AmpE - PFAM28P - GREMLIN Contacts

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AmpE - Regulatory signalling modulator protein AmpE

PFAM:	PF17113	Sequences: MTLISLLLALIIERLFTLGEHWQLDRYLDRYFRRLERFSLIRTLLLALLPVLLVALLLWLLGGLLFGLPYLLLWVLVLLLCLGPRDLREHYKAYLQALERGDEEAAREYAKELTLIHGVPADASERERLREVQEALLWANNRRYFAVIFWFVVLGPAGAVLYRLYALLRARAVWLARRETPLERAQSGADRLLHWLDWIPARLTALGYALVGHFEDALPAWRASLLDFHTSNYQVLTRVAQAALAREPHEDEVETPRAAVRLVKRNLLIWLVVIALLTLYGTLV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	284 (281)
Sequences:	792 (575)
Seq/√Len:	34.3
META:	0.593

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
162_Y	165_Y	6.732	1.00
159_A	162_Y	5.526	1.00
139_A	142_R	5.028	1.00
140_N	143_R	4.733	1.00
159_A	163_R	4.119	1.00
163_R	166_A	3.797	1.00
162_Y	166_A	3.455	1.00
159_A	165_Y	3.382	1.00
155_G	159_A	3.176	1.00
139_A	143_R	3.132	1.00
156_P	159_A	2.897	1.00
159_A	166_A	2.731	1.00
160_V	167_L	2.661	1.00
19_G	23_Q	2.635	1.00
47_A	50_P	2.577	1.00
18_L	23_Q	2.558	1.00
138_W	143_R	2.547	1.00
18_L	22_W	2.420	1.00
138_W	144_Y	2.419	1.00
160_V	166_A	2.386	0.99
160_V	163_R	2.366	0.99
17_T	23_Q	2.328	0.99
140_N	144_Y	2.250	0.99
132_V	135_A	2.106	0.99
19_G	22_W	2.067	0.98
78_L	83_G	2.048	0.98
163_R	167_L	1.996	0.98
97_A	105_A	1.966	0.98
160_V	165_Y	1.942	0.98
114_T	118_G	1.926	0.98
6_L	148_I	1.921	0.98
262_L	265_R	1.899	0.97
161_L	165_Y	1.881	0.97
239_V	243_A	1.817	0.97
213_H	216_D	1.773	0.96
50_P	54_V	1.761	0.96
98_L	106_A	1.733	0.95
45_L	50_P	1.685	0.95
240_A	243_A	1.681	0.95
32_F	35_L	1.674	0.94
141_N	197_D	1.618	0.93
240_A	245_A	1.610	0.93
5_S	74_W	1.599	0.93
260_V	264_K	1.589	0.93
246_R	252_E	1.585	0.93
240_A	244_L	1.563	0.92
20_E	23_Q	1.556	0.92
140_N	145_F	1.555	0.92
129_L	132_V	1.549	0.92
17_T	21_H	1.545	0.92
155_G	161_L	1.505	0.91
104_E	108_E	1.495	0.90
160_V	164_L	1.474	0.90
113_L	116_I	1.450	0.89
100_R	105_A	1.442	0.89
46_L	50_P	1.441	0.89
207_G	266_N	1.423	0.88
1_M	13_E	1.408	0.87
256_P	263_V	1.394	0.87
10_L	13_E	1.379	0.86
16_F	19_G	1.359	0.85
239_V	242_A	1.358	0.85
55_A	59_W	1.355	0.85
132_V	136_L	1.351	0.85
247_E	252_E	1.350	0.85
247_E	250_E	1.348	0.85
165_Y	168_L	1.336	0.84
260_V	263_V	1.336	0.84
153_V	199_I	1.333	0.84
17_T	20_E	1.329	0.84
106_A	110_A	1.320	0.84
155_G	162_Y	1.318	0.84
30_R	34_R	1.316	0.83
31_Y	34_R	1.316	0.83
16_F	23_Q	1.311	0.83
166_A	169_R	1.308	0.83
30_R	33_R	1.307	0.83
133_Q	136_L	1.299	0.83
110_A	154_L	1.297	0.83
17_T	22_W	1.272	0.81
188_G	193_L	1.267	0.81
233_Y	238_R	1.248	0.80
16_F	20_E	1.239	0.80
90_H	93_A	1.237	0.79
18_L	21_H	1.220	0.78
1_M	10_L	1.209	0.78
39_S	45_L	1.206	0.78
253_V	257_R	1.203	0.77
138_W	142_R	1.200	0.77
161_L	166_A	1.199	0.77
