YPGQ - BACSU - GREMLIN Contacts

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YPGQ - Uncharacterized protein YpgQ

UniProt:	P54168	Sequences: MKELKQAEQIRTWVQSILTDESSGHDWHHVSRVADLAAYIGEKEKADLFIVETAALVHDLIDVKLPDTVRLSVSEVYDQLVFFGVGKENADRVIHIITRMSFRDRGKLAKEPLSIEGKAVQDADRLDAIGAVGIARAFMFAGAKGHGLYGDEQSAYAHFFHKLLRLKDMMNTDTARELAEERHNFMLQFVRQLEKDIPGIDAETS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	205 (189)
Sequences:	1524 (1149)
Seq/√Len:	83.6

ECOLI - YEDJ
BACSU - YPGQ
HALSA - Q9HRV0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
141_A	155_A	4.089	1.00
164_L	190_V	3.233	1.00
44_E	174_T	2.703	1.00
40_I	174_T	2.641	1.00
121_Q	171_N	2.593	1.00
41_G	46_A	2.570	1.00
10_I	53_T	2.535	1.00
11_R	34_A	2.386	1.00
9_Q	83_F	2.378	1.00
174_T	177_E	2.313	1.00
34_A	52_E	2.286	1.00
86_G	89_N	2.273	1.00
47_D	89_N	2.220	1.00
185_F	192_Q	2.181	1.00
37_A	51_V	2.163	1.00
135_A	138_F	2.154	1.00
170_M	179_A	2.140	1.00
147_G	150_G	2.129	1.00
156_Y	190_V	2.058	1.00
38_A	52_E	2.017	1.00
170_M	175_A	1.973	1.00
51_V	120_V	1.971	1.00
167_K	183_H	1.958	1.00
184_N	188_Q	1.942	1.00
171_N	175_A	1.936	1.00
53_T	93_V	1.931	1.00
146_H	155_A	1.916	1.00
13_W	79_Q	1.864	1.00
17_I	75_E	1.838	1.00
34_A	38_A	1.807	1.00
41_G	48_L	1.802	1.00
193_L	197_I	1.795	1.00
163_L	186_M	1.778	1.00
167_K	180_E	1.776	1.00
121_Q	125_R	1.760	1.00
181_E	192_Q	1.721	1.00
115_I	118_K	1.718	1.00
43_K	177_E	1.696	1.00
183_H	187_L	1.639	1.00
112_P	117_G	1.636	1.00
99_R	117_G	1.619	1.00
157_A	161_H	1.600	1.00
68_T	71_L	1.565	1.00
185_F	188_Q	1.558	1.00
180_E	184_N	1.556	1.00
46_A	51_V	1.520	0.99
154_S	157_A	1.504	0.99
34_A	56_L	1.495	0.99
184_N	187_L	1.486	0.99
166_L	170_M	1.482	0.99
24_G	65_L	1.479	0.99
100_M	117_G	1.426	0.99
49_F	89_N	1.421	0.99
46_A	119_A	1.409	0.99
185_F	189_F	1.409	0.99
178_L	181_E	1.391	0.99
165_R	169_M	1.352	0.99
77_Y	94_I	1.323	0.99
188_Q	192_Q	1.320	0.99
141_A	146_H	1.310	0.98
10_I	79_Q	1.310	0.98
138_F	142_G	1.307	0.98
43_K	174_T	1.305	0.98
95_H	99_R	1.278	0.98
137_A	155_A	1.275	0.98
156_Y	193_L	1.262	0.98
61_I	72_S	1.258	0.98
11_R	15_Q	1.245	0.98
36_L	178_L	1.230	0.98
81_V	87_K	1.224	0.98
53_T	85_V	1.216	0.98
187_L	191_R	1.193	0.97
61_I	76_V	1.188	0.97
181_E	195_K	1.168	0.97
87_K	91_D	1.168	0.97
186_M	190_V	1.160	0.97
36_L	39_Y	1.142	0.96
129_I	183_H	1.121	0.96
158_H	162_K	1.115	0.96
42_E	48_L	1.112	0.96
173_D	176_R	1.110	0.96
85_V	89_N	1.109	0.96
41_G	51_V	1.104	0.96
23_S	139_M	1.091	0.95
46_A	115_I	1.090	0.95
