YDEO - ECOLI - GREMLIN Contacts

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YDEO - HTH-type transcriptional regulator YdeO

UniProt:	P76135	Sequences: MSLVCSVIFIHHAFNANILDKDYAFSDGEILMVDNAVRTHFEPYERHFKEIGFTENTIKKYLQCTNIQTVTVPVPAKFLRASNVPTGLLNEMIAYLNSEERNHHNFSELLLFSCLSIFAACKGFITLLTNGVLSVSGKVRNIVNMKPAHPWKLKDICDCLYISESLLKKKLKQEQTTFSQILLDARMQHAKNLIRVEGSVNKIAEQCGYASTSYFIYAFRKHFGNSPKRVSKEYRCQSHTGMNTGNTMNALAI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13797
Length:	253 (223)
Sequences:	34216 (29426)
Seq/√Len:	1970.5

ECOLI - YDEO APPY GADW YBCM YDIP YQHC RHAR YIDL ARAC FEAR MELR ENVY YIJO GADX ADIY RHAS CHBR YPDC RCLR YEAM EUTR MARA YKGA SOXS ROB XYLR
BACSU - YBFI YDEC YFIF YISR BTR YOBQ ADAA YTDP YDEE YESN YESS

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
191_K	223_F	3.233	1.00
176_T	184_D	3.184	1.00
144_N	185_A	3.000	1.00
187_M	223_F	2.852	1.00
142_I	146_K	2.763	1.00
189_H	192_N	2.733	1.00
154_K	164_E	2.712	1.00
184_D	222_H	2.501	1.00
146_K	149_H	2.484	1.00
219_F	230_V	2.479	1.00
139_V	167_L	2.246	1.00
190_A	215_F	2.162	1.00
193_L	206_Q	2.155	1.00
171_L	181_I	2.118	1.00
147_P	185_A	2.013	1.00
193_L	207_C	1.968	1.00
225_N	233_E	1.946	1.00
152_K	155_D	1.944	1.00
15_N	22_D	1.850	1.00
142_I	159_C	1.844	1.00
179_S	183_L	1.798	1.00
143_V	182_L	1.783	1.00
187_M	222_H	1.781	1.00
139_V	160_L	1.770	1.00
140_R	174_E	1.735	1.00
212_T	216_I	1.702	1.00
199_S	202_K	1.691	1.00
15_N	24_A	1.689	1.00
156_I	178_F	1.658	1.00
191_K	230_V	1.654	1.00
153_L	168_K	1.646	1.00
141_N	145_M	1.642	1.00
17_N	22_D	1.624	1.00
136_S	174_E	1.616	1.00
166_L	170_K	1.610	1.00
110_L	113_S	1.577	1.00
192_N	196_V	1.569	1.00
11_H	47_H	1.567	1.00
218_A	221_K	1.564	1.00
109_L	116_S	1.557	1.00
13_A	24_A	1.548	1.00
189_H	193_L	1.547	1.00
26_S	29_E	1.533	1.00
176_T	180_Q	1.526	1.00
142_I	151_W	1.520	1.00
167_L	178_F	1.515	1.00
201_N	212_T	1.510	1.00
185_A	189_H	1.497	1.00
178_F	182_L	1.480	1.00
109_L	113_S	1.477	1.00
225_N	229_R	1.459	1.00
214_Y	218_A	1.452	1.00
144_N	181_I	1.450	1.00
194_I	200_V	1.445	1.00
147_P	189_H	1.440	1.00
10_I	49_K	1.436	1.00
116_S	120_A	1.428	1.00
228_K	232_K	1.423	1.00
166_L	169_K	1.422	1.00
202_K	205_E	1.418	1.00
164_E	168_K	1.413	1.00
113_S	117_I	1.406	1.00
13_A	26_S	1.399	1.00
201_N	205_E	1.391	1.00
148_A	206_Q	1.385	1.00
143_V	185_A	1.383	1.00
139_V	156_I	1.374	1.00
168_K	178_F	1.371	1.00
190_A	207_C	1.357	1.00
162_I	166_L	1.357	1.00
165_S	169_K	1.356	1.00
112_F	116_S	1.350	1.00
140_R	144_N	1.346	1.00
209_Y	218_A	1.341	1.00
17_N	40_H	1.340	1.00
203_I	207_C	1.316	1.00
184_D	188_Q	1.310	1.00
154_K	158_D	1.309	1.00
202_K	206_Q	1.302	1.00
189_H	207_C	1.294	1.00
197_E	231_S	1.289	1.00
90_N	94_A	1.279	1.00
177_T	180_Q	1.268	1.00
213_S	216_I	1.265	1.00
19_L	37_V	1.263	1.00
155_D	159_C	1.261	1.00
34_D	37_V	1.257	1.00
183_L	218_A	1.241	1.00
149_H	155_D	1.240	1.00
86_T	90_N	1.224	1.00
185_A	188_Q	1.202	1.00
216_I	226_S	1.169	1.00
216_I	228_K	1.154	1.00
163_S	166_L	1.152	1.00
11_H	27_D	1.149	1.00
