YOHK - ECOLI - GREMLIN Contacts

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YOHK - Inner membrane protein YohK

UniProt:	P0AD19	Sequences: MMANIWWSLPLTLIVFFAARKLAARYKFPLLNPLLVAMVVIIPFLMLTGISYDSYFKGSEVLNDLLQPAVVALAYPLYEQLHQIRARWKSIITICFIGSVVAMVTGTSVALLMGASPEIAASILPKSVTTPIAMAVGGSIGGIPAISAVCVIFVGILGAVFGHTLLNAMRIRTKAARGLAMGTASHALGTARCAELDYQEGAFSSLALVLCGIITSLIAPFLFPIILAVMG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12024
Length:	231 (220)
Sequences:	1920 (1346)
Seq/√Len:	90.8

ECOLI - YOHK
BACSU - YXAC LRGB YWBG

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
132_I	212_G	5.800	1.00
133_A	151_V	5.074	1.00
135_A	138_G	4.267	1.00
137_G	147_S	3.758	1.00
125_P	137_G	3.307	1.00
174_K	197_D	3.169	1.00
162_G	181_M	3.147	1.00
181_M	193_C	3.106	1.00
12_T	55_Y	3.066	1.00
158_G	185_S	2.816	1.00
15_V	40_V	2.714	1.00
190_T	204_S	2.564	1.00
128_V	136_V	2.470	1.00
167_N	177_R	2.422	1.00
192_R	195_E	2.296	1.00
110_A	115_A	2.230	1.00
162_G	166_L	2.219	1.00
110_A	120_A	2.072	1.00
19_A	36_V	2.040	1.00
15_V	37_A	2.000	1.00
166_L	181_M	1.934	1.00
177_R	200_E	1.896	1.00
121_A	140_I	1.869	1.00
21_K	25_R	1.862	1.00
36_V	40_V	1.847	1.00
197_D	200_E	1.831	1.00
122_S	142_G	1.801	1.00
19_A	37_A	1.757	1.00
122_S	143_I	1.756	1.00
97_I	101_V	1.750	1.00
99_S	211_C	1.731	1.00
56_F	63_N	1.729	1.00
15_V	41_I	1.695	1.00
43_P	47_L	1.658	1.00
82_H	86_A	1.650	1.00
18_A	22_L	1.641	1.00
8_S	50_I	1.621	1.00
43_P	46_M	1.615	1.00
15_V	44_F	1.606	1.00
110_A	123_I	1.602	1.00
127_S	154_V	1.594	1.00
87_R	90_S	1.594	1.00
206_L	212_G	1.589	1.00
179_L	183_T	1.565	1.00
15_V	19_A	1.564	1.00
106_G	154_V	1.523	1.00
164_T	168_A	1.514	1.00
117_P	121_A	1.496	1.00
96_F	214_I	1.470	1.00
108_S	112_L	1.457	0.99
129_T	132_I	1.445	0.99
107_T	124_L	1.420	0.99
44_F	48_T	1.398	0.99
18_A	40_V	1.385	0.99
39_V	43_P	1.384	0.99
56_F	59_S	1.372	0.99
57_K	60_E	1.360	0.99
14_I	18_A	1.345	0.99
128_V	132_I	1.341	0.99
179_L	207_A	1.340	0.99
99_S	103_M	1.318	0.99
81_L	85_R	1.314	0.99
88_W	92_I	1.304	0.99
125_P	147_S	1.302	0.99
21_K	26_Y	1.299	0.99
131_P	135_A	1.293	0.99
179_L	203_F	1.288	0.99
45_L	52_Y	1.283	0.99
104_V	108_S	1.280	0.99
70_V	75_Y	1.266	0.99
126_K	154_V	1.261	0.99
103_M	219_A	1.258	0.99
87_R	203_F	1.255	0.98
134_M	148_A	1.252	0.98
56_F	60_E	1.239	0.98
185_S	204_S	1.238	0.98
136_V	215_T	1.226	0.98
130_T	152_I	1.200	0.98
67_Q	131_P	1.183	0.98
144_P	148_A	1.181	0.98
146_I	150_C	1.163	0.97
116_S	119_I	1.158	0.97
11_L	41_I	1.152	0.97
18_A	21_K	1.151	0.97
152_I	156_I	1.141	0.97
108_S	111_L	1.132	0.97
23_A	31_L	1.109	0.97
70_V	154_V	1.093	0.96
66_L	187_A	1.069	0.96
76_P	205_S	1.063	0.96
154_V	185_S	1.056	0.96
42_I	46_M	1.054	0.96
28_F	31_L	1.043	0.95
103_M	124_L	1.040	0.95
193_C	197_D	1.036	0.95
166_L	171_I	1.036	0.95
48_T	51_S	1.033	0.95
26_Y	31_L	1.029	0.95
119_I	122_S	1.029	0.95
20_R	24_A	1.023	0.95
54_S	59_S	1.015	0.94
