YDHC - BACSU - GREMLIN Contacts

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YDHC - Uncharacterized HTH-type transcriptional regulator YdhC

UniProt:	O05494	Sequences: MDDFKLDKPTPYYLQFYNQLKKMIFNGTFKPGERINETQLAKSFGVSRSPIREAMRLLEKDGLLKADDRNGFSITSLTAKDVDEIYKIRIPLEQLAVELVIDEADEEELTILEKQLEETEKAIHNGTEDTEIIRLNQKFHELLVDFSHNRHLKNLLEHVNDLIHFCRILNYTGDHRAETILREHRRIFEEVKKKNKEAAKQHVLAHFNHDCEHLKHVLEEGKEN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	224 (203)
Sequences:	23625 (17424)
Seq/√Len:	1222.9

ECOLI - MCBR YDFH YJJM NANR PDHR CSIR GLCC EXUR DGOR YIEP UXUR LLDR FADR FRLR YEGW YIDP
BACSU - YDHC GNTR YCBG LUTR YVOA YMFC YURK TRER YYDK
SULSO - Q97YR4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
113_E	192_K	3.778	1.00
98_E	200_K	3.296	1.00
195_N	198_A	2.916	1.00
120_E	185_R	2.789	1.00
23_M	28_T	2.717	1.00
30_K	33_E	2.687	1.00
23_M	43_S	2.390	1.00
91_P	95_L	2.299	1.00
37_E	48_R	2.232	1.00
111_I	142_L	2.214	1.00
84_E	150_R	2.188	1.00
90_I	208_N	2.093	1.00
17_Y	57_L	2.073	1.00
65_K	75_T	2.019	1.00
21_K	61_D	1.962	1.00
16_F	46_V	1.956	1.00
87_K	99_L	1.952	1.00
102_D	196_K	1.949	1.00
66_A	72_F	1.828	1.00
145_D	153_K	1.821	1.00
109_L	192_K	1.797	1.00
16_F	44_F	1.791	1.00
190_E	198_A	1.783	1.00
108_E	148_H	1.738	1.00
142_L	145_D	1.722	1.00
105_D	108_E	1.712	1.00
19_Q	23_M	1.679	1.00
94_Q	204_L	1.663	1.00
116_L	188_F	1.653	1.00
183_E	209_H	1.607	1.00
98_E	196_K	1.607	1.00
88_I	155_L	1.587	1.00
200_K	204_L	1.587	1.00
128_E	131_E	1.577	1.00
198_A	202_H	1.558	1.00
22_K	26_N	1.555	1.00
10_T	18_N	1.553	1.00
94_Q	200_K	1.543	1.00
140_H	184_H	1.542	1.00
95_L	98_E	1.536	1.00
186_R	202_H	1.476	1.00
144_V	156_L	1.434	1.00
120_E	181_L	1.417	1.00
118_E	135_L	1.417	1.00
141_E	157_E	1.416	1.00
154_N	158_H	1.406	1.00
97_V	199_A	1.398	1.00
189_E	193_K	1.396	1.00
151_H	162_L	1.395	1.00
90_I	204_L	1.394	1.00
67_D	70_N	1.389	1.00
17_Y	61_D	1.388	1.00
115_Q	135_L	1.372	1.00
108_E	146_F	1.371	1.00
113_E	188_F	1.366	1.00
193_K	198_A	1.363	1.00
90_I	211_C	1.360	1.00
38_T	42_K	1.335	1.00
84_E	151_H	1.312	1.00
185_R	189_E	1.307	1.00
104_A	109_L	1.306	1.00
196_K	200_K	1.270	1.00
118_E	138_K	1.259	1.00
113_E	117_E	1.258	1.00
114_K	118_E	1.252	1.00
39_Q	43_S	1.230	1.00
36_N	39_Q	1.204	1.00
40_L	51_I	1.200	1.00
90_I	94_Q	1.197	1.00
115_Q	142_L	1.197	1.00
34_R	73_S	1.194	1.00
116_L	185_R	1.191	1.00
15_Q	19_Q	1.182	1.00
19_Q	22_K	1.182	1.00
183_E	206_H	1.181	1.00
201_Q	205_A	1.179	1.00
67_D	73_S	1.164	1.00
204_L	208_N	1.144	1.00
23_M	44_F	1.142	1.00
89_R	93_E	1.140	1.00
59_E	66_A	1.139	1.00
104_A	194_K	1.138	1.00
138_K	142_L	1.138	1.00
19_Q	44_F	1.133	1.00
141_E	145_D	1.131	1.00
198_A	201_Q	1.131	1.00
84_E	149_N	1.119	1.00
104_A	146_F	1.119	1.00