135_V	162_I	1.144	1.00
217_Y	221_K	1.144	1.00
162_I	167_L	1.141	1.00
191_K	195_R	1.141	1.00
99_E	103_H	1.137	1.00
109_L	112_F	1.127	1.00
188_Q	191_K	1.109	1.00
211_S	217_Y	1.099	1.00
157_C	164_E	1.090	1.00
15_N	42_E	1.085	1.00
142_I	160_L	1.082	1.00
153_L	178_F	1.082	1.00
229_R	232_K	1.076	1.00
91_E	95_Y	1.070	1.00
151_W	156_I	1.062	1.00
197_E	203_I	1.058	1.00
148_A	189_H	1.052	1.00
134_S	138_K	1.049	1.00
200_V	203_I	1.042	1.00
29_E	80_R	1.042	1.00
183_L	221_K	1.028	1.00
106_F	113_S	1.024	1.00
170_K	173_Q	1.023	1.00
156_I	159_C	1.022	1.00
135_V	160_L	1.015	1.00
228_K	231_S	1.015	1.00
226_S	229_R	1.008	1.00
193_L	203_I	1.006	1.00
137_G	141_N	0.990	1.00
10_I	47_H	0.984	1.00
180_Q	183_L	0.982	1.00
216_I	220_R	0.978	1.00
87_G	90_N	0.976	1.00
138_K	159_C	0.974	1.00
95_Y	99_E	0.970	1.00
150_P	155_D	0.969	1.00
155_D	158_D	0.969	1.00
135_V	170_K	0.968	1.00
140_R	181_I	0.966	1.00
81_A	85_P	0.963	1.00
150_P	210_A	0.960	1.00
218_A	222_H	0.937	1.00
191_K	219_F	0.933	1.00
108_E	112_F	0.932	1.00
180_Q	184_D	0.928	1.00
165_S	168_K	0.920	1.00
143_V	178_F	0.916	1.00
9_F	14_F	0.914	1.00
142_I	156_I	0.906	1.00
87_G	91_E	0.904	1.00
105_N	109_L	0.901	1.00
106_F	110_L	0.895	1.00
18_I	21_K	0.892	1.00
153_L	164_E	0.892	1.00
17_N	20_D	0.889	1.00
147_P	151_W	0.888	1.00
223_F	230_V	0.885	1.00
160_L	167_L	0.884	1.00
136_S	170_K	0.878	1.00
186_R	207_C	0.875	1.00
187_M	218_A	0.874	1.00
171_L	178_F	0.867	1.00
179_S	214_Y	0.864	1.00
138_K	141_N	0.864	1.00
138_K	160_L	0.855	1.00
75_P	78_F	0.854	1.00
113_S	116_S	0.850	1.00
183_L	222_H	0.848	1.00
229_R	233_E	0.847	1.00
214_Y	217_Y	0.845	1.00
14_F	25_F	0.837	1.00
162_I	170_K	0.832	1.00
137_G	140_R	0.831	1.00
179_S	182_L	0.820	1.00
33_V	39_T	0.818	1.00
147_P	182_L	0.817	1.00
146_K	159_C	0.808	1.00
220_R	226_S	0.806	1.00
136_S	139_V	0.804	1.00
105_N	108_E	0.803	1.00
194_I	203_I	0.795	1.00
14_F	24_A	0.791	1.00
91_E	94_A	0.791	1.00
195_R	230_V	0.789	1.00
140_R	171_L	0.786	1.00
194_I	231_S	0.786	1.00
16_A	31_L	0.784	1.00
55_E	59_K	0.778	1.00
168_K	177_T	0.777	1.00
180_Q	222_H	0.776	1.00
187_M	215_F	0.773	1.00
78_F	81_A	0.770	1.00
205_E	210_A	0.769	1.00
181_I	185_A	0.766	1.00
146_K	155_D	0.760	1.00
139_V	142_I	0.759	1.00
168_K	172_K	0.757	1.00
135_V	138_K	0.755	1.00
77_K	80_R	0.754	1.00
143_V	181_I	0.754	1.00
190_A	193_L	0.754	1.00
171_L	174_E	0.752	1.00
100_E	103_H	0.750	1.00
105_N	116_S	0.749	1.00
133_L	170_K	0.748	1.00
147_P	207_C	0.747	1.00
225_N	230_V	0.746	1.00
88_L	91_E	0.742	1.00
8_I	30_I	0.742	1.00
130_N	133_L	0.737	1.00
156_I	167_L	0.733	1.00
13_A	44_Y	0.732	1.00
147_P	186_R	0.727	1.00
106_F	116_S	0.726	1.00
220_R	229_R	0.726	1.00
88_L	96_L	0.723	1.00
136_S	140_R	0.723	1.00
78_F	85_P	0.718	1.00
139_V	171_L	0.712	1.00
210_A	214_Y	0.712	1.00
88_L	95_Y	0.702	1.00
82_S	85_P	0.701	1.00
169_K	173_Q	0.700	1.00
99_E	102_N	0.697	1.00
139_V	178_F	0.696	1.00
94_A	98_S	0.695	1.00
7_V	50_E	0.694	1.00
204_A	212_T	0.691	1.00
14_F	41_F	0.689	1.00
212_T	215_F	0.689	1.00
