YDIR - ECOLI - GREMLIN Contacts

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YDIR - Putative electron transfer flavoprotein subunit YdiR

UniProt:	P77378	Sequences: MSQLNSVWVFSDNPERYAELFGGAQQWGQQVYAIVQNTDQAQAVMPYGPKCLYVLAQNDALQRTENYAESIAALLKDKHPAMLLLAATKRGKALAARLSVQLNAALVNDATAVDIVDGHICAEHRMYGGLAFAQEKINSPLAIITLAPGVQEPCTSDTSHQCPTETVPYVAPRHEILCRERRAKAASSVDLSKAKRVVGVGRGLAAQDDLKMVHELAAVLNAEVGCSRPIAEGENWMERERYIGVSGVLLKSDLYLTLGISGQIQHMVGGNGAKVIVAINKDKNAPIFNYADYGLVGDIYKVVPALISQLSR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13977
Length:	312 (300)
Sequences:	4064 (2435)
Seq/√Len:	140.6

ECOLI - YDIR FIXB YGCQ
BACSU - ETFA
HALSA - Q9HND2
SULSO - Q97V19 Q97V72

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
297_G	302_V	4.972	1.00
288_F	294_G	3.671	1.00
258_L	279_I	3.472	1.00
195_K	253_D	3.429	1.00
199_G	260_I	3.314	1.00
85_L	95_A	3.116	1.00
23_G	26_Q	2.658	1.00
197_V	250_L	2.647	1.00
258_L	303_V	2.622	1.00
51_C	165_E	2.587	1.00
32_Y	53_Y	2.570	1.00
24_A	31_V	2.551	1.00
200_V	210_L	2.548	1.00
219_V	307_I	2.510	1.00
75_L	83_L	2.401	1.00
22_G	154_C	2.338	1.00
45_M	162_C	2.322	1.00
51_C	163_P	2.174	1.00
38_T	56_A	2.167	1.00
157_D	160_H	2.152	1.00
211_K	214_H	2.144	1.00
237_M	241_R	2.137	1.00
11_S	17_Y	2.133	1.00
267_M	290_Y	2.095	1.00
11_S	33_A	2.078	1.00
211_K	215_E	2.062	1.00
226_C	237_M	2.055	1.00
275_V	293_Y	2.005	1.00
215_E	307_I	2.004	1.00
278_A	291_A	1.999	1.00
30_Q	51_C	1.980	1.00
200_V	213_V	1.958	1.00
209_D	300_Y	1.937	1.00
254_L	277_V	1.927	1.00
196_R	222_A	1.920	1.00
258_L	299_I	1.913	1.00
227_S	260_I	1.884	1.00
214_H	224_V	1.883	1.00
216_L	307_I	1.877	1.00
110_A	144_I	1.868	1.00
20_L	84_L	1.850	1.00
204_L	213_V	1.809	1.00
199_G	257_T	1.775	1.00
38_T	61_L	1.751	1.00
213_V	258_L	1.745	1.00
112_A	123_E	1.741	1.00
72_A	101_Q	1.740	1.00
6_S	30_Q	1.724	1.00
68_A	101_Q	1.721	1.00
255_Y	266_H	1.715	1.00
253_D	274_K	1.710	1.00
72_A	98_L	1.705	1.00
123_E	132_F	1.700	1.00
38_T	58_N	1.675	1.00
278_A	287_I	1.673	1.00
216_L	303_V	1.670	1.00
199_G	243_I	1.666	1.00
60_A	70_S	1.658	1.00
190_D	193_K	1.657	1.00
250_L	270_G	1.632	1.00
305_A	308_S	1.627	1.00
32_Y	80_P	1.622	1.00
191_L	197_V	1.597	1.00
197_V	225_G	1.571	1.00
216_L	220_L	1.558	1.00
270_G	273_A	1.548	1.00
198_V	216_L	1.533	1.00
63_R	66_N	1.531	1.00
