YAGS - ECOLI - GREMLIN Contacts

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YAGS - Putative xanthine dehydrogenase YagS FAD-binding subunit

UniProt:	P77324	Sequences: MKAFTYERVNTPAEAALSAQRVPGAKFIAGGTNLLDLMKLEIETPTHLIDVNGLGLDKIEVTDAGGLRIGALVRNTDLAAHERVRRDYAVLSRALLAGASGQLRNQATTAGNLLQRTRCPYFYDTNQPCNKRLPGSGCAALEGFSRQHAVVGVSEACIATHPSDMAVAMRLLDAVVETITPEGKTRSITLADFYHPPGKTPHIETALLPGELIVAVTLPPPLGGKHIYRKVRDRASYAFALVSVAAIIQPDGSGRVALGGVAHKPWRIEAADAQLSQGAQAVYDTLFASAHPTAENTFKLLLAKRTLASVLAEARAQA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13558
Length:	318 (311)
Sequences:	1425 (871)
Seq/√Len:	49.4

ECOLI - YAGS XDHB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
67_L	84_V	5.139	1.00
73_V	78_L	4.990	1.00
178_T	188_I	4.084	1.00
26_K	43_E	3.629	1.00
158_I	293_T	3.331	1.00
19_A	27_F	3.170	1.00
177_E	217_T	3.122	1.00
91_L	165_M	2.860	1.00
287_F	290_A	2.756	1.00
284_D	304_K	2.687	1.00
11_T	14_E	2.678	1.00
292_P	297_T	2.661	1.00
292_P	300_L	2.632	1.00
258_L	303_A	2.565	1.00
253_S	276_S	2.422	1.00
282_V	290_A	2.419	1.00
294_A	297_T	2.417	1.00
74_R	77_D	2.394	1.00
69_I	78_L	2.333	1.00
258_L	261_V	2.326	1.00
19_A	49_I	2.326	1.00
78_L	109_T	2.319	1.00
68_R	215_A	2.277	1.00
69_I	109_T	2.167	1.00
246_A	256_V	2.164	1.00
258_L	307_L	2.139	1.00
189_T	192_D	2.136	1.00
10_N	14_E	2.089	1.00
161_H	166_A	2.087	1.00
109_T	216_V	2.083	1.00
175_V	187_S	2.002	1.00
145_S	294_A	1.998	1.00
204_E	263_H	1.974	0.99
128_P	139_A	1.971	0.99
177_E	215_A	1.931	0.99
16_A	180_T	1.914	0.99
301_L	305_R	1.912	0.99
153_V	263_H	1.895	0.99
229_R	309_S	1.846	0.99
146_R	298_F	1.835	0.99
194_Y	264_K	1.830	0.99
231_V	306_T	1.824	0.99
268_I	286_L	1.820	0.99
146_R	233_D	1.818	0.99
186_R	211_E	1.805	0.99
120_P	147_Q	1.796	0.99
14_E	18_S	1.786	0.99
68_R	177_E	1.777	0.99
88_Y	218_L	1.758	0.99
74_R	95_L	1.756	0.99
267_R	272_D	1.740	0.99
52_N	74_R	1.729	0.99
145_S	293_T	1.724	0.99
177_E	184_K	1.715	0.98
187_S	217_T	1.646	0.98
179_I	184_K	1.633	0.98
274_Q	285_T	1.625	0.98
61_V	83_R	1.622	0.98
191_A	269_E	1.585	0.97
12_P	179_I	1.567	0.97
27_F	212_L	1.549	0.97
51_V	72_L	1.548	0.97
24_G	46_T	1.542	0.97
278_G	281_A	1.532	0.97
90_V	171_L	1.525	0.97
93_R	227_I	1.519	0.97
33_N	238_A	1.514	0.97
114_L	193_F	1.500	0.96
177_E	187_S	1.483	0.96
200_T	203_I	1.474	0.96
33_N	123_Y	1.473	0.96
195_H	204_E	1.466	0.96
178_T	211_E	1.459	0.96
