YCBO - BACSU - GREMLIN Contacts

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YCBO - Uncharacterized protein YcbO

UniProt:	P42247	Sequences: MNLIRIELRKMKMGWYIRGALIANVIIMGFMWLISYSEKADGGVSFQSTDEAFLIIGTFVRAVFIVFGAVLIVKLVISEYKNKTILVMFTYPISRKKLLTAKLMIAGGLTFITILLSNILIAAGFFWLNSICHFIPGELTSEIISQQAVKMAVFAFGAAGTSLVPIFFGMRRHSVPATIISSVVIVMLISSTSPGFSISSVVYIPLSLAAFGLFFSYMAIRNADKQDA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	228 (226)
Sequences:	244 (194)
Seq/√Len:	12.9

BACSU - YCBO

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
23_A	63_V	4.042	1.00
168_F	181_S	3.504	0.99
80_Y	173_H	3.421	0.99
24_N	117_S	3.194	0.98
152_A	156_F	2.722	0.94
24_N	93_I	2.474	0.90
73_V	78_S	2.374	0.88
70_V	179_I	2.371	0.88
98_L	183_V	2.363	0.88
80_Y	87_V	2.336	0.87
12_K	117_S	2.334	0.87
80_Y	223_A	2.201	0.84
77_I	181_S	2.197	0.84
94_S	123_A	2.184	0.83
19_G	23_A	2.150	0.82
116_L	204_I	2.038	0.79
161_T	182_S	2.029	0.79
84_T	165_P	1.967	0.76
88_M	162_S	1.908	0.74
104_M	191_S	1.905	0.74
68_G	110_T	1.873	0.73
170_M	227_D	1.834	0.71
198_I	201_V	1.803	0.70
30_F	59_F	1.795	0.69
121_I	124_G	1.782	0.69
114_I	155_A	1.767	0.68
84_T	227_D	1.757	0.67
115_L	119_I	1.756	0.67
79_E	102_K	1.745	0.67
15_W	63_V	1.719	0.66
100_T	113_T	1.708	0.65
176_P	179_I	1.704	0.65
26_I	69_A	1.683	0.64
84_T	170_M	1.669	0.63
19_G	108_G	1.664	0.63
116_L	119_I	1.655	0.63
168_F	209_A	1.636	0.62
2_N	29_G	1.612	0.61
79_E	89_F	1.610	0.60
114_I	191_S	1.590	0.59
16_Y	20_A	1.566	0.58
12_K	19_G	1.556	0.58
4_I	146_Q	1.517	0.56
22_I	26_I	1.477	0.54
50_D	120_L	1.463	0.53
75_L	105_I	1.459	0.53
13_M	116_L	1.457	0.53
131_I	180_I	1.449	0.52
66_V	121_I	1.448	0.52
62_A	187_M	1.448	0.52
159_A	183_V	1.434	0.51
204_I	209_A	1.433	0.51
3_L	111_F	1.420	0.51
180_I	186_V	1.414	0.50
73_V	88_M	1.405	0.50
22_I	131_I	1.387	0.49
8_L	23_A	1.385	0.49
10_K	208_L	1.384	0.49
62_A	74_K	1.378	0.48
107_G	156_F	1.374	0.48
6_I	70_V	1.374	0.48
11_M	184_V	1.370	0.48
156_F	185_I	1.364	0.48
71_L	85_I	1.360	0.48
5_R	104_M	1.359	0.47
30_F	87_V	1.350	0.47
7_E	10_K	1.335	0.46
70_V	73_V	1.332	0.46
21_L	28_M	1.324	0.46
85_I	165_P	1.323	0.46
49_T	139_L	1.311	0.45
82_N	170_M	1.290	0.44
107_G	159_A	1.284	0.44
66_V	129_N	1.264	0.43
2_N	80_Y	1.248	0.42
58_T	161_T	1.215	0.40
94_S	98_L	1.211	0.40
44_V	213_L	1.211	0.40
84_T	167_F	1.210	0.40
53_F	69_A	1.208	0.40
88_M	210_A	1.206	0.40
49_T	137_G	1.206	0.40
65_I	158_A	1.200	0.39
24_N	120_L	1.195	0.39
219_A	227_D	1.191	0.39
5_R	184_V	1.191	0.39
35_S	125_F	1.189	0.39
78_S	88_M	1.186	0.39
73_V	210_A	1.177	0.38
201_V	204_I	1.174	0.38
45_S	94_S	1.173	0.38
125_F	135_I	1.168	0.38
32_W	125_F	1.164	0.38
75_L	80_Y	1.158	0.37
216_S	226_Q	1.146	0.37
176_P	181_S	1.137	0.36
111_F	212_G	1.125	0.36
20_A	220_I	1.123	0.36
18_R	83_K	1.123	0.36
87_V	106_A	1.110	0.35
29_G	152_A	1.102	0.35
76_V	100_T	1.101	0.35
207_S	211_F	1.088	0.34
172_R	178_T	1.067	0.33
2_N	218_M	1.066	0.33
