	1.00
38_Q	80_A	3.070	1.00
21_T	50_N	3.057	1.00
167_A	204_T	2.900	1.00
90_A	94_R	2.776	1.00
167_A	206_E	2.766	1.00
24_S	242_V	2.573	1.00
60_F	112_Q	2.476	1.00
193_E	207_W	2.420	1.00
167_A	202_S	2.399	1.00
199_R	207_W	2.295	1.00
87_G	91_T	2.286	1.00
202_S	206_E	2.285	1.00
137_V	214_T	2.256	1.00
70_A	112_Q	2.254	1.00
40_M	89_L	2.199	1.00
193_E	197_H	2.135	1.00
83_L	130_C	2.099	1.00
90_A	130_C	2.089	1.00
164_G	172_V	2.071	1.00
143_E	146_R	2.062	1.00
135_I	156_R	2.056	1.00
41_Q	96_Q	2.052	1.00
117_A	143_E	2.036	1.00
45_R	96_Q	2.022	1.00
191_T	215_V	1.993	1.00
159_V	212_A	1.991	1.00
61_P	71_M	1.960	1.00
65_N	69_S	1.960	1.00
79_Y	129_A	1.936	1.00
79_Y	125_R	1.928	1.00
166_Q	173_P	1.887	1.00
44_V	92_I	1.858	1.00
164_G	178_G	1.839	1.00
41_Q	80_A	1.791	1.00
15_S	18_E	1.763	1.00
121_D	150_Q	1.737	1.00
4_D	25_S	1.710	1.00
23_V	26_A	1.705	1.00
32_F	84_Y	1.704	1.00
201_K	207_W	1.702	1.00
12_G	39_I	1.696	1.00
166_Q	176_Q	1.648	1.00
124_A	147_A	1.636	1.00
164_G	180_L	1.630	1.00
54_I	98_G	1.624	1.00
193_E	199_R	1.620	1.00
20_L	23_V	1.609	1.00
232_R	236_A	1.601	1.00
166_Q	170_S	1.586	1.00
113_A	123_I	1.582	1.00
184_E	188_L	1.577	1.00
217_L	228_A	1.575	1.00
166_Q	172_V	1.563	1.00
44_V	93_A	1.558	1.00
93_A	98_G	1.543	1.00
138_G	155_T	1.509	1.00
187_A	227_F	1.502	1.00
115_K	170_S	1.495	1.00
61_P	81_Q	1.485	1.00
78_V	119_L	1.479	1.00
73_L	78_V	1.475	1.00
41_Q	45_R	1.426	1.00
164_G	190_Q	1.420	1.00
156_R	213_Q	1.418	1.00
138_G	145_I	1.405	1.00
173_P	176_Q	1.398	1.00
188_L	234_A	1.382	1.00
164_G	203_I	1.381	1.00
145_I	157_E	1.380	1.00
192_L	234_A	1.374	1.00
193_E	201_K	1.372	1.00
199_R	209_T	1.361	0.99
70_A	116_E	1.360	0.99
4_D	24_S	1.355	0.99
125_R	129_A	1.354	0.99
145_I	155_T	1.300	0.99
185_E	230_R	1.292	0.99
17_A	46_E	1.288	0.99
70_A	115_K	1.286	0.99
64_E	81_Q	1.283	0.99
181_I	187_A	1.275	0.99
197_H	207_W	1.270	0.99
86_I	130_C	1.263	0.99
221_G	227_F	1.256	0.99
112_Q	119_L	1.255	0.99
104_K	216_C	1.254	0.99
121_D	151_Y	1.251	0.99
20_L	50_N	1.246	0.99
121_D	147_A	1.243	0.99
196_Q	238_K	1.242	0.99
113_A	144_L	1.234	0.99
161_A	215_V	1.229	0.99
226_A	229_R	1.224	0.99
234_A	238_K	1.220	0.99
184_E	230_R	1.218	0.99
84_Y	88_A	1.198	0.99
143_E	147_A	1.192	0.99
44_V	54_I	1.191	0.99
103_V	127_V	1.169	0.98
200_V	208_A	1.164	0.98
112_Q	116_E	1.150	0.98
53_A	101_R	1.141	0.98
121_D	125_R	1.136	0.98
38_Q	77_T	1.121	0.98
73_L	81_Q	1.120	0.98
46_E	49_K	1.115	0.98
93_A	100_M	1.103	0.98
46_E	50_N	1.094	0.98
44_V	89_L	1.092	0.98
183_N	186_Q	1.071	0.97
236_A	242_V	1.068	0.97
125_R	151_Y	1.068	0.97
157_E	213_Q	1.065	0.97
147_A	150_Q	1.065	0.97
202_S	208_A	1.061	0.97
42_A	46_E	1.060	0.97
3_I	195_V	1.059	0.97
158_E	216_C	1.055	0.97
124_A	153_L	1.052	0.97
145_I	149_K	1.047	0.97
102_H	137_V	1.046	0.97
148_G	155_T	1.040	0.97
104_K	158_E	1.030	0.96
124_A	148_G	1.029	0.96
76_E	80_A	1.029	0.96
74_P	77_T	1.028	0.96
128_Y	151_Y	1.020	0.96