25_Q	50_K	1.527	1.00
84_L	144_I	1.523	1.00
30_Q	50_K	1.518	1.00
32_Y	50_K	1.504	1.00
64_T	93_A	1.472	1.00
238_E	241_R	1.455	1.00
95_A	145_T	1.449	1.00
72_A	76_K	1.443	1.00
77_D	167_V	1.439	1.00
210_L	224_V	1.419	1.00
214_H	218_A	1.418	1.00
73_A	77_D	1.400	1.00
226_C	230_I	1.385	1.00
57_Q	60_A	1.379	1.00
39_D	42_Q	1.364	1.00
43_A	46_P	1.357	1.00
54_V	166_T	1.351	1.00
114_D	123_E	1.342	1.00
215_E	219_V	1.337	1.00
257_T	260_I	1.332	1.00
219_V	310_L	1.315	1.00
107_V	137_I	1.312	1.00
53_Y	165_E	1.312	1.00
212_M	303_V	1.304	1.00
188_S	218_A	1.297	1.00
7_V	24_A	1.291	1.00
204_L	299_I	1.290	1.00
71_I	98_L	1.290	1.00
10_F	94_L	1.287	1.00
257_T	266_H	1.284	1.00
46_P	156_S	1.274	1.00
20_L	86_A	1.268	1.00
73_A	76_K	1.268	1.00
53_Y	167_V	1.266	1.00
12_D	88_T	1.264	1.00
204_L	209_D	1.247	1.00
295_L	302_V	1.244	1.00
55_L	70_S	1.237	1.00
212_M	215_E	1.236	1.00
45_M	160_H	1.232	1.00
172_P	175_E	1.231	1.00
226_C	231_A	1.217	1.00
225_G	243_I	1.216	1.00
98_L	143_I	1.203	1.00
200_V	230_I	1.200	1.00
192_S	248_V	1.198	1.00
19_E	149_G	1.196	1.00
111_T	123_E	1.176	1.00
67_Y	94_L	1.171	1.00
11_S	44_V	1.167	1.00
199_G	250_L	1.166	0.99
301_K	305_A	1.163	0.99
25_Q	31_V	1.163	0.99
81_A	141_L	1.159	0.99
210_L	230_I	1.156	0.99
111_T	132_F	1.156	0.99
109_D	147_A	1.155	0.99
21_F	49_P	1.144	0.99
305_A	309_Q	1.130	0.99
26_Q	112_A	1.128	0.99
227_S	243_I	1.119	0.99
8_W	74_L	1.116	0.99
6_S	32_Y	1.110	0.99
58_N	61_L	1.107	0.99
110_A	146_L	1.105	0.99
36_Q	70_S	1.104	0.99
13_N	40_Q	1.103	0.99
303_V	307_I	1.093	0.99
288_F	296_V	1.090	0.99
34_I	71_I	1.081	0.99
17_Y	33_A	1.068	0.99
40_Q	43_A	1.062	0.99
126_M	131_A	1.059	0.99
45_M	52_L	1.058	0.99
212_M	307_I	1.057	0.99
299_I	304_P	1.054	0.99
114_D	134_Q	1.045	0.99
74_L	167_V	1.045	0.99
53_Y	78_K	1.044	0.99
43_A	156_S	1.044	0.99
206_A	209_D	1.037	0.99
46_P	157_D	1.036	0.99
71_I	94_L	1.028	0.99
52_L	162_C	1.022	0.99
243_I	257_T	1.017	0.99
68_A	98_L	1.011	0.99
199_G	225_G	1.004	0.98
217_A	224_V	1.003	0.98
10_F	71_I	1.000	0.98
206_A	236_W	0.999	0.98
75_L	102_L	0.998	0.98
231_A	242_Y	0.997	0.98
205_A	300_Y	0.991	0.98
203_G	236_W	0.991	0.98
229_P	234_E	0.990	0.98
115_I	118_G	0.990	0.98
297_G	301_K	0.988	0.98
62_Q	67_Y	0.985	0.98
200_V	204_L	0.981	0.98
171_A	174_H	0.973	0.98
199_G	227_S	0.971	0.98
102_L	143_I	0.970	0.98