4_I	211_F	1.064	0.33
162_S	168_F	1.063	0.33
118_N	125_F	1.063	0.33
25_V	43_G	1.061	0.33
105_I	119_I	1.060	0.33
77_I	172_R	1.059	0.33
10_K	84_T	1.051	0.32
169_G	174_S	1.045	0.32
134_F	183_V	1.044	0.32
13_M	184_V	1.042	0.32
76_V	85_I	1.041	0.32
9_R	150_K	1.039	0.32
156_F	225_K	1.037	0.32
58_T	125_F	1.027	0.31
56_I	125_F	1.024	0.31
99_L	190_S	1.019	0.31
32_W	133_H	1.005	0.30
32_W	129_N	1.004	0.30
54_L	74_K	1.000	0.30
80_Y	84_T	0.993	0.30
109_L	203_Y	0.985	0.29
136_P	175_V	0.979	0.29
66_V	162_S	0.978	0.29
96_K	160_G	0.975	0.29
87_V	142_E	0.968	0.29
90_T	93_I	0.965	0.28
77_I	85_I	0.962	0.28
64_F	89_F	0.961	0.28
101_A	119_I	0.958	0.28
126_F	146_Q	0.947	0.28
6_I	68_G	0.940	0.27
110_T	179_I	0.940	0.27
92_P	95_R	0.937	0.27
89_F	92_P	0.934	0.27
71_L	165_P	0.927	0.27
72_I	166_I	0.926	0.27
61_R	165_P	0.916	0.26
8_L	20_A	0.910	0.26
8_L	125_F	0.907	0.26
69_A	213_L	0.902	0.26
8_L	158_A	0.899	0.26
16_Y	135_I	0.899	0.26
71_L	163_L	0.898	0.26
90_T	194_P	0.897	0.26
106_A	109_L	0.894	0.26
162_S	178_T	0.894	0.26
192_T	213_L	0.891	0.25
19_G	67_F	0.889	0.25
106_A	128_L	0.888	0.25
157_G	209_A	0.888	0.25
90_T	159_A	0.883	0.25
42_G	185_I	0.882	0.25
197_S	205_P	0.882	0.25
25_V	127_W	0.879	0.25
59_F	188_L	0.878	0.25
119_I	188_L	0.878	0.25
98_L	117_S	0.875	0.25
26_I	83_K	0.874	0.25
128_L	165_P	0.873	0.25
126_F	203_Y	0.871	0.25
21_L	25_V	0.869	0.25
3_L	7_E	0.858	0.24
45_S	200_S	0.845	0.24
158_A	213_L	0.838	0.23
8_L	87_V	0.837	0.23
21_L	221_R	0.835	0.23
46_F	115_L	0.835	0.23
63_V	103_L	0.835	0.23
133_H	207_S	0.835	0.23
103_L	161_T	0.833	0.23
164_V	224_D	0.833	0.23
86_L	90_T	0.830	0.23
77_I	165_P	0.827	0.23
9_R	161_T	0.825	0.23
199_S	203_Y	0.817	0.23
85_I	170_M	0.816	0.23
13_M	213_L	0.815	0.23
49_T	66_V	0.815	0.23
22_I	97_K	0.812	0.22
5_R	48_S	0.811	0.22
195_G	213_L	0.799	0.22
57_G	154_F	0.796	0.22
155_A	160_G	0.795	0.22
201_V	205_P	0.795	0.22
223_A	226_Q	0.791	0.22
15_W	106_A	0.779	0.21
2_N	50_D	0.778	0.21
73_V	124_G	0.776	0.21
28_M	88_M	0.774	0.21
120_L	129_N	0.773	0.21
136_P	211_F	0.771	0.21
52_A	58_T	0.769	0.21
69_A	214_F	0.763	0.21
11_M	99_L	0.763	0.21
14_G	18_R	0.759	0.21
8_L	146_Q	0.756	0.20
5_R	136_P	0.755	0.20
35_S	113_T	0.754	0.20
52_A	78_S	0.753	0.20
115_L	152_A	0.751	0.20
2_N	26_I	0.748	0.20
116_L	196_F	0.747	0.20
81_K	111_F	0.738	0.20
185_I	190_S	0.736	0.20
48_S	108_G	0.732	0.20
13_M	130_S	0.727	0.20
119_I	140_T	0.724	0.19
6_I	198_I	0.723	0.19
202_V	205_P	0.720	0.19
107_G	119_I	0.715	0.19
75_L	180_I	0.713	0.19
71_L	144_I	0.711	0.19
10_K	214_F	0.710	0.19
171_R	191_S	0.708	0.19
120_L	147_Q	0.708	0.19
93_I	97_K	0.704	0.19
62_A	93_I	0.703	0.19
82_N	227_D	0.702	0.19
29_G	33_L	0.701	0.19
80_Y	89_F	0.701	0.19
72_I	165_P	0.700	0.19
59_F	215_F	0.699	0.19
212_G	216_S	0.699	0.19
197_S	213_L	0.698	0.19
159_A	201_V	0.697	0.19
99_L	120_L	0.696	0.19
75_L	173_H	0.692	0.18
166_I	191_S	0.690	0.18
12_K	211_F	0.688	0.18
