YPEP - BACSU - GREMLIN Contacts

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YPEP - Uncharacterized protein YpeP

UniProt:	P54164	Sequences: MKLRPHLKIEAKGTGSVSFFSEDWLTAQQARTFARELGRFPYMKELEFEDEKGGSWTLKELEKLTEELAQEPDDITVYFDGSFDKESELAGLGIVIYYSLGGTRHRLRKNKSFRLKTNNEAEYAALYEAIREVRELGASRNSITIKGDSLVVLNQLDGSWPCYDPSHNEWLDKIEALLESLKLTPTYETIQRKDNQEADGLAKKILSHQFVESHTKLDRNGDDDIG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	226 (181)
Sequences:	428 (337)
Seq/√Len:	25.0

BACSU - YPEP RNHL
HALSA - RNH

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
79_F	147_G	4.823	1.00
126_L	145_I	4.209	1.00
77_V	129_A	3.781	1.00
128_E	131_R	2.323	0.98
117_T	129_A	2.319	0.98
113_F	121_A	2.300	0.98
127_Y	177_L	2.292	0.98
155_Q	192_R	2.268	0.98
96_I	164_D	2.249	0.97
117_T	157_D	2.242	0.97
123_Y	151_V	2.166	0.97
36_E	42_Y	2.136	0.97
138_A	143_I	2.129	0.96
126_L	152_V	2.089	0.96
91_G	95_V	2.054	0.96
123_Y	152_V	2.029	0.95
165_P	168_N	2.028	0.95
32_T	37_L	1.938	0.94
131_R	173_K	1.885	0.93
35_R	38_G	1.853	0.92
127_Y	174_I	1.853	0.92
123_Y	155_Q	1.844	0.92
167_H	171_L	1.840	0.92
79_F	123_Y	1.830	0.92
148_D	195_N	1.781	0.91
130_I	181_L	1.715	0.89
37_L	46_L	1.715	0.89
174_I	187_Y	1.706	0.89
122_E	195_N	1.665	0.88
150_L	154_N	1.654	0.87
152_V	171_L	1.639	0.87
93_G	199_D	1.610	0.86
121_A	198_A	1.595	0.85
75_I	138_A	1.557	0.84
129_A	199_D	1.549	0.83
31_R	38_G	1.548	0.83
73_D	173_K	1.515	0.82
89_L	207_S	1.459	0.80
144_T	188_E	1.439	0.79
26_T	29_Q	1.436	0.78
45_E	57_T	1.434	0.78
89_L	107_L	1.425	0.78
146_K	188_E	1.422	0.78
122_E	148_D	1.386	0.76
52_K	66_E	1.372	0.75
156_L	174_I	1.358	0.74
80_D	148_D	1.356	0.74
37_L	40_F	1.355	0.74
151_V	189_T	1.340	0.73
33_F	40_F	1.332	0.73
92_L	198_A	1.321	0.72
88_E	207_S	1.275	0.70
93_G	198_A	1.261	0.69
172_D	176_A	1.256	0.68
113_F	116_K	1.247	0.68
53_G	64_L	1.237	0.67
153_L	189_T	1.225	0.66
95_V	108_R	1.224	0.66
92_L	111_K	1.220	0.66
82_S	203_K	1.220	0.66
92_L	113_F	1.206	0.65
57_T	60_E	1.197	0.65
25_L	29_Q	1.194	0.64
123_Y	147_G	1.187	0.64
96_I	145_I	1.186	0.64
34_A	143_I	1.177	0.63
139_S	182_K	1.172	0.63
130_I	178_L	1.160	0.62
151_V	171_L	1.154	0.62
123_Y	192_R	1.147	0.61
117_T	166_S	1.144	0.61
75_I	143_I	1.143	0.61
45_E	51_E	1.142	0.61
202_A	206_L	1.138	0.61
87_S	116_K	1.115	0.59
93_G	202_A	1.114	0.59
190_I	209_Q	1.108	0.58
77_V	187_Y	1.094	0.57
33_F	44_K	1.094	0.57
28_Q	31_R	1.094	0.57
30_A	36_E	1.078	0.56
