HCR - ECOLI - GREMLIN Contacts

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HCR - NADH oxidoreductase HCR

UniProt:	P75824	Sequences: MTMPTNQCPWRMQVHHITQETPDVWTISLICHDYYPYRAGQYALVSVRNSAETLRAYTISSTPGVSEYITLTVRRIDDGVGSQWLTRDVKRGDYLWLSDAMGEFTCDDKAEDKFLLLAAGCGVTPIMSMRRWLAKNRPQADVRVIYNVRTPQDVIFADEWRNYPVTLVAENNVTEGFIAGRLTRELLAGVPDLASRTVMTCGPAPYMDWVEQEVKALGVTRFFKEKFFTPVAEAATSGLKFTKLQPAREFYAPVGTTLLEALESNNVPVVAACRAGVCGCCKTKVVSGEYTVSSTMTLTDAEIAEGYVLACSCHPQGDLVLA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13691
Length:	322 (303)
Sequences:	5383 (3931)
Seq/√Len:	225.8

ECOLI - HCR PAAE YEAX
BACSU - PYRK HMP

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
256_T	264_S	4.073	1.00
113_K	141_D	3.439	1.00
75_R	87_R	3.227	1.00
20_E	26_T	3.225	1.00
15_H	30_I	3.126	1.00
12_M	97_L	2.962	1.00
263_E	274_R	2.762	1.00
14_V	89_V	2.754	1.00
253_P	256_T	2.728	1.00
11_R	94_Y	2.634	1.00
27_I	85_L	2.598	1.00
131_R	159_E	2.581	1.00
90_K	93_D	2.558	1.00
17_I	25_W	2.537	1.00
250_F	261_A	2.483	1.00
240_K	251_Y	2.477	1.00
132_W	136_N	2.459	1.00
283_T	310_A	2.398	1.00
259_L	271_A	2.396	1.00
26_T	70_T	2.393	1.00
123_V	144_V	2.312	1.00
19_Q	25_W	2.312	1.00
289_E	316_Q	2.297	1.00
16_H	91_R	2.295	1.00
148_V	154_V	2.247	1.00
240_K	249_E	2.216	1.00
285_V	308_V	2.159	1.00
13_Q	94_Y	2.152	1.00
13_Q	30_I	2.127	1.00
75_R	83_Q	2.121	1.00
11_R	96_W	2.105	1.00
204_A	208_D	2.101	1.00
197_T	223_F	2.039	1.00
241_F	258_L	2.028	1.00
118_A	146_Y	1.962	1.00
85_L	89_V	1.934	1.00
28_S	68_Y	1.914	1.00
45_V	71_L	1.908	1.00
200_T	210_V	1.886	1.00
77_D	80_V	1.871	1.00
117_L	206_Y	1.814	1.00
258_L	308_V	1.761	1.00
256_T	261_A	1.742	1.00
17_I	91_R	1.735	1.00
44_L	56_A	1.722	1.00
113_K	143_R	1.707	1.00
16_H	28_S	1.704	1.00
150_T	153_D	1.702	1.00
285_V	290_Y	1.700	1.00
242_T	249_E	1.673	1.00
299_T	302_E	1.629	1.00
43_A	97_L	1.625	1.00
26_T	156_F	1.619	1.00
83_Q	87_R	1.619	1.00
116_L	130_R	1.609	1.00
243_K	262_L	1.605	1.00
260_E	274_R	1.598	1.00
147_N	206_Y	1.593	1.00
119_A	206_Y	1.593	1.00
157_A	161_R	1.592	1.00
22_P	152_Q	1.590	1.00
258_L	310_A	1.573	1.00
28_S	70_T	1.560	1.00
118_A	126_I	1.559	1.00
117_L	210_V	1.551	1.00
46_S	96_W	1.513	1.00
243_K	246_P	1.505	1.00
47_V	81_G	1.499	1.00
18_T	26_T	1.497	1.00
300_D	304_A	1.481	1.00
115_L	198_V	1.462	1.00
250_F	265_N	1.458	1.00
