YDFH - ECOLI - GREMLIN Contacts

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YDFH - Uncharacterized HTH-type transcriptional regulator YdfH

UniProt:	P0ACM2	Sequences: MTVETQLNPTQPVNQQIYRILRRDIVHCLIAPGTPLSEKEVSVRFNVSRQPVREAFIKLAENGLIQIRPQRGSYVNKISMAQVRNGSFIRQAIECAVARRAASMITESQCYQLEQNLHQQRIAIERKQLDDFFELDDNFHQLLTQIADCQLAWDTIENLKATVDRVRYMSFDHVSPPEMLLRQHLDIFSALQKRDGDAVERAMTQHLQEISESVRQIRQENSDWFSEE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13820
Length:	228 (205)
Sequences:	23719 (17643)
Seq/√Len:	1232.2

ECOLI - YDFH MCBR PDHR YJJM NANR CSIR GLCC EXUR LLDR UXUR YIEP DGOR FADR FRLR YEGW YIDP
BACSU - GNTR YDHC 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
114_E	192_Q	3.771	1.00
99_R	200_E	3.296	1.00
195_D	198_A	2.957	1.00
121_R	185_L	2.800	1.00
24_D	29_L	2.730	1.00
31_A	34_T	2.681	1.00
24_D	44_R	2.412	1.00
92_A	96_A	2.325	1.00
38_E	49_R	2.273	1.00
112_Q	142_L	2.233	1.00
85_N	150_Q	2.147	1.00
91_Q	208_Q	2.092	1.00
18_Y	58_K	2.078	1.00
66_Q	76_N	2.054	1.00
88_F	100_R	1.976	1.00
22_R	62_N	1.968	1.00
17_I	47_V	1.965	1.00
103_S	196_G	1.961	1.00
145_Q	153_W	1.818	1.00
17_I	45_F	1.807	1.00
190_A	198_A	1.794	1.00
110_C	192_Q	1.790	1.00
109_Q	148_D	1.751	1.00
67_I	73_S	1.742	1.00
142_L	145_Q	1.739	1.00
20_I	24_D	1.710	1.00
95_C	204_T	1.708	1.00
106_T	109_Q	1.687	1.00
117_L	188_F	1.659	1.00
183_Q	209_E	1.636	1.00
99_R	196_G	1.626	1.00
128_Q	131_D	1.625	1.00
89_I	155_T	1.595	1.00
200_E	204_T	1.589	1.00
198_A	202_A	1.576	1.00
95_C	200_E	1.576	1.00
96_A	99_R	1.560	1.00
11_Q	19_R	1.558	1.00
23_R	27_H	1.537	1.00
140_H	184_H	1.528	1.00
186_D	202_A	1.484	1.00
144_T	156_I	1.442	1.00
119_Q	135_L	1.442	1.00
109_Q	146_I	1.436	1.00
121_R	181_L	1.426	1.00
98_A	199_V	1.421	1.00
154_D	158_N	1.419	1.00
141_Q	157_E	1.413	1.00
91_Q	204_T	1.405	1.00
114_E	188_F	1.393	1.00
151_L	162_T	1.393	1.00
18_Y	62_N	1.386	1.00
189_S	193_K	1.372	1.00
116_N	135_L	1.365	1.00
39_K	43_V	1.357	1.00
68_R	71_R	1.354	1.00
91_Q	211_S	1.353	1.00
193_K	198_A	1.336	1.00
105_I	110_C	1.332	1.00
85_N	151_L	1.308	1.00
185_L	189_S	1.290	1.00
196_G	200_E	1.271	1.00
114_E	118_H	1.253	1.00
115_Q	119_Q	1.247	1.00
40_E	44_R	1.240	1.00
37_S	40_E	1.232	1.00
35_P	74_Y	1.218	1.00
119_Q	138_N	1.215	1.00
116_N	142_L	1.201	1.00
183_Q	206_H	1.200	1.00
16_Q	20_I	1.196	1.00
91_Q	95_C	1.195	1.00
117_L	185_L	1.190	1.00
41_V	52_V	1.187	1.00
201_R	205_Q	1.181	1.00
20_I	23_R	1.169	1.00
90_R	94_E	1.165	1.00
24_D	45_F	1.158	1.00
84_R	215_R	1.155	1.00
141_Q	145_Q	1.153	1.00
138_N	142_L	1.151	1.00
20_I	45_F	1.139	1.00
68_R	74_Y	1.137	1.00
105_I	194_R	1.136	1.00
95_C	99_R	1.130	1.00
198_A	201_R	1.126	1.00
60_A	67_I	1.118	1.00
204_T	208_Q	1.118	1.00
84_R	211_S	1.109	1.00
105_I	146_I	1.107	1.00
