YDDK - BACSU - GREMLIN Contacts

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YDDK - Uncharacterized protein YddK

UniProt:	P96648	Sequences: MDTLKKLKFEANGIIGVLLDYSREPVLTNIIDQFRTSLESNDIELIRYSLEQLKTWYARNRNEIYKNEFVFNEFEHHETENKIKKFLDELPVVDETEKSSITHFSSDQNRELEKKIFISHSSKDKIVCNAFVELLEDIGVSSEDIIYTSSPYHGIPGDEDIFEYLKKHLFKGAYVFYMLSDNYYDSVYCLNEMGATWVNSNNCSTFILPGFKGEIKGVIDKNKKAFSLEEPIDLFNLKEKILRMYDLTLEDKKWERIKAKFNTKLK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	266 (211)
Sequences:	163 (150)
Seq/√Len:	10.3

BACSU - YDDK

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
119_S	192_E	4.334	0.99
158_D	192_E	3.348	0.96
116_I	176_F	2.917	0.92
204_S	208_L	2.851	0.91
79_T	82_K	2.843	0.91
118_I	139_G	2.738	0.89
205_T	209_P	2.690	0.89
205_T	208_L	2.602	0.87
177_Y	193_M	2.565	0.86
186_S	189_C	2.434	0.83
188_Y	192_E	2.434	0.83
158_D	168_H	2.125	0.73
74_F	148_T	2.108	0.73
119_S	165_L	2.010	0.69
129_N	152_Y	1.959	0.67
32_D	43_I	1.955	0.66
235_F	239_E	1.941	0.66
121_S	155_I	1.887	0.64
77_H	80_E	1.877	0.63
155_I	188_Y	1.870	0.63
151_P	192_E	1.842	0.62
117_F	193_M	1.820	0.61
149_S	168_H	1.818	0.61
202_N	206_F	1.814	0.60
124_D	155_I	1.781	0.59
131_F	178_M	1.750	0.58
127_V	178_M	1.715	0.56
117_F	169_L	1.712	0.56
117_F	165_L	1.708	0.56
203_C	208_L	1.680	0.54
124_D	192_E	1.668	0.54
160_D	169_L	1.660	0.53
204_S	207_I	1.645	0.53
60_N	127_V	1.625	0.52
161_I	165_L	1.548	0.48
155_I	224_K	1.527	0.47
121_S	124_D	1.510	0.46
175_V	219_I	1.496	0.46
122_S	169_L	1.494	0.46
75_E	78_E	1.475	0.45
188_Y	224_K	1.475	0.45
161_I	224_K	1.469	0.45
120_H	150_S	1.458	0.44
155_I	159_E	1.455	0.44
202_N	205_T	1.451	0.44
77_H	221_K	1.449	0.44
159_E	208_L	1.437	0.43
26_V	29_N	1.405	0.42
49_S	59_R	1.380	0.40
61_R	97_E	1.380	0.40
24_E	36_T	1.370	0.40
124_D	188_Y	1.366	0.40
25_P	30_I	1.360	0.40
100_S	104_F	1.345	0.39
234_L	238_K	1.322	0.38
212_K	221_K	1.314	0.38
56_W	70_V	1.291	0.37
175_V	215_I	1.286	0.36
172_G	188_Y	1.279	0.36
129_N	150_S	1.269	0.36
58_A	118_I	1.256	0.35
121_S	188_Y	1.246	0.35
69_F	94_D	1.241	0.34
165_L	168_H	1.230	0.34
27_L	31_I	1.224	0.34
27_L	30_I	1.223	0.34
151_P	172_G	1.222	0.34
22_S	25_P	1.217	0.33
23_R	29_N	1.204	0.33
126_I	181_D	1.204	0.33
206_F	225_A	1.204	0.33
88_D	91_P	1.198	0.33
22_S	41_N	1.189	0.32
116_I	140_V	1.179	0.32
28_T	36_T	1.174	0.32
124_D	131_F	1.169	0.31
149_S	166_K	1.162	0.31
34_F	54_K	1.157	0.31
151_P	178_M	1.157	0.31
192_E	214_E	1.154	0.31
155_I	229_E	1.153	0.31
117_F	180_S	1.150	0.31
233_D	237_L	1.148	0.31
61_R	172_G	1.143	0.30
169_L	195_A	1.141	0.30
23_R	26_V	1.138	0.30
130_A	226_F	1.132	0.30
78_E	82_K	1.123	0.30
33_Q	83_I	1.111	0.29
83_I	215_I	1.110	0.29
135_L	155_I	1.105	0.29
206_F	209_P	1.096	0.29
110_R	126_I	1.095	0.29
162_F	210_G	1.079	0.28
49_S	53_L	1.072	0.28