145_S	295_E	1.447	0.96
170_R	190_L	1.440	0.95
178_T	207_L	1.419	0.95
142_E	145_S	1.416	0.95
254_G	282_V	1.390	0.95
282_V	286_L	1.371	0.94
2_K	46_T	1.350	0.94
33_N	36_D	1.346	0.94
127_Q	139_A	1.344	0.93
56_L	72_L	1.341	0.93
188_I	206_A	1.339	0.93
273_A	276_S	1.338	0.93
68_R	217_T	1.337	0.93
66_G	88_Y	1.332	0.93
12_P	56_L	1.329	0.93
33_N	75_N	1.322	0.93
283_Y	307_L	1.322	0.93
286_L	290_A	1.315	0.93
61_V	87_D	1.302	0.92
74_R	108_T	1.296	0.92
191_A	194_Y	1.294	0.92
75_N	98_G	1.285	0.92
5_T	47_H	1.272	0.91
19_A	209_P	1.268	0.91
249_Q	253_S	1.264	0.91
67_L	83_R	1.260	0.91
58_K	73_V	1.256	0.91
268_I	289_S	1.252	0.91
275_L	282_V	1.251	0.91
286_L	289_S	1.244	0.90
256_V	268_I	1.235	0.90
176_V	190_L	1.226	0.90
90_V	172_L	1.220	0.90
145_S	148_H	1.209	0.89
155_E	291_H	1.203	0.89
19_A	210_G	1.191	0.88
7_E	47_H	1.189	0.88
52_N	72_L	1.186	0.88
16_A	179_I	1.182	0.88
133_L	136_S	1.179	0.88
195_H	203_I	1.173	0.88
73_V	109_T	1.168	0.87
83_R	87_D	1.167	0.87
2_K	41_E	1.164	0.87
193_F	206_A	1.154	0.87
166_A	190_L	1.150	0.87
268_I	271_A	1.149	0.87
282_V	287_F	1.148	0.87
13_A	179_I	1.141	0.86
57_D	74_R	1.140	0.86
282_V	289_S	1.140	0.86
222_L	247_I	1.139	0.86
123_Y	238_A	1.136	0.86
113_L	190_L	1.136	0.86
57_D	77_D	1.106	0.84
41_E	44_T	1.105	0.84
28_I	35_L	1.105	0.84
283_Y	287_F	1.103	0.84
190_L	194_Y	1.102	0.84
233_D	298_F	1.092	0.84
25_A	49_I	1.084	0.83
254_G	276_S	1.083	0.83
12_P	212_L	1.082	0.83
170_R	191_A	1.081	0.83
223_G	249_Q	1.071	0.82
75_N	97_A	1.069	0.82
29_A	72_L	1.067	0.82
261_V	307_L	1.066	0.82
76_T	80_A	1.064	0.82
29_A	51_V	1.061	0.82
221_P	224_G	1.046	0.81
268_I	285_T	1.042	0.81
28_I	48_L	1.039	0.81
114_L	213_I	1.039	0.81
283_Y	290_A	1.039	0.81
261_V	303_A	1.037	0.80
110_A	169_M	1.034	0.80
242_V	246_A	1.023	0.79
178_T	208_L	1.022	0.79
188_I	193_F	1.014	0.79
187_S	215_A	1.014	0.79
310_V	314_A	1.012	0.79
180_T	211_E	1.008	0.78
153_V	293_T	1.004	0.78
175_V	189_T	1.001	0.78
193_F	211_E	1.000	0.78
141_L	293_T	0.999	0.78
19_A	22_V	0.998	0.78
294_A	300_L	0.993	0.77
59_I	81_H	0.982	0.77
244_V	306_T	0.979	0.76
208_L	211_E	0.973	0.76
150_V	300_L	0.964	0.75
182_E	210_G	0.962	0.75
75_N	165_M	0.955	0.75
164_D	239_F	0.951	0.74
153_V	160_T	0.951	0.74
83_R	86_R	0.948	0.74
244_V	314_A	0.937	0.73
287_F	303_A	0.934	0.73
123_Y	242_V	0.933	0.73
29_A	52_N	0.932	0.73
190_L	193_F	0.931	0.73
255_R	267_R	0.929	0.73
