DEDD - ECOLI - GREMLIN Contacts

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DEDD - Protein DedD

UniProt:	P09549	Sequences: MASKFQNRLVGTIVLVALGVIVLPGLLDGQKKHYQDEFAAIPLVPKAGDRDEPDMMPAATQALPTQPPEGAAEEVRAGDAAAPSLDPATIAANNTEFEPEPAPVAPPKPKPVEPPKPKVEAPPAPKPEPKPVVEEKAAPTGKAYVVQLGALKNADKVNEIVGKLRGAGYRVYTSPSTPVQGKITRILVGPDASKDKLKGSLGELKQLSGLSGVVMGYTPN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10218
Length:	220 (202)
Sequences:	1054 (983)
Seq/√Len:	69.2

ECOLI - DEDD FTSN

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
146_V	197_L	4.245	1.00
173_T	184_T	3.993	1.00
178_P	181_G	3.962	1.00
161_V	165_R	2.956	1.00
191_D	200_S	2.868	1.00
205_K	211_S	2.555	1.00
201_L	205_K	2.435	1.00
146_V	201_L	2.377	1.00
150_A	213_V	2.237	1.00
150_A	156_K	2.215	1.00
191_D	196_K	2.199	1.00
144_Y	194_K	2.192	1.00
193_S	196_K	2.120	1.00
98_E	102_A	2.083	1.00
20_V	27_L	2.069	1.00
162_G	166_G	2.012	1.00
194_K	198_K	1.992	1.00
151_L	156_K	1.987	1.00
21_I	24_P	1.931	1.00
16_V	20_V	1.910	1.00
20_V	24_P	1.863	1.00
145_V	172_Y	1.841	1.00
24_P	27_L	1.829	1.00
12_T	23_L	1.812	1.00
201_L	212_G	1.776	1.00
194_K	197_L	1.768	1.00
12_T	25_G	1.716	1.00
148_L	164_L	1.683	1.00
157_V	171_V	1.666	0.99
157_V	173_T	1.664	0.99
198_K	201_L	1.656	0.99
66_Q	70_G	1.646	0.99
161_V	214_V	1.631	0.99
16_V	23_L	1.628	0.99
149_G	162_G	1.567	0.99
90_I	94_N	1.524	0.99
154_A	158_N	1.507	0.99
154_A	184_T	1.506	0.99
12_T	197_L	1.489	0.99
13_I	27_L	1.486	0.99
116_K	120_E	1.479	0.99
180_Q	203_E	1.470	0.99
19_G	25_G	1.424	0.98
105_A	112_V	1.422	0.98
148_L	210_L	1.417	0.98
158_N	162_G	1.391	0.98
102_A	105_A	1.384	0.98
94_N	106_P	1.379	0.98
105_A	108_K	1.372	0.98
119_V	123_P	1.367	0.98
65_T	68_P	1.367	0.98
12_T	15_L	1.364	0.98
28_D	41_I	1.361	0.98
148_L	169_Y	1.360	0.98
97_F	101_P	1.357	0.98
96_E	100_E	1.329	0.97
152_K	183_I	1.329	0.97
118_K	121_A	1.316	0.97
21_I	26_L	1.308	0.97
43_L	47_A	1.297	0.97
122_P	126_K	1.272	0.97
71_A	74_E	1.262	0.96
174_S	185_R	1.258	0.96
177_T	182_K	1.246	0.96
118_K	122_P	1.244	0.96
174_S	187_L	1.240	0.96
157_V	184_T	1.235	0.96
25_G	29_G	1.231	0.96
151_L	159_E	1.229	0.96
100_E	105_A	1.224	0.96
68_P	76_R	1.206	0.95
92_A	104_V	1.203	0.95
28_D	31_K	1.192	0.95
174_S	194_K	1.192	0.95
69_E	75_V	1.186	0.95
16_V	27_L	1.185	0.95
118_K	123_P	1.178	0.95
100_E	103_P	1.178	0.95
22_V	26_L	1.176	0.95
19_G	30_Q	1.174	0.95
54_D	59_A	1.172	0.95
14_V	22_V	1.172	0.95
119_V	122_P	1.172	0.95
93_N	98_E	1.171	0.95
147_Q	185_R	1.170	0.95
94_N	98_E	1.166	0.94
145_V	215_M	1.162	0.94
156_K	173_T	1.162	0.94
82_A	104_V	1.142	0.94
15_L	23_L	1.142	0.94
176_S	183_I	1.141	0.94
24_P	28_D	1.140	0.94
