YBHN - ECOLI - GREMLIN Contacts

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YBHN - Inner membrane protein YbhN

UniProt:	P75770	Sequences: MSKSHPRWRLAKKILTWLFFIAVIVLLVVYAKKVDWEEVWKVIRDYNRVALLSAVGLVVVSYLIYGCYDLLARFYCGHKLAKRQVMLVSFICYAFNLTLSTWVGGIGMRYRLYSRLGLPGSTITRIFSLSITTNWLGYILLAGIIFTAGVVELPDHWYVDQTTLRILGIGLLMIIAVYLWFCAFAKHRHMTIKGQKLVLPSWKFALAQMLISSVNWMVMGAIIWLLLGQSVNYFFVLGVLLVSSIAGVIVHIPAGIGVLEAVFIALLAGEHTSKGTIIAALLAYRVLYYFIPLLLALICYLLLESQAKKLRAKNEAAM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13670
Length:	318 (287)
Sequences:	3764 (3023)
Seq/√Len:	178.4

ECOLI - YBHN
BACSU - MPRF
HALSA - Q9HSJ6 Q9HS48

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
25_V	29_V	3.515	1.00
57_L	225_L	3.379	1.00
35_D	38_E	2.749	1.00
21_I	25_V	2.729	1.00
105_G	108_M	2.695	1.00
224_W	228_G	2.558	1.00
40_W	44_R	2.524	1.00
24_I	28_V	2.502	1.00
261_A	265_A	2.446	1.00
105_G	109_R	2.436	1.00
227_L	280_A	2.423	1.00
54_A	287_L	2.392	1.00
47_N	50_A	2.328	1.00
64_I	218_V	2.328	1.00
178_Y	182_C	2.260	1.00
119_P	122_T	2.209	1.00
67_C	211_I	2.202	1.00
134_N	216_W	2.202	1.00
60_V	218_V	2.174	1.00
106_I	109_R	2.174	1.00
84_Q	116_L	2.168	1.00
70_L	74_F	2.138	1.00
50_A	225_L	2.109	1.00
99_L	104_G	2.068	1.00
53_S	225_L	2.067	1.00
277_I	281_L	2.064	1.00
232_N	235_F	2.018	1.00
260_E	285_R	2.005	1.00
86_M	90_F	1.946	1.00
105_G	113_Y	1.940	1.00
253_P	285_R	1.919	1.00
81_A	84_Q	1.861	1.00
243_S	247_G	1.837	1.00
68_Y	134_N	1.833	1.00
68_Y	130_S	1.824	1.00
66_G	86_M	1.818	1.00
65_Y	134_N	1.814	1.00
64_I	211_I	1.812	1.00
259_L	285_R	1.808	1.00
20_F	24_I	1.789	1.00
101_T	104_G	1.771	1.00
166_I	170_G	1.702	1.00
64_I	214_V	1.699	1.00
52_L	56_G	1.697	1.00
54_A	226_L	1.671	1.00
203_K	207_A	1.661	1.00
49_V	53_S	1.645	1.00
57_L	218_V	1.644	1.00
69_D	126_I	1.640	1.00
40_W	43_I	1.635	1.00
162_T	166_I	1.631	1.00
90_F	299_C	1.625	1.00
50_A	53_S	1.614	1.00
78_H	118_L	1.612	1.00
63_L	82_K	1.597	1.00
145_I	241_L	1.567	1.00
250_V	258_V	1.563	1.00
23_V	27_L	1.548	1.00
281_L	285_R	1.535	1.00
29_V	32_K	1.535	1.00
55_V	287_L	1.530	1.00
66_G	85_V	1.514	1.00
106_I	131_I	1.498	1.00
71_L	207_A	1.497	1.00
80_L	85_V	1.492	1.00
16_T	20_F	1.486	1.00
165_R	169_I	1.474	1.00
131_I	134_N	1.467	1.00
259_L	284_Y	1.467	1.00
294_L	298_I	1.450	1.00
223_I	263_F	1.442	1.00
82_K	86_M	1.439	1.00
273_S	276_T	1.427	1.00
25_V	28_V	1.426	1.00
58_V	287_L	1.425	1.00
71_L	211_I	1.411	1.00
25_V	30_Y	1.410	1.00
286_V	290_F	1.404	1.00
95_F	99_L	1.387	1.00
298_I	302_L	1.382	1.00
19_F	23_V	1.377	1.00
66_G	82_K	1.374	1.00
46_Y	229_Q	1.365	1.00
137_G	212_S	1.364	1.00
94_A	297_L	1.359	1.00
23_V	26_L	1.355	1.00
67_C	70_L	1.340	1.00
239_V	266_L	1.334	1.00
207_A	210_L	1.326	1.00
68_Y	212_S	1.321	1.00
134_N	212_S	1.309	1.00