22_S	65_L	1.088	0.95
172_T	175_A	1.086	0.95
54_A	96_I	1.083	0.95
77_Y	81_V	1.059	0.94
39_Y	43_K	1.055	0.94
190_V	194_E	1.033	0.94
15_Q	27_W	1.030	0.94
77_Y	90_A	1.025	0.93
118_K	171_N	1.022	0.93
99_R	110_K	1.020	0.93
92_R	116_E	1.012	0.93
78_D	82_F	1.004	0.93
21_E	24_G	0.988	0.92
164_L	183_H	0.983	0.92
14_V	18_L	0.979	0.92
79_Q	83_F	0.967	0.91
139_M	155_A	0.960	0.91
76_V	80_L	0.953	0.91
73_V	98_T	0.952	0.91
160_F	190_V	0.941	0.90
30_V	34_A	0.940	0.90
99_R	113_L	0.935	0.90
135_A	148_L	0.922	0.89
128_A	158_H	0.917	0.89
49_F	85_V	0.913	0.89
140_F	144_K	0.899	0.88
77_Y	91_D	0.885	0.87
76_V	97_I	0.883	0.87
134_I	189_F	0.876	0.87
40_I	178_L	0.874	0.87
30_V	127_D	0.873	0.86
28_H	31_S	0.870	0.86
126_L	175_A	0.865	0.86
31_S	35_D	0.858	0.86
129_I	137_A	0.857	0.85
164_L	187_L	0.855	0.85
69_V	72_S	0.851	0.85
160_F	194_E	0.840	0.84
156_Y	160_F	0.833	0.84
10_I	57_V	0.829	0.84
131_A	196_D	0.821	0.83
25_H	136_R	0.821	0.83
75_E	78_D	0.819	0.83
138_F	178_L	0.818	0.83
39_Y	174_T	0.810	0.82
49_F	53_T	0.806	0.82
47_D	92_R	0.801	0.81
54_A	100_M	0.796	0.81
73_V	76_V	0.796	0.81
113_L	118_K	0.793	0.81
105_R	109_A	0.793	0.81
14_V	27_W	0.793	0.81
39_Y	178_L	0.790	0.80
37_A	120_V	0.788	0.80
150_G	157_A	0.783	0.80
10_I	13_W	0.781	0.80
175_A	178_L	0.780	0.80
165_R	168_D	0.778	0.79
128_A	162_K	0.769	0.79
36_L	40_I	0.763	0.78
187_L	194_E	0.762	0.78
40_I	175_A	0.756	0.77
103_R	158_H	0.752	0.77
61_I	73_V	0.752	0.77
95_H	114_S	0.751	0.77
164_L	186_M	0.747	0.77
151_D	197_I	0.744	0.76
65_L	101_S	0.740	0.76
153_Q	157_A	0.737	0.76
101_S	125_R	0.735	0.75
176_R	180_E	0.731	0.75
158_H	166_L	0.729	0.75
188_Q	191_R	0.728	0.75
18_L	100_M	0.727	0.75
182_R	192_Q	0.724	0.74
45_K	115_I	0.723	0.74
57_V	76_V	0.723	0.74
94_I	98_T	0.722	0.74
121_Q	158_H	0.715	0.73
24_G	171_N	0.713	0.73
50_I	92_R	0.710	0.73
90_A	94_I	0.709	0.73
96_I	100_M	0.708	0.73
164_L	179_A	0.707	0.73
103_R	121_Q	0.707	0.73
62_D	65_L	0.707	0.73
25_H	162_K	0.706	0.73
89_N	93_V	0.704	0.72
11_R	31_S	0.702	0.72
61_I	66_P	0.698	0.72
127_D	133_G	0.697	0.72
41_G	55_A	0.695	0.71
57_V	60_L	0.694	0.71
133_G	170_M	0.694	0.71
159_F	164_L	0.692	0.71
41_G	45_K	0.690	0.71
61_I	75_E	0.684	0.70
102_F	165_R	0.683	0.70
162_K	166_L	0.682	0.70
131_A	185_F	0.675	0.69
97_I	100_M	0.675	0.69
18_L	30_V	0.675	0.69
101_S	158_H	0.674	0.69
21_E	65_L	0.669	0.68
66_P	72_S	0.669	0.68
36_L	192_Q	0.660	0.67
66_P	75_E	0.657	0.67
31_S	34_A	0.654	0.67
195_K	198_P	0.653	0.67
62_D	161_H	0.647	0.66
77_Y	88_E	0.646	0.66
