YUXN - BACSU - GREMLIN Contacts

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YUXN - Uncharacterized HTH-type transcriptional regulator YuxN

UniProt:	P40950	Sequences: MKEKEKLIIETALKLFAQKGYNSTSVQEIAKECKISKGAFYIYFPSKEALLLSMLNYYYDKTFTRILNIKTKGDSPRTAYRKQLTVLYENILEHKDFISMQLKEGSLPYTEEVEQCAKKIRQSSLQFHIDSLLNIYGKKAEPYTAELCFLIEGISQIYLECMILLGYTVKPSQLADIIMNRIDDMVKGMSERNDKPFITLEEASSLFGPLTHGRPDPLTESIVKSLRDKINSLNTNSSLELSESLDILEAEMKKKTPKLAIIKGMIHNLTESEALAKDAEQLKYLLKQQHI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	291 (276)
Sequences:	426 (363)
Seq/√Len:	21.9

BACSU - YUXN YCNC YERO

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
136_Y	183_D	7.164	1.00
26_V	40_F	5.105	1.00
19_K	28_E	4.361	1.00
138_K	141_E	4.192	1.00
30_A	40_F	3.489	1.00
77_R	183_D	3.456	1.00
270_T	283_K	3.347	1.00
36_S	40_F	2.888	0.99
254_K	258_K	2.836	0.99
244_S	268_N	2.823	0.99
37_K	41_Y	2.752	0.99
247_I	265_M	2.736	0.99
264_G	268_N	2.716	0.99
11_T	32_E	2.691	0.99
146_E	177_I	2.678	0.99
72_K	82_K	2.655	0.99
16_F	24_T	2.596	0.98
247_I	261_I	2.493	0.98
251_E	258_K	2.480	0.98
31_K	185_M	2.381	0.97
81_R	176_D	2.373	0.97
241_L	269_L	2.320	0.97
42_I	264_G	2.247	0.96
23_S	146_E	2.219	0.96
269_L	282_L	2.217	0.96
177_I	181_R	2.205	0.96
227_R	249_E	2.200	0.96
184_D	188_G	2.109	0.94
250_A	254_K	2.047	0.93
11_T	35_I	2.036	0.93
36_S	39_A	1.985	0.92
247_I	260_A	1.957	0.92
198_I	250_A	1.927	0.91
94_H	261_I	1.857	0.90
42_I	45_P	1.836	0.89
85_T	172_S	1.836	0.89
38_G	83_Q	1.834	0.89
27_Q	38_G	1.802	0.88
39_A	42_I	1.780	0.87
244_S	264_G	1.778	0.87
226_L	230_I	1.767	0.87
26_V	38_G	1.722	0.86
36_S	41_Y	1.644	0.83
243_E	260_A	1.614	0.82
38_G	41_Y	1.611	0.81
219_T	230_I	1.578	0.80
38_G	46_S	1.541	0.78
204_S	225_S	1.537	0.78
150_L	154_I	1.509	0.77
83_Q	131_S	1.495	0.76
275_L	278_D	1.486	0.76
243_E	247_I	1.474	0.75
7_L	84_L	1.464	0.75
66_I	69_I	1.463	0.75
240_E	263_K	1.435	0.73
17_A	28_E	1.422	0.72
83_Q	135_I	1.407	0.72
29_I	44_F	1.406	0.72
39_A	175_A	1.404	0.72
3_E	52_L	1.402	0.71
53_S	261_I	1.394	0.71
4_K	36_S	1.381	0.70
39_A	157_I	1.370	0.70
42_I	83_Q	1.361	0.69
137_G	143_Y	1.355	0.69
69_I	179_M	1.354	0.69
8_I	136_Y	1.347	0.68
4_K	8_I	1.341	0.68
260_A	268_N	1.336	0.68
38_G	42_I	1.335	0.68
16_F	47_K	1.322	0.67
133_L	144_T	1.320	0.67
9_I	250_A	1.315	0.66
223_V	226_L	1.293	0.65
27_Q	37_K	1.291	0.65
230_I	249_E	1.274	0.64
23_S	174_L	1.270	0.64
262_I	266_I	1.269	0.64
8_I	22_N	1.266	0.63
142_P	227_R	1.263	0.63
17_A	98_I	1.246	0.62
8_I	268_N	1.228	0.61
55_L	107_L	1.214	0.60
25_S	29_I	1.213	0.60
158_Y	244_S	1.206	0.59
269_L	283_K	1.196	0.59
27_Q	31_K	1.195	0.59
37_K	153_G	1.194	0.59
