YDHK - BACSU - GREMLIN Contacts

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YDHK - Uncharacterized protein YdhK

UniProt:	O05503	Sequences: MSAGKSYRKKMKQRRMNMKISKYALGILMLSLVFVLSACGNNNSTKESTHDNHSDSSTHEEMDHSGSADVPEGLQESKNPKYKVGSQVIINTSHMKGMKGAEATVTGAYDTTAYVVSYTPTNGGQRVDHHKWVIQEEIKDAGDKTLQPGDQVILEASHMKGMKGATAEIDSAEKTTVYMVDYTSTTSGEKVKNHKWVTEDELSAK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	205 (182)
Sequences:	209 (186)
Seq/√Len:	13.8

BACSU - YDHK

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
116_V	154_L	9.042	1.00
138_I	141_A	5.010	1.00
88_V	105_V	4.254	1.00
74_L	134_I	4.220	1.00
117_S	170_D	4.089	1.00
139_K	155_E	3.113	0.98
119_T	126_R	3.083	0.98
138_I	152_V	3.034	0.97
138_I	146_L	2.974	0.97
146_L	150_D	2.899	0.97
87_Q	102_E	2.704	0.95
151_Q	166_T	2.586	0.93
90_I	202_L	2.468	0.92
154_L	167_A	2.411	0.91
133_V	146_L	2.364	0.90
83_K	86_S	2.191	0.86
148_P	172_A	2.166	0.85
173_E	200_D	2.114	0.84
74_L	179_M	2.062	0.82
120_P	123_G	2.056	0.82
105_V	202_L	1.764	0.71
31_S	40_G	1.761	0.70
26_G	30_L	1.732	0.69
135_Q	144_K	1.690	0.67
113_A	170_D	1.689	0.67
141_A	144_K	1.598	0.63
115_V	129_H	1.556	0.60
130_H	194_H	1.542	0.60
139_K	163_K	1.513	0.58
117_S	198_T	1.505	0.58
135_Q	145_T	1.499	0.58
65_S	88_V	1.497	0.57
112_T	172_A	1.488	0.57
66_G	192_K	1.480	0.57
90_I	180_V	1.435	0.54
130_H	159_M	1.428	0.54
159_M	194_H	1.365	0.50
134_I	172_A	1.350	0.50
117_S	126_R	1.345	0.49
189_E	198_T	1.343	0.49
108_A	176_T	1.342	0.49
106_T	109_Y	1.326	0.48
70_V	74_L	1.316	0.48
66_G	70_V	1.310	0.47
113_A	173_E	1.300	0.47
96_K	180_V	1.241	0.44
21_S	38_A	1.233	0.43
109_Y	179_M	1.202	0.42
34_F	38_A	1.200	0.42
134_I	179_M	1.193	0.41
59_H	70_V	1.192	0.41
134_I	175_T	1.178	0.40
62_M	182_Y	1.169	0.40
38_A	166_T	1.154	0.39
164_G	171_S	1.144	0.39
88_V	103_A	1.137	0.38
133_V	138_I	1.126	0.38
155_E	182_Y	1.122	0.38
23_Y	38_A	1.121	0.37
96_K	153_I	1.103	0.37
143_D	192_K	1.102	0.37
88_V	202_L	1.094	0.36
113_A	175_T	1.086	0.36
67_S	148_P	1.067	0.35
67_S	74_L	1.066	0.35
59_H	113_A	1.064	0.35
112_T	136_E	1.061	0.35
45_T	116_V	1.057	0.34
77_S	110_D	1.057	0.34
83_K	153_I	1.050	0.34
121_T	166_T	1.029	0.33
75_Q	79_N	1.028	0.33
141_A	146_L	1.022	0.33
23_Y	29_M	1.009	0.32
49_T	106_T	1.006	0.32
49_T	157_S	0.998	0.32
151_Q	169_I	0.995	0.31
138_I	190_K	0.995	0.31
92_T	126_R	0.987	0.31
75_Q	81_K	0.980	0.31
105_V	108_A	0.977	0.31
117_S	128_D	0.973	0.30
173_E	189_E	0.973	0.30