211_E	226_K	1.439	1.00
89_V	93_D	1.431	1.00
34_Y	69_I	1.428	1.00
45_V	85_L	1.427	1.00
282_K	307_Y	1.426	1.00
113_K	196_R	1.423	1.00
151_P	157_A	1.415	1.00
60_S	72_T	1.409	1.00
289_E	317_G	1.395	1.00
253_P	261_A	1.391	1.00
23_D	153_D	1.388	1.00
89_V	95_L	1.385	1.00
118_A	144_V	1.384	1.00
14_V	29_L	1.368	1.00
211_E	224_K	1.356	1.00
269_V	310_A	1.343	1.00
73_V	85_L	1.332	1.00
111_E	114_F	1.311	1.00
106_C	133_L	1.294	1.00
263_E	271_A	1.287	1.00
208_D	212_Q	1.237	1.00
282_K	309_L	1.226	1.00
116_L	142_V	1.217	1.00
17_I	27_I	1.212	1.00
20_E	156_F	1.201	1.00
72_T	155_I	1.201	1.00
291_T	316_Q	1.196	1.00
84_W	88_D	1.195	1.00
192_D	196_R	1.191	1.00
17_I	90_K	1.191	1.00
12_M	34_Y	1.190	1.00
24_V	155_I	1.190	1.00
198_V	214_V	1.184	1.00
32_H	94_Y	1.180	1.00
242_T	247_A	1.177	1.00
13_Q	32_H	1.176	1.00
130_R	142_V	1.167	1.00
200_T	207_M	1.161	1.00
252_A	261_A	1.157	1.00
12_M	29_L	1.156	1.00
290_Y	315_P	1.154	1.00
37_Y	59_I	1.151	1.00
211_E	215_K	1.149	1.00
207_M	224_K	1.147	1.00
147_N	182_L	1.146	1.00
12_M	32_H	1.142	1.00
260_E	263_E	1.140	1.00
49_N	84_W	1.135	1.00
151_P	178_I	1.134	1.00
243_K	250_F	1.133	1.00
74_R	153_D	1.132	1.00
37_Y	61_S	1.121	1.00
26_T	72_T	1.117	1.00
39_A	132_W	1.105	1.00
154_V	169_A	1.104	1.00
14_V	27_I	1.101	1.00
27_I	89_V	1.095	1.00
211_E	222_F	1.087	1.00
148_V	153_D	1.083	1.00
176_G	181_R	1.079	1.00
114_F	140_A	1.077	1.00
151_P	161_R	1.064	1.00
27_I	73_V	1.062	1.00
186_L	189_G	1.057	1.00
290_Y	313_C	1.052	1.00
29_L	71_L	1.051	1.00
198_V	219_V	1.050	1.00
154_V	157_A	1.047	1.00
127_M	156_F	1.045	1.00
168_V	171_N	1.040	1.00
298_L	302_E	1.038	1.00
212_Q	216_A	1.036	1.00
184_R	188_A	1.034	1.00
257_T	260_E	1.034	1.00
293_S	314_H	1.025	1.00
62_T	131_R	1.024	1.00
209_W	213_E	1.023	1.00
59_I	69_I	1.017	1.00
15_H	68_Y	1.016	1.00
47_V	53_T	1.014	1.00
82_S	86_T	1.014	1.00
238_G	251_Y	1.006	1.00
18_T	28_S	1.000	1.00
298_L	306_G	0.994	1.00
262_L	269_V	0.994	1.00
106_C	129_M	0.982	1.00
261_A	265_N	0.975	1.00
188_A	217_L	0.969	1.00
126_I	144_V	0.964	1.00
70_T	159_E	0.957	1.00
45_V	95_L	0.956	1.00
185_E	188_A	0.955	1.00
23_D	74_R	0.951	1.00
187_L	190_V	0.947	1.00
271_A	274_R	0.944	1.00
24_V	121_C	0.943	1.00
284_K	307_Y	0.942	1.00
12_M	95_L	0.942	1.00
176_G	180_G	0.941	1.00
181_R	205_P	0.938	1.00
240_K	318_D	0.937	1.00
53_T	80_V	0.929	1.00