23_S	262_I	1.193	0.59
53_S	197_F	1.190	0.58
59_Y	117_A	1.189	0.58
148_C	157_I	1.185	0.58
181_R	186_V	1.180	0.58
170_K	221_S	1.179	0.58
39_A	43_Y	1.179	0.58
12_A	176_D	1.177	0.58
30_A	48_E	1.175	0.57
5_E	30_A	1.173	0.57
150_L	177_I	1.170	0.57
94_H	255_K	1.167	0.57
54_M	100_M	1.164	0.57
37_K	47_K	1.161	0.56
156_Q	160_E	1.161	0.56
173_Q	195_K	1.160	0.56
27_Q	46_S	1.151	0.56
198_I	203_A	1.141	0.55
50_L	94_H	1.135	0.55
242_S	266_I	1.128	0.54
100_M	104_E	1.126	0.54
170_K	245_L	1.118	0.54
181_R	188_G	1.117	0.54
157_I	268_N	1.108	0.53
52_L	116_C	1.103	0.53
15_L	40_F	1.093	0.52
49_A	248_L	1.093	0.52
174_L	197_F	1.084	0.51
112_E	234_N	1.067	0.50
78_T	190_S	1.065	0.50
33_C	40_F	1.060	0.50
36_S	42_I	1.055	0.49
12_A	49_A	1.053	0.49
137_G	140_A	1.039	0.48
75_S	130_D	1.032	0.48
48_E	66_I	1.029	0.48
5_E	49_A	1.027	0.47
15_L	24_T	1.027	0.47
95_K	161_C	1.026	0.47
210_L	248_L	1.024	0.47
43_Y	97_F	1.010	0.46
21_Y	157_I	1.008	0.46
21_Y	48_E	1.006	0.46
46_S	137_G	1.005	0.46
247_I	268_N	1.000	0.46
17_A	39_A	0.997	0.45
38_G	45_P	0.994	0.45
273_E	276_A	0.993	0.45
37_K	97_F	0.991	0.45
43_Y	135_I	0.986	0.45
256_T	259_L	0.982	0.44
143_Y	150_L	0.979	0.44
227_R	270_T	0.979	0.44
143_Y	186_V	0.976	0.44
260_A	263_K	0.960	0.43
10_E	26_V	0.957	0.43
50_L	269_L	0.954	0.43
249_E	265_M	0.949	0.42
24_T	40_F	0.947	0.42
6_K	151_I	0.945	0.42
137_G	142_P	0.945	0.42
66_I	161_C	0.944	0.42
33_C	175_A	0.939	0.42
101_Q	104_E	0.937	0.41
97_F	101_Q	0.937	0.41
27_Q	36_S	0.930	0.41
173_Q	227_R	0.927	0.41
229_K	278_D	0.924	0.41
8_I	43_Y	0.923	0.41
28_E	103_K	0.921	0.40
223_V	282_L	0.920	0.40
237_S	277_K	0.918	0.40
127_F	131_S	0.916	0.40
233_L	256_T	0.902	0.39
55_L	179_M	0.897	0.39
55_L	208_G	0.897	0.39
144_T	148_C	0.895	0.39
111_E	122_Q	0.894	0.39
158_Y	177_I	0.888	0.38
69_I	203_A	0.885	0.38
42_I	268_N	0.882	0.38
170_K	230_I	0.879	0.38
201_E	233_L	0.879	0.38
27_Q	83_Q	0.878	0.38
23_S	116_C	0.877	0.38
132_L	216_D	0.875	0.37
59_Y	98_I	0.874	0.37
242_S	259_L	0.873	0.37
258_K	262_I	0.872	0.37
16_F	20_G	0.867	0.37
5_E	127_F	0.859	0.36
83_Q	95_K	0.856	0.36
133_L	242_S	0.852	0.36
250_A	279_A	0.850	0.36
36_S	96_D	0.849	0.36
226_L	245_L	0.847	0.36
251_E	269_L	0.840	0.35
17_A	104_E	0.836	0.35
251_E	257_P	0.834	0.35
243_E	258_K	0.828	0.34
57_Y	136_Y	0.826	0.34
250_A	263_K	0.823	0.34
22_N	51_L	0.818	0.34
147_L	186_V	0.815	0.34
191_E	216_D	0.814	0.34
130_D	148_C	0.810	0.33
52_L	122_Q	0.803	0.33
54_M	61_K	0.799	0.33
12_A	137_G	0.796	0.33
239_L	242_S	0.795	0.32
48_E	177_I	0.791	0.32
78_T	159_L	0.788	0.32
65_R	228_D	0.785	0.32
28_E	96_D	0.783	0.32
73_G	248_L	0.783	0.32
6_K	59_Y	0.778	0.31