88_R	94_Y	1.197	0.77
110_A	113_L	1.190	0.77
53_L	58_L	1.187	0.77
159_A	164_L	1.186	0.76
41_I	45_L	1.181	0.76
145_F	208_Y	1.175	0.76
81_C	160_V	1.175	0.76
246_R	251_D	1.165	0.75
131_E	134_E	1.145	0.74
28_L	31_Y	1.143	0.74
123_A	153_V	1.142	0.74
271_L	274_I	1.130	0.73
276_L	279_L	1.125	0.73
193_L	197_D	1.123	0.72
158_G	221_W	1.115	0.72
185_A	188_G	1.106	0.71
13_E	197_D	1.103	0.71
57_L	191_R	1.097	0.71
156_P	163_R	1.091	0.70
235_V	238_R	1.089	0.70
81_C	86_D	1.088	0.70
242_A	246_R	1.080	0.69
170_A	174_W	1.079	0.69
120_P	124_S	1.070	0.69
228_F	232_N	1.069	0.69
129_L	133_Q	1.068	0.69
70_Y	74_W	1.052	0.67
128_R	132_V	1.052	0.67
164_L	167_L	1.049	0.67
223_A	226_L	1.047	0.67
65_L	72_L	1.042	0.67
268_L	275_A	1.039	0.66
92_K	95_L	1.033	0.66
38_F	41_I	1.029	0.66
57_L	199_I	1.028	0.66
165_Y	169_R	1.026	0.65
105_A	108_E	1.025	0.65
259_A	263_V	1.020	0.65
238_R	242_A	1.020	0.65
25_D	30_R	1.015	0.65
171_R	174_W	1.015	0.65
162_Y	167_L	1.004	0.64
34_R	37_R	0.998	0.63
46_L	51_V	0.995	0.63
25_D	28_L	0.990	0.63
88_R	92_K	0.984	0.62
7_L	12_I	0.981	0.62
150_W	196_L	0.980	0.62
254_E	257_R	0.976	0.61
205_A	217_A	0.975	0.61
252_E	268_L	0.975	0.61
185_A	189_A	0.975	0.61
16_F	22_W	0.959	0.60
44_L	47_A	0.959	0.60
137_L	142_R	0.959	0.60
44_L	49_L	0.959	0.60
188_G	194_H	0.956	0.60
70_Y	160_V	0.951	0.59
233_Y	236_L	0.945	0.59
24_L	27_Y	0.939	0.58
78_L	81_C	0.936	0.58
238_R	241_Q	0.932	0.58
94_Y	140_N	0.925	0.57
246_R	249_H	0.925	0.57
138_W	141_N	0.919	0.57
278_T	281_G	0.917	0.57
262_L	268_L	0.914	0.56
80_L	204_T	0.912	0.56
45_L	51_V	0.910	0.56
148_I	274_I	0.908	0.56
134_E	137_L	0.892	0.55
135_A	138_W	0.889	0.54
257_R	268_L	0.889	0.54
155_G	163_R	0.889	0.54
87_L	210_L	0.881	0.54
217_A	239_V	0.881	0.54
157_A	192_L	0.875	0.53
241_Q	244_L	0.870	0.53
102_D	105_A	0.869	0.53
139_A	144_Y	0.865	0.52
147_V	159_A	0.862	0.52
7_L	39_S	0.859	0.52
159_A	167_L	0.858	0.52
84_P	141_N	0.853	0.51
232_N	240_A	0.851	0.51
196_L	211_V	0.849	0.51
78_L	151_F	0.844	0.50
204_T	210_L	0.842	0.50
48_L	190_D	0.840	0.50
137_L	144_Y	0.836	0.50
44_L	50_P	0.835	0.50
101_G	106_A	0.834	0.50
130_R	134_E	0.834	0.50
44_L	48_L	0.833	0.50
27_Y	31_Y	0.827	0.49
169_R	172_A	0.824	0.49
110_A	114_T	0.821	0.48
149_F	270_W	0.818	0.48
127_E	130_R	0.817	0.48
243_A	246_R	0.817	0.48
28_L	38_F	0.811	0.48
12_I	54_V	0.810	0.48
256_P	264_K	0.809	0.47
58_L	61_L	0.805	0.47
140_N	207_G	0.805	0.47
100_R	108_E	0.803	0.47
271_L	277_L	0.799	0.47
69_P	101_G	0.799	0.47
190_D	194_H	0.796	0.46
79_L	110_A	0.794	0.46
182_L	185_A	0.794	0.46
112_E	118_G	0.791	0.46
16_F	21_H	0.791	0.46
56_L	59_W	0.791	0.46
136_L	144_Y	0.789	0.46
150_W	239_V	0.789	0.46
83_G	150_W	0.788	0.46
77_V	172_A	0.787	0.46