103_L	237_Y	0.922	0.72
95_L	169_M	0.916	0.71
65_G	218_L	0.914	0.71
191_A	267_R	0.912	0.71
256_V	307_L	0.911	0.71
200_T	206_A	0.910	0.71
246_A	310_V	0.910	0.71
182_E	208_L	0.908	0.71
258_L	268_I	0.906	0.71
75_N	238_A	0.904	0.70
274_Q	278_G	0.900	0.70
280_Q	304_K	0.891	0.69
75_N	123_Y	0.890	0.69
248_I	254_G	0.890	0.69
148_H	160_T	0.885	0.69
33_N	242_V	0.882	0.69
242_V	260_G	0.881	0.68
36_D	98_G	0.872	0.68
153_V	204_E	0.871	0.68
281_A	284_D	0.871	0.68
37_L	42_I	0.865	0.67
270_A	289_S	0.864	0.67
94_A	98_G	0.863	0.67
7_E	18_S	0.860	0.67
203_I	208_L	0.853	0.66
61_V	66_G	0.852	0.66
181_P	211_E	0.849	0.66
284_D	287_F	0.849	0.66
80_A	85_R	0.848	0.65
142_E	293_T	0.848	0.65
139_A	142_E	0.843	0.65
116_R	204_E	0.841	0.65
92_S	96_L	0.840	0.65
57_D	72_L	0.836	0.64
90_V	245_A	0.826	0.63
243_S	259_G	0.825	0.63
40_L	123_Y	0.823	0.63
129_C	140_A	0.822	0.63
256_V	271_A	0.820	0.63
297_T	301_L	0.820	0.63
16_A	212_L	0.819	0.63
109_T	165_M	0.816	0.62
149_A	263_H	0.806	0.62
156_A	199_K	0.805	0.61
116_R	122_F	0.802	0.61
75_N	94_A	0.801	0.61
51_V	110_A	0.800	0.61
180_T	184_K	0.799	0.61
8_R	53_G	0.798	0.61
164_D	230_K	0.797	0.61
170_R	194_Y	0.797	0.61
77_D	101_G	0.797	0.61
274_Q	281_A	0.792	0.60
145_S	296_N	0.791	0.60
147_Q	160_T	0.791	0.60
268_I	288_A	0.783	0.59
173_D	191_A	0.783	0.59
195_H	206_A	0.782	0.59
151_V	292_P	0.777	0.59
229_R	310_V	0.774	0.58
22_V	47_H	0.774	0.58
8_R	50_D	0.773	0.58
51_V	212_L	0.771	0.58
280_Q	297_T	0.771	0.58
223_G	247_I	0.765	0.57
117_T	159_A	0.764	0.57
283_Y	308_A	0.763	0.57
51_V	271_A	0.763	0.57
90_V	226_H	0.761	0.57
138_C	157_C	0.758	0.57
113_L	216_V	0.754	0.56
76_T	101_G	0.754	0.56
51_V	56_L	0.747	0.56
37_L	122_F	0.746	0.56
229_R	313_E	0.745	0.55
151_V	303_A	0.744	0.55
195_H	263_H	0.742	0.55
196_P	264_K	0.742	0.55
9_V	14_E	0.742	0.55
302_L	305_R	0.742	0.55
27_F	210_G	0.741	0.55
90_V	247_I	0.739	0.55
229_R	306_T	0.738	0.55
28_I	314_A	0.736	0.55
57_D	73_V	0.735	0.54
59_I	78_L	0.735	0.54
80_A	166_A	0.734	0.54
301_L	304_K	0.728	0.54
40_L	101_G	0.728	0.54
82_E	86_R	0.725	0.53
260_G	298_F	0.721	0.53
117_T	131_K	0.720	0.53
250_P	277_Q	0.716	0.53
282_V	285_T	0.715	0.52
17_L	110_A	0.714	0.52
142_E	294_A	0.711	0.52
88_Y	220_P	0.711	0.52
254_G	275_L	0.710	0.52
274_Q	279_A	0.706	0.52
87_D	222_L	0.703	0.51
154_S	198_G	0.702	0.51
148_H	263_H	0.701	0.51
4_F	29_A	0.701	0.51
241_L	298_F	0.701	0.51