84_Y	87_G	1.018	0.96
124_A	151_Y	1.017	0.96
172_V	203_I	1.015	0.96
233_S	237_E	1.013	0.96
191_T	195_V	1.005	0.96
32_F	81_Q	1.002	0.96
180_L	221_G	0.998	0.96
83_L	95_A	0.993	0.96
138_G	144_L	0.992	0.96
117_A	147_A	0.984	0.95
131_D	134_L	0.974	0.95
233_S	236_A	0.974	0.95
122_A	126_A	0.961	0.95
159_V	194_M	0.950	0.94
48_I	54_I	0.944	0.94
36_D	65_N	0.942	0.94
86_I	103_V	0.934	0.94
185_E	189_A	0.933	0.94
28_I	43_C	0.930	0.94
154_T	213_Q	0.928	0.94
45_R	49_K	0.921	0.93
17_A	42_A	0.909	0.93
26_A	52_V	0.906	0.93
156_R	214_T	0.903	0.93
161_A	191_T	0.895	0.92
12_G	43_C	0.894	0.92
192_L	196_Q	0.892	0.92
18_E	21_T	0.877	0.92
137_V	156_R	0.872	0.91
194_M	212_A	0.872	0.91
99_V	131_D	0.859	0.91
59_S	71_M	0.858	0.91
127_V	153_L	0.854	0.91
114_A	170_S	0.851	0.90
149_K	211_A	0.850	0.90
101_R	137_V	0.848	0.90
131_D	154_T	0.848	0.90
163_R	174_R	0.847	0.90
10_G	43_C	0.841	0.90
37_A	84_Y	0.840	0.90
22_L	228_A	0.832	0.89
20_L	47_A	0.830	0.89
186_Q	189_A	0.830	0.89
53_A	102_H	0.828	0.89
92_I	96_Q	0.826	0.89
186_Q	190_Q	0.825	0.89
133_A	154_T	0.824	0.89
28_I	54_I	0.823	0.89
117_A	146_R	0.820	0.89
111_N	174_R	0.818	0.89
117_A	121_D	0.804	0.88
9_L	20_L	0.801	0.88
42_A	45_R	0.797	0.87
12_G	19_L	0.783	0.86
166_Q	203_I	0.782	0.86
235_F	240_I	0.779	0.86
13_C	57_H	0.779	0.86
79_Y	83_L	0.779	0.86
229_R	233_S	0.774	0.86
60_F	78_V	0.772	0.86
113_A	119_L	0.767	0.85
7_A	19_L	0.764	0.85
194_M	200_V	0.763	0.85
135_I	154_T	0.761	0.85
124_A	128_Y	0.761	0.85
104_K	110_Y	0.753	0.84
159_V	215_V	0.748	0.84
30_C	56_A	0.744	0.83
61_P	64_E	0.742	0.83
190_Q	194_M	0.742	0.83
196_Q	240_I	0.741	0.83
192_L	238_K	0.741	0.83
48_I	93_A	0.741	0.83
22_L	225_L	0.738	0.83
189_A	234_A	0.737	0.83
120_A	147_A	0.736	0.83
200_V	210_V	0.734	0.83
64_E	73_L	0.734	0.83
157_E	211_A	0.730	0.82
149_K	157_E	0.728	0.82
187_A	190_Q	0.723	0.82
105_P	123_I	0.723	0.82
110_Y	160_F	0.723	0.82
102_H	135_I	0.719	0.81
22_L	232_R	0.718	0.81
40_M	57_H	0.718	0.81
47_A	54_I	0.710	0.81
75_P	122_A	0.707	0.80
78_V	81_Q	0.704	0.80
182_E	223_H	0.704	0.80
105_P	110_Y	0.700	0.80
142_S	145_I	0.698	0.79
136_L	144_L	0.697	0.79
140_A	157_E	0.697	0.79
110_Y	158_E	0.695	0.79
185_E	234_A	0.686	0.78
21_T	229_R	0.685	0.78
111_N	163_R	0.683	0.78
54_I	93_A	0.681	0.78
115_K	168_D	0.677	0.77
83_L	129_A	0.677	0.77
171_L	174_R	0.666	0.76
161_A	231_L	0.666	0.76
111_N	173_P	0.665	0.76
128_Y	132_P	0.665	0.76
20_L	26_A	0.664	0.76
77_T	175_S	0.658	0.75
184_E	223_H	0.655	0.75
111_N	171_L	0.653	0.75
111_N	114_A	0.652	0.75
188_L	230_R	0.646	0.74
139_L	160_F	0.644	0.74
114_A	142_S	0.642	0.74
22_L	229_R	0.641	0.73
195_V	240_I	0.640	0.73
176_Q	203_I	0.640	0.73
174_R	179_A	0.639	0.73
147_A	151_Y	0.639	0.73
14_A	65_N	0.638	0.73
9_L	26_A	0.638	0.73
110_Y	138_G	0.638	0.73
183_N	190_Q	0.634	0.73
88_A	91_T	0.632	0.72
84_Y	91_T	0.632	0.72
14_A	69_S	0.628	0.72
90_A	131_D	0.628	0.72
104_K	160_F	0.627	0.72