12_M	31_C	0.927	1.00
245_Q	248_R	0.926	1.00
184_R	213_E	0.926	1.00
253_P	264_S	0.925	1.00
296_M	309_L	0.915	0.99
200_T	211_E	0.915	0.99
284_K	306_G	0.912	0.99
302_E	305_E	0.908	0.99
15_H	28_S	0.907	0.99
145_I	190_V	0.906	0.99
183_T	186_L	0.903	0.99
214_V	222_F	0.903	0.99
134_A	142_V	0.902	0.99
25_W	86_T	0.896	0.99
291_T	314_H	0.894	0.99
130_R	144_V	0.892	0.99
47_V	84_W	0.892	0.99
184_R	216_A	0.891	0.99
108_D	132_W	0.889	0.99
200_T	222_F	0.886	0.99
175_E	178_I	0.882	0.99
195_S	221_R	0.880	0.99
61_S	70_T	0.871	0.99
30_I	68_Y	0.865	0.99
57_Y	82_S	0.863	0.99
112_D	197_T	0.862	0.99
262_L	310_A	0.862	0.99
175_E	179_A	0.860	0.99
209_W	212_Q	0.859	0.99
243_K	248_R	0.857	0.99
212_Q	215_K	0.854	0.99
207_M	226_K	0.853	0.99
21_T	153_D	0.849	0.99
177_F	180_G	0.848	0.99
116_L	133_L	0.843	0.99
259_L	263_E	0.842	0.99
38_R	105_T	0.837	0.99
268_P	271_A	0.837	0.99
61_S	65_V	0.836	0.99
158_D	162_N	0.836	0.99
48_R	84_W	0.831	0.99
37_Y	128_S	0.830	0.99
116_L	129_M	0.827	0.99
46_S	54_L	0.826	0.99
290_Y	317_G	0.825	0.99
127_M	131_R	0.820	0.99
197_T	221_R	0.819	0.99
208_D	226_K	0.819	0.99
248_R	267_V	0.818	0.99
248_R	265_N	0.814	0.99
10_W	35_Y	0.814	0.99
112_D	195_S	0.813	0.99
116_L	126_I	0.812	0.99
31_C	34_Y	0.812	0.99
113_K	193_L	0.807	0.99
108_D	136_N	0.805	0.99
177_F	181_R	0.805	0.99
165_V	170_E	0.803	0.99
44_L	101_M	0.802	0.99
193_L	196_R	0.799	0.99
17_I	93_D	0.799	0.99
176_G	179_A	0.796	0.99
23_D	75_R	0.795	0.99
214_V	219_V	0.793	0.99
117_L	187_L	0.793	0.99
263_E	268_P	0.792	0.99
107_D	110_A	0.787	0.98
41_Q	102_G	0.785	0.98
114_F	197_T	0.784	0.98
130_R	134_A	0.782	0.98
106_C	114_F	0.778	0.98
62_T	135_K	0.775	0.98
158_D	161_R	0.774	0.98
176_G	182_L	0.773	0.98
134_A	163_Y	0.773	0.98
217_L	220_T	0.771	0.98
47_V	85_L	0.771	0.98
237_S	318_D	0.770	0.98
205_P	209_W	0.770	0.98
10_W	31_C	0.768	0.98
146_Y	155_I	0.767	0.98
60_S	70_T	0.766	0.98
239_L	317_G	0.766	0.98
232_A	235_A	0.765	0.98
208_D	211_E	0.758	0.98
167_L	170_E	0.753	0.98
117_L	145_I	0.748	0.98
76_I	83_Q	0.744	0.98
256_T	260_E	0.741	0.98
46_S	98_S	0.738	0.98
298_L	303_I	0.732	0.98
213_E	216_A	0.732	0.98
119_A	205_P	0.732	0.98
302_E	306_G	0.730	0.98
44_L	54_L	0.729	0.97
164_P	167_L	0.727	0.97
297_T	302_E	0.721	0.97
22_P	153_D	0.720	0.97
200_T	224_K	0.720	0.97
69_I	97_L	0.719	0.97
63_P	66_S	0.719	0.97