75_N	218_L	0.701	0.51
7_E	82_E	0.699	0.51
284_D	290_A	0.698	0.51
240_A	243_S	0.696	0.51
293_T	297_T	0.693	0.50
18_S	47_H	0.693	0.50
224_G	310_V	0.693	0.50
150_V	261_V	0.692	0.50
175_V	217_T	0.688	0.50
49_I	136_S	0.685	0.49
280_Q	290_A	0.684	0.49
42_I	125_T	0.684	0.49
77_D	95_L	0.682	0.49
223_G	226_H	0.680	0.49
250_P	279_A	0.679	0.49
280_Q	284_D	0.679	0.49
194_Y	263_H	0.675	0.48
93_R	286_L	0.674	0.48
115_Q	162_P	0.672	0.48
23_P	209_P	0.670	0.48
9_V	85_R	0.669	0.48
151_V	268_I	0.667	0.48
158_I	294_A	0.667	0.48
269_E	286_L	0.661	0.47
8_R	106_Q	0.660	0.47
65_G	220_P	0.658	0.47
227_I	313_E	0.656	0.46
148_H	153_V	0.654	0.46
136_S	139_A	0.654	0.46
200_T	204_E	0.651	0.46
203_I	256_V	0.650	0.46
1_M	4_F	0.650	0.46
33_N	98_G	0.647	0.46
49_I	94_A	0.645	0.45
270_A	288_A	0.644	0.45
12_P	27_F	0.641	0.45
227_I	310_V	0.641	0.45
75_N	95_L	0.641	0.45
153_V	233_D	0.637	0.45
60_E	68_R	0.636	0.44
247_I	255_R	0.636	0.44
113_L	194_Y	0.635	0.44
15_A	65_G	0.635	0.44
36_D	238_A	0.635	0.44
11_T	225_K	0.634	0.44
230_K	239_F	0.632	0.44
29_A	108_T	0.630	0.44
66_G	94_A	0.629	0.44
269_E	273_A	0.629	0.44
144_F	233_D	0.627	0.44
14_E	17_L	0.625	0.43
221_P	249_Q	0.624	0.43
61_V	184_K	0.624	0.43
256_V	282_V	0.623	0.43
93_R	305_R	0.623	0.43
120_P	292_P	0.619	0.43
109_T	247_I	0.619	0.43
41_E	226_H	0.619	0.43
93_R	235_A	0.617	0.43
160_T	262_A	0.617	0.43
124_D	146_R	0.616	0.42
66_G	218_L	0.615	0.42
192_D	291_H	0.611	0.42
150_V	303_A	0.610	0.42
36_D	237_Y	0.610	0.42
178_T	206_A	0.609	0.42
167_V	257_A	0.607	0.42
303_A	307_L	0.607	0.42
130_N	137_G	0.607	0.42
43_E	122_F	0.606	0.41
12_P	279_A	0.604	0.41
188_I	207_L	0.603	0.41
93_R	313_E	0.603	0.41
93_R	226_H	0.602	0.41
7_E	14_E	0.601	0.41
58_K	81_H	0.601	0.41
178_T	210_G	0.601	0.41
204_E	262_A	0.598	0.41
98_G	238_A	0.598	0.41
158_I	292_P	0.593	0.40
94_A	161_H	0.592	0.40
35_L	55_G	0.592	0.40
190_L	263_H	0.592	0.40
12_P	16_A	0.591	0.40
75_N	109_T	0.591	0.40
116_R	237_Y	0.590	0.40
281_A	285_T	0.590	0.40
163_S	166_A	0.586	0.39
11_T	49_I	0.586	0.39
226_H	247_I	0.584	0.39
285_T	288_A	0.582	0.39
78_L	95_L	0.581	0.39
90_V	227_I	0.579	0.39
98_G	165_M	0.577	0.39
34_L	38_M	0.575	0.38
33_N	97_A	0.574	0.38
16_A	181_P	0.572	0.38
78_L	169_M	0.572	0.38
76_T	109_T	0.571	0.38
241_L	306_T	0.569	0.38
51_V	213_I	0.566	0.38
2_K	120_P	0.566	0.38
14_E	215_A	0.566	0.38
59_I	83_R	0.565	0.37
