YERO - BACSU - GREMLIN Contacts

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YERO - Uncharacterized HTH-type transcriptional regulator YerO

UniProt:	O31500	Sequences: MNEKKERIIKTSIRLFAKKGFAATTIQEIASECGISKGAFYLHFKSKEALLLSACEYYIGMSMNKMKNIEEDLAGKPPKEVLKKQIGAQFEDFRDHKDFIVLLLTENIIPENQEIKQYFYKVTMETDKLYRNALLVSYGEGIERYVADLSIMARGIVHSYMNVMVFNGELNIDAEEISAFIIERLDDLVQGLSRSALNPIVSKDIFNPMPAGKDQLLEDIQKVKENSTLPEDITVSLDVIEEELTQDKPRKPIIKGMLSNLAGTNDKEVERLRALILSLSQFDHKKSSL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	289 (269)
Sequences:	391 (351)
Seq/√Len:	21.4

BACSU - YERO YUXN YCNC

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
138_Y	186_D	7.455	1.00
26_I	40_F	4.816	1.00
140_E	143_E	4.107	1.00
79_K	186_D	3.667	1.00
19_K	28_E	3.602	1.00
148_D	180_F	3.507	1.00
262_A	276_I	3.407	1.00
36_S	40_F	3.393	1.00
30_A	40_F	3.375	1.00
256_G	260_N	3.098	1.00
83_K	179_A	2.991	0.99
239_V	257_M	2.940	0.99
236_S	260_N	2.903	0.99
36_S	39_A	2.783	0.99
246_Q	250_R	2.632	0.98
11_T	32_E	2.583	0.98
239_V	253_I	2.543	0.98
233_I	261_L	2.500	0.98
37_K	41_Y	2.423	0.97
42_L	256_G	2.391	0.97
72_D	84_K	2.357	0.97
87_G	175_E	2.353	0.97
242_E	246_Q	2.280	0.96
31_S	188_L	2.238	0.96
39_A	42_L	2.144	0.95
23_A	148_D	2.073	0.94
201_V	242_E	2.068	0.93
96_H	253_I	2.031	0.93
239_V	252_P	2.024	0.93
243_E	250_R	1.992	0.92
187_D	191_G	1.987	0.92
39_A	43_H	1.967	0.92
180_F	184_R	1.963	0.92
42_L	45_K	1.943	0.91
261_L	276_I	1.912	0.90
236_S	256_G	1.897	0.90
16_F	24_T	1.879	0.90
15_L	24_T	1.845	0.89
216_L	254_I	1.821	0.88
27_Q	38_G	1.798	0.87
11_T	35_I	1.639	0.82
227_S	263_G	1.632	0.82
38_G	85_Q	1.627	0.81
160_Y	177_I	1.622	0.81
221_Q	241_E	1.618	0.81
85_Q	133_A	1.616	0.81
85_Q	137_S	1.600	0.80
27_Q	37_K	1.566	0.79
139_G	145_Y	1.522	0.77
38_G	46_S	1.490	0.75
235_V	252_P	1.478	0.75
261_L	275_L	1.465	0.74
103_L	106_E	1.444	0.73
252_P	260_N	1.436	0.72
176_E	198_N	1.435	0.72
27_Q	46_S	1.428	0.72
158_H	162_N	1.414	0.71
235_V	239_V	1.392	0.70
49_A	147_A	1.379	0.69
134_L	198_N	1.365	0.68
38_G	42_L	1.358	0.68
25_T	97_K	1.344	0.67
59_I	119_F	1.335	0.67
9_I	242_E	1.315	0.66
36_S	50_L	1.310	0.65
210_P	215_Q	1.308	0.65
243_E	249_P	1.301	0.65
139_G	144_R	1.298	0.64
25_T	155_G	1.296	0.64
232_D	255_K	1.283	0.64
152_M	156_I	1.275	0.63
159_S	260_N	1.265	0.62
8_I	260_N	1.256	0.62
12_S	49_A	1.243	0.61
219_D	223_V	1.237	0.61
50_L	96_H	1.227	0.60
217_L	224_K	1.225	0.60
139_G	142_I	1.222	0.60
82_L	90_F	1.211	0.59
25_T	36_S	1.206	0.59
23_A	254_I	1.206	0.59
99_F	103_L	1.190	0.58
53_S	253_I	1.185	0.57
210_P	275_L	1.179	0.57
