YCNC - BACSU - GREMLIN Contacts

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YCNC - Uncharacterized HTH-type transcriptional regulator YcnC

UniProt:	P94423	Sequences: MLDKKTDILLAARKLFSEKDFTSVSMQAIAEECKMSKASIYKLFQSKEDLLLELLSFNQKQMVAAASRLQENTALTPEERLTQKVKMELEGFRRNQQFFNMLTYGNPKLHNDRVKQHIHQTRSTIICWHRDSLIQAYGETILPFVWDLVIILHGMMREFLMLIKIEEKPLELDPIAEFIISTLNQIIKNRETRQSLLPPEAIELYIHSASSYKPKDKSVLLSESLKELHKGISSLSAADYDVDELTSAAAMLEEEAKKEEPRAFLLKSLIGYLEQTGVLTQPVSMLKTLLIT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	292 (268)
Sequences:	457 (377)
Seq/√Len:	23.0

BACSU - YCNC YUXN 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
137_Y	184_N	6.420	1.00
26_M	40_I	5.334	1.00
19_K	28_A	4.691	1.00
139_E	142_L	3.779	1.00
30_A	40_I	3.369	1.00
78_E	184_N	3.215	1.00
248_A	272_Y	2.992	1.00
37_K	41_Y	2.888	0.99
251_M	269_L	2.868	0.99
229_H	253_E	2.784	0.99
11_A	32_E	2.723	0.99
268_S	272_Y	2.700	0.99
258_K	262_R	2.619	0.99
147_D	178_F	2.596	0.99
72_N	83_Q	2.562	0.99
31_E	186_I	2.282	0.97
254_E	258_K	2.259	0.97
95_N	265_L	2.236	0.97
245_L	273_L	2.217	0.96
255_E	262_R	2.172	0.96
251_M	264_F	2.130	0.95
251_M	265_L	2.100	0.95
82_T	177_E	2.092	0.95
178_F	182_T	2.064	0.95
16_F	24_V	2.062	0.95
42_K	268_S	2.025	0.94
36_S	40_I	2.020	0.94
38_A	84_K	1.930	0.92
248_A	268_S	1.883	0.91
86_K	173_D	1.867	0.91
39_S	42_K	1.860	0.91
26_M	38_A	1.846	0.90
151_I	155_M	1.827	0.90
42_K	45_Q	1.804	0.89
244_E	267_K	1.729	0.87
185_Q	189_N	1.728	0.87
247_S	264_F	1.693	0.86
84_K	136_A	1.681	0.86
4_K	36_S	1.665	0.85
11_A	35_M	1.637	0.84
27_Q	36_S	1.618	0.83
81_L	89_L	1.614	0.83
36_S	39_S	1.600	0.83
277_G	280_T	1.553	0.81
37_K	154_G	1.546	0.81
38_A	41_Y	1.544	0.80
175_I	196_L	1.543	0.80
264_F	272_Y	1.540	0.80
53_E	265_L	1.536	0.80
138_G	144_F	1.474	0.77
102_L	105_G	1.460	0.76
16_F	47_K	1.444	0.76
54_L	101_M	1.442	0.76
38_A	42_K	1.433	0.75
12_A	49_D	1.422	0.75
27_Q	37_K	1.418	0.74
38_A	46_S	1.397	0.73
133_L	194_Q	1.390	0.73
129_H	133_L	1.386	0.73
23_S	147_D	1.381	0.72
218_S	222_S	1.379	0.72
134_I	145_V	1.368	0.72
15_L	40_I	1.363	0.71
203_E	227_E	1.361	0.71
16_F	20_D	1.356	0.71
246_T	270_I	1.350	0.71
43_L	136_A	1.340	0.70
255_E	273_L	1.318	0.69
5_K	49_D	1.315	0.68
50_L	95_N	1.305	0.68
149_V	158_E	1.304	0.68
9_L	254_E	1.294	0.67
247_S	251_M	1.292	0.67
84_K	132_S	1.274	0.66
50_L	273_L	1.273	0.66
8_I	272_Y	1.267	0.66
178_F	187_I	1.264	0.65
23_S	266_L	1.238	0.64
53_E	196_L	1.235	0.63
144_F	147_D	1.233	0.63
49_D	146_W	1.226	0.63
260_E	263_A	1.219	0.62
39_S	43_L	1.215	0.62
8_I	43_L	1.214	0.62