108_R	197_E	1.078	0.56
117_T	136_L	1.076	0.56
24_W	29_Q	1.074	0.56
152_V	155_Q	1.072	0.56
129_A	167_H	1.070	0.56
93_G	201_L	1.056	0.55
80_D	195_N	1.054	0.55
111_K	128_E	1.054	0.55
68_L	72_P	1.053	0.55
33_F	145_I	1.052	0.54
122_E	199_D	1.051	0.54
153_L	171_L	1.050	0.54
97_Y	144_T	1.028	0.53
91_G	147_G	1.027	0.53
154_N	178_L	1.024	0.52
79_F	167_H	1.012	0.52
83_F	196_Q	1.005	0.51
81_G	122_E	1.005	0.51
130_I	154_N	0.980	0.49
86_E	190_I	0.978	0.49
102_G	139_S	0.977	0.49
146_K	190_I	0.972	0.49
44_K	59_K	0.972	0.49
56_W	59_K	0.969	0.48
190_I	207_S	0.966	0.48
126_L	147_G	0.965	0.48
131_R	143_I	0.938	0.46
110_N	197_E	0.935	0.46
147_G	167_H	0.934	0.46
112_S	116_K	0.928	0.45
80_D	149_S	0.922	0.45
81_G	90_A	0.921	0.45
28_Q	38_G	0.910	0.44
95_V	205_I	0.909	0.44
30_A	34_A	0.908	0.44
118_N	160_W	0.896	0.43
66_E	69_A	0.894	0.43
167_H	170_W	0.894	0.43
109_K	113_F	0.890	0.43
201_L	204_K	0.885	0.42
151_V	155_Q	0.880	0.42
110_N	201_L	0.880	0.42
85_K	117_T	0.878	0.42
158_G	162_C	0.874	0.42
77_V	157_D	0.872	0.41
147_G	205_I	0.868	0.41
113_F	209_Q	0.862	0.41
123_Y	171_L	0.855	0.40
31_R	35_R	0.853	0.40
58_L	66_E	0.846	0.40
161_P	164_D	0.842	0.39
121_A	171_L	0.839	0.39
34_A	40_F	0.838	0.39
159_S	163_Y	0.837	0.39
30_A	33_F	0.833	0.39
91_G	108_R	0.822	0.38
174_I	196_Q	0.816	0.38
69_A	102_G	0.812	0.37
52_K	55_S	0.807	0.37
97_Y	101_G	0.807	0.37
33_F	42_Y	0.805	0.37
80_D	122_E	0.803	0.37
82_S	175_E	0.799	0.36
168_N	172_D	0.799	0.36
124_A	185_P	0.793	0.36
88_E	153_L	0.790	0.36
129_A	145_I	0.789	0.36
31_R	36_E	0.789	0.36
39_R	42_Y	0.788	0.36
155_Q	171_L	0.785	0.36
30_A	35_R	0.779	0.35
79_F	129_A	0.778	0.35
43_M	46_L	0.777	0.35
143_I	196_Q	0.771	0.35
38_G	44_K	0.765	0.34
119_N	152_V	0.762	0.34
132_E	136_L	0.762	0.34
174_I	201_L	0.751	0.33
134_R	180_S	0.748	0.33
151_V	192_R	0.745	0.33
91_G	100_L	0.744	0.33
77_V	89_L	0.739	0.33
109_K	132_E	0.738	0.32
39_R	49_E	0.735	0.32
135_E	180_S	0.735	0.32
42_Y	57_T	0.735	0.32
130_I	172_D	0.730	0.32
165_P	171_L	0.722	0.31
157_D	179_E	0.720	0.31
46_L	166_S	0.720	0.31
152_V	197_E	0.719	0.31
91_G	119_N	0.714	0.31
158_G	168_N	0.705	0.30
94_I	113_F	0.704	0.30
35_R	47_E	0.701	0.30
77_V	101_G	0.701	0.30
92_L	109_K	0.699	0.30
158_G	163_Y	0.698	0.30
87_S	112_S	0.696	0.30
33_F	41_P	0.694	0.30
51_E	56_W	0.691	0.30
95_V	116_K	0.690	0.29
149_S	195_N	0.688	0.29
34_A	37_L	0.685	0.29
90_A	186_T	0.685	0.29
97_Y	181_L	0.684	0.29
25_L	30_A	0.684	0.29