239_V	260_N	1.160	0.56
42_L	85_Q	1.149	0.55
243_E	261_L	1.141	0.54
49_A	240_I	1.140	0.54
25_T	37_K	1.140	0.54
7_R	86_I	1.135	0.54
102_L	106_E	1.130	0.54
54_A	102_L	1.127	0.53
30_A	39_A	1.127	0.53
200_I	258_L	1.127	0.53
72_D	78_P	1.109	0.52
95_D	247_D	1.098	0.51
12_S	179_A	1.082	0.50
108_I	157_V	1.081	0.50
95_D	201_V	1.079	0.50
42_L	260_N	1.070	0.50
184_R	191_G	1.067	0.49
10_K	26_I	1.061	0.49
52_L	124_M	1.060	0.49
27_Q	31_S	1.055	0.49
33_C	178_S	1.055	0.49
218_E	223_V	1.053	0.48
82_L	118_Y	1.045	0.48
29_I	44_F	1.045	0.48
25_T	29_I	1.045	0.48
171_N	222_K	1.043	0.48
177_I	200_I	1.040	0.48
33_C	131_R	1.033	0.47
66_M	98_D	1.030	0.47
33_C	148_D	1.029	0.47
51_L	163_V	1.027	0.47
82_L	142_I	1.023	0.46
254_I	258_L	1.022	0.46
272_L	277_L	1.010	0.46
135_L	146_V	1.006	0.45
145_Y	189_V	1.006	0.45
213_K	227_S	1.004	0.45
121_K	219_D	0.993	0.44
52_L	118_Y	0.992	0.44
235_V	250_R	0.990	0.44
17_A	39_A	0.988	0.44
50_L	261_L	0.981	0.44
21_F	51_L	0.973	0.43
5_K	110_P	0.972	0.43
62_S	153_A	0.969	0.43
54_A	61_M	0.956	0.42
84_K	204_D	0.953	0.42
24_T	40_F	0.953	0.42
149_L	189_V	0.952	0.42
38_G	41_Y	0.951	0.42
71_E	223_V	0.945	0.41
66_M	163_V	0.943	0.41
184_R	189_V	0.941	0.41
4_K	8_I	0.939	0.41
20_G	47_K	0.938	0.41
148_D	184_R	0.934	0.41
27_Q	36_S	0.931	0.40
103_L	182_I	0.929	0.40
30_A	48_E	0.928	0.40
53_S	200_I	0.921	0.40
252_P	255_K	0.919	0.40
80_E	175_E	0.919	0.40
248_K	251_K	0.919	0.40
145_Y	152_M	0.918	0.40
234_T	258_L	0.917	0.39
43_H	153_A	0.915	0.39
57_Y	138_Y	0.914	0.39
3_E	52_L	0.913	0.39
254_I	271_R	0.912	0.39
267_K	271_R	0.911	0.39
12_S	34_G	0.899	0.38
49_A	70_E	0.897	0.38
241_E	249_P	0.896	0.38
21_F	159_S	0.895	0.38
102_L	105_T	0.894	0.38
66_M	69_I	0.891	0.38
99_F	256_G	0.891	0.38
43_H	137_S	0.884	0.37
27_Q	85_Q	0.882	0.37
4_K	42_L	0.881	0.37
36_S	42_L	0.879	0.37
144_R	241_E	0.879	0.37
26_I	41_Y	0.872	0.37
23_A	177_I	0.870	0.37
137_S	141_G	0.863	0.36
17_A	100_I	0.857	0.36
241_E	257_M	0.853	0.35
16_F	20_G	0.852	0.35
162_N	202_S	0.850	0.35
40_F	43_H	0.847	0.35
29_I	41_Y	0.846	0.35
212_G	216_L	0.838	0.35
212_G	223_V	0.837	0.34
160_Y	236_S	0.836	0.34
179_A	203_K	0.832	0.34
219_D	222_K	0.827	0.34
18_K	32_E	0.825	0.34
69_I	76_K	0.825	0.34
152_M	206_F	0.824	0.34
5_K	129_L	0.823	0.34
65_K	103_L	0.821	0.34
14_R	102_L	0.818	0.33
80_E	161_M	0.818	0.33
34_G	199_P	0.815	0.33
240_I	254_I	0.810	0.33
55_C	216_L	0.810	0.33
129_L	133_A	0.810	0.33
99_F	106_E	0.807	0.33
48_E	112_N	0.807	0.33
17_A	28_E	0.805	0.33
9_I	106_E	0.794	0.32
8_I	93_F	0.794	0.32
26_I	39_A	0.794	0.32
234_T	251_K	0.793	0.32
180_F	189_V	0.790	0.32