68_Y	131_I	1.309	1.00
46_Y	283_A	1.306	1.00
48_R	52_L	1.304	1.00
54_A	222_I	1.300	1.00
56_G	60_V	1.288	1.00
46_Y	50_A	1.285	1.00
97_L	293_L	1.285	1.00
73_R	118_L	1.277	1.00
92_C	109_R	1.276	1.00
243_S	262_V	1.272	1.00
130_S	134_N	1.254	1.00
103_V	106_I	1.253	1.00
163_T	167_L	1.250	1.00
246_A	262_V	1.235	1.00
83_R	87_L	1.224	1.00
18_L	25_V	1.214	1.00
264_I	278_I	1.209	1.00
180_W	184_F	1.203	1.00
28_V	31_A	1.197	1.00
71_L	204_F	1.193	1.00
173_M	176_A	1.190	1.00
219_M	288_Y	1.189	1.00
240_L	244_S	1.182	1.00
104_G	109_R	1.182	1.00
247_G	255_G	1.161	1.00
94_A	296_A	1.154	1.00
16_T	19_F	1.149	1.00
72_A	208_Q	1.146	1.00
180_W	183_A	1.145	1.00
108_M	113_Y	1.139	1.00
170_G	174_I	1.129	1.00
79_K	83_R	1.115	1.00
96_N	105_G	1.107	1.00
168_G	172_L	1.095	1.00
164_L	167_L	1.095	1.00
162_T	165_R	1.089	1.00
265_A	268_A	1.085	1.00
50_A	54_A	1.075	1.00
134_N	215_N	1.072	1.00
105_G	110_Y	1.067	1.00
102_W	105_G	1.057	1.00
221_A	233_Y	1.055	1.00
225_L	229_Q	1.050	1.00
272_T	277_I	1.048	1.00
41_K	44_R	1.044	1.00
99_L	107_G	1.037	1.00
13_K	16_T	1.034	1.00
22_A	26_L	1.032	0.99
224_W	233_Y	1.031	0.99
78_H	122_T	1.030	0.99
91_I	95_F	1.029	0.99
62_Y	90_F	1.029	0.99
253_P	281_L	1.025	0.99
220_G	237_L	1.019	0.99
251_H	258_V	1.018	0.99
264_I	277_I	1.017	0.99
28_V	32_K	1.015	0.99
263_F	281_L	1.013	0.99
210_L	214_V	1.007	0.99
224_W	236_V	1.000	0.99
55_V	291_I	0.998	0.99
262_V	265_A	0.997	0.99
53_S	56_G	0.989	0.99
177_V	180_W	0.986	0.99
14_I	18_L	0.983	0.99
94_A	100_S	0.981	0.99
184_F	189_H	0.980	0.99
285_R	288_Y	0.977	0.99
58_V	219_M	0.977	0.99
65_Y	215_N	0.967	0.99
17_W	21_I	0.966	0.99
38_E	275_G	0.965	0.99
109_R	113_Y	0.963	0.99
78_H	119_P	0.961	0.99
38_E	41_K	0.958	0.99
201_S	204_F	0.947	0.99
70_L	85_V	0.945	0.99
169_I	173_M	0.944	0.99
253_P	259_L	0.938	0.99
69_D	284_Y	0.938	0.99
190_M	194_G	0.935	0.99
260_E	281_L	0.934	0.99
92_C	131_I	0.932	0.99
108_M	112_L	0.932	0.99
263_F	267_L	0.931	0.99
54_A	229_Q	0.925	0.99
243_S	255_G	0.924	0.99
89_S	215_N	0.920	0.99
240_L	243_S	0.914	0.99
205_A	208_Q	0.909	0.99
220_G	224_W	0.903	0.99
88_V	112_L	0.903	0.99
202_W	206_L	0.899	0.99
222_I	284_Y	0.897	0.99
263_F	280_A	0.896	0.99
69_D	109_R	0.891	0.99
167_L	171_L	0.891	0.99
70_L	82_K	0.889	0.98
168_G	171_L	0.882	0.98
18_L	22_A	0.881	0.98
43_I	283_A	0.875	0.98
65_Y	131_I	0.874	0.98
183_A	189_H	0.871	0.98
87_L	302_L	0.871	0.98
206_L	210_L	0.869	0.98
179_L	182_C	0.860	0.98
223_I	280_A	0.857	0.98
175_I	184_F	0.856	0.98
62_Y	93_Y	0.854	0.98
284_Y	288_Y	0.853	0.98
50_A	228_G	0.849	0.98
227_L	272_T	0.849	0.98
138_Y	142_A	0.843	0.98
22_A	27_L	0.833	0.98
38_E	42_V	0.833	0.98
85_V	89_S	0.829	0.98
68_Y	215_N	0.829	0.98
141_L	217_M	0.829	0.98
184_F	188_R	0.825	0.98
165_R	168_G	0.824	0.98
217_M	221_A	0.822	0.97