214_F	265_R	0.786	0.46
272_V	281_G	0.780	0.45
175_L	181_P	0.780	0.45
45_L	49_L	0.778	0.45
133_Q	140_N	0.777	0.45
253_V	256_P	0.777	0.45
192_L	195_W	0.776	0.45
50_P	53_L	0.773	0.44
276_L	280_Y	0.773	0.44
6_L	17_T	0.772	0.44
35_L	42_R	0.766	0.44
46_L	49_L	0.764	0.44
80_L	217_A	0.763	0.44
209_A	217_A	0.762	0.44
81_C	84_P	0.748	0.42
142_R	217_A	0.746	0.42
238_R	243_A	0.746	0.42
4_I	10_L	0.742	0.42
2_T	206_L	0.741	0.42
247_E	254_E	0.741	0.42
84_P	91_Y	0.739	0.42
88_R	91_Y	0.733	0.41
155_G	160_V	0.731	0.41
213_H	218_L	0.730	0.41
54_V	62_G	0.729	0.41
6_L	142_R	0.728	0.41
11_I	199_I	0.728	0.41
51_V	55_A	0.725	0.40
43_T	50_P	0.725	0.40
256_P	261_R	0.723	0.40
194_H	208_Y	0.723	0.40
158_G	214_F	0.721	0.40
254_E	266_N	0.720	0.40
178_R	181_P	0.717	0.40
83_G	151_F	0.716	0.40
263_V	270_W	0.715	0.40
113_L	117_H	0.715	0.40
28_L	32_F	0.712	0.39
188_G	191_R	0.712	0.39
44_L	53_L	0.708	0.39
256_P	260_V	0.706	0.39
40_L	53_L	0.705	0.39
41_I	49_L	0.703	0.39
76_L	152_V	0.702	0.39
168_L	173_V	0.702	0.39
91_Y	95_L	0.699	0.38
54_V	221_W	0.699	0.38
266_N	270_W	0.696	0.38
96_Q	100_R	0.688	0.37
49_L	53_L	0.683	0.37
136_L	143_R	0.683	0.37
89_E	92_K	0.682	0.37
266_N	276_L	0.676	0.37
246_R	250_E	0.676	0.37
94_Y	98_L	0.676	0.37
236_L	241_Q	0.674	0.36
241_Q	246_R	0.673	0.36
13_E	204_T	0.671	0.36
263_V	269_I	0.671	0.36
6_L	21_H	0.670	0.36
265_R	270_W	0.670	0.36
242_A	277_L	0.668	0.36
135_A	143_R	0.667	0.36
33_R	38_F	0.664	0.36
100_R	206_L	0.664	0.36
67_G	73_L	0.663	0.36
74_W	151_F	0.659	0.35
154_L	159_A	0.657	0.35
52_L	199_I	0.654	0.35
236_L	243_A	0.654	0.35
26_R	29_D	0.653	0.35
232_N	236_L	0.653	0.35
90_H	160_V	0.650	0.34
4_I	23_Q	0.650	0.34
157_A	161_L	0.645	0.34
182_L	186_Q	0.645	0.34
141_N	150_W	0.643	0.34
74_W	78_L	0.641	0.34
6_L	207_G	0.641	0.34
237_T	244_L	0.640	0.34
160_V	174_W	0.639	0.34
153_V	271_L	0.638	0.34
211_V	269_I	0.638	0.34
129_L	134_E	0.636	0.33
37_R	42_R	0.635	0.33
51_V	66_F	0.634	0.33
89_E	93_A	0.634	0.33
197_D	217_A	0.633	0.33
274_I	281_G	0.633	0.33
213_H	219_P	0.631	0.33
236_L	280_Y	0.631	0.33
4_I	56_L	0.629	0.33
186_Q	190_D	0.629	0.33
65_L	176_A	0.628	0.33
35_L	38_F	0.625	0.33
84_P	90_H	0.624	0.33
252_E	255_T	0.624	0.33
130_R	133_Q	0.622	0.32
11_I	35_L	0.622	0.32
81_C	144_Y	0.621	0.32
273_V	281_G	0.621	0.32
3_L	7_L	0.621	0.32
259_A	266_N	0.619	0.32
84_P	211_V	0.615	0.32
98_L	213_H	0.615	0.32
91_Y	260_V	0.614	0.32
57_L	149_F	0.613	0.32
15_L	18_L	0.609	0.31
24_L	82_L	0.608	0.31
247_E	269_I	0.608	0.31
28_L	34_R	0.607	0.31
137_L	143_R	0.607	0.31
262_L	278_T	0.606	0.31
218_L	260_V	0.605	0.31
28_L	35_L	0.604	0.31
242_A	245_A	0.603	0.31
87_L	195_W	0.603	0.31
27_Y	30_R	0.603	0.31
84_P	87_L	0.602	0.31