97_V	101_I	1.105	1.00
143_L	191_V	1.102	1.00
98_E	197_E	1.091	1.00
94_Q	98_E	1.091	1.00
136_N	140_H	1.090	1.00
142_L	146_F	1.074	1.00
97_V	203_V	1.070	1.00
116_L	119_T	1.069	1.00
131_E	134_R	1.069	1.00
115_Q	138_K	1.064	1.00
109_L	188_F	1.062	1.00
189_E	192_K	1.062	1.00
104_A	108_E	1.056	1.00
29_F	74_I	1.054	1.00
113_E	185_R	1.052	1.00
188_F	192_K	1.048	1.00
111_I	145_D	1.035	1.00
96_A	144_V	1.033	1.00
87_K	149_N	1.030	1.00
116_L	120_E	1.017	1.00
184_H	206_H	1.011	1.00
83_D	211_C	1.009	1.00
117_E	120_E	1.005	1.00
109_L	194_K	1.002	1.00
65_K	73_S	0.997	1.00
135_L	138_K	0.987	1.00
190_E	195_N	0.975	1.00
53_E	56_R	0.973	1.00
111_I	114_K	0.972	1.00
140_H	206_H	0.970	1.00
155_L	158_H	0.968	1.00
59_E	64_L	0.967	1.00
10_T	15_Q	0.967	1.00
99_L	103_E	0.959	1.00
182_R	186_R	0.959	1.00
95_L	200_K	0.950	1.00
55_M	72_F	0.948	1.00
24_I	74_I	0.947	1.00
121_K	125_N	0.947	1.00
110_T	114_K	0.947	1.00
147_S	153_K	0.946	1.00
67_D	71_G	0.941	1.00
186_R	205_A	0.940	1.00
101_I	196_K	0.937	1.00
23_M	29_F	0.929	1.00
139_F	188_F	0.926	1.00
134_R	138_K	0.924	1.00
13_Y	57_L	0.923	1.00
93_E	140_H	0.922	1.00
186_R	198_A	0.920	1.00
111_I	115_Q	0.916	1.00
64_L	72_F	0.904	1.00
153_K	157_E	0.902	1.00
78_T	81_D	0.900	1.00
186_R	189_E	0.900	1.00
197_E	201_Q	0.896	1.00
34_R	71_G	0.892	1.00
37_E	52_R	0.886	1.00
17_Y	21_K	0.884	1.00
101_I	191_V	0.881	1.00
57_L	60_K	0.877	1.00
109_L	113_E	0.876	1.00
187_I	203_V	0.875	1.00
88_I	151_H	0.867	1.00
103_E	148_H	0.864	1.00
70_N	73_S	0.863	1.00
104_A	191_V	0.857	1.00
41_A	51_I	0.855	1.00
115_Q	118_E	0.855	1.00
81_D	151_H	0.855	1.00
21_K	63_L	0.847	1.00
95_L	99_L	0.839	1.00
181_L	185_R	0.836	1.00
113_E	189_E	0.835	1.00
197_E	200_K	0.834	1.00
21_K	25_F	0.825	1.00
101_I	194_K	0.825	1.00
89_R	207_F	0.825	1.00
106_E	110_T	0.825	1.00
47_S	50_P	0.824	1.00
118_E	121_K	0.817	1.00
122_A	131_E	0.816	1.00
56_R	59_E	0.814	1.00
39_Q	42_K	0.814	1.00
100_V	146_F	0.802	1.00
108_E	111_I	0.800	1.00
117_E	121_K	0.795	1.00
55_M	64_L	0.792	1.00
12_Y	15_Q	0.791	1.00
187_I	202_H	0.788	1.00
80_K	148_H	0.784	1.00
136_N	184_H	0.783	1.00
46_V	51_I	0.781	1.00
112_L	142_L	0.777	1.00
186_R	190_E	0.776	1.00
56_R	66_A	0.776	1.00
190_E	202_H	0.772	1.00
11_P	14_L	0.772	1.00
151_H	155_L	0.771	1.00
14_L	57_L	0.771	1.00
100_V	104_A	0.770	1.00
87_K	211_C	0.764	1.00
112_L	188_F	0.763	1.00
106_E	194_K	0.763	1.00
40_L	55_M	0.758	1.00
12_Y	50_P	0.756	1.00
178_E	182_R	0.749	1.00
13_Y	17_Y	0.748	1.00
119_T	132_I	0.748	1.00
117_E	185_R	0.745	1.00
101_I	199_A	0.741	1.00
151_H	154_N	0.735	1.00
98_E	102_D	0.732	1.00
80_K	84_E	0.731	1.00
141_E	160_N	0.730	1.00
88_I	152_L	0.730	1.00
202_H	205_A	0.723	1.00
87_K	103_E	0.718	1.00
99_L	102_D	0.718	1.00