28_E	79_K	0.787	0.32
54_A	161_M	0.783	0.31
203_K	214_D	0.780	0.31
250_R	254_I	0.780	0.31
75_G	141_G	0.779	0.31
159_S	253_I	0.778	0.31
9_I	224_K	0.778	0.31
35_I	39_A	0.775	0.31
85_Q	97_K	0.768	0.30
8_I	45_K	0.768	0.30
8_I	138_Y	0.765	0.30
51_L	249_P	0.762	0.30
56_E	61_M	0.760	0.30
26_I	184_R	0.756	0.30
42_L	159_S	0.754	0.30
242_E	255_K	0.752	0.30
149_L	192_L	0.751	0.29
183_E	229_L	0.751	0.29
69_I	88_A	0.748	0.29
31_S	235_V	0.747	0.29
160_Y	180_F	0.746	0.29
8_I	22_A	0.745	0.29
220_I	225_E	0.740	0.29
28_E	185_L	0.738	0.29
152_M	180_F	0.731	0.28
134_L	240_I	0.730	0.28
99_F	112_N	0.730	0.28
85_Q	129_L	0.728	0.28
43_H	244_L	0.726	0.28
21_F	48_E	0.723	0.28
6_E	153_A	0.720	0.28
40_F	110_P	0.718	0.28
58_Y	102_L	0.711	0.27
257_M	260_N	0.711	0.27
116_K	189_V	0.706	0.27
30_A	42_L	0.705	0.27
252_P	257_M	0.705	0.27
137_S	198_N	0.703	0.27
82_L	162_N	0.702	0.27
39_A	58_Y	0.701	0.27
43_H	85_Q	0.701	0.27
17_A	186_D	0.700	0.27
211_A	221_Q	0.699	0.27
104_L	107_N	0.697	0.27
237_L	241_E	0.697	0.27
156_I	181_I	0.693	0.26
63_M	187_D	0.693	0.26
91_E	95_D	0.691	0.26
50_L	180_F	0.690	0.26
175_E	179_A	0.690	0.26
91_E	188_L	0.690	0.26
151_I	201_V	0.688	0.26
239_V	256_G	0.687	0.26
101_V	181_I	0.686	0.26
89_Q	156_I	0.684	0.26
121_K	198_N	0.684	0.26
24_T	35_I	0.677	0.26
207_N	221_Q	0.677	0.26
75_G	215_Q	0.675	0.25
173_D	237_L	0.674	0.25
30_A	50_L	0.674	0.25
59_I	122_V	0.673	0.25
135_L	234_T	0.670	0.25
4_K	252_P	0.669	0.25
18_K	45_K	0.669	0.25
26_I	38_G	0.669	0.25
37_K	139_G	0.667	0.25
132_N	210_P	0.662	0.25
31_S	272_L	0.662	0.25
24_T	38_G	0.661	0.25
59_I	100_I	0.661	0.25
207_N	238_D	0.660	0.25
36_S	41_Y	0.660	0.25
33_C	180_F	0.659	0.25
141_G	272_L	0.658	0.25
49_A	200_I	0.658	0.25
246_Q	253_I	0.657	0.25
37_K	155_G	0.653	0.24
22_A	153_A	0.652	0.24
21_F	150_S	0.652	0.24
265_N	268_E	0.648	0.24
33_C	276_I	0.648	0.24
89_Q	155_G	0.647	0.24
9_I	254_I	0.645	0.24
26_I	81_V	0.645	0.24
174_A	207_N	0.641	0.24
72_D	216_L	0.638	0.24
127_D	188_L	0.638	0.24
48_E	66_M	0.637	0.24
38_G	148_D	0.636	0.23
21_F	127_D	0.633	0.23
190_Q	261_L	0.632	0.23
57_Y	256_G	0.632	0.23
42_L	257_M	0.631	0.23
4_K	256_G	0.630	0.23
171_N	220_I	0.628	0.23
159_S	256_G	0.626	0.23
150_S	159_S	0.622	0.23
32_E	51_L	0.622	0.23
262_A	269_V	0.620	0.23
265_N	277_L	0.615	0.22
84_K	248_K	0.615	0.22
68_N	77_P	0.614	0.22
174_A	204_D	0.613	0.22
79_K	138_Y	0.613	0.22
9_I	44_F	0.610	0.22
43_H	97_K	0.606	0.22
223_V	269_V	0.604	0.22
62_S	237_L	0.601	0.22
20_G	24_T	0.599	0.22
41_Y	47_K	0.598	0.22
19_K	188_L	0.598	0.22
141_G	203_K	0.596	0.22
37_K	48_E	0.596	0.22