17_A	21_I	1.130	0.93
91_A	104_V	1.124	0.93
114_P	118_K	1.114	0.93
160_I	186_I	1.108	0.93
69_E	73_E	1.108	0.93
22_V	25_G	1.101	0.93
153_N	184_T	1.073	0.92
199_G	202_G	1.063	0.91
23_L	28_D	1.062	0.91
23_L	27_L	1.036	0.90
18_L	22_V	1.033	0.90
74_E	78_G	1.025	0.90
112_V	122_P	1.024	0.90
157_V	186_I	1.024	0.90
100_E	104_V	1.021	0.89
83_P	118_K	1.012	0.89
170_R	204_L	1.001	0.88
16_V	32_K	1.000	0.88
21_I	29_G	0.995	0.88
124_A	131_P	0.993	0.88
60_T	65_T	0.983	0.88
125_P	129_P	0.977	0.87
94_N	97_F	0.974	0.87
16_V	30_Q	0.974	0.87
70_G	74_E	0.969	0.87
100_E	106_P	0.965	0.87
93_N	135_E	0.953	0.86
110_K	118_K	0.947	0.86
77_A	83_P	0.939	0.85
100_E	111_P	0.931	0.85
161_V	171_V	0.929	0.84
13_I	146_V	0.928	0.84
10_V	181_G	0.923	0.84
39_A	42_P	0.921	0.84
89_T	94_N	0.916	0.84
151_L	160_I	0.913	0.83
169_Y	204_L	0.912	0.83
167_A	207_L	0.902	0.83
115_P	119_V	0.894	0.82
76_R	79_D	0.891	0.82
77_A	81_A	0.890	0.82
156_K	159_E	0.888	0.82
40_A	43_L	0.871	0.80
109_P	121_A	0.867	0.80
150_A	173_T	0.866	0.80
23_L	36_D	0.857	0.79
143_A	169_Y	0.853	0.79
21_I	25_G	0.844	0.78
105_A	109_P	0.843	0.78
158_N	161_V	0.842	0.78
108_K	112_V	0.842	0.78
191_D	197_L	0.839	0.78
98_E	106_P	0.837	0.78
72_A	82_A	0.837	0.78
148_L	184_T	0.836	0.78
108_K	118_K	0.836	0.78
108_K	121_A	0.835	0.78
108_K	116_K	0.834	0.77
138_A	141_G	0.833	0.77
112_V	133_V	0.825	0.77
62_A	66_Q	0.824	0.77
22_V	29_G	0.821	0.76
109_P	113_E	0.820	0.76
103_P	107_P	0.818	0.76
124_A	132_V	0.818	0.76
154_A	175_P	0.812	0.76
156_K	184_T	0.806	0.75
181_G	184_T	0.806	0.75
97_F	105_A	0.801	0.75
147_Q	168_G	0.801	0.75
12_T	194_K	0.797	0.74
111_P	115_P	0.794	0.74
165_R	200_S	0.791	0.74
20_V	25_G	0.789	0.73
166_G	171_V	0.787	0.73
107_P	127_P	0.786	0.73
157_V	178_P	0.784	0.73
73_E	77_A	0.782	0.73
47_A	50_R	0.773	0.72
68_P	72_A	0.773	0.72
127_P	131_P	0.771	0.72
98_E	105_A	0.771	0.72
102_A	106_P	0.764	0.71
88_A	116_K	0.761	0.71
153_N	169_Y	0.756	0.70
106_P	110_K	0.755	0.70
96_E	99_P	0.755	0.70
148_L	160_I	0.752	0.70
107_P	125_P	0.744	0.69
165_R	171_V	0.739	0.68
95_T	98_E	0.737	0.68
151_L	201_L	0.734	0.68
95_T	99_P	0.731	0.68
169_Y	187_L	0.730	0.68
32_K	37_E	0.730	0.68
12_T	28_D	0.727	0.67
61_Q	64_P	0.724	0.67
117_P	131_P	0.720	0.66
112_V	116_K	0.719	0.66
22_V	27_L	0.718	0.66
164_L	171_V	0.712	0.66
30_Q	37_E	0.709	0.65
151_L	213_V	0.706	0.65
53_P	56_M	0.703	0.65
95_T	135_E	0.699	0.64
41_I	45_P	0.695	0.64
61_Q	69_E	0.693	0.63
106_P	109_P	0.690	0.63
131_P	134_E	0.690	0.63
90_I	95_T	0.688	0.63
78_G	81_A	0.686	0.63
160_I	183_I	0.685	0.63
21_I	28_D	0.685	0.63
115_P	118_K	0.684	0.62
14_V	144_Y	0.683	0.62
177_T	180_Q	0.681	0.62
149_G	190_P	0.677	0.62