133_T	208_Q	0.822	0.97
58_V	222_I	0.821	0.97
243_S	263_F	0.820	0.97
23_V	31_A	0.820	0.97
175_I	179_L	0.819	0.97
145_I	238_G	0.817	0.97
23_V	28_V	0.810	0.97
27_L	30_Y	0.808	0.97
105_G	131_I	0.803	0.97
252_I	281_L	0.802	0.97
252_I	262_V	0.801	0.97
141_L	241_L	0.801	0.97
114_S	120_G	0.801	0.97
69_D	106_I	0.800	0.97
26_L	29_V	0.797	0.97
89_S	134_N	0.794	0.97
127_F	131_I	0.788	0.97
239_V	243_S	0.788	0.97
73_R	126_I	0.788	0.97
250_V	253_P	0.783	0.97
110_Y	113_Y	0.780	0.97
239_V	267_L	0.779	0.97
99_L	103_V	0.776	0.96
106_I	113_Y	0.775	0.96
166_I	169_I	0.775	0.96
247_G	250_V	0.772	0.96
252_I	258_V	0.763	0.96
215_N	219_M	0.762	0.96
243_S	258_V	0.762	0.96
256_I	284_Y	0.761	0.96
226_L	229_Q	0.760	0.96
74_F	79_K	0.757	0.96
212_S	220_G	0.755	0.96
120_G	123_I	0.749	0.96
27_L	31_A	0.748	0.96
173_M	177_V	0.744	0.95
57_L	60_V	0.743	0.95
32_K	35_D	0.741	0.95
221_A	224_W	0.741	0.95
102_W	106_I	0.734	0.95
65_Y	69_D	0.734	0.95
138_Y	216_W	0.732	0.95
97_L	292_P	0.728	0.95
46_Y	54_A	0.724	0.95
90_F	295_L	0.723	0.95
26_L	30_Y	0.722	0.95
234_F	238_G	0.718	0.95
13_K	210_L	0.718	0.95
55_V	157_W	0.717	0.95
100_S	215_N	0.716	0.94
93_Y	284_Y	0.716	0.94
149_G	153_L	0.715	0.94
19_F	22_A	0.714	0.94
91_I	112_L	0.714	0.94
144_I	148_A	0.713	0.94
216_W	219_M	0.711	0.94
171_L	174_I	0.710	0.94
65_Y	89_S	0.707	0.94
15_L	140_L	0.706	0.94
97_L	289_Y	0.706	0.94
175_I	178_Y	0.703	0.94
61_S	97_L	0.703	0.94
50_A	229_Q	0.702	0.94
96_N	106_I	0.699	0.94
259_L	281_L	0.696	0.94
221_A	225_L	0.696	0.94
48_R	51_L	0.695	0.94
120_G	124_T	0.694	0.93
41_K	45_D	0.694	0.93
109_R	131_I	0.694	0.93
174_I	178_Y	0.694	0.93
69_D	131_I	0.692	0.93
100_S	104_G	0.691	0.93
195_Q	198_V	0.690	0.93
69_D	281_L	0.688	0.93
168_G	183_A	0.687	0.93
297_L	301_L	0.682	0.93
130_S	252_I	0.682	0.93
140_L	209_M	0.681	0.93
19_F	29_V	0.680	0.93
113_Y	127_F	0.677	0.93
126_I	290_F	0.677	0.93
68_Y	109_R	0.676	0.93
52_L	151_V	0.676	0.93
299_C	303_L	0.676	0.93
210_L	217_M	0.673	0.92
109_R	263_F	0.672	0.92
302_L	305_S	0.672	0.92
65_Y	216_W	0.671	0.92
98_T	254_A	0.670	0.92
110_Y	127_F	0.669	0.92
98_T	293_L	0.668	0.92
252_I	285_R	0.665	0.92
57_L	221_A	0.665	0.92
276_T	279_A	0.664	0.92
32_K	179_L	0.663	0.92
264_I	281_L	0.662	0.92
102_W	108_M	0.661	0.92
88_V	92_C	0.661	0.92
167_L	184_F	0.659	0.92
208_Q	281_L	0.659	0.92
118_L	122_T	0.659	0.92
212_S	216_W	0.657	0.92
288_Y	292_P	0.655	0.91
168_G	184_F	0.654	0.91
49_V	52_L	0.653	0.91
14_I	56_G	0.652	0.91
173_M	180_W	0.651	0.91
20_F	23_V	0.650	0.91
197_L	200_P	0.647	0.91
131_I	250_V	0.646	0.91
146_F	150_V	0.644	0.91
167_L	179_L	0.643	0.91
179_L	183_A	0.643	0.91
25_V	32_K	0.641	0.91
249_I	289_Y	0.641	0.91
96_N	104_G	0.638	0.90
168_G	174_I	0.636	0.90
285_R	289_Y	0.633	0.90
101_T	109_R	0.633	0.90