131_E	135_L	0.716	1.00
208_N	212_E	0.713	1.00
118_E	131_E	0.710	1.00
86_Y	210_D	0.709	1.00
110_T	192_K	0.707	1.00
201_Q	204_L	0.706	1.00
122_A	135_L	0.698	1.00
99_L	149_N	0.696	1.00
137_Q	160_N	0.694	1.00
111_I	138_K	0.693	1.00
110_T	113_E	0.692	1.00
141_E	153_K	0.690	1.00
116_L	181_L	0.686	1.00
88_I	96_A	0.677	1.00
28_T	43_S	0.676	1.00
137_Q	164_H	0.672	1.00
187_I	199_A	0.672	1.00
100_V	147_S	0.660	1.00
109_L	191_V	0.660	1.00
114_K	117_E	0.659	1.00
205_A	209_H	0.657	1.00
57_L	61_D	0.656	1.00
10_T	14_L	0.656	1.00
108_E	142_L	0.651	1.00
118_E	122_A	0.649	1.00
50_P	54_A	0.647	1.00
108_E	145_D	0.645	1.00
208_N	211_C	0.643	1.00
81_D	150_R	0.642	1.00
138_K	141_E	0.638	1.00
209_H	213_H	0.638	1.00
120_E	124_H	0.634	1.00
91_P	152_L	0.633	1.00
183_E	186_R	0.630	1.00
29_F	33_E	0.628	1.00
87_K	95_L	0.623	1.00
69_R	72_F	0.622	1.00
97_V	196_K	0.622	1.00
88_I	92_L	0.616	1.00
90_I	207_F	0.615	1.00
187_I	206_H	0.610	1.00
96_A	147_S	0.604	1.00
93_E	184_H	0.601	1.00
96_A	152_L	0.597	1.00
125_N	128_E	0.595	1.00
122_A	128_E	0.594	1.00
13_Y	53_E	0.593	1.00
132_I	180_I	0.592	1.00
23_M	27_G	0.590	1.00
94_Q	203_V	0.584	1.00
154_N	162_L	0.574	1.00
32_G	76_S	0.573	1.00
94_Q	196_K	0.571	1.00
107_E	111_I	0.568	1.00
119_T	181_L	0.568	1.00
44_F	51_I	0.566	1.00
80_K	83_D	0.561	1.00
31_P	76_S	0.556	1.00
100_V	143_L	0.549	1.00
92_L	156_L	0.546	1.00
91_P	94_Q	0.543	1.00
112_L	116_L	0.541	1.00
38_T	41_A	0.541	1.00
20_L	40_L	0.539	1.00
80_K	150_R	0.539	1.00
112_L	146_F	0.538	1.00
56_R	60_K	0.536	1.00
106_E	192_K	0.535	1.00
42_K	45_G	0.534	1.00
73_S	76_S	0.532	1.00
179_T	182_R	0.529	1.00
14_L	18_N	0.527	1.00
98_E	204_L	0.525	1.00
176_R	179_T	0.521	1.00
29_F	35_I	0.520	1.00
203_V	207_F	0.519	1.00
88_I	91_P	0.519	1.00
97_V	143_L	0.518	1.00
165_F	169_L	0.517	1.00
182_R	185_R	0.516	1.00
130_T	168_I	0.515	1.00
150_R	153_K	0.515	1.00
35_I	64_L	0.514	1.00
137_Q	141_E	0.511	1.00
112_L	115_Q	0.511	1.00
87_K	90_I	0.510	1.00
205_A	208_N	0.510	1.00
209_H	212_E	0.507	1.00
95_L	152_L	0.505	1.00
81_D	162_L	0.505	1.00
68_D	71_G	0.504	1.00
175_H	178_E	0.504	1.00
154_N	157_E	0.503	1.00
199_A	203_V	0.503	1.00
23_M	26_N	0.502	1.00
121_K	124_H	0.501	1.00
94_Q	97_V	0.500	1.00

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
3sxyA	2	0.8929	100	0.133	Contact Map
2hs5A	1	0.9241	100	0.138	Contact Map
3ihuA	1	0.9107	100	0.147	Contact Map
3c7jA	4	0.9821	100	0.148	Contact Map
4p9fA	1	0.933	100	0.156	Contact Map
4p96A	2	0.9777	100	0.171	Contact Map
2di3A	2	0.9241	100	0.196	Contact Map
1hw1A	2	0.9196	100	0.216	Contact Map
3by6A	2	0.5491	99.8	0.537	Contact Map
4r1hA	2	0.5045	99.8	0.54	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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