34_A	60_E	0.677	0.29
155_Q	158_G	0.670	0.28
60_E	68_L	0.668	0.28
117_T	167_H	0.667	0.28
93_G	153_L	0.659	0.28
26_T	31_R	0.656	0.27
23_D	26_T	0.655	0.27
91_G	205_I	0.653	0.27
175_E	179_E	0.653	0.27
78_Y	175_E	0.650	0.27
28_Q	32_T	0.647	0.27
113_F	198_A	0.646	0.27
92_L	125_A	0.641	0.27
145_I	185_P	0.638	0.26
27_A	68_L	0.637	0.26
44_K	50_D	0.636	0.26
54_G	65_T	0.635	0.26
151_V	167_H	0.629	0.26
198_A	202_A	0.628	0.26
24_W	28_Q	0.627	0.26
67_E	139_S	0.626	0.26
48_F	61_L	0.624	0.26
88_E	198_A	0.622	0.26
50_D	59_K	0.621	0.25
110_N	124_A	0.620	0.25
56_W	60_E	0.612	0.25
35_R	62_E	0.609	0.25
34_A	39_R	0.606	0.25
86_E	114_R	0.602	0.24
24_W	27_A	0.600	0.24
156_L	189_T	0.600	0.24
195_N	202_A	0.599	0.24
25_L	28_Q	0.599	0.24
151_V	159_S	0.597	0.24
35_R	46_L	0.594	0.24
47_E	57_T	0.593	0.24
39_R	90_A	0.592	0.24
51_E	58_L	0.591	0.24
126_L	171_L	0.590	0.24
151_V	170_W	0.587	0.24
90_A	165_P	0.584	0.24
123_Y	167_H	0.583	0.23
64_L	173_K	0.574	0.23
125_A	130_I	0.573	0.23
147_G	152_V	0.571	0.23
82_S	185_P	0.568	0.23
33_F	163_Y	0.566	0.23
79_F	155_Q	0.563	0.22
125_A	201_L	0.561	0.22
87_S	194_D	0.560	0.22
91_G	123_Y	0.549	0.22
88_E	132_E	0.549	0.22
79_F	152_V	0.546	0.22
34_A	48_F	0.543	0.21
87_S	108_R	0.543	0.21
63_K	67_E	0.540	0.21
195_N	199_D	0.540	0.21
127_Y	203_K	0.536	0.21
104_R	128_E	0.536	0.21
80_D	199_D	0.536	0.21
79_F	151_V	0.531	0.21
24_W	51_E	0.531	0.21
129_A	200_G	0.531	0.21
111_K	166_S	0.531	0.21
138_A	170_W	0.530	0.21
64_L	67_E	0.528	0.21
112_S	156_L	0.527	0.21
27_A	61_L	0.527	0.21
92_L	95_V	0.526	0.21
95_V	194_D	0.525	0.21
81_G	198_A	0.524	0.21
36_E	67_E	0.523	0.20
43_M	50_D	0.514	0.20
36_E	48_F	0.512	0.20
127_Y	186_T	0.510	0.20
157_D	167_H	0.507	0.20
56_W	161_P	0.506	0.20
94_I	121_A	0.506	0.20
127_Y	170_W	0.505	0.20
82_S	140_R	0.503	0.20
57_T	163_Y	0.503	0.20
163_Y	200_G	0.503	0.20
147_G	191_Q	0.502	0.19
53_G	62_E	0.500	0.19

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
3u3gD	1	0.5973	100	0.507	Contact Map
2lsnA	1	0.6062	100	0.512	Contact Map
2e4lA	1	0.6195	100	0.512	Contact Map
3hstB	1	0.6106	100	0.515	Contact Map
1jl1A	1	0.6062	100	0.518	Contact Map
2ehgA	1	0.6283	100	0.523	Contact Map
3h08A	1	0.5664	100	0.523	Contact Map
1rilA	1	0.5796	100	0.524	Contact Map
2qkbA	1	0.5973	100	0.524	Contact Map
4e19A	1	0.5885	100	0.533	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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