67_S	134_I	0.970	0.30
70_V	134_I	0.969	0.30
125_Q	200_D	0.967	0.30
115_V	122_N	0.951	0.29
24_A	34_F	0.951	0.29
74_L	186_T	0.949	0.29
147_Q	187_S	0.940	0.29
118_Y	127_V	0.928	0.28
79_N	157_S	0.927	0.28
72_E	125_Q	0.927	0.28
146_L	152_V	0.925	0.28
156_A	159_M	0.921	0.28
106_T	181_D	0.916	0.28
62_M	161_G	0.915	0.28
150_D	186_T	0.913	0.28
70_V	182_Y	0.910	0.28
89_I	144_K	0.910	0.28
112_T	145_T	0.910	0.28
67_S	191_V	0.909	0.28
175_T	191_V	0.905	0.27
122_N	138_I	0.904	0.27
82_Y	160_K	0.903	0.27
78_K	109_Y	0.901	0.27
147_Q	150_D	0.896	0.27
175_T	200_D	0.880	0.26
76_E	81_K	0.874	0.26
172_A	186_T	0.871	0.26
74_L	185_T	0.867	0.26
170_D	198_T	0.866	0.26
99_K	168_E	0.860	0.25
164_G	167_A	0.853	0.25
72_E	171_S	0.852	0.25
179_M	195_K	0.851	0.25
66_G	195_K	0.846	0.25
46_K	79_N	0.842	0.25
93_S	133_V	0.838	0.25
173_E	191_V	0.837	0.25
70_V	179_M	0.836	0.24
131_K	171_S	0.836	0.24
40_G	112_T	0.834	0.24
67_S	175_T	0.833	0.24
35_V	64_H	0.829	0.24
86_S	128_D	0.828	0.24
65_S	134_I	0.824	0.24
113_A	177_V	0.819	0.24
96_K	151_Q	0.818	0.24
116_V	133_V	0.817	0.24
63_D	168_E	0.816	0.24
72_E	144_K	0.812	0.24
25_L	28_L	0.810	0.23
106_T	173_E	0.809	0.23
69_D	198_T	0.809	0.23
155_E	163_K	0.809	0.23
92_T	182_Y	0.802	0.23
89_I	168_E	0.801	0.23
175_T	189_E	0.798	0.23
29_M	34_F	0.797	0.23
133_V	161_G	0.792	0.23
93_S	99_K	0.782	0.22
78_K	140_D	0.782	0.22
65_S	175_T	0.780	0.22
57_S	60_E	0.778	0.22
53_H	116_V	0.777	0.22
58_T	160_K	0.775	0.22
24_A	50_H	0.770	0.22
32_L	66_G	0.769	0.22
92_T	99_K	0.763	0.22
66_G	134_I	0.756	0.21
51_D	182_Y	0.750	0.21
90_I	115_V	0.745	0.21
93_S	127_V	0.743	0.21
105_V	169_I	0.743	0.21
113_A	134_I	0.731	0.21
70_V	180_V	0.728	0.20
112_T	141_A	0.724	0.20
137_E	192_K	0.718	0.20
42_N	138_I	0.716	0.20
37_S	43_N	0.714	0.20
115_V	155_E	0.713	0.20
173_E	202_L	0.710	0.20
46_K	58_T	0.706	0.20
115_V	171_S	0.702	0.20
33_V	121_T	0.699	0.19
142_G	146_L	0.698	0.19
133_V	163_K	0.692	0.19
104_T	195_K	0.688	0.19
106_T	157_S	0.682	0.19
27_I	38_A	0.682	0.19
138_I	154_L	0.679	0.19
109_Y	140_D	0.670	0.18
67_S	173_E	0.669	0.18
131_K	182_Y	0.668	0.18
36_L	136_E	0.665	0.18
153_I	167_A	0.663	0.18
26_G	40_G	0.652	0.18
82_Y	118_Y	0.648	0.18
147_Q	172_A	0.646	0.18
73_G	168_E	0.640	0.18
116_V	126_R	0.632	0.17
150_D	169_I	0.630	0.17
29_M	52_N	0.624	0.17
168_E	180_V	0.624	0.17
113_A	129_H	0.616	0.17
59_H	169_I	0.610	0.17
152_V	182_Y	0.609	0.17
33_V	192_K	0.607	0.17