191_S	195_G	0.683	0.18
52_A	193_S	0.677	0.18
78_S	167_F	0.677	0.18
41_D	161_T	0.676	0.18
25_V	108_G	0.673	0.18
49_T	53_F	0.673	0.18
217_Y	222_N	0.672	0.18
73_V	216_S	0.672	0.18
55_I	139_L	0.664	0.18
98_L	112_I	0.661	0.17
20_A	173_H	0.658	0.17
86_L	159_A	0.655	0.17
81_K	165_P	0.649	0.17
75_L	203_Y	0.647	0.17
206_L	210_A	0.646	0.17
67_F	162_S	0.645	0.17
86_L	125_F	0.644	0.17
108_G	127_W	0.644	0.17
76_V	160_G	0.643	0.17
27_I	63_V	0.643	0.17
15_W	109_L	0.641	0.17
134_F	182_S	0.635	0.17
71_L	87_V	0.635	0.17
146_Q	210_A	0.634	0.17
21_L	162_S	0.629	0.16
6_I	95_R	0.624	0.16
165_P	217_Y	0.624	0.16
164_V	184_V	0.623	0.16
36_Y	100_T	0.621	0.16
98_L	201_V	0.621	0.16
22_I	145_S	0.618	0.16
202_V	219_A	0.617	0.16
24_N	121_I	0.614	0.16
79_E	165_P	0.612	0.16
49_T	135_I	0.610	0.16
28_M	34_I	0.610	0.16
51_E	72_I	0.609	0.16
194_P	200_S	0.607	0.16
165_P	170_M	0.607	0.16
25_V	153_V	0.604	0.16
65_I	84_T	0.601	0.16
76_V	148_A	0.598	0.16
49_T	122_A	0.598	0.16
23_A	93_I	0.598	0.16
164_V	212_G	0.594	0.16
46_F	51_E	0.593	0.15
41_D	44_V	0.590	0.15
63_V	208_L	0.586	0.15
120_L	202_V	0.586	0.15
73_V	175_V	0.585	0.15
210_A	213_L	0.584	0.15
65_I	117_S	0.584	0.15
66_V	76_V	0.583	0.15
171_R	196_F	0.581	0.15
73_V	179_I	0.578	0.15
149_V	222_N	0.577	0.15
68_G	86_L	0.577	0.15
15_W	74_K	0.573	0.15
67_F	168_F	0.573	0.15
32_W	124_G	0.569	0.15
116_L	222_N	0.568	0.15
48_S	59_F	0.568	0.15
170_M	226_Q	0.565	0.15
104_M	142_E	0.560	0.15
8_L	110_T	0.560	0.15
32_W	136_P	0.559	0.15
62_A	190_S	0.559	0.15
115_L	220_I	0.559	0.15
30_F	137_G	0.559	0.15
2_N	6_I	0.553	0.14
57_G	197_S	0.551	0.14
80_Y	92_P	0.550	0.14
143_I	148_A	0.547	0.14
147_Q	185_I	0.546	0.14
105_I	210_A	0.546	0.14
39_K	216_S	0.544	0.14
98_L	167_F	0.543	0.14
63_V	124_G	0.542	0.14
156_F	210_A	0.542	0.14
69_A	136_P	0.540	0.14
151_M	173_H	0.536	0.14
113_T	176_P	0.536	0.14
26_I	124_G	0.534	0.14
117_S	191_S	0.533	0.14
122_A	183_V	0.532	0.14
101_A	193_S	0.531	0.14
155_A	164_V	0.530	0.14
14_G	69_A	0.523	0.14
109_L	113_T	0.520	0.14
59_F	189_I	0.517	0.14
164_V	216_S	0.516	0.13
23_A	209_A	0.514	0.13
148_A	214_F	0.513	0.13
112_I	119_I	0.512	0.13
47_Q	145_S	0.512	0.13
217_Y	224_D	0.510	0.13
203_Y	207_S	0.509	0.13
74_K	184_V	0.509	0.13
103_L	179_I	0.509	0.13
101_A	190_S	0.508	0.13
12_K	208_L	0.508	0.13
6_I	92_P	0.504	0.13
121_I	185_I	0.503	0.13
68_G	131_I	0.502	0.13
43_G	146_Q	0.500	0.13

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
3tdsE	3	0.9518	14.4	0.957	Contact Map
2xq2A	2	0.8553	7.3	0.963	Contact Map
1orqC	4	0.4649	6.4	0.964	Contact Map
2cfqA	1	0.7895	6.1	0.964	Contact Map
3dh4A	3	0.864	5.8	0.964	Contact Map
4pypA	1	0.7895	5.8	0.964	Contact Map
4tphA	2	0.7939	4.6	0.966	Contact Map
4ikvA	1	0.8333	4	0.967	Contact Map
4httA	1	0.8553	3.9	0.967	Contact Map
4cadC	1	0.8509	3.6	0.968	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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