7_A	217_L	0.626	0.72
44_V	98_G	0.619	0.71
171_L	179_A	0.617	0.71
41_Q	92_I	0.617	0.71
69_S	77_T	0.613	0.70
78_V	82_T	0.612	0.70
7_A	23_V	0.611	0.70
16_D	43_C	0.610	0.70
12_G	63_R	0.609	0.70
136_L	148_G	0.609	0.70
37_A	88_A	0.608	0.69
94_R	99_V	0.608	0.69
83_L	126_A	0.608	0.69
139_L	142_S	0.607	0.69
41_Q	95_A	0.606	0.69
163_R	173_P	0.604	0.69
61_P	73_L	0.604	0.69
160_F	216_C	0.604	0.69
44_V	96_Q	0.602	0.69
110_Y	139_L	0.600	0.68
29_A	36_D	0.597	0.68
94_R	130_C	0.594	0.68
59_S	63_R	0.592	0.67
87_G	92_I	0.591	0.67
164_G	181_I	0.590	0.67
75_P	118_Q	0.590	0.67
32_F	37_A	0.587	0.67
188_L	227_F	0.585	0.67
4_D	53_A	0.585	0.67
120_A	144_L	0.585	0.67
36_D	39_I	0.584	0.66
19_L	228_A	0.583	0.66
195_V	235_F	0.580	0.66
6_N	104_K	0.579	0.66
110_Y	216_C	0.578	0.66
19_L	22_L	0.578	0.66
73_L	77_T	0.577	0.65
3_I	215_V	0.574	0.65
13_C	219_G	0.573	0.65
164_G	179_A	0.572	0.65
186_Q	201_K	0.571	0.65
78_V	122_A	0.570	0.65
91_T	130_C	0.570	0.65
46_E	52_V	0.569	0.64
82_T	122_A	0.569	0.64
58_P	82_T	0.569	0.64
192_L	235_F	0.568	0.64
136_L	153_L	0.568	0.64
6_N	216_C	0.567	0.64
221_G	224_A	0.567	0.64
172_V	176_Q	0.566	0.64
197_H	200_V	0.566	0.64
232_R	242_V	0.565	0.64
189_A	193_E	0.564	0.64
39_I	64_E	0.563	0.64
230_R	234_A	0.563	0.64
236_A	241_V	0.561	0.63
7_A	219_G	0.560	0.63
54_I	100_M	0.559	0.63
60_F	73_L	0.558	0.63
144_L	148_G	0.557	0.63
87_G	95_A	0.550	0.62
128_Y	133_A	0.550	0.62
44_V	57_H	0.548	0.61
75_P	125_R	0.548	0.61
174_R	178_G	0.548	0.61
119_L	214_T	0.543	0.61
74_P	78_V	0.543	0.61
37_A	87_G	0.535	0.60
98_G	101_R	0.534	0.60
60_F	70_A	0.533	0.59
48_I	97_G	0.532	0.59
83_L	90_A	0.532	0.59
222_E	226_A	0.531	0.59
36_D	69_S	0.530	0.59
225_L	228_A	0.529	0.59
146_R	150_Q	0.529	0.59
86_I	90_A	0.527	0.59
146_R	149_K	0.527	0.59
234_A	237_E	0.527	0.59
191_T	194_M	0.526	0.58
84_Y	92_I	0.523	0.58
39_I	92_I	0.523	0.58
26_A	47_A	0.521	0.58
172_V	190_Q	0.518	0.57
105_P	144_L	0.517	0.57
164_G	175_S	0.516	0.57
63_R	69_S	0.516	0.57
43_C	191_T	0.515	0.57
10_G	29_A	0.515	0.57
32_F	39_I	0.514	0.57
127_V	131_D	0.514	0.57
76_E	79_Y	0.513	0.57
5_L	217_L	0.511	0.56
118_Q	121_D	0.511	0.56
126_A	130_C	0.508	0.56
226_A	233_S	0.505	0.55
42_A	76_E	0.504	0.55
14_A	84_Y	0.504	0.55
174_R	177_S	0.503	0.55
105_P	113_A	0.502	0.55
79_Y	126_A	0.502	0.55
28_I	98_G	0.502	0.55
82_T	126_A	0.500	0.55
65_N	91_T	0.500	0.55

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
1xw8A	2	0.9303	100	0.006	Contact Map
1v6tA	4	0.9795	100	0.011	Contact Map
2dfaA	4	0.9877	100	0.012	Contact Map
2xu2A	4	0.9549	100	0.036	Contact Map
2i5iA	4	0.8811	96.6	0.93	Contact Map
4m1bA	1	0.7008	88.6	0.95	Contact Map
2vyoA	1	0.7336	84.1	0.953	Contact Map
1ny1A	1	0.7131	73.7	0.957	Contact Map
2qv5A	1	0.8156	66	0.96	Contact Map
2e67A	2	0.8197	64.5	0.96	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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