YEDJ - ECOLI - GREMLIN Contacts

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YEDJ - Uncharacterized protein YedJ

UniProt:	P46144	Sequences: MDLQHWQAQFENWLKNHHQHQDAAHDVCHFRRVWATAQKLAADDDVDMLVILTACYFHDIVSLAKNHPQRQRSSILAAEETRRLLREEFEQFPAEKIEAVCHAIAAHSFSAQIAPLTTEAKIVQDADRLEALGAIGLARVFAVSGALGVALFDGEDPFAQHRPLDDKRYALDHFQTKLLKLPQTMQTARGKQLAQHNAHFLVEFMAKLSAELAGENEGVDHKVIDAFSSAG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12710
Length:	231 (202)
Sequences:	1508 (1124)
Seq/√Len:	79.1

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
144_S	170_A	4.070	1.00
179_L	205_M	3.290	1.00
41_A	46_V	2.725	1.00
44_D	189_R	2.656	1.00
40_L	189_R	2.639	1.00
11_E	34_W	2.501	1.00
10_F	53_T	2.493	1.00
124_Q	186_Q	2.469	1.00
34_W	52_L	2.302	1.00
9_Q	88_E	2.300	1.00
37_A	51_I	2.248	1.00
47_D	96_K	2.245	1.00
189_R	192_Q	2.239	1.00
51_I	123_V	2.211	1.00
138_A	141_F	2.208	1.00
93_P	96_K	2.194	1.00
185_M	194_A	2.167	1.00
171_L	205_M	2.072	1.00
150_A	153_D	2.049	1.00
46_V	51_I	2.044	1.00
200_F	207_K	2.042	1.00
38_Q	52_L	2.035	1.00
159_A	162_R	2.021	1.00
185_M	190_G	2.004	1.00
53_T	100_V	1.993	1.00
186_Q	190_G	1.978	1.00
159_A	163_P	1.925	1.00
149_V	170_A	1.923	1.00
182_P	198_A	1.919	1.00
41_A	48_M	1.875	1.00
34_W	38_Q	1.838	1.00
17_H	80_E	1.809	1.00
196_H	207_K	1.799	1.00
124_Q	128_R	1.795	1.00
208_L	212_L	1.792	1.00
199_H	203_E	1.768	1.00
178_L	201_L	1.746	1.00
43_D	192_Q	1.729	1.00
182_P	195_Q	1.718	1.00
181_L	185_M	1.705	1.00
13_W	84_L	1.701	1.00
118_T	121_K	1.685	1.00
106_A	120_A	1.677	1.00
198_A	202_V	1.653	1.00
195_Q	199_H	1.626	1.00
115_P	120_A	1.620	1.00
200_F	203_E	1.581	1.00
199_H	202_V	1.522	0.99
34_W	56_Y	1.516	0.99
24_A	65_K	1.496	0.99
158_F	162_R	1.450	0.99
141_F	145_G	1.432	0.99
200_F	204_F	1.411	0.99
49_L	96_K	1.409	0.99
158_F	163_P	1.403	0.99
46_V	122_I	1.389	0.99
193_L	196_H	1.385	0.99
107_H	120_A	1.384	0.99
169_Y	172_D	1.363	0.99
171_L	208_L	1.362	0.99
159_A	164_L	1.361	0.99
162_R	166_D	1.359	0.99
53_T	92_F	1.359	0.99
144_S	149_V	1.351	0.99
172_D	176_T	1.338	0.98
10_F	84_L	1.338	0.98
102_H	106_A	1.317	0.98
180_K	184_T	1.270	0.98
203_E	207_K	1.267	0.98
61_V	77_A	1.258	0.98
82_R	101_C	1.252	0.98
202_V	206_A	1.250	0.98
43_D	189_R	1.220	0.97
86_R	94_A	1.219	0.97
36_T	193_L	1.210	0.97
41_A	51_I	1.206	0.97
11_E	15_K	1.178	0.96
22_D	65_K	1.177	0.96
36_T	39_K	1.171	0.96
94_A	98_E	1.171	0.96
201_L	205_M	1.140	0.96
61_V	81_T	1.140	0.96
138_A	151_L	1.131	0.96
188_A	191_K	1.100	0.95
42_A	48_M	1.087	0.94
140_V	170_A	1.086	0.94
121_K	186_Q	1.065	0.94
14_L	18_H	1.040	0.93
179_L	198_A	1.040	0.93
84_L	88_E	1.032	0.93
78_A	105_A	1.031	0.93
162_R	165_D	1.027	0.93