234_L	237_L	1.069	0.28
189_C	199_N	1.068	0.28
127_V	182_N	1.067	0.28
121_S	192_E	1.064	0.27
104_F	173_A	1.062	0.27
102_T	106_S	1.060	0.27
39_E	47_R	1.059	0.27
104_F	107_D	1.040	0.27
197_W	228_L	1.039	0.27
23_R	27_L	1.037	0.26
164_Y	175_V	1.037	0.26
107_D	113_E	1.035	0.26
26_V	30_I	1.034	0.26
114_K	172_G	1.033	0.26
119_S	151_P	1.029	0.26
43_I	58_A	1.026	0.26
24_E	32_D	1.021	0.26
85_K	176_F	1.021	0.26
193_M	213_G	1.018	0.26
121_S	179_L	1.012	0.26
112_L	176_F	1.006	0.25
107_D	111_E	1.003	0.25
82_K	86_F	1.002	0.25
178_M	229_E	1.002	0.25
133_E	136_E	0.998	0.25
87_L	118_I	0.996	0.25
120_H	224_K	0.995	0.25
168_H	192_E	0.994	0.25
107_D	221_K	0.993	0.25
155_I	192_E	0.985	0.25
51_E	66_K	0.981	0.24
119_S	158_D	0.977	0.24
132_V	150_S	0.975	0.24
119_S	155_I	0.974	0.24
137_D	178_M	0.973	0.24
120_H	165_L	0.972	0.24
53_L	60_N	0.972	0.24
165_L	220_D	0.960	0.24
165_L	224_K	0.956	0.24
163_E	194_G	0.954	0.24
26_V	33_Q	0.950	0.23
33_Q	37_S	0.945	0.23
121_S	228_L	0.942	0.23
26_V	37_S	0.934	0.23
24_E	28_T	0.930	0.23
70_V	102_T	0.926	0.23
122_S	194_G	0.926	0.23
122_S	193_M	0.919	0.22
167_K	203_C	0.916	0.22
52_Q	70_V	0.914	0.22
155_I	196_T	0.912	0.22
150_S	155_I	0.896	0.22
119_S	188_Y	0.894	0.22
56_W	59_R	0.889	0.21
120_H	179_L	0.885	0.21
120_H	183_Y	0.881	0.21
116_I	179_L	0.874	0.21
24_E	31_I	0.868	0.21
26_V	34_F	0.866	0.21
183_Y	189_C	0.863	0.21
127_V	208_L	0.858	0.20
159_E	176_F	0.844	0.20
118_I	132_V	0.842	0.20
203_C	207_I	0.839	0.20
168_H	222_N	0.835	0.20
132_V	155_I	0.835	0.20
69_F	201_N	0.832	0.20
90_L	211_F	0.830	0.20
47_R	72_N	0.827	0.20
208_L	212_K	0.826	0.20
49_S	101_I	0.826	0.20
78_E	84_K	0.825	0.20
235_F	238_K	0.823	0.19
115_K	172_G	0.820	0.19
187_V	191_N	0.820	0.19
186_S	207_I	0.820	0.19
158_D	165_L	0.819	0.19
27_L	34_F	0.819	0.19
155_I	161_I	0.817	0.19
149_S	195_A	0.815	0.19
124_D	180_S	0.813	0.19
45_L	49_S	0.809	0.19
177_Y	188_Y	0.804	0.19
175_V	196_T	0.803	0.19
169_L	191_N	0.801	0.19
183_Y	188_Y	0.795	0.19
181_D	209_P	0.794	0.19
104_F	229_E	0.790	0.18
194_G	197_W	0.788	0.18
204_S	209_P	0.787	0.18
29_N	61_R	0.784	0.18
76_H	79_T	0.783	0.18
202_N	207_I	0.777	0.18
201_N	206_F	0.774	0.18
26_V	178_M	0.773	0.18
115_K	204_S	0.771	0.18
189_C	192_E	0.766	0.18
115_K	157_G	0.766	0.18
149_S	175_V	0.764	0.18
33_Q	36_T	0.760	0.18
194_G	228_L	0.760	0.18
197_W	221_K	0.755	0.18
233_D	239_E	0.737	0.17
115_K	180_S	0.735	0.17
226_F	238_K	0.733	0.17
113_E	171_K	0.732	0.17
97_E	100_S	0.727	0.17
206_F	212_K	0.727	0.17
150_S	225_A	0.727	0.17
64_I	100_S	0.717	0.17
80_E	187_V	0.717	0.17
67_N	84_K	0.716	0.17
28_T	37_S	0.711	0.16
45_L	59_R	0.709	0.16
121_S	168_H	0.708	0.16
165_L	193_M	0.701	0.16
182_N	190_L	0.697	0.16
24_E	27_L	0.693	0.16
140_V	193_M	0.692	0.16
79_T	109_N	0.690	0.16
22_S	46_I	0.686	0.16
134_L	198_V	0.682	0.16