99_R	197_D	1.104	1.00
105_I	109_Q	1.103	1.00
85_N	149_C	1.094	1.00
143_L	191_L	1.092	1.00
116_N	138_N	1.089	1.00
98_A	102_A	1.087	1.00
30_I	75_V	1.087	1.00
136_D	140_H	1.086	1.00
98_A	203_M	1.075	1.00
131_D	134_E	1.075	1.00
142_L	146_I	1.069	1.00
117_L	121_R	1.065	1.00
97_V	144_T	1.063	1.00
110_C	188_F	1.061	1.00
188_F	192_Q	1.057	1.00
189_S	192_Q	1.054	1.00
117_L	120_Q	1.043	1.00
114_E	185_L	1.041	1.00
112_Q	145_Q	1.020	1.00
110_C	194_R	1.018	1.00
88_F	149_C	1.017	1.00
66_Q	74_Y	1.011	1.00
211_S	215_R	1.010	1.00
135_L	138_N	1.001	1.00
155_T	158_N	0.993	1.00
60_A	65_I	0.993	1.00
112_Q	115_Q	0.986	1.00
54_E	57_I	0.985	1.00
118_H	121_R	0.984	1.00
11_Q	16_Q	0.984	1.00
190_A	195_D	0.980	1.00
184_H	206_H	0.979	1.00
140_H	206_H	0.972	1.00
24_D	30_I	0.969	1.00
94_E	140_H	0.965	1.00
96_A	200_E	0.955	1.00
186_D	205_Q	0.954	1.00
100_R	104_M	0.951	1.00
102_A	196_G	0.945	1.00
56_F	73_S	0.942	1.00
147_A	153_W	0.942	1.00
14_N	58_K	0.940	1.00
25_I	75_V	0.936	1.00
112_Q	116_N	0.934	1.00
139_F	188_F	0.931	1.00
182_R	186_D	0.930	1.00
134_E	138_N	0.924	1.00
111_Y	115_Q	0.916	1.00
65_I	73_S	0.912	1.00
38_E	53_R	0.911	1.00
186_D	198_A	0.910	1.00
186_D	189_S	0.908	1.00
79_S	82_Q	0.907	1.00
35_P	72_G	0.906	1.00
153_W	157_E	0.906	1.00
102_A	191_L	0.896	1.00
58_K	61_E	0.890	1.00
68_R	72_G	0.888	1.00
110_C	114_E	0.874	1.00
18_Y	22_R	0.874	1.00
197_D	201_R	0.870	1.00
104_M	148_D	0.870	1.00
71_R	74_Y	0.867	1.00
116_N	119_Q	0.863	1.00
187_I	203_M	0.863	1.00
96_A	100_R	0.852	1.00
22_R	64_L	0.851	1.00
42_S	52_V	0.851	1.00
89_I	151_L	0.849	1.00
109_Q	112_Q	0.840	1.00
114_E	189_S	0.836	1.00
181_L	185_L	0.835	1.00
90_R	207_L	0.834	1.00
48_S	51_P	0.834	1.00
13_V	16_Q	0.833	1.00
105_I	191_L	0.832	1.00
22_R	26_V	0.827	1.00
82_Q	151_L	0.827	1.00
136_D	184_H	0.822	1.00
197_D	200_E	0.822	1.00
107_E	111_Y	0.820	1.00
119_Q	122_I	0.820	1.00
57_I	60_A	0.820	1.00
102_A	194_R	0.815	1.00
56_F	65_I	0.802	1.00
118_H	122_I	0.797	1.00
123_A	131_D	0.796	1.00
186_D	190_A	0.796	1.00
40_E	43_V	0.794	1.00
151_L	155_T	0.793	1.00
187_I	202_A	0.793	1.00
101_A	146_I	0.786	1.00
122_I	126_R	0.783	1.00
41_V	56_F	0.780	1.00
15_Q	58_K	0.772	1.00
81_A	148_D	0.772	1.00
113_L	142_L	0.769	1.00
88_F	211_S	0.763	1.00
13_V	51_P	0.763	1.00
178_E	182_R	0.761	1.00
12_P	15_Q	0.761	1.00
190_A	202_A	0.758	1.00
121_R	125_E	0.757	1.00
151_L	154_D	0.756	1.00
120_Q	132_F	0.756	1.00
107_E	194_R	0.755	1.00
113_L	188_F	0.755	1.00
102_A	199_V	0.754	1.00
47_V	52_V	0.753	1.00
57_I	67_I	0.746	1.00
88_F	104_M	0.744	1.00
118_H	185_L	0.741	1.00
14_N	18_Y	0.740	1.00
202_A	205_Q	0.737	1.00
100_R	103_S	0.734	1.00
99_R	103_S	0.734	1.00
87_S	210_I	0.731	1.00
81_A	85_N	0.727	1.00
208_Q	212_E	0.724	1.00
141_Q	160_K	0.723	1.00