225_K	314_A	0.565	0.37
91_L	97_A	0.564	0.37
186_R	208_L	0.563	0.37
22_V	209_P	0.561	0.37
196_P	263_H	0.561	0.37
115_Q	163_S	0.560	0.37
29_A	170_R	0.559	0.37
139_A	148_H	0.559	0.37
55_G	72_L	0.557	0.37
106_Q	226_H	0.557	0.37
44_T	133_L	0.556	0.37
156_A	202_H	0.554	0.36
66_G	69_I	0.552	0.36
270_A	314_A	0.551	0.36
298_F	306_T	0.550	0.36
28_I	268_I	0.550	0.36
33_N	237_Y	0.549	0.36
51_V	69_I	0.549	0.36
190_L	264_K	0.548	0.36
167_V	243_S	0.547	0.36
39_K	109_T	0.545	0.36
36_D	75_N	0.544	0.35
123_Y	204_E	0.543	0.35
150_V	293_T	0.542	0.35
69_I	217_T	0.541	0.35
193_F	208_L	0.541	0.35
222_L	225_K	0.539	0.35
164_D	243_S	0.539	0.35
248_I	311_L	0.539	0.35
91_L	218_L	0.539	0.35
176_V	193_F	0.538	0.35
129_C	138_C	0.537	0.35
11_T	18_S	0.537	0.35
37_L	43_E	0.536	0.35
306_T	309_S	0.536	0.35
39_K	45_P	0.535	0.35
44_T	193_F	0.533	0.34
35_L	39_K	0.530	0.34
95_L	103_L	0.530	0.34
27_F	49_I	0.529	0.34
77_D	100_S	0.529	0.34
75_N	96_L	0.529	0.34
35_L	106_Q	0.528	0.34
29_A	109_T	0.528	0.34
33_N	263_H	0.527	0.34
69_I	216_V	0.527	0.34
37_L	302_L	0.527	0.34
97_A	235_A	0.526	0.34
114_L	206_A	0.524	0.34
5_T	48_L	0.522	0.33
252_G	278_G	0.522	0.33
37_L	204_E	0.521	0.33
17_L	136_S	0.520	0.33
80_A	231_V	0.520	0.33
18_S	49_I	0.518	0.33
296_N	300_L	0.518	0.33
147_Q	305_R	0.517	0.33
198_G	201_P	0.517	0.33
49_I	269_E	0.517	0.33
155_E	192_D	0.516	0.33
5_T	202_H	0.515	0.33
35_L	254_G	0.514	0.33
258_L	271_A	0.512	0.33
274_Q	282_V	0.511	0.32
82_E	288_A	0.510	0.32
100_S	124_D	0.509	0.32
122_F	131_K	0.509	0.32
72_L	123_Y	0.509	0.32
92_S	109_T	0.509	0.32
280_Q	289_S	0.508	0.32
6_Y	22_V	0.507	0.32
179_I	211_E	0.507	0.32
152_G	266_W	0.506	0.32
254_G	278_G	0.506	0.32
69_I	73_V	0.506	0.32
39_K	294_A	0.503	0.32
33_N	205_T	0.503	0.32
95_L	114_L	0.501	0.32
39_K	127_Q	0.501	0.32
186_R	197_P	0.501	0.32
29_A	309_S	0.500	0.31

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
1rm6B	1	0.956	100	0.307	Contact Map
1t3qC	1	0.8365	100	0.482	Contact Map
1n62C	1	0.8396	100	0.485	Contact Map
3hrdC	1	0.8522	100	0.487	Contact Map
2w3sA	1	0.8208	100	0.508	Contact Map
1ffvC	1	0.8396	100	0.509	Contact Map
3nvzB	1	0.8428	100	0.524	Contact Map
3zyvA	3	0.8333	100	0.548	Contact Map
3uncA	2	0.8428	100	0.583	Contact Map
3tx1A	1	0.7264	97.5	0.933	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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