174_K	200_E	1.015	0.94
79_E	198_Y	1.013	0.94
22_L	36_V	1.008	0.94
8_S	58_G	1.003	0.94
193_C	201_G	1.002	0.94
194_A	202_A	0.995	0.94
205_S	209_V	0.993	0.94
21_K	24_A	0.977	0.93
159_A	188_L	0.976	0.93
134_M	144_P	0.972	0.93
103_M	218_I	0.968	0.93
78_Y	81_L	0.964	0.93
99_S	215_T	0.952	0.92
82_H	85_R	0.948	0.92
134_M	137_G	0.941	0.92
107_T	120_A	0.932	0.92
190_T	201_G	0.932	0.92
66_L	131_P	0.931	0.92
32_N	36_V	0.927	0.91
183_T	211_C	0.921	0.91
98_G	183_T	0.918	0.91
95_C	211_C	0.905	0.90
187_A	205_S	0.903	0.90
147_S	151_V	0.898	0.90
186_H	189_G	0.895	0.90
26_Y	29_P	0.882	0.89
122_S	147_S	0.878	0.89
156_I	188_L	0.874	0.89
173_T	176_A	0.867	0.88
32_N	35_L	0.867	0.88
89_K	92_I	0.862	0.88
177_R	196_L	0.860	0.88
154_V	157_L	0.859	0.88
34_L	188_L	0.859	0.88
111_L	120_A	0.858	0.88
88_W	152_I	0.857	0.88
175_A	203_F	0.857	0.88
148_A	151_V	0.839	0.87
17_F	21_K	0.839	0.87
106_G	126_K	0.838	0.87
91_I	179_L	0.837	0.87
31_L	36_V	0.836	0.86
161_F	164_T	0.834	0.86
194_A	201_G	0.831	0.86
40_V	43_P	0.831	0.86
8_S	59_S	0.830	0.86
37_A	40_V	0.830	0.86
204_S	207_A	0.829	0.86
72_A	148_A	0.828	0.86
119_I	143_I	0.825	0.86
158_G	204_S	0.820	0.85
217_L	221_F	0.820	0.85
155_G	158_G	0.819	0.85
95_C	183_T	0.814	0.85
135_A	139_S	0.809	0.85
87_R	175_A	0.800	0.84
31_L	162_G	0.800	0.84
51_S	54_S	0.799	0.84
180_A	184_A	0.799	0.84
46_M	49_G	0.798	0.84
77_L	220_P	0.790	0.83
16_F	20_R	0.789	0.83
32_N	203_F	0.788	0.83
93_T	97_I	0.785	0.83
203_F	208_L	0.784	0.83
199_Q	213_I	0.782	0.83
94_I	203_F	0.772	0.82
158_G	186_H	0.772	0.82
52_Y	71_V	0.762	0.81
106_G	109_V	0.757	0.80
58_G	125_P	0.753	0.80
136_V	219_A	0.751	0.80
140_I	219_A	0.749	0.80
37_A	41_I	0.749	0.80
71_V	146_I	0.744	0.79
103_M	208_L	0.739	0.79
23_A	28_F	0.738	0.79
113_M	213_I	0.736	0.79
129_T	212_G	0.733	0.78
102_A	105_T	0.732	0.78
137_G	142_G	0.731	0.78
126_K	216_S	0.730	0.78
183_T	205_S	0.730	0.78
121_A	223_F	0.725	0.78
82_H	97_I	0.724	0.77
131_P	144_P	0.721	0.77
121_A	142_G	0.718	0.77
23_A	26_Y	0.713	0.76
73_L	126_K	0.712	0.76
122_S	137_G	0.708	0.76
130_T	151_V	0.707	0.76
24_A	27_K	0.706	0.76
49_G	167_N	0.704	0.75
83_Q	175_A	0.704	0.75
157_L	161_F	0.703	0.75
124_L	223_F	0.700	0.75
128_V	215_T	0.697	0.75
124_L	219_A	0.695	0.75
221_F	225_I	0.694	0.74
54_S	57_K	0.694	0.74
56_F	61_V	0.691	0.74
197_D	203_F	0.690	0.74
123_I	150_C	0.686	0.74
80_Q	199_Q	0.680	0.73
100_V	109_V	0.679	0.73
161_F	165_L	0.679	0.73
109_V	113_M	0.677	0.73
186_H	190_T	0.677	0.73
11_L	44_F	0.670	0.72
23_A	131_P	0.669	0.72
136_V	223_F	0.669	0.72
31_L	91_I	0.668	0.72
108_S	225_I	0.668	0.72
99_S	214_I	0.665	0.71
62_L	65_L	0.663	0.71
71_V	76_P	0.663	0.71
117_P	225_I	0.660	0.71
100_V	168_A	0.656	0.70
155_G	186_H	0.656	0.70
46_M	118_E	0.652	0.70
94_I	102_A	0.652	0.70
212_G	216_S	0.646	0.69
75_Y	102_A	0.646	0.69
52_Y	149_V	0.638	0.68
12_T	187_A	0.636	0.68
221_F	224_P	0.636	0.68