89_I	97_V	0.718	1.00
89_I	152_A	0.709	1.00
111_Y	192_Q	0.702	1.00
201_R	204_T	0.701	1.00
100_R	149_C	0.697	1.00
11_Q	15_Q	0.697	1.00
112_Q	138_N	0.691	1.00
131_D	135_L	0.687	1.00
111_Y	114_E	0.684	1.00
187_I	199_V	0.682	1.00
141_Q	153_W	0.682	1.00
123_A	135_L	0.681	1.00
119_Q	131_D	0.676	1.00
117_L	181_L	0.674	1.00
205_Q	209_E	0.674	1.00
208_Q	211_S	0.671	1.00
137_D	160_K	0.670	1.00
110_C	191_L	0.669	1.00
51_P	55_A	0.666	1.00
29_L	44_R	0.663	1.00
88_F	96_A	0.663	1.00
109_Q	145_Q	0.662	1.00
119_Q	123_A	0.662	1.00
109_Q	142_L	0.659	1.00
137_D	164_D	0.658	1.00
58_K	62_N	0.652	1.00
209_E	213_S	0.650	1.00
138_N	141_Q	0.643	1.00
115_Q	118_H	0.643	1.00
183_Q	186_D	0.642	1.00
92_A	152_A	0.635	1.00
30_I	34_T	0.629	1.00
187_I	206_H	0.626	1.00
97_V	147_A	0.620	1.00
97_V	152_A	0.619	1.00
89_I	93_I	0.616	1.00
98_A	196_G	0.614	1.00
70_Q	73_S	0.610	1.00
91_Q	207_L	0.610	1.00
14_N	54_E	0.606	1.00
94_E	184_H	0.606	1.00
95_C	203_M	0.604	1.00
101_A	105_I	0.598	1.00
101_A	147_A	0.591	1.00
24_D	28_C	0.590	1.00
120_Q	181_L	0.588	1.00
123_A	127_K	0.587	1.00
154_D	162_T	0.586	1.00
82_Q	150_Q	0.581	1.00
212_E	215_R	0.580	1.00
33_G	77_K	0.578	1.00
108_S	112_Q	0.568	1.00
113_L	146_I	0.568	1.00
93_I	156_I	0.567	1.00
32_P	77_K	0.563	1.00
123_A	128_Q	0.563	1.00
176_P	179_M	0.560	1.00
45_F	52_V	0.559	1.00
132_F	180_L	0.559	1.00
92_A	95_C	0.558	1.00
95_C	196_G	0.546	1.00
57_I	61_E	0.545	1.00
39_K	42_S	0.543	1.00
21_L	41_V	0.541	1.00
74_Y	77_K	0.537	1.00
36_L	65_I	0.535	1.00
99_R	204_T	0.535	1.00
182_R	185_L	0.534	1.00
107_E	192_Q	0.530	1.00
98_A	143_L	0.529	1.00
205_Q	208_Q	0.526	1.00
15_Q	19_R	0.525	1.00
43_V	46_N	0.524	1.00
113_L	117_L	0.521	1.00
89_I	92_A	0.520	1.00
26_V	64_L	0.520	1.00
100_R	147_A	0.519	1.00
187_I	190_A	0.518	1.00
150_Q	153_W	0.517	1.00
84_R	88_F	0.517	1.00
30_I	36_L	0.516	1.00
183_Q	205_Q	0.515	1.00
154_D	157_E	0.514	1.00
165_R	169_M	0.512	1.00
122_I	125_E	0.510	1.00
94_E	207_L	0.510	1.00
101_A	143_L	0.510	1.00
209_E	212_E	0.509	1.00
38_E	73_S	0.509	1.00
144_T	160_K	0.508	1.00
130_D	168_Y	0.507	1.00
203_M	207_L	0.507	1.00
82_Q	162_T	0.506	1.00
88_F	91_Q	0.504	1.00
179_M	182_R	0.503	1.00
24_D	27_H	0.502	1.00
191_L	199_V	0.502	1.00
30_I	44_R	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	0.8772	100	0.141	Contact Map
2hs5A	1	0.9079	100	0.151	Contact Map
3ihuA	1	0.8947	100	0.155	Contact Map
4p96A	2	0.9737	100	0.155	Contact Map
3c7jA	4	0.9781	100	0.163	Contact Map
4p9fA	1	0.9167	100	0.168	Contact Map
1hw1A	2	0.9035	100	0.202	Contact Map
2di3A	2	0.9079	100	0.209	Contact Map
3by6A	2	0.5395	99.8	0.546	Contact Map
3ic7A	2	0.4825	99.8	0.551	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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