30_F	34_W	1.021	0.92
173_H	177_K	1.017	0.92
21_Q	24_A	1.013	0.92
23_A	142_A	1.011	0.92
46_V	118_T	1.002	0.92
99_A	119_E	1.000	0.92
54_A	103_A	0.996	0.91
39_K	43_D	0.995	0.91
175_Q	205_M	0.994	0.91
92_F	96_K	0.994	0.91
205_M	209_S	0.990	0.91
81_T	85_L	0.988	0.91
163_P	166_D	0.977	0.91
196_H	210_A	0.977	0.91
15_K	27_V	0.966	0.90
82_R	97_I	0.962	0.90
132_L	198_A	0.961	0.90
82_R	86_R	0.959	0.90
106_A	116_L	0.949	0.89
187_T	190_G	0.941	0.89
6_W	88_E	0.927	0.88
81_T	104_I	0.925	0.88
6_W	49_L	0.925	0.88
132_L	140_V	0.923	0.88
171_L	175_Q	0.914	0.87
137_L	204_F	0.910	0.87
37_A	123_V	0.902	0.87
60_I	77_A	0.901	0.87
179_L	202_V	0.896	0.86
40_L	193_L	0.886	0.86
190_G	193_L	0.885	0.86
142_A	170_A	0.883	0.86
49_L	53_T	0.880	0.85
28_C	31_R	0.880	0.85
131_A	173_H	0.878	0.85
149_V	167_K	0.874	0.85
31_R	35_A	0.868	0.85
156_D	172_D	0.863	0.84
30_F	130_E	0.861	0.84
83_R	87_E	0.860	0.84
61_V	78_A	0.857	0.84
106_A	113_I	0.855	0.84
109_F	180_K	0.849	0.83
39_K	189_R	0.842	0.83
203_E	206_A	0.840	0.83
80_E	83_R	0.838	0.82
134_A	211_E	0.838	0.82
143_V	147_L	0.836	0.82
180_K	183_Q	0.832	0.82
14_L	27_V	0.827	0.82
40_L	190_G	0.818	0.81
49_L	92_F	0.816	0.81
10_F	57_F	0.814	0.81
78_A	81_T	0.811	0.80
45_D	118_T	0.803	0.80
103_A	107_H	0.798	0.79
11_E	31_R	0.795	0.79
36_T	40_L	0.792	0.79
54_A	107_H	0.791	0.79
24_A	186_Q	0.787	0.78
175_Q	209_S	0.785	0.78
25_H	139_R	0.783	0.78
57_F	81_T	0.777	0.77
129_L	190_G	0.775	0.77
174_F	179_L	0.773	0.77
173_H	181_L	0.769	0.77
47_D	99_A	0.767	0.76
108_S	128_R	0.764	0.76
109_F	181_L	0.758	0.76
102_H	117_T	0.754	0.75
21_Q	65_K	0.751	0.75
84_L	87_E	0.739	0.74
101_C	105_A	0.739	0.74
141_F	193_L	0.738	0.74
41_A	45_D	0.737	0.74
66_N	77_A	0.736	0.73
179_L	194_A	0.735	0.73
154_G	212_L	0.733	0.73
61_V	66_N	0.731	0.73
97_I	101_C	0.730	0.73
131_A	177_K	0.729	0.73
202_V	209_S	0.725	0.72
39_K	193_L	0.720	0.72
179_L	201_L	0.718	0.72
18_H	30_F	0.718	0.72
31_R	34_W	0.717	0.72
41_A	122_I	0.717	0.72
23_A	146_A	0.717	0.72
124_Q	173_H	0.716	0.71
210_A	214_G	0.711	0.71
116_L	121_K	0.707	0.70
110_S	173_H	0.706	0.70
57_F	60_I	0.703	0.70
50_V	99_A	0.701	0.70
10_F	88_E	0.700	0.70
88_E	91_Q	0.699	0.70
130_E	136_G	0.699	0.70
14_L	17_H	0.697	0.69
112_Q	186_Q	0.696	0.69
62_S	176_T	0.696	0.69
65_K	108_S	0.691	0.69
6_W	92_F	0.689	0.68
108_S	173_H	0.681	0.68
41_A	55_C	0.681	0.68
182_P	194_A	0.679	0.67
82_R	98_E	0.673	0.67
66_N	80_E	0.672	0.67
173_H	176_T	0.667	0.66
10_F	13_W	0.663	0.66
140_V	174_F	0.661	0.65
131_A	181_L	0.660	0.65
62_S	123_V	0.660	0.65
134_A	200_F	0.652	0.64
18_H	61_V	0.651	0.64
136_G	185_M	0.651	0.64
175_Q	179_L	0.650	0.64
110_S	124_Q	0.646	0.64