89_E	93_E	0.770	0.31
137_G	282_L	0.767	0.31
49_A	70_K	0.766	0.31
80_Y	88_Y	0.763	0.31
111_E	136_Y	0.760	0.30
28_E	77_R	0.758	0.30
51_L	257_P	0.758	0.30
113_V	247_I	0.757	0.30
8_I	35_I	0.755	0.30
29_I	46_S	0.755	0.30
88_Y	104_E	0.752	0.30
30_A	50_L	0.748	0.30
142_P	190_S	0.748	0.30
8_I	269_L	0.748	0.30
48_E	110_T	0.747	0.30
40_F	156_Q	0.745	0.30
43_Y	252_M	0.744	0.30
263_K	283_K	0.743	0.29
82_K	256_T	0.743	0.29
118_K	173_Q	0.742	0.29
219_T	249_E	0.740	0.29
24_T	163_I	0.739	0.29
93_E	142_P	0.737	0.29
132_L	195_K	0.736	0.29
97_F	264_G	0.735	0.29
130_D	162_M	0.733	0.29
154_I	178_I	0.729	0.29
4_K	99_S	0.729	0.29
72_K	232_S	0.728	0.29
158_Y	174_L	0.726	0.29
13_L	21_Y	0.726	0.29
134_N	230_I	0.726	0.29
274_A	280_E	0.725	0.28
39_A	58_Y	0.725	0.28
143_Y	257_P	0.725	0.28
11_T	61_K	0.721	0.28
97_F	104_E	0.716	0.28
39_A	97_F	0.712	0.28
3_E	156_Q	0.704	0.27
45_P	244_S	0.703	0.27
49_A	197_F	0.700	0.27
41_Y	47_K	0.700	0.27
37_K	146_E	0.699	0.27
177_I	189_M	0.694	0.27
260_A	265_M	0.694	0.27
6_K	113_V	0.690	0.27
35_I	218_L	0.689	0.27
93_E	198_I	0.688	0.26
249_E	269_L	0.686	0.26
198_I	206_L	0.686	0.26
20_G	24_T	0.684	0.26
218_L	224_K	0.684	0.26
42_I	97_F	0.682	0.26
165_L	172_S	0.681	0.26
87_L	154_I	0.681	0.26
40_F	50_L	0.679	0.26
135_I	195_K	0.677	0.26
69_I	155_S	0.672	0.26
77_R	179_M	0.670	0.26
46_S	146_E	0.669	0.25
276_A	279_A	0.666	0.25
249_E	257_P	0.666	0.25
240_E	275_L	0.663	0.25
21_Y	125_L	0.662	0.25
9_I	220_E	0.662	0.25
43_Y	83_Q	0.662	0.25
217_P	222_I	0.658	0.25
130_D	179_M	0.656	0.25
157_I	264_G	0.653	0.25
42_I	157_I	0.652	0.25
75_S	178_I	0.645	0.24
21_Y	51_L	0.643	0.24
9_I	272_S	0.643	0.24
83_Q	127_F	0.643	0.24
16_F	37_K	0.642	0.24
32_E	133_L	0.641	0.24
153_G	181_R	0.640	0.24
30_A	39_A	0.637	0.24
83_Q	148_C	0.636	0.24
146_E	260_A	0.634	0.24
25_S	37_K	0.632	0.24
133_L	192_R	0.629	0.23
100_M	103_K	0.626	0.23
4_K	62_T	0.622	0.23
32_E	132_L	0.620	0.23
40_F	43_Y	0.620	0.23
4_K	264_G	0.619	0.23
41_Y	80_Y	0.619	0.23
247_I	264_G	0.618	0.23
27_Q	100_M	0.615	0.23
130_D	142_P	0.614	0.23
8_I	45_P	0.609	0.23
77_R	136_Y	0.609	0.23
54_M	154_I	0.608	0.22
248_L	262_I	0.607	0.22
149_F	276_A	0.606	0.22
82_K	227_R	0.605	0.22
5_E	108_P	0.601	0.22
80_Y	160_E	0.600	0.22
28_E	104_E	0.597	0.22
17_A	183_D	0.596	0.22
260_A	267_H	0.595	0.22
29_I	38_G	0.593	0.22
191_E	255_K	0.591	0.22
33_C	146_E	0.590	0.22
57_Y	264_G	0.590	0.22
197_F	266_I	0.590	0.22
79_A	94_H	0.587	0.21
151_I	258_K	0.587	0.21
86_V	98_I	0.587	0.21
10_E	34_K	0.586	0.21
143_Y	156_Q	0.585	0.21
182_I	217_P	0.580	0.21
170_K	173_Q	0.578	0.21
22_N	113_V	0.578	0.21
43_Y	95_K	0.577	0.21
117_A	211_T	0.576	0.21