64_H	154_L	0.604	0.16
133_V	154_L	0.604	0.16
157_S	192_K	0.601	0.16
69_D	175_T	0.600	0.16
27_I	33_V	0.596	0.16
143_D	174_K	0.592	0.16
80_P	197_V	0.590	0.16
73_G	157_S	0.587	0.16
113_A	150_D	0.587	0.16
69_D	148_P	0.585	0.16
75_Q	106_T	0.584	0.16
76_E	128_D	0.583	0.16
65_S	191_V	0.583	0.16
136_E	145_T	0.581	0.16
45_T	110_D	0.579	0.16
67_S	189_E	0.578	0.16
79_N	170_D	0.576	0.16
30_L	82_Y	0.574	0.16
28_L	82_Y	0.572	0.16
175_T	202_L	0.571	0.15
83_K	163_K	0.571	0.15
65_S	103_A	0.569	0.15
27_I	41_N	0.567	0.15
31_S	38_A	0.566	0.15
74_L	88_V	0.565	0.15
119_T	142_G	0.565	0.15
106_T	185_T	0.563	0.15
31_S	72_E	0.563	0.15
145_T	183_T	0.561	0.15
61_E	144_K	0.560	0.15
156_A	195_K	0.560	0.15
91_N	155_E	0.559	0.15
89_I	103_A	0.558	0.15
115_V	170_D	0.557	0.15
75_Q	122_N	0.555	0.15
140_D	190_K	0.555	0.15
172_A	203_S	0.555	0.15
111_T	124_G	0.554	0.15
65_S	202_L	0.549	0.15
91_N	203_S	0.548	0.15
128_D	160_K	0.542	0.15
22_K	180_V	0.540	0.15
66_G	191_V	0.539	0.15
47_E	58_T	0.536	0.15
25_L	30_L	0.536	0.15
26_G	50_H	0.532	0.14
22_K	109_Y	0.531	0.14
145_T	174_K	0.530	0.14
69_D	171_S	0.529	0.14
156_A	161_G	0.529	0.14
99_K	186_T	0.528	0.14
128_D	163_K	0.528	0.14
104_T	200_D	0.526	0.14
37_S	75_Q	0.526	0.14
34_F	142_G	0.525	0.14
40_G	45_T	0.524	0.14
119_T	140_D	0.523	0.14
82_Y	110_D	0.522	0.14
60_E	91_N	0.521	0.14
139_K	153_I	0.520	0.14
70_V	109_Y	0.520	0.14
112_T	174_K	0.520	0.14
67_S	70_V	0.519	0.14
137_E	156_A	0.518	0.14
26_G	168_E	0.517	0.14
70_V	175_T	0.517	0.14
29_M	40_G	0.513	0.14
148_P	180_V	0.512	0.14
43_N	168_E	0.511	0.14
70_V	169_I	0.511	0.14
72_E	173_E	0.510	0.14
67_S	172_A	0.508	0.14
148_P	189_E	0.507	0.14
157_S	163_K	0.507	0.14
93_S	157_S	0.507	0.14
92_T	119_T	0.507	0.14
48_S	81_K	0.507	0.14
102_E	170_D	0.506	0.14
130_H	156_A	0.506	0.14
67_S	88_V	0.504	0.14
138_I	144_K	0.503	0.14
103_A	108_A	0.501	0.14
62_M	103_A	0.500	0.14
115_V	119_T	0.500	0.14

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
4mdwA	1	0.6488	100	0.254	Contact Map
4fibA	1	0.6049	100	0.364	Contact Map
4r2fA	1	0.3902	83.3	0.952	Contact Map
2ltjA	1	0.4	78	0.954	Contact Map
3k6vA	1	0.4732	76.8	0.955	Contact Map
4wzzA	1	0.5268	73.8	0.956	Contact Map
3ucpA	1	0.4878	73.4	0.956	Contact Map
3ombA	1	0.4293	72.5	0.956	Contact Map
4r9fA	1	0.5561	72.4	0.956	Contact Map
3uorA	1	0.3902	70.7	0.957	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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