157_R	161_M	1.212	0.62
264_F	267_K	1.210	0.62
27_Q	38_A	1.210	0.62
23_S	117_H	1.182	0.60
46_S	147_D	1.168	0.59
159_F	178_F	1.166	0.59
52_L	117_H	1.166	0.59
69_L	75_L	1.158	0.58
101_M	104_Y	1.151	0.58
95_N	259_E	1.145	0.58
15_L	24_V	1.139	0.57
251_M	272_Y	1.139	0.57
3_D	52_L	1.138	0.57
17_S	28_A	1.138	0.57
159_F	175_I	1.135	0.57
36_S	42_K	1.135	0.57
158_E	272_Y	1.128	0.56
262_R	266_L	1.121	0.56
42_K	84_K	1.118	0.56
27_Q	31_E	1.116	0.56
40_I	157_R	1.113	0.55
49_D	70_Q	1.103	0.55
39_S	158_E	1.094	0.54
30_A	48_E	1.093	0.54
136_A	194_Q	1.087	0.54
12_A	34_K	1.087	0.54
8_I	22_T	1.084	0.53
81_L	122_R	1.084	0.53
72_N	77_P	1.083	0.53
12_A	177_E	1.061	0.52
254_E	267_K	1.060	0.52
99_F	185_Q	1.050	0.51
15_L	47_K	1.047	0.51
81_L	117_H	1.046	0.51
78_E	180_I	1.042	0.50
148_L	187_I	1.041	0.50
128_W	132_S	1.034	0.50
7_D	85_V	1.029	0.50
199_P	230_K	1.028	0.49
6_T	152_L	1.023	0.49
59_Q	118_I	1.020	0.49
246_T	263_A	1.019	0.49
231_G	235_L	1.018	0.49
243_D	246_T	1.017	0.49
66_A	97_Q	1.014	0.48
66_A	69_L	1.009	0.48
155_M	179_I	0.999	0.47
166_E	202_I	0.998	0.47
40_I	50_L	0.994	0.47
26_M	30_A	0.992	0.47
182_T	189_N	0.989	0.47
20_D	24_V	0.988	0.47
33_C	40_I	0.985	0.46
235_L	279_L	0.981	0.46
49_D	252_L	0.981	0.46
84_K	96_Q	0.981	0.46
266_L	270_I	0.980	0.46
122_R	125_I	0.979	0.46
197_L	254_E	0.978	0.46
66_A	162_L	0.974	0.46
228_L	249_A	0.973	0.46
174_P	194_Q	0.971	0.45
17_S	105_G	0.968	0.45
246_T	279_L	0.963	0.45
252_L	266_L	0.960	0.45
253_E	261_P	0.955	0.44
54_L	61_Q	0.955	0.44
45_Q	49_D	0.952	0.44
181_S	193_R	0.949	0.44
21_F	48_E	0.948	0.44
149_V	173_D	0.940	0.43
18_E	108_K	0.925	0.42
182_T	187_I	0.922	0.42
102_L	180_I	0.920	0.42
262_R	273_L	0.920	0.42
22_T	114_V	0.920	0.42
29_I	44_F	0.916	0.42
197_L	202_I	0.915	0.42
94_R	259_E	0.914	0.42
4_K	8_I	0.913	0.42
122_R	161_M	0.902	0.41
88_E	155_M	0.901	0.41
33_C	176_A	0.899	0.41
112_D	123_S	0.893	0.40
42_K	272_Y	0.893	0.40
172_L	224_S	0.886	0.40
74_A	129_H	0.882	0.39
210_S	246_T	0.876	0.39
39_S	58_N	0.874	0.39
25_S	96_Q	0.866	0.38
57_F	137_Y	0.852	0.37
39_S	176_A	0.852	0.37
65_A	230_K	0.852	0.37
144_F	157_R	0.851	0.37
255_E	261_P	0.851	0.37
144_F	151_I	0.851	0.37
114_V	251_M	0.847	0.37
36_S	133_L	0.847	0.37
52_L	123_S	0.846	0.37
83_Q	235_L	0.836	0.36
34_K	65_A	0.836	0.36
249_A	253_E	0.831	0.36
112_D	137_Y	0.821	0.35
25_S	29_I	0.820	0.35
48_E	95_N	0.818	0.35
25_S	154_G	0.812	0.35
253_E	275_Q	0.812	0.35
138_G	141_I	0.811	0.35
4_K	62_M	0.809	0.35
172_L	180_I	0.808	0.35
248_A	264_F	0.807	0.35
38_A	54_L	0.806	0.35
98_F	104_Y	0.803	0.34
269_L	272_Y	0.801	0.34