144_Y	156_K	0.675	0.61
29_G	34_Y	0.669	0.61
14_V	17_A	0.667	0.61
19_G	193_S	0.666	0.60
144_Y	150_A	0.665	0.60
29_G	32_K	0.665	0.60
148_L	158_N	0.659	0.60
88_A	92_A	0.657	0.59
121_A	131_P	0.654	0.59
55_M	59_A	0.654	0.59
98_E	104_V	0.653	0.59
41_I	44_V	0.648	0.58
165_R	170_R	0.646	0.58
160_I	176_S	0.643	0.58
110_K	113_E	0.642	0.58
162_G	204_L	0.636	0.57
101_P	122_P	0.633	0.57
99_P	107_P	0.631	0.56
89_T	93_N	0.631	0.56
157_V	175_P	0.631	0.56
159_E	163_K	0.630	0.56
106_P	115_P	0.630	0.56
104_V	110_K	0.620	0.55
67_P	75_V	0.620	0.55
156_K	187_L	0.619	0.55
95_T	125_P	0.616	0.55
124_A	128_E	0.614	0.54
76_R	81_A	0.609	0.54
173_T	182_K	0.607	0.53
14_V	29_G	0.603	0.53
184_T	201_L	0.600	0.53
23_L	26_L	0.598	0.52
148_L	168_G	0.596	0.52
123_P	129_P	0.596	0.52
110_K	114_P	0.593	0.52
42_P	190_P	0.592	0.52
25_G	201_L	0.591	0.52
146_V	172_Y	0.589	0.51
106_P	127_P	0.587	0.51
196_K	199_G	0.586	0.51
102_A	116_K	0.583	0.51
28_D	156_K	0.583	0.51
10_V	148_L	0.582	0.50
69_E	81_A	0.582	0.50
95_T	102_A	0.572	0.49
17_A	24_P	0.572	0.49
92_A	96_E	0.571	0.49
158_N	166_G	0.569	0.49
152_K	170_R	0.567	0.49
188_V	204_L	0.566	0.49
19_G	43_L	0.564	0.48
100_E	115_P	0.564	0.48
41_I	50_R	0.559	0.48
105_A	116_K	0.558	0.48
14_V	167_A	0.556	0.47
191_D	207_L	0.555	0.47
123_P	126_K	0.555	0.47
92_A	95_T	0.555	0.47
62_A	73_E	0.552	0.47
72_A	77_A	0.549	0.46
149_G	160_I	0.548	0.46
20_V	26_L	0.546	0.46
195_D	199_G	0.546	0.46
21_I	165_R	0.546	0.46
33_H	36_D	0.544	0.46
16_V	193_S	0.543	0.46
44_V	49_D	0.543	0.46
98_E	127_P	0.540	0.45
94_N	99_P	0.538	0.45
10_V	157_V	0.537	0.45
93_N	111_P	0.536	0.45
64_P	112_V	0.534	0.45
145_V	187_L	0.532	0.44
10_V	13_I	0.531	0.44
30_Q	33_H	0.531	0.44
97_F	131_P	0.530	0.44
98_E	108_K	0.528	0.44
121_A	124_A	0.527	0.44
64_P	107_P	0.525	0.44
119_V	124_A	0.524	0.44
92_A	121_A	0.522	0.43
111_P	121_A	0.522	0.43
149_G	213_V	0.521	0.43
70_G	75_V	0.519	0.43
16_V	35_Q	0.519	0.43
24_P	41_I	0.516	0.43
61_Q	65_T	0.515	0.42
49_D	53_P	0.513	0.42
53_P	58_A	0.509	0.42
101_P	104_V	0.507	0.41
10_V	37_E	0.502	0.41
13_I	157_V	0.502	0.41
98_E	117_P	0.501	0.41
156_K	166_G	0.500	0.41

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
1x60A	1	0.3591	99.7	0.621	Contact Map
1utaA	1	0.35	99.7	0.623	Contact Map
2lfvA	1	0.4545	98.9	0.761	Contact Map
4zpjA	1	0.3364	78.7	0.909	Contact Map
2lepA	1	0.2727	43.6	0.928	Contact Map
4s1aA	2	0.3409	31.1	0.934	Contact Map
4hddA	6	0.3	28.5	0.935	Contact Map
2hfvA	1	0.4136	26.3	0.936	Contact Map
5bmqA	3	0.2955	19.8	0.939	Contact Map
4hnoA	1	0.3182	19.5	0.94	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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