106_I	110_Y	0.633	0.90
65_Y	130_S	0.630	0.90
37_E	42_V	0.627	0.90
227_L	236_V	0.626	0.89
295_L	299_C	0.622	0.89
107_G	282_L	0.621	0.89
95_F	108_M	0.621	0.89
113_Y	123_I	0.621	0.89
254_A	259_L	0.620	0.89
47_N	52_L	0.618	0.89
254_A	289_Y	0.618	0.89
91_I	299_C	0.616	0.89
103_V	109_R	0.613	0.88
135_W	219_M	0.612	0.88
170_G	178_Y	0.612	0.88
233_Y	237_L	0.612	0.88
176_A	180_W	0.610	0.88
202_W	232_N	0.608	0.88
143_G	147_T	0.608	0.88
292_P	295_L	0.606	0.88
72_A	130_S	0.605	0.88
290_F	294_L	0.605	0.88
20_F	25_V	0.603	0.88
194_G	197_L	0.600	0.87
145_I	149_G	0.597	0.87
193_K	197_L	0.594	0.87
256_I	285_R	0.593	0.87
100_S	250_V	0.593	0.87
133_T	212_S	0.591	0.87
223_I	244_S	0.589	0.86
213_S	217_M	0.589	0.86
20_F	27_L	0.589	0.86
98_T	104_G	0.588	0.86
177_V	181_F	0.579	0.86
244_S	247_G	0.578	0.85
75_Y	201_S	0.576	0.85
263_F	285_R	0.575	0.85
249_I	300_Y	0.575	0.85
62_Y	288_Y	0.567	0.84
166_I	198_V	0.566	0.84
104_G	263_F	0.566	0.84
156_H	159_V	0.565	0.84
219_M	222_I	0.563	0.84
76_C	122_T	0.563	0.84
58_V	62_Y	0.561	0.84
264_I	268_A	0.560	0.84
36_W	40_W	0.559	0.83
212_S	215_N	0.555	0.83
165_R	181_F	0.555	0.83
246_A	266_L	0.553	0.83
127_F	215_N	0.552	0.83
168_G	176_A	0.552	0.83
134_N	138_Y	0.550	0.82
92_C	96_N	0.549	0.82
53_S	57_L	0.549	0.82
193_K	198_V	0.548	0.82
72_A	220_G	0.548	0.82
244_S	263_F	0.547	0.82
96_N	259_L	0.547	0.82
218_V	222_I	0.547	0.82
62_Y	222_I	0.546	0.82
92_C	105_G	0.544	0.82
88_V	109_R	0.542	0.82
44_R	48_R	0.541	0.81
102_W	109_R	0.541	0.81
267_L	277_I	0.540	0.81
168_G	181_F	0.540	0.81
141_L	213_S	0.539	0.81
100_S	251_H	0.538	0.81
169_I	178_Y	0.537	0.81
177_V	183_A	0.536	0.81
88_V	111_R	0.533	0.81
17_W	20_F	0.532	0.80
48_R	301_L	0.530	0.80
126_I	260_E	0.530	0.80
107_G	289_Y	0.529	0.80
218_V	221_A	0.528	0.80
176_A	184_F	0.528	0.80
16_T	30_Y	0.524	0.79
16_T	24_I	0.524	0.79
55_V	59_V	0.524	0.79
237_L	241_L	0.523	0.79
163_T	166_I	0.522	0.79
69_D	130_S	0.522	0.79
65_Y	102_W	0.517	0.78
212_S	223_I	0.516	0.78
96_N	131_I	0.513	0.78
204_F	208_Q	0.512	0.78
37_E	40_W	0.508	0.77
12_K	16_T	0.507	0.77
59_V	86_M	0.507	0.77
89_S	292_P	0.506	0.77
15_L	40_W	0.506	0.77
292_P	296_A	0.505	0.77
173_M	228_G	0.505	0.77
109_R	137_G	0.500	0.76
58_V	284_Y	0.500	0.76
135_W	148_A	0.500	0.76

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	0.8648	60.8	0.932	Contact Map
2rddB	1	0.1069	39	0.94	Contact Map
4n7wA	2	0.8616	21.8	0.947	Contact Map
2zy9A	2	0.4245	10.8	0.954	Contact Map
3wdoA	1	0.9371	7.4	0.958	Contact Map
2kluA	1	0.1384	6.4	0.959	Contact Map
2l2tA	2	0.1352	5.9	0.959	Contact Map
3qe7A	2	0.7233	5.8	0.959	Contact Map
2kncA	1	0.1541	5.6	0.96	Contact Map
4u9nA	2	0.4277	5.5	0.96	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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