UXUR - ECOLI - GREMLIN Contacts

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UXUR - Uxu operon transcriptional regulator

UniProt:	P39161	Sequences: MKSATSAQRPYQEVGAMIRDLIIKTPYNPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVRRGAGIYVLDNSGSQNTDSPDANVCNDAGPFELLQARQLLESNIAEFAALQATREDIVKMRQALQLEERELASSAPGSSESGDMQFHLAIAEATHNSMLVELFRQSWQWRENNPMWIQLHSHLDDSLYRKEWLGDHKQILAALIKKDARAAKLAMWQHLENVKQRLLEFSNVDDIYFDGYLFDSWPLDKVDA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG20249
Length:	257 (207)
Sequences:	23156 (16963)
Seq/√Len:	1179.0

ECOLI - UXUR PDHR GLCC EXUR LLDR NANR YJJM YDFH FADR YIEP MCBR DGOR CSIR FRLR YIDP YEGW
BACSU - GNTR YDHC YCBG LUTR YMFC YURK YVOA 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
126_R	209_I	3.746	1.00
111_E	217_K	3.353	1.00
212_D	215_A	2.936	1.00
133_E	202_K	2.796	1.00
21_L	26_P	2.754	1.00
28_N	31_E	2.712	1.00
21_L	42_M	2.437	1.00
104_L	108_N	2.394	1.00
36_E	47_R	2.265	1.00
124_K	154_A	2.260	1.00
97_E	162_S	2.177	1.00
15_G	56_M	2.109	1.00
103_Q	225_E	2.104	1.00
64_E	74_L	2.051	1.00
19_R	60_K	2.017	1.00
115_L	213_A	1.987	1.00
100_Q	112_F	1.955	1.00
14_V	45_V	1.945	1.00
122_I	209_I	1.882	1.00
121_D	160_H	1.841	1.00
157_E	165_V	1.830	1.00
207_A	215_A	1.777	1.00
154_A	157_E	1.769	1.00
14_V	43_L	1.768	1.00
65_V	71_I	1.752	1.00
17_M	21_L	1.744	1.00
107_S	221_W	1.713	1.00
118_T	121_D	1.701	1.00
129_L	205_L	1.679	1.00
111_E	213_A	1.664	1.00
200_D	226_N	1.640	1.00
108_N	111_E	1.612	1.00
140_A	143_S	1.606	1.00
101_A	167_L	1.601	1.00
215_A	219_A	1.592	1.00
217_K	221_W	1.584	1.00
107_S	217_K	1.577	1.00
20_D	24_K	1.561	1.00
203_Q	219_A	1.518	1.00
8_Q	16_A	1.499	1.00
66_R	69_A	1.464	1.00
166_E	170_Q	1.457	1.00
131_L	147_G	1.448	1.00
152_H	201_H	1.432	1.00
121_D	158_A	1.430	1.00
156_A	168_F	1.426	1.00
110_A	216_A	1.419	1.00
153_L	169_R	1.418	1.00
163_M	174_W	1.414	1.00
103_Q	221_W	1.412	1.00
126_R	205_L	1.411	1.00
128_A	147_G	1.411	1.00
15_G	60_K	1.402	1.00
206_A	210_K	1.397	1.00
133_E	198_L	1.387	1.00
210_K	215_A	1.335	1.00
103_Q	228_K	1.329	1.00
213_A	217_K	1.325	1.00
37_R	41_E	1.318	1.00
117_A	122_I	1.314	1.00
97_E	163_M	1.306	1.00
202_K	206_A	1.290	1.00
129_L	202_K	1.259	1.00
131_L	150_Q	1.252	1.00
127_Q	131_L	1.244	1.00
38_E	42_M	1.235	1.00
32_R	72_Y	1.217	1.00
39_I	50_V	1.211	1.00