251_K	272_G	0.962	0.98
207_Q	237_M	0.961	0.98
76_K	79_H	0.959	0.98
41_A	45_M	0.958	0.98
42_Q	46_P	0.955	0.98
27_W	84_L	0.953	0.98
279_I	302_V	0.952	0.98
47_Y	155_T	0.950	0.98
208_D	211_K	0.949	0.98
107_V	110_A	0.947	0.98
117_D	136_K	0.944	0.98
36_Q	67_Y	0.943	0.98
95_A	106_L	0.938	0.98
45_M	157_D	0.929	0.97
72_A	102_L	0.927	0.97
210_L	237_M	0.921	0.97
225_G	241_R	0.915	0.97
9_V	21_F	0.908	0.97
97_R	101_Q	0.905	0.97
213_V	224_V	0.904	0.97
68_A	97_R	0.903	0.97
218_A	221_N	0.899	0.97
106_L	143_I	0.898	0.97
191_L	225_G	0.895	0.97
148_P	249_L	0.894	0.97
223_E	241_R	0.894	0.97
77_D	165_E	0.891	0.97
32_Y	51_C	0.891	0.97
56_A	166_T	0.886	0.97
209_D	212_M	0.884	0.97
92_K	109_D	0.880	0.97
104_A	143_I	0.877	0.96
200_V	237_M	0.875	0.96
230_I	236_W	0.873	0.96
230_I	237_M	0.870	0.96
256_L	279_I	0.867	0.96
29_Q	81_A	0.865	0.96
87_A	109_D	0.852	0.96
210_L	213_V	0.848	0.96
122_A	144_I	0.847	0.96
42_Q	45_M	0.836	0.95
204_L	207_Q	0.836	0.95
10_F	33_A	0.835	0.95
106_L	145_T	0.830	0.95
212_M	304_P	0.824	0.95
105_A	137_I	0.822	0.95
215_E	224_V	0.816	0.95
191_L	248_V	0.809	0.94
69_E	73_A	0.808	0.94
212_M	258_L	0.803	0.94
178_C	181_R	0.799	0.94
204_L	210_L	0.798	0.94
73_A	170_V	0.793	0.94
8_W	78_K	0.792	0.94
81_A	140_P	0.791	0.94
110_A	113_V	0.789	0.94
62_Q	93_A	0.786	0.94
99_S	106_L	0.786	0.94
35_V	40_Q	0.779	0.93
85_L	145_T	0.778	0.93
270_G	290_Y	0.770	0.93
43_A	47_Y	0.768	0.93
21_F	154_C	0.768	0.93
175_E	178_C	0.765	0.93
25_Q	47_Y	0.764	0.93
33_A	49_P	0.761	0.92
171_A	175_E	0.758	0.92
35_V	52_L	0.758	0.92
113_V	122_A	0.757	0.92
6_S	29_Q	0.756	0.92
123_E	134_Q	0.756	0.92
197_V	223_E	0.752	0.92
9_V	84_L	0.751	0.92
203_G	209_D	0.749	0.92
122_A	142_A	0.749	0.92
203_G	207_Q	0.744	0.92
252_S	273_A	0.743	0.92
53_Y	74_L	0.742	0.91
18_A	43_A	0.741	0.91
232_E	242_Y	0.735	0.91
10_F	85_L	0.731	0.91
46_P	158_T	0.731	0.91
207_Q	236_W	0.729	0.91
87_A	91_G	0.725	0.91
78_K	165_E	0.724	0.90
8_W	34_I	0.723	0.90
39_D	43_A	0.722	0.90
11_S	35_V	0.721	0.90
41_A	52_L	0.721	0.90
204_L	212_M	0.718	0.90
64_T	97_R	0.718	0.90
73_A	168_P	0.716	0.90
45_M	164_T	0.716	0.90
36_Q	60_A	0.715	0.90
125_R	147_A	0.710	0.90
105_A	139_S	0.709	0.90
37_N	56_A	0.708	0.89
204_L	300_Y	0.706	0.89
137_I	142_A	0.705	0.89
78_K	167_V	0.704	0.89
10_F	83_L	0.703	0.89
227_S	267_M	0.702	0.89