106_F	109_L	0.688	1.00
15_N	44_Y	0.685	1.00
168_K	179_S	0.678	1.00
211_S	214_Y	0.677	1.00
106_F	120_A	0.677	1.00
213_S	226_S	0.673	1.00
176_T	181_I	0.671	1.00
203_I	231_S	0.663	1.00
43_P	46_R	0.661	1.00
25_F	31_L	0.659	1.00
215_F	219_F	0.658	1.00
151_W	186_R	0.657	1.00
117_I	121_C	0.657	1.00
9_F	48_F	0.650	1.00
59_K	63_Q	0.650	1.00
79_L	85_P	0.647	1.00
16_A	39_T	0.646	1.00
215_F	227_P	0.642	1.00
151_W	155_D	0.640	1.00
183_L	214_Y	0.637	1.00
41_F	48_F	0.635	1.00
153_L	179_S	0.633	1.00
172_K	177_T	0.632	1.00
57_T	60_K	0.628	1.00
56_N	59_K	0.628	1.00
18_I	33_V	0.626	1.00
136_S	167_L	0.623	1.00
188_Q	223_F	0.622	1.00
193_L	196_V	0.622	1.00
96_L	99_E	0.622	1.00
144_N	189_H	0.619	1.00
7_V	16_A	0.618	1.00
187_M	209_Y	0.616	1.00
190_A	203_I	0.616	1.00
194_I	230_V	0.614	1.00
213_S	217_Y	0.613	1.00
41_F	50_E	0.612	1.00
183_L	187_M	0.611	1.00
7_V	48_F	0.610	1.00
9_F	25_F	0.609	1.00
198_G	203_I	0.608	1.00
7_V	33_V	0.605	1.00
42_E	45_E	0.603	1.00
76_A	80_R	0.600	1.00
60_K	63_Q	0.599	1.00
107_S	110_L	0.599	1.00
117_I	120_A	0.598	1.00
199_S	203_I	0.598	1.00
139_V	159_C	0.596	1.00
219_F	225_N	0.595	1.00
188_Q	222_H	0.595	1.00
115_L	118_F	0.593	1.00
156_I	160_L	0.593	1.00
92_M	96_L	0.592	1.00
139_V	143_V	0.587	1.00
151_W	182_L	0.587	1.00
157_C	160_L	0.586	1.00
81_A	84_V	0.585	1.00
211_S	221_K	0.585	1.00
158_D	161_Y	0.584	1.00
74_V	77_K	0.582	1.00
7_V	31_L	0.580	1.00
92_M	95_Y	0.579	1.00
16_A	41_F	0.576	1.00
142_I	155_D	0.575	1.00
74_V	81_A	0.574	1.00
132_V	173_Q	0.568	1.00
167_L	174_E	0.567	1.00
47_H	50_E	0.563	1.00
94_A	97_N	0.559	1.00
153_L	165_S	0.556	1.00
80_R	85_P	0.554	1.00
143_V	151_W	0.553	1.00
174_E	181_I	0.552	1.00
192_N	195_R	0.550	1.00
141_N	144_N	0.547	1.00
200_V	228_K	0.546	1.00
73_P	77_K	0.545	1.00
209_Y	214_Y	0.542	1.00
213_S	220_R	0.540	1.00
146_K	151_W	0.540	1.00
191_K	225_N	0.539	1.00
183_L	209_Y	0.538	1.00
109_L	118_F	0.535	1.00
107_S	118_F	0.535	1.00
93_I	96_L	0.534	1.00
83_N	86_T	0.534	1.00
87_G	94_A	0.532	1.00
139_V	170_K	0.531	1.00
182_L	186_R	0.531	1.00
219_F	223_F	0.530	1.00
105_N	112_F	0.529	1.00
182_L	185_A	0.527	1.00
10_I	90_N	0.524	1.00
180_Q	221_K	0.524	1.00
111_L	115_L	0.523	1.00
143_V	156_I	0.521	1.00
48_F	52_G	0.521	1.00
194_I	197_E	0.520	1.00
107_S	111_L	0.519	1.00
16_A	33_V	0.518	1.00
156_I	186_R	0.518	1.00
101_R	104_H	0.513	1.00
35_N	40_H	0.508	1.00
201_N	213_S	0.506	1.00
88_L	117_I	0.504	1.00
188_Q	192_N	0.502	1.00
136_S	160_L	0.502	1.00
113_S	120_A	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
3gbgA	1	0.9051	100	0.237	Contact Map
3mklA	1	0.4348	99.9	0.47	Contact Map
3oouA	1	0.4071	99.9	0.474	Contact Map
3mn2A	1	0.4111	99.9	0.476	Contact Map
1bl0A	1	0.4506	99.9	0.476	Contact Map
3w6vA	1	0.4308	99.9	0.482	Contact Map
3oioA	1	0.4348	99.9	0.483	Contact Map
2k9sA	1	0.4111	99.9	0.487	Contact Map
3lsgA	2	0.3953	99.9	0.495	Contact Map
4fe7A	2	0.8775	99.9	0.505	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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