272_A	280_C	0.718	0.97
43_A	59_I	0.718	0.97
277_V	280_C	0.718	0.97
35_Y	99_D	0.716	0.97
303_I	306_G	0.714	0.97
271_A	277_V	0.710	0.97
244_L	286_V	0.710	0.97
119_A	203_P	0.710	0.97
169_A	173_V	0.706	0.97
119_A	147_N	0.706	0.97
65_V	68_Y	0.704	0.97
104_F	129_M	0.701	0.97
147_N	176_G	0.700	0.97
151_P	177_F	0.699	0.97
29_L	95_L	0.696	0.97
123_V	146_Y	0.690	0.97
24_V	72_T	0.689	0.96
38_R	102_G	0.689	0.96
70_T	131_R	0.688	0.96
174_T	179_A	0.688	0.96
38_R	41_Q	0.686	0.96
186_L	190_V	0.684	0.96
10_W	99_D	0.682	0.96
74_R	155_I	0.679	0.96
62_T	65_V	0.677	0.96
173_V	179_A	0.668	0.96
262_L	267_V	0.667	0.96
259_L	269_V	0.664	0.96
251_Y	254_V	0.663	0.96
204_A	226_K	0.661	0.96
290_Y	308_V	0.661	0.96
147_N	170_E	0.660	0.96
258_L	283_T	0.657	0.95
45_V	97_L	0.656	0.95
136_N	140_A	0.656	0.95
43_A	69_I	0.655	0.95
252_A	258_L	0.654	0.95
173_V	176_G	0.653	0.95
283_T	308_V	0.652	0.95
294_S	297_T	0.651	0.95
76_I	79_G	0.649	0.95
44_L	98_S	0.648	0.95
12_M	43_A	0.647	0.95
178_I	184_R	0.645	0.95
55_R	129_M	0.644	0.95
119_A	181_R	0.643	0.95
77_D	83_Q	0.642	0.95
53_T	81_G	0.640	0.95
58_T	126_I	0.640	0.95
205_P	208_D	0.637	0.95
301_A	304_A	0.637	0.95
43_A	71_L	0.637	0.95
230_P	234_A	0.633	0.94
64_G	135_K	0.631	0.94
208_D	224_K	0.630	0.94
159_E	162_N	0.630	0.94
315_P	318_D	0.629	0.94
207_M	210_V	0.626	0.94
213_E	217_L	0.625	0.94
307_Y	310_A	0.624	0.94
63_P	132_W	0.624	0.94
308_V	313_C	0.621	0.94
36_P	66_S	0.621	0.94
133_L	140_A	0.620	0.94
261_A	264_S	0.619	0.94
198_V	210_V	0.618	0.94
258_L	262_L	0.616	0.94
129_M	199_M	0.613	0.93
112_D	196_R	0.611	0.93
192_D	195_S	0.606	0.93
167_L	171_N	0.603	0.93
257_T	314_H	0.601	0.93
170_E	173_V	0.597	0.92
210_V	213_E	0.597	0.92
175_E	180_G	0.597	0.92
181_R	209_W	0.596	0.92
145_I	186_L	0.596	0.92
126_I	130_R	0.595	0.92
75_R	86_T	0.595	0.92
131_R	163_Y	0.593	0.92
119_A	209_W	0.592	0.92
134_A	166_T	0.592	0.92
144_V	160_W	0.592	0.92
257_T	312_S	0.589	0.92
297_T	301_A	0.589	0.92
270_V	310_A	0.588	0.92
114_F	133_L	0.587	0.92
35_Y	69_I	0.587	0.92
242_T	287_S	0.587	0.92
309_L	312_S	0.587	0.92
49_N	53_T	0.586	0.92
130_R	163_Y	0.586	0.92
14_V	17_I	0.585	0.92
290_Y	305_E	0.584	0.92
114_F	199_M	0.583	0.92
88_D	93_D	0.582	0.92
177_F	183_T	0.582	0.92
113_K	195_S	0.579	0.91
20_E	72_T	0.575	0.91
297_T	303_I	0.575	0.91
113_K	140_A	0.574	0.91