98_F	268_S	0.796	0.34
81_L	141_I	0.787	0.33
247_S	262_R	0.784	0.33
150_I	280_T	0.781	0.33
148_L	190_R	0.780	0.33
30_A	39_S	0.773	0.32
69_L	180_I	0.772	0.32
17_S	99_F	0.771	0.32
30_A	42_K	0.770	0.32
254_E	262_R	0.766	0.32
17_S	26_M	0.765	0.32
151_I	211_S	0.765	0.32
27_Q	84_K	0.763	0.32
81_L	84_K	0.762	0.32
79_E	173_D	0.760	0.32
17_S	184_N	0.756	0.31
253_E	269_L	0.755	0.31
246_T	257_K	0.755	0.31
276_T	280_T	0.751	0.31
8_I	40_I	0.750	0.31
264_F	271_G	0.746	0.31
131_D	180_I	0.745	0.31
24_V	40_I	0.745	0.31
10_L	26_M	0.743	0.31
50_L	54_L	0.740	0.31
220_L	228_L	0.737	0.30
134_I	246_T	0.737	0.30
81_L	161_M	0.736	0.30
85_V	278_V	0.734	0.30
6_T	59_Q	0.734	0.30
84_K	128_W	0.733	0.30
36_S	41_Y	0.733	0.30
10_L	152_L	0.731	0.30
66_A	251_M	0.727	0.30
69_L	202_I	0.726	0.30
28_A	78_E	0.721	0.29
38_A	45_Q	0.721	0.29
83_Q	260_E	0.719	0.29
224_S	277_G	0.719	0.29
83_Q	229_H	0.718	0.29
183_L	246_T	0.718	0.29
25_S	37_K	0.718	0.29
186_I	225_L	0.715	0.29
8_I	273_L	0.712	0.29
48_E	66_A	0.711	0.29
150_I	197_L	0.710	0.29
24_V	34_K	0.710	0.29
19_K	262_R	0.708	0.29
16_F	37_K	0.708	0.29
159_F	248_A	0.707	0.29
133_L	252_L	0.705	0.28
253_E	273_L	0.702	0.28
79_E	160_L	0.701	0.28
76_T	179_I	0.700	0.28
76_T	79_E	0.698	0.28
24_V	46_S	0.697	0.28
83_Q	233_S	0.694	0.28
113_R	177_E	0.693	0.28
105_G	108_K	0.690	0.28
176_A	179_I	0.687	0.27
154_G	182_T	0.685	0.27
57_F	268_S	0.682	0.27
26_M	182_T	0.682	0.27
261_P	265_L	0.679	0.27
7_D	42_K	0.679	0.27
74_A	210_S	0.678	0.27
14_K	78_E	0.677	0.27
97_Q	149_V	0.677	0.27
41_Y	50_L	0.674	0.27
264_F	269_L	0.674	0.27
81_L	134_I	0.673	0.27
21_F	126_I	0.671	0.27
34_K	105_G	0.669	0.26
12_A	138_G	0.669	0.26
192_T	229_H	0.668	0.26
225_L	228_L	0.664	0.26
28_A	117_H	0.660	0.26
39_S	98_F	0.659	0.26
4_K	42_K	0.656	0.26
117_H	121_T	0.651	0.26
8_I	137_Y	0.650	0.25
74_A	250_A	0.650	0.25
57_F	101_M	0.649	0.25
43_L	256_A	0.649	0.25
251_M	268_S	0.648	0.25
246_T	250_A	0.648	0.25
171_E	174_P	0.647	0.25
37_K	50_L	0.646	0.25
54_L	91_G	0.645	0.25
254_E	279_L	0.644	0.25
235_L	254_E	0.644	0.25
23_S	175_I	0.642	0.25
37_K	42_K	0.642	0.25
33_C	130_R	0.639	0.25
9_L	276_T	0.636	0.25
4_K	148_L	0.634	0.25
158_E	268_S	0.633	0.25
254_E	278_V	0.633	0.25
37_K	47_K	0.632	0.25
53_E	86_K	0.632	0.25
55_L	108_K	0.631	0.24
138_G	143_P	0.629	0.24
142_L	235_L	0.629	0.24
39_S	49_D	0.627	0.24
144_F	187_I	0.627	0.24
80_R	230_K	0.626	0.24
40_I	44_F	0.625	0.24
197_L	205_Y	0.625	0.24
25_S	71_E	0.624	0.24
104_Y	109_L	0.624	0.24
74_A	252_L	0.619	0.24
9_L	165_I	0.618	0.24
236_S	277_G	0.618	0.24