155_I	164_Y	0.681	0.16
148_T	196_T	0.681	0.16
25_P	28_T	0.677	0.16
165_L	237_L	0.676	0.16
77_H	103_H	0.675	0.15
166_K	191_N	0.674	0.15
184_Y	189_C	0.672	0.15
117_F	131_F	0.669	0.15
138_I	204_S	0.661	0.15
32_D	36_T	0.659	0.15
41_N	205_T	0.656	0.15
20_D	23_R	0.655	0.15
38_L	102_T	0.654	0.15
27_L	35_R	0.653	0.15
102_T	202_N	0.649	0.15
160_D	222_N	0.649	0.15
193_M	200_S	0.649	0.15
72_N	105_S	0.647	0.15
58_A	62_N	0.643	0.15
121_S	224_K	0.642	0.15
86_F	112_L	0.640	0.15
58_A	61_R	0.640	0.15
92_V	176_F	0.637	0.15
179_L	237_L	0.637	0.15
117_F	127_V	0.635	0.15
21_Y	37_S	0.635	0.15
130_A	238_K	0.635	0.15
28_T	38_L	0.632	0.14
139_G	153_H	0.632	0.14
193_M	215_I	0.630	0.14
31_I	34_F	0.627	0.14
188_Y	196_T	0.625	0.14
161_I	178_M	0.625	0.14
90_L	107_D	0.623	0.14
59_R	98_K	0.621	0.14
170_F	192_E	0.610	0.14
55_T	58_A	0.607	0.14
128_C	178_M	0.601	0.14
184_Y	212_K	0.601	0.14
192_E	228_L	0.595	0.14
138_I	194_G	0.592	0.14
160_D	166_K	0.590	0.14
124_D	165_L	0.589	0.14
22_S	118_I	0.588	0.13
162_F	172_G	0.587	0.13
85_K	111_E	0.585	0.13
99_S	113_E	0.584	0.13
44_E	48_Y	0.583	0.13
44_E	90_L	0.583	0.13
175_V	186_S	0.582	0.13
175_V	188_Y	0.580	0.13
24_E	39_E	0.580	0.13
81_N	90_L	0.579	0.13
60_N	63_E	0.577	0.13
45_L	202_N	0.576	0.13
135_L	201_N	0.573	0.13
129_N	206_F	0.572	0.13
77_H	214_E	0.571	0.13
124_D	148_T	0.571	0.13
30_I	33_Q	0.569	0.13
158_D	189_C	0.569	0.13
56_W	178_M	0.569	0.13
178_M	204_S	0.564	0.13
20_D	37_S	0.561	0.13
22_S	30_I	0.560	0.13
23_R	31_I	0.559	0.13
150_S	158_D	0.558	0.13
186_S	196_T	0.557	0.13
122_S	228_L	0.556	0.13
94_D	97_E	0.556	0.13
163_E	213_G	0.555	0.13
151_P	208_L	0.552	0.13
97_E	181_D	0.550	0.13
132_V	169_L	0.549	0.13
192_E	197_W	0.548	0.13
186_S	238_K	0.547	0.13
55_T	85_K	0.546	0.13
86_F	176_F	0.542	0.13
91_P	167_K	0.539	0.12
121_S	165_L	0.537	0.12
74_F	81_N	0.537	0.12
45_L	101_I	0.532	0.12
148_T	205_T	0.525	0.12
42_D	53_L	0.523	0.12
175_V	187_V	0.522	0.12
85_K	99_S	0.521	0.12
115_K	168_H	0.521	0.12
24_E	53_L	0.520	0.12
58_A	84_K	0.516	0.12
41_N	53_L	0.516	0.12
158_D	205_T	0.516	0.12
97_E	235_F	0.515	0.12
64_I	94_D	0.513	0.12
121_S	166_K	0.512	0.12
25_P	36_T	0.510	0.12
219_I	227_S	0.508	0.12
51_E	55_T	0.503	0.12
156_P	222_N	0.502	0.12
41_N	140_V	0.500	0.12

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
3oziA	2	0.5564	100	0.531	Contact Map
4c6rA	1	0.5451	100	0.55	Contact Map
3jrnA	1	0.5	100	0.552	Contact Map
4lzpB	2	0.609	100	0.586	Contact Map
4c6sA	2	0.4662	100	0.605	Contact Map
4lqcA	2	0.485	99.9	0.613	Contact Map
3h16A	2	0.4925	99.9	0.623	Contact Map
3ub2A	2	0.4474	99.9	0.643	Contact Map
2js7A	1	0.5564	99.9	0.645	Contact Map
1fyxA	2	0.4925	99.9	0.654	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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