75_L	141_L	0.701	0.89
256_L	277_V	0.699	0.89
91_G	94_L	0.694	0.89
19_E	153_P	0.694	0.89
287_I	294_G	0.690	0.88
67_Y	90_R	0.688	0.88
110_A	122_A	0.687	0.88
8_W	83_L	0.685	0.88
23_G	151_Q	0.680	0.88
202_R	229_P	0.676	0.87
76_K	102_L	0.675	0.87
85_L	91_G	0.674	0.87
171_A	176_I	0.674	0.87
41_A	162_C	0.671	0.87
257_T	287_I	0.671	0.87
62_Q	94_L	0.667	0.86
44_V	52_L	0.665	0.86
13_N	16_R	0.664	0.86
200_V	226_C	0.658	0.86
114_D	117_D	0.654	0.85
102_L	141_L	0.652	0.85
203_G	212_M	0.651	0.85
207_Q	211_K	0.651	0.85
47_Y	156_S	0.644	0.85
227_S	257_T	0.642	0.84
118_G	136_K	0.642	0.84
156_S	160_H	0.639	0.84
175_E	179_R	0.639	0.84
176_I	179_R	0.637	0.84
298_D	301_K	0.636	0.84
76_K	141_L	0.634	0.84
250_L	273_A	0.633	0.84
117_D	142_A	0.632	0.83
18_A	47_Y	0.630	0.83
75_L	80_P	0.629	0.83
267_M	289_N	0.627	0.83
50_K	160_H	0.626	0.83
41_A	164_T	0.624	0.83
302_V	305_A	0.624	0.83
275_V	292_D	0.623	0.83
33_A	36_Q	0.623	0.83
9_V	20_L	0.621	0.82
65_E	175_E	0.618	0.82
147_A	245_V	0.617	0.82
210_L	245_V	0.615	0.82
34_I	74_L	0.614	0.82
55_L	74_L	0.612	0.81
33_A	44_V	0.611	0.81
21_F	33_A	0.611	0.81
204_L	236_W	0.609	0.81
68_A	72_A	0.609	0.81
59_D	173_R	0.608	0.81
207_Q	214_H	0.607	0.81
137_I	140_P	0.607	0.81
171_A	178_C	0.606	0.81
174_H	178_C	0.606	0.81
198_V	303_V	0.603	0.80
210_L	226_C	0.602	0.80
31_V	49_P	0.602	0.80
22_G	25_Q	0.600	0.80
40_Q	44_V	0.599	0.80
128_G	147_A	0.598	0.80
18_A	153_P	0.598	0.80
200_V	258_L	0.596	0.80
199_G	266_H	0.596	0.80
216_L	219_V	0.594	0.79
255_Y	260_I	0.590	0.79
267_M	270_G	0.589	0.79
227_S	268_V	0.587	0.79
198_V	224_V	0.584	0.78
69_E	170_V	0.584	0.78
106_L	110_A	0.584	0.78
110_A	115_I	0.584	0.78
115_I	136_K	0.583	0.78
95_A	98_L	0.582	0.78
246_S	264_I	0.581	0.78
24_A	84_L	0.579	0.78
22_G	155_T	0.578	0.78
71_I	75_L	0.576	0.77
13_N	17_Y	0.575	0.77
209_D	215_E	0.575	0.77
57_Q	168_P	0.575	0.77
184_K	283_K	0.574	0.77
85_L	98_L	0.572	0.77
152_E	155_T	0.572	0.77
36_Q	55_L	0.569	0.77
196_R	221_N	0.569	0.77
49_P	52_L	0.568	0.76
157_D	161_Q	0.567	0.76
107_V	135_E	0.566	0.76
182_R	185_A	0.566	0.76
107_V	222_A	0.565	0.76
74_L	78_K	0.564	0.76
62_Q	90_R	0.563	0.76
190_D	248_V	0.562	0.76
82_M	113_V	0.561	0.76
38_T	57_Q	0.561	0.76
203_G	299_I	0.560	0.75
66_N	176_I	0.560	0.75
104_A	139_S	0.560	0.75
204_L	303_V	0.558	0.75