26_M	223_E	0.615	0.24
19_K	77_P	0.611	0.23
158_E	265_L	0.610	0.23
243_D	271_G	0.610	0.23
21_F	51_L	0.609	0.23
41_Y	81_L	0.609	0.23
81_L	206_I	0.609	0.23
4_K	268_S	0.608	0.23
94_R	220_L	0.607	0.23
221_L	228_L	0.606	0.23
41_Y	47_K	0.606	0.23
234_S	275_Q	0.605	0.23
177_E	199_P	0.605	0.23
30_A	251_M	0.604	0.23
90_E	179_I	0.600	0.23
250_A	280_T	0.600	0.23
84_K	88_E	0.597	0.23
143_P	229_H	0.596	0.23
152_L	167_E	0.596	0.23
43_L	96_Q	0.594	0.23
34_K	106_N	0.594	0.23
171_E	244_E	0.593	0.23
151_I	182_T	0.592	0.23
50_L	178_F	0.592	0.23
172_L	176_A	0.591	0.22
116_Q	120_Q	0.589	0.22
136_A	140_T	0.589	0.22
69_L	114_V	0.586	0.22
52_L	279_L	0.584	0.22
228_L	279_L	0.584	0.22
249_A	278_V	0.581	0.22
52_L	114_V	0.578	0.22
107_P	156_M	0.574	0.22
42_K	66_A	0.572	0.22
18_E	32_E	0.571	0.22
96_Q	162_L	0.567	0.21
39_S	125_I	0.563	0.21
48_E	111_N	0.562	0.21
63_V	185_Q	0.562	0.21
152_L	262_R	0.561	0.21
37_K	98_F	0.561	0.21
119_H	206_I	0.558	0.21
138_G	142_L	0.558	0.21
37_K	138_G	0.558	0.21
228_L	232_I	0.557	0.21
58_N	155_M	0.556	0.21
26_M	66_A	0.556	0.21
26_M	83_Q	0.555	0.21
244_E	279_L	0.551	0.21
22_T	51_L	0.547	0.20
26_M	221_L	0.546	0.20
183_L	219_V	0.545	0.20
17_S	57_F	0.544	0.20
32_E	51_L	0.544	0.20
4_K	37_K	0.542	0.20
233_S	243_D	0.541	0.20
65_A	68_R	0.541	0.20
13_R	58_N	0.537	0.20
34_K	96_Q	0.536	0.20
86_K	269_L	0.534	0.20
76_T	228_L	0.533	0.20
60_K	155_M	0.532	0.20
34_K	275_Q	0.531	0.20
217_K	232_I	0.530	0.20
51_L	162_L	0.530	0.20
39_S	100_N	0.529	0.20
78_E	95_N	0.526	0.19
26_M	46_S	0.526	0.19
200_E	266_L	0.523	0.19
232_I	280_T	0.518	0.19
25_S	80_R	0.518	0.19
74_A	236_S	0.517	0.19
9_L	266_L	0.515	0.19
58_N	98_F	0.515	0.19
11_A	61_Q	0.515	0.19
263_A	274_E	0.513	0.19
124_T	133_L	0.513	0.19
102_L	192_T	0.512	0.19
267_K	272_Y	0.511	0.19
28_A	104_Y	0.510	0.19
145_V	148_L	0.508	0.19
151_I	178_F	0.507	0.19
42_K	158_E	0.507	0.19
246_T	260_E	0.506	0.19
36_S	154_G	0.506	0.19
90_E	94_R	0.505	0.19
171_E	249_A	0.504	0.19
25_S	52_L	0.502	0.18
13_R	97_Q	0.502	0.18
82_T	176_A	0.501	0.18
27_Q	46_S	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	0.6233	100	0.592	Contact Map
2ibdA	2	0.6438	100	0.594	Contact Map
2g3bA	2	0.6301	100	0.603	Contact Map
4udsA	2	0.6233	100	0.604	Contact Map
2id6A	2	0.6507	100	0.605	Contact Map
1vi0A	2	0.637	100	0.605	Contact Map
4gckA	2	0.637	100	0.606	Contact Map
3bqzB	3	0.6301	100	0.611	Contact Map
2genA	2	0.637	100	0.612	Contact Map
3himA	2	0.6438	100	0.612	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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