102_F	166_L	0.644	0.66
80_L	90_A	0.641	0.65
74_S	98_T	0.634	0.64
146_H	154_S	0.631	0.64
60_L	72_S	0.630	0.64
135_A	178_L	0.627	0.63
74_S	77_Y	0.626	0.63
127_D	149_Y	0.624	0.63
23_S	143_A	0.622	0.63
10_I	83_F	0.620	0.63
137_A	159_F	0.619	0.62
128_A	166_L	0.619	0.62
158_H	164_L	0.615	0.62
114_S	117_G	0.615	0.62
32_R	127_D	0.611	0.61
160_F	164_L	0.607	0.61
71_L	74_S	0.607	0.61
8_E	31_S	0.606	0.61
158_H	163_L	0.605	0.61
105_R	169_M	0.603	0.60
18_L	61_I	0.603	0.60
134_I	164_L	0.602	0.60
41_G	119_A	0.599	0.60
81_V	90_A	0.599	0.60
80_L	93_V	0.596	0.60
12_T	177_E	0.595	0.59
167_K	179_A	0.592	0.59
8_E	12_T	0.591	0.59
46_A	116_E	0.587	0.58
96_I	99_R	0.584	0.58
28_H	151_D	0.583	0.58
105_R	112_P	0.582	0.58
138_F	141_A	0.580	0.58
79_Q	82_F	0.579	0.57
63_V	105_R	0.579	0.57
14_V	30_V	0.577	0.57
39_Y	92_R	0.573	0.57
191_R	195_K	0.572	0.56
34_A	55_A	0.572	0.56
13_W	82_F	0.571	0.56
115_I	119_A	0.569	0.56
84_G	173_D	0.568	0.56
22_S	139_M	0.567	0.56
53_T	89_N	0.567	0.56
14_V	17_I	0.565	0.56
135_A	142_G	0.564	0.55
25_H	128_A	0.564	0.55
174_T	178_L	0.563	0.55
125_R	171_N	0.563	0.55
16_S	19_T	0.561	0.55
104_D	110_K	0.556	0.54
57_V	193_L	0.555	0.54
98_T	110_K	0.555	0.54
62_D	125_R	0.553	0.54
54_A	120_V	0.551	0.54
42_E	74_S	0.549	0.53
7_A	11_R	0.549	0.53
141_A	157_A	0.548	0.53
137_A	166_L	0.546	0.53
35_D	198_P	0.544	0.53
62_D	120_V	0.543	0.53
117_G	139_M	0.538	0.52
103_R	125_R	0.538	0.52
35_D	38_A	0.537	0.52
151_D	157_A	0.536	0.52
95_H	98_T	0.534	0.51
40_I	120_V	0.534	0.51
70_R	74_S	0.534	0.51
70_R	98_T	0.531	0.51
38_A	48_L	0.531	0.51
17_I	20_D	0.530	0.51
64_K	161_H	0.526	0.50
158_H	161_H	0.526	0.50
78_D	81_V	0.525	0.50
8_E	16_S	0.518	0.49
95_H	117_G	0.518	0.49
117_G	171_N	0.515	0.49
149_Y	197_I	0.508	0.48
129_I	179_A	0.506	0.48
16_S	20_D	0.505	0.48
8_E	88_E	0.504	0.47
138_F	181_E	0.504	0.47
44_E	119_A	0.503	0.47
141_A	150_G	0.501	0.47
181_E	184_N	0.501	0.47
62_D	140_F	0.501	0.47
114_S	118_K	0.500	0.47
14_V	56_L	0.500	0.47

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
2pjqA	2	0.9561	100	0.283	Contact Map
2qgsA	2	0.9415	100	0.287	Contact Map
3b57A	2	0.8683	100	0.291	Contact Map
3dtoA	2	0.8537	100	0.295	Contact Map
3djbA	2	0.8976	100	0.298	Contact Map
3gw7A	2	0.9073	100	0.299	Contact Map
2pq7A	2	0.7902	100	0.336	Contact Map
2hekA	4	0.8829	99.6	0.751	Contact Map
2q14A	4	0.9024	99.6	0.754	Contact Map
2cqzA	5	0.7854	99.5	0.76	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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