70_V	215_T	0.636	0.68
163_H	192_R	0.635	0.68
14_I	49_G	0.634	0.68
80_Q	134_M	0.633	0.68
139_S	209_V	0.631	0.67
130_T	134_M	0.628	0.67
100_V	104_V	0.627	0.67
29_P	32_N	0.623	0.66
83_Q	199_Q	0.620	0.66
154_V	186_H	0.620	0.66
21_K	161_F	0.620	0.66
32_N	38_M	0.614	0.65
94_I	141_G	0.614	0.65
166_L	180_A	0.614	0.65
96_F	210_L	0.613	0.65
35_L	160_V	0.611	0.65
163_H	167_N	0.609	0.65
18_A	225_I	0.609	0.65
166_L	170_R	0.608	0.64
83_Q	203_F	0.608	0.64
84_I	202_A	0.607	0.64
97_I	108_S	0.606	0.64
16_F	173_T	0.605	0.64
75_Y	206_L	0.602	0.64
74_A	128_V	0.602	0.64
49_G	153_F	0.601	0.64
95_C	207_A	0.601	0.64
216_S	219_A	0.599	0.63
21_K	27_K	0.599	0.63
87_R	173_T	0.594	0.63
158_G	190_T	0.591	0.62
82_H	172_R	0.587	0.62
67_Q	126_K	0.586	0.62
194_A	205_S	0.586	0.62
185_S	189_G	0.580	0.61
38_M	130_T	0.578	0.61
13_L	17_F	0.575	0.60
73_L	194_A	0.574	0.60
6_W	17_F	0.573	0.60
187_A	190_T	0.573	0.60
208_L	212_G	0.573	0.60
192_R	196_L	0.572	0.60
105_T	109_V	0.572	0.60
129_T	163_H	0.572	0.60
111_L	225_I	0.570	0.59
45_L	50_I	0.570	0.59
101_V	105_T	0.567	0.59
109_V	115_A	0.560	0.58
175_A	207_A	0.559	0.58
7_W	48_T	0.558	0.58
188_L	191_A	0.557	0.58
187_A	195_E	0.555	0.57
20_R	126_K	0.553	0.57
132_I	136_V	0.552	0.57
163_H	212_G	0.551	0.57
13_L	22_L	0.550	0.57
26_Y	188_L	0.547	0.56
192_R	198_Y	0.547	0.56
32_N	185_S	0.546	0.56
148_A	201_G	0.545	0.56
61_V	100_V	0.544	0.56
11_L	14_I	0.543	0.56
11_L	40_V	0.539	0.55
8_S	94_I	0.538	0.55
128_V	151_V	0.536	0.55
95_C	122_S	0.535	0.55
85_R	184_A	0.535	0.55
6_W	10_P	0.534	0.55
152_I	188_L	0.534	0.55
73_L	190_T	0.531	0.54
77_L	110_A	0.531	0.54
18_A	44_F	0.530	0.54
6_W	58_G	0.528	0.54
49_G	53_D	0.525	0.53
16_F	23_A	0.525	0.53
108_S	167_N	0.525	0.53
49_G	138_G	0.522	0.53
108_S	118_E	0.521	0.53
38_M	65_L	0.521	0.53
110_A	146_I	0.521	0.53
84_I	93_T	0.518	0.52
185_S	218_I	0.518	0.52
204_S	211_C	0.517	0.52
37_A	207_A	0.515	0.52
136_V	216_S	0.513	0.52
84_I	203_F	0.513	0.52
104_V	107_T	0.513	0.52
137_G	144_P	0.512	0.52
98_G	105_T	0.512	0.52
178_G	190_T	0.511	0.51
130_T	147_S	0.511	0.51
90_S	209_V	0.510	0.51
23_A	195_E	0.510	0.51
107_T	223_F	0.508	0.51
207_A	216_S	0.507	0.51
99_S	184_A	0.506	0.51
96_F	218_I	0.505	0.51
159_A	205_S	0.505	0.51
18_A	26_Y	0.504	0.50
102_A	180_A	0.504	0.50
123_I	191_A	0.503	0.50
54_S	168_A	0.500	0.50
159_A	191_A	0.500	0.50

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
3zuxA	1	0.7446	94.1	0.918	Contact Map
4n7wA	2	0.7229	91.9	0.924	Contact Map
4cz8A	2	0.9437	44.3	0.95	Contact Map
4bwzA	2	0.9134	37.6	0.952	Contact Map
2zy9A	2	0.7316	26.5	0.956	Contact Map
4czbA	2	0.9481	23.8	0.957	Contact Map
2a65A	2	0.3766	14.6	0.961	Contact Map
3nd0A	2	0.9048	12.8	0.962	Contact Map
4humA	1	0.697	7.2	0.966	Contact Map
2gfpA	2	0.8052	6.7	0.966	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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