260_E	264_S	0.573	0.91
38_R	108_D	0.571	0.91
239_L	247_A	0.569	0.91
115_L	196_R	0.568	0.91
292_V	296_M	0.566	0.90
291_T	313_C	0.566	0.90
56_A	101_M	0.565	0.90
173_V	178_I	0.565	0.90
21_T	155_I	0.563	0.90
37_Y	65_V	0.563	0.90
42_Y	292_V	0.562	0.90
118_A	148_V	0.562	0.90
301_A	305_E	0.561	0.90
293_S	313_C	0.561	0.90
60_S	156_F	0.560	0.90
275_A	295_T	0.558	0.90
165_V	168_V	0.557	0.90
251_Y	265_N	0.557	0.90
282_K	302_E	0.551	0.89
248_R	262_L	0.551	0.89
108_D	140_A	0.550	0.89
177_F	182_L	0.550	0.89
304_A	307_Y	0.549	0.89
148_V	169_A	0.547	0.89
156_F	160_W	0.545	0.89
292_V	303_I	0.545	0.89
141_D	196_R	0.544	0.89
32_H	97_L	0.544	0.89
23_D	149_R	0.543	0.89
21_T	24_V	0.543	0.89
280_C	309_L	0.542	0.88
39_A	63_P	0.541	0.88
169_A	175_E	0.540	0.88
277_V	295_T	0.539	0.88
241_F	250_F	0.538	0.88
112_D	140_A	0.535	0.88
106_C	199_M	0.534	0.88
115_L	145_I	0.534	0.88
206_Y	209_W	0.534	0.88
232_A	236_T	0.533	0.88
25_W	73_V	0.532	0.87
292_V	312_S	0.530	0.87
230_P	295_T	0.528	0.87
283_T	286_V	0.526	0.87
180_G	183_T	0.522	0.87
192_D	217_L	0.520	0.86
292_V	313_C	0.520	0.86
237_S	254_V	0.520	0.86
239_L	314_H	0.519	0.86
60_S	128_S	0.518	0.86
64_G	136_N	0.517	0.86
174_T	178_I	0.517	0.86
282_K	296_M	0.516	0.86
71_L	75_R	0.515	0.86
19_Q	23_D	0.515	0.86
300_D	303_I	0.515	0.86
75_R	82_S	0.513	0.86
275_A	280_C	0.512	0.85
218_G	221_R	0.512	0.85
229_T	277_V	0.512	0.85
129_M	148_V	0.511	0.85
83_Q	88_D	0.511	0.85
132_W	135_K	0.511	0.85
178_I	186_L	0.510	0.85
169_A	174_T	0.510	0.85
25_W	85_L	0.508	0.85
238_G	254_V	0.507	0.85
128_S	131_R	0.507	0.85
188_A	216_A	0.506	0.85
107_D	223_F	0.504	0.85
250_F	262_L	0.503	0.84
146_Y	154_V	0.503	0.84
15_H	91_R	0.502	0.84
121_C	155_I	0.502	0.84
160_W	163_Y	0.502	0.84
110_A	140_A	0.501	0.84
277_V	296_M	0.501	0.84
115_L	143_R	0.500	0.84

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
2piaA	1	0.9658	100	0.307	Contact Map
1gvhA	3	0.7205	100	0.499	Contact Map
1cqxA	2	0.7205	100	0.504	Contact Map
1ep3B	2	0.7826	100	0.515	Contact Map
4g1vA	3	0.7267	100	0.524	Contact Map
1krhA	1	0.705	100	0.525	Contact Map
4ylfA	1	0.7702	100	0.529	Contact Map
1tvcA	1	0.7205	100	0.53	Contact Map
1qfjA	1	0.6677	100	0.538	Contact Map
4eh1A	2	0.6801	100	0.543	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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