158_F	161_H	0.643	0.63
28_C	154_G	0.640	0.63
173_H	179_L	0.637	0.62
96_K	100_V	0.636	0.62
140_V	181_L	0.636	0.62
153_D	172_D	0.634	0.62
104_I	107_H	0.629	0.61
197_N	207_K	0.629	0.61
191_K	195_Q	0.627	0.61
103_A	106_A	0.626	0.61
144_S	153_D	0.624	0.61
12_N	192_Q	0.624	0.61
34_W	55_C	0.624	0.61
79_E	82_R	0.623	0.61
168_R	172_D	0.623	0.61
85_L	100_V	0.622	0.61
36_T	207_K	0.621	0.60
160_Q	163_P	0.620	0.60
18_H	107_H	0.619	0.60
7_Q	11_E	0.617	0.60
86_R	97_I	0.616	0.60
177_K	181_L	0.616	0.60
141_F	151_L	0.615	0.60
82_R	95_E	0.613	0.59
120_A	186_Q	0.611	0.59
68_P	77_A	0.611	0.59
25_H	177_K	0.609	0.59
83_R	86_R	0.608	0.59
8_A	12_N	0.608	0.59
62_S	128_R	0.608	0.59
138_A	193_L	0.605	0.58
141_F	144_S	0.604	0.58
107_H	123_V	0.603	0.58
130_E	152_F	0.603	0.58
61_V	80_E	0.598	0.58
8_A	31_R	0.596	0.57
173_H	178_L	0.596	0.57
62_S	65_K	0.595	0.57
32_R	130_E	0.590	0.57
6_W	53_T	0.588	0.56
39_K	99_A	0.587	0.56
64_A	176_T	0.585	0.56
156_D	164_L	0.584	0.56
85_L	97_I	0.584	0.56
87_E	91_Q	0.582	0.56
118_T	122_I	0.582	0.56
149_V	169_Y	0.577	0.55
128_R	186_Q	0.576	0.55
62_S	107_H	0.570	0.54
152_F	212_L	0.567	0.54
27_V	148_G	0.565	0.53
159_A	165_D	0.565	0.53
10_F	18_H	0.564	0.53
6_W	10_F	0.564	0.53
57_F	208_L	0.559	0.53
53_T	96_K	0.559	0.53
54_A	123_V	0.558	0.53
138_A	145_G	0.558	0.53
117_T	120_A	0.555	0.52
60_I	80_E	0.551	0.52
12_N	20_H	0.544	0.51
152_F	213_A	0.541	0.50
86_R	93_P	0.539	0.50
206_A	210_A	0.537	0.50
60_I	92_F	0.536	0.50
210_A	213_A	0.535	0.50
137_L	179_L	0.532	0.49
93_P	98_E	0.530	0.49
161_H	168_R	0.527	0.49
160_Q	165_D	0.526	0.48
132_L	182_P	0.525	0.48
17_H	20_H	0.521	0.48
62_S	108_S	0.520	0.48
22_D	142_A	0.518	0.47
189_R	193_L	0.516	0.47
18_H	21_Q	0.515	0.47
154_G	172_D	0.515	0.47
50_V	100_V	0.514	0.47
77_A	80_E	0.514	0.47
94_A	210_A	0.511	0.46
117_T	121_K	0.511	0.46
7_Q	52_L	0.511	0.46
8_A	16_N	0.510	0.46
45_D	189_R	0.508	0.46
128_R	173_H	0.507	0.46
14_L	30_F	0.506	0.46
130_E	135_I	0.503	0.45
16_N	35_A	0.502	0.45
134_A	185_M	0.502	0.45
120_A	142_A	0.502	0.45
88_E	170_A	0.501	0.45
39_K	51_I	0.500	0.45
16_N	20_H	0.500	0.45
137_L	181_L	0.500	0.45

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
3gw7A	2	0.8961	100	0.3	Contact Map
2pjqA	2	0.8874	100	0.336	Contact Map
2qgsA	2	0.8831	100	0.338	Contact Map
3dtoA	2	0.8095	100	0.346	Contact Map
3b57A	2	0.7792	100	0.351	Contact Map
3djbA	2	0.8139	100	0.351	Contact Map
2pq7A	2	0.71	100	0.37	Contact Map
2q14A	4	0.9264	99.6	0.778	Contact Map
2cqzA	5	0.697	99.5	0.785	Contact Map
2hekA	4	0.9134	99.5	0.785	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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