92_K	108_N	0.558	0.75
10_F	17_Y	0.555	0.75
243_I	270_G	0.554	0.75
171_A	179_R	0.554	0.75
239_R	243_I	0.554	0.75
69_E	172_P	0.553	0.75
122_A	146_L	0.551	0.74
160_H	163_P	0.551	0.74
199_G	255_Y	0.550	0.74
206_A	300_Y	0.550	0.74
212_M	219_V	0.549	0.74
45_M	49_P	0.548	0.74
205_A	209_D	0.548	0.74
46_P	155_T	0.546	0.74
293_Y	300_Y	0.545	0.73
276_I	290_Y	0.545	0.73
300_Y	304_P	0.545	0.73
7_V	84_L	0.545	0.73
124_H	265_Q	0.543	0.73
69_E	173_R	0.543	0.73
55_L	167_V	0.540	0.73
18_A	156_S	0.540	0.73
206_A	230_I	0.539	0.73
70_S	73_A	0.537	0.72
99_S	143_I	0.536	0.72
69_E	174_H	0.535	0.72
75_L	143_I	0.534	0.72
172_P	176_I	0.533	0.72
127_Y	135_E	0.533	0.72
60_A	170_V	0.531	0.72
198_V	219_V	0.530	0.71
227_S	281_K	0.530	0.71
228_R	242_Y	0.529	0.71
189_V	197_V	0.528	0.71
51_C	78_K	0.527	0.71
188_S	214_H	0.527	0.71
295_L	309_Q	0.526	0.71
232_E	239_R	0.526	0.71
196_R	253_D	0.526	0.71
224_V	241_R	0.525	0.71
158_T	161_Q	0.525	0.71
189_V	223_E	0.525	0.71
7_V	30_Q	0.523	0.70
214_H	222_A	0.523	0.70
204_L	230_I	0.522	0.70
9_V	24_A	0.521	0.70
220_L	256_L	0.521	0.70
14_P	87_A	0.521	0.70
10_F	13_N	0.521	0.70
219_V	222_A	0.520	0.70
232_E	246_S	0.517	0.70
203_G	227_S	0.517	0.70
27_W	115_I	0.516	0.69
198_V	307_I	0.516	0.69
69_E	101_Q	0.515	0.69
7_V	31_V	0.515	0.69
198_V	204_L	0.514	0.69
105_A	133_A	0.514	0.69
196_R	220_L	0.513	0.69
200_V	224_V	0.513	0.69
283_K	286_P	0.512	0.69
188_S	191_L	0.512	0.69
10_F	67_Y	0.510	0.69
7_V	27_W	0.510	0.69
200_V	246_S	0.510	0.69
97_R	100_V	0.510	0.69
205_A	216_L	0.510	0.69
197_V	243_I	0.510	0.69
250_L	290_Y	0.508	0.68
107_V	122_A	0.507	0.68
278_A	288_F	0.507	0.68
124_H	135_E	0.506	0.68
74_L	77_D	0.506	0.68
286_P	289_N	0.506	0.68
60_A	66_N	0.506	0.68
198_V	220_L	0.502	0.67
214_H	241_R	0.500	0.67

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
4l2iA	1	0.9936	100	0.055	Contact Map
1efvA	1	0.9679	100	0.076	Contact Map
1o97D	1	0.9551	100	0.077	Contact Map
1efpA	1	0.9487	100	0.09	Contact Map
3ih5A	6	0.5929	100	0.664	Contact Map
3fetA	2	0.5288	99.9	0.727	Contact Map
1efvB	1	0.6474	99.9	0.76	Contact Map
4l2iB	1	0.6987	99.9	0.766	Contact Map
1efpB	1	0.6378	99.9	0.766	Contact Map
1o97C	1	0.6474	99.9	0.769	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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