30_A	255_K	0.596	0.22
22_A	51_L	0.594	0.22
97_K	163_V	0.594	0.22
77_P	157_V	0.593	0.21
194_R	222_K	0.592	0.21
96_H	247_D	0.586	0.21
9_I	220_I	0.585	0.21
39_A	178_S	0.585	0.21
16_F	47_K	0.582	0.21
28_E	105_T	0.581	0.21
61_M	262_A	0.581	0.21
123_T	150_S	0.580	0.21
144_R	193_S	0.580	0.21
113_Q	124_M	0.577	0.21
228_T	259_S	0.575	0.21
139_G	201_V	0.574	0.21
4_K	101_V	0.572	0.21
101_V	104_L	0.569	0.20
40_F	158_H	0.568	0.20
57_Y	186_D	0.568	0.20
65_K	219_D	0.567	0.20
9_I	264_T	0.566	0.20
227_S	244_L	0.561	0.20
95_D	215_Q	0.561	0.20
155_G	208_P	0.558	0.20
16_F	44_F	0.557	0.20
54_A	134_L	0.557	0.20
264_T	268_E	0.556	0.20
25_T	35_I	0.555	0.20
218_E	248_K	0.554	0.20
81_V	136_V	0.554	0.20
41_Y	44_F	0.554	0.20
153_A	250_R	0.553	0.20
160_Y	201_V	0.549	0.20
8_I	261_L	0.548	0.20
138_Y	240_I	0.548	0.20
146_V	151_I	0.546	0.19
204_D	244_L	0.546	0.19
161_M	269_V	0.545	0.19
99_F	104_L	0.544	0.19
54_A	92_D	0.543	0.19
213_K	217_L	0.540	0.19
21_F	103_L	0.540	0.19
132_N	150_S	0.540	0.19
42_L	252_P	0.540	0.19
87_G	257_M	0.540	0.19
180_F	192_L	0.539	0.19
28_E	118_Y	0.539	0.19
45_K	232_D	0.534	0.19
26_I	84_K	0.532	0.19
173_D	232_D	0.531	0.19
85_Q	89_Q	0.530	0.19
117_Q	121_K	0.529	0.19
91_E	174_A	0.529	0.19
188_L	254_I	0.528	0.19
75_G	240_I	0.528	0.19
79_K	182_I	0.528	0.19
201_V	235_V	0.527	0.19
135_L	191_G	0.525	0.19
139_G	143_E	0.525	0.19
65_K	68_N	0.525	0.19
119_F	158_H	0.525	0.19
37_K	47_K	0.521	0.18
80_E	207_N	0.518	0.18
148_D	201_V	0.518	0.18
93_F	98_D	0.517	0.18
33_C	70_E	0.517	0.18
207_N	215_Q	0.517	0.18
242_E	266_D	0.516	0.18
84_K	221_Q	0.515	0.18
252_P	259_S	0.513	0.18
30_A	43_H	0.513	0.18
95_D	175_E	0.513	0.18
26_I	30_A	0.512	0.18
100_I	163_V	0.512	0.18
50_L	192_L	0.510	0.18
40_F	50_L	0.510	0.18
79_K	243_E	0.510	0.18
46_S	148_D	0.509	0.18
150_S	164_M	0.508	0.18
71_E	214_D	0.507	0.18
115_I	239_V	0.506	0.18
4_K	36_S	0.506	0.18
25_T	42_L	0.504	0.18
64_N	158_H	0.504	0.18
35_I	159_S	0.503	0.18
210_P	220_I	0.503	0.18
80_E	193_S	0.502	0.18
13_I	26_I	0.501	0.18
17_A	106_E	0.501	0.18
43_H	60_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	0.6298	100	0.621	Contact Map
2ibdA	2	0.6505	100	0.627	Contact Map
4udsA	2	0.6298	100	0.63	Contact Map
2id6A	2	0.6574	99.9	0.632	Contact Map
2g3bA	2	0.6401	99.9	0.636	Contact Map
4gckA	2	0.6436	99.9	0.636	Contact Map
1vi0A	2	0.6436	99.9	0.637	Contact Map
3himA	2	0.6505	99.9	0.639	Contact Map
3ccyA	2	0.6574	99.9	0.64	Contact Map
2genA	2	0.6436	99.9	0.64	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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