146_A	216_D	0.601	0.31
7_L	73_L	0.599	0.31
209_A	216_D	0.597	0.31
31_Y	35_L	0.594	0.30
33_R	36_E	0.593	0.30
48_L	51_V	0.591	0.30
67_G	182_L	0.590	0.30
83_G	136_L	0.588	0.30
58_L	62_G	0.587	0.30
47_A	53_L	0.587	0.30
137_L	140_N	0.586	0.30
62_G	67_G	0.585	0.30
14_R	87_L	0.582	0.29
14_R	17_T	0.581	0.29
42_R	50_P	0.581	0.29
252_E	258_A	0.580	0.29
72_L	118_G	0.579	0.29
21_H	33_R	0.579	0.29
131_E	136_L	0.578	0.29
41_I	53_L	0.578	0.29
272_V	280_Y	0.578	0.29
253_V	274_I	0.577	0.29
82_L	148_I	0.577	0.29
270_W	274_I	0.576	0.29
141_N	259_A	0.575	0.29
264_K	268_L	0.575	0.29
131_E	135_A	0.574	0.29
149_F	259_A	0.573	0.29
242_A	247_E	0.572	0.29
40_L	44_L	0.571	0.29
167_L	170_A	0.569	0.29
88_R	140_N	0.567	0.28
14_R	84_P	0.566	0.28
93_A	97_A	0.565	0.28
16_F	69_P	0.564	0.28
241_Q	245_A	0.563	0.28
213_H	272_V	0.562	0.28
266_N	271_L	0.561	0.28
181_P	188_G	0.560	0.28
133_Q	142_R	0.560	0.28
86_D	91_Y	0.560	0.28
237_T	241_Q	0.556	0.28
68_L	72_L	0.555	0.28
24_L	28_L	0.554	0.28
63_G	156_P	0.553	0.27
9_A	13_E	0.553	0.27
193_L	217_A	0.551	0.27
139_A	207_G	0.550	0.27
137_L	145_F	0.550	0.27
224_S	236_L	0.549	0.27
270_W	273_V	0.549	0.27
5_S	151_F	0.546	0.27
78_L	84_P	0.545	0.27
118_G	227_D	0.545	0.27
121_A	124_S	0.544	0.27
78_L	155_G	0.544	0.27
84_P	197_D	0.544	0.27
136_L	140_N	0.541	0.27
90_H	221_W	0.541	0.27
6_L	152_V	0.540	0.27
72_L	76_L	0.540	0.27
239_V	245_A	0.540	0.27
124_S	136_L	0.537	0.26
267_L	276_L	0.534	0.26
133_Q	144_Y	0.534	0.26
56_L	187_S	0.534	0.26
249_H	252_E	0.533	0.26
197_D	211_V	0.530	0.26
41_I	65_L	0.528	0.26
69_P	72_L	0.527	0.26
91_Y	94_Y	0.525	0.26
81_C	85_R	0.523	0.25
233_Y	239_V	0.522	0.25
82_L	145_F	0.521	0.25
82_L	147_V	0.520	0.25
128_R	131_E	0.520	0.25
37_R	41_I	0.519	0.25
125_E	129_L	0.519	0.25
265_R	278_T	0.518	0.25
13_E	133_Q	0.517	0.25
228_F	233_Y	0.516	0.25
256_P	269_I	0.510	0.25
157_A	162_Y	0.510	0.25
105_A	110_A	0.509	0.25
76_L	125_E	0.508	0.25
13_E	97_A	0.507	0.24
234_Q	238_R	0.505	0.24
185_A	194_H	0.505	0.24
14_R	88_R	0.505	0.24
141_N	163_R	0.504	0.24
224_S	249_H	0.502	0.24
254_E	258_A	0.502	0.24
68_L	186_Q	0.501	0.24
123_A	229_H	0.501	0.24
235_V	239_V	0.500	0.24

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
1xnfA	2	0.3099	12.2	0.965	Contact Map
2mn6B	2	0.1408	11.8	0.965	Contact Map
1qleD	1	0.1514	10.8	0.966	Contact Map
4a1sA	1	0.3028	10.4	0.966	Contact Map
2l16A	1	0.1585	9.8	0.966	Contact Map
2jlnA	1	0.3556	9.6	0.966	Contact Map
2vsyA	1	0.2923	6	0.969	Contact Map
2lzrA	1	0.1725	5.4	0.97	Contact Map
3gw4A	2	0.3838	4.6	0.971	Contact Map
4pypA	1	0.2993	4.5	0.971	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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