98_I	149_F	0.574	0.21
28_E	116_C	0.573	0.21
155_S	164_L	0.572	0.21
147_L	189_M	0.570	0.21
17_A	26_V	0.568	0.21
25_S	36_S	0.568	0.21
4_K	147_L	0.567	0.21
62_T	245_L	0.567	0.21
57_Y	97_F	0.566	0.21
30_A	196_P	0.564	0.20
34_K	196_P	0.564	0.20
147_L	277_K	0.564	0.20
136_Y	198_I	0.563	0.20
57_Y	183_D	0.563	0.20
82_K	231_N	0.562	0.20
75_S	172_S	0.561	0.20
163_I	231_N	0.560	0.20
146_E	181_R	0.560	0.20
258_K	269_L	0.560	0.20
7_L	22_N	0.560	0.20
136_Y	179_M	0.559	0.20
60_D	222_I	0.558	0.20
219_T	226_L	0.557	0.20
89_E	171_P	0.556	0.20
6_K	120_I	0.555	0.20
25_S	44_F	0.555	0.20
52_L	113_V	0.555	0.20
12_A	34_K	0.554	0.20
35_I	39_A	0.553	0.20
17_A	100_M	0.553	0.20
265_M	268_N	0.550	0.20
125_L	159_L	0.550	0.20
256_T	280_E	0.550	0.20
53_S	229_K	0.550	0.20
182_I	242_S	0.549	0.20
249_E	271_E	0.547	0.20
37_K	137_G	0.547	0.20
119_K	195_K	0.545	0.20
152_E	283_K	0.545	0.20
3_E	198_I	0.545	0.20
35_I	154_I	0.543	0.20
24_T	35_I	0.542	0.20
177_I	186_V	0.541	0.19
180_N	194_D	0.540	0.19
37_K	50_L	0.539	0.19
154_I	233_L	0.538	0.19
95_K	160_E	0.537	0.19
34_K	271_E	0.537	0.19
197_F	282_L	0.536	0.19
272_S	276_A	0.536	0.19
195_K	220_E	0.534	0.19
158_Y	196_P	0.534	0.19
135_I	139_K	0.533	0.19
62_T	218_L	0.533	0.19
45_P	240_E	0.531	0.19
60_D	196_P	0.531	0.19
157_I	261_I	0.531	0.19
93_E	255_K	0.526	0.19
279_A	282_L	0.526	0.19
32_E	51_L	0.526	0.19
101_Q	107_L	0.522	0.19
138_K	145_A	0.520	0.19
20_G	47_K	0.519	0.19
75_S	206_L	0.519	0.19
107_L	147_L	0.519	0.19
49_A	145_A	0.519	0.19
39_A	194_D	0.518	0.19
99_S	102_L	0.516	0.18
230_I	246_D	0.516	0.18
51_L	264_G	0.514	0.18
132_L	250_A	0.514	0.18
209_P	240_E	0.512	0.18
19_K	258_K	0.511	0.18
77_R	94_H	0.511	0.18
93_E	257_P	0.510	0.18
146_E	150_L	0.510	0.18
25_S	71_T	0.509	0.18
154_I	230_I	0.509	0.18
82_K	201_E	0.509	0.18
99_S	148_C	0.507	0.18
80_Y	140_A	0.507	0.18
131_S	247_I	0.507	0.18
24_T	34_K	0.505	0.18
73_G	139_K	0.505	0.18
272_S	281_Q	0.504	0.18
8_I	40_F	0.504	0.18
88_Y	97_F	0.504	0.18
59_Y	120_I	0.503	0.18
222_I	226_L	0.503	0.18
99_S	178_I	0.502	0.18
245_L	249_E	0.502	0.18
58_Y	196_P	0.502	0.18
133_L	166_G	0.500	0.18

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
3dcfA	2	0.6254	100	0.622	Contact Map
2ibdA	2	0.646	100	0.624	Contact Map
4udsA	2	0.6254	100	0.626	Contact Map
2id6A	2	0.6495	100	0.629	Contact Map
2g3bA	2	0.6357	100	0.63	Contact Map
4gckA	2	0.6392	100	0.63	Contact Map
1vi0A	2	0.6392	100	0.631	Contact Map
3lsjA	2	0.6632	99.9	0.634	Contact Map
2genA	2	0.6392	99.9	0.636	Contact Map
3himA	2	0.646	99.9	0.636	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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