126_R	130_Q	1.207	1.00
13_E	17_M	1.203	1.00
128_A	154_A	1.200	1.00
66_R	72_Y	1.199	1.00
218_L	222_Q	1.182	1.00
96_F	232_L	1.177	1.00
103_Q	107_S	1.176	1.00
221_W	225_E	1.176	1.00
96_F	228_K	1.170	1.00
153_L	157_E	1.158	1.00
17_M	43_L	1.152	1.00
150_Q	154_A	1.152	1.00
200_D	223_H	1.146	1.00
21_L	43_L	1.144	1.00
117_A	121_D	1.141	1.00
107_S	111_E	1.137	1.00
17_M	20_D	1.134	1.00
102_R	106_E	1.129	1.00
117_A	211_K	1.121	1.00
215_A	218_L	1.115	1.00
117_A	158_A	1.114	1.00
110_A	220_M	1.108	1.00
27_Y	73_V	1.104	1.00
111_E	214_R	1.102	1.00
122_I	205_L	1.100	1.00
155_I	208_L	1.100	1.00
58_E	65_V	1.093	1.00
206_A	209_I	1.075	1.00
143_S	146_S	1.072	1.00
110_A	114_A	1.071	1.00
97_E	161_N	1.069	1.00
129_L	133_E	1.063	1.00
147_G	150_Q	1.063	1.00
109_I	156_A	1.058	1.00
129_L	132_E	1.057	1.00
205_L	209_I	1.056	1.00
154_A	158_A	1.055	1.00
148_D	152_H	1.055	1.00
228_K	232_L	1.048	1.00
126_R	202_K	1.041	1.00
128_A	150_Q	1.037	1.00
122_I	211_K	1.032	1.00
100_Q	161_N	1.019	1.00
124_K	157_E	1.018	1.00
58_E	63_V	1.015	1.00
64_E	72_Y	1.014	1.00
167_L	170_Q	1.008	1.00
130_Q	133_E	1.003	1.00
124_K	127_Q	1.001	1.00
52_E	55_I	0.994	1.00
152_H	223_H	0.988	1.00
207_A	212_D	0.979	1.00
108_N	217_K	0.977	1.00
21_L	27_Y	0.973	1.00
112_F	116_Q	0.970	1.00
114_A	213_A	0.969	1.00
36_E	51_R	0.957	1.00
201_H	223_H	0.954	1.00
22_I	73_V	0.953	1.00
8_Q	13_E	0.953	1.00
151_F	205_L	0.943	1.00
199_G	203_Q	0.942	1.00
203_Q	222_Q	0.942	1.00
203_Q	215_A	0.931	1.00
146_S	150_Q	0.926	1.00
124_K	128_A	0.926	1.00
106_E	152_H	0.923	1.00
56_M	59_I	0.917	1.00
123_V	127_Q	0.917	1.00
54_L	71_I	0.916	1.00
159_T	165_V	0.913	1.00
11_Y	56_M	0.909	1.00
116_Q	160_H	0.905	1.00
114_A	208_L	0.898	1.00
66_R	70_G	0.895	1.00
108_N	112_F	0.894	1.00
203_Q	206_A	0.889	1.00
165_V	169_R	0.884	1.00
204_I	220_M	0.884	1.00
122_I	126_R	0.883	1.00
63_V	71_I	0.878	1.00
15_G	19_R	0.877	1.00
128_A	131_L	0.877	1.00
214_R	218_L	0.875	1.00
94_G	163_M	0.872	1.00
32_R	70_G	0.860	1.00
69_A	72_Y	0.854	1.00
134_R	138_S	0.854	1.00
40_A	50_V	0.849	1.00
19_R	23_I	0.847	1.00
102_R	224_L	0.841	1.00
135_E	143_S	0.838	1.00
93_A	160_H	0.837	1.00
214_R	217_K	0.835	1.00
101_A	163_M	0.832	1.00
126_R	206_A	0.823	1.00
19_R	62_L	0.822	1.00
131_L	134_R	0.821	1.00
198_L	202_K	0.818	1.00
114_A	211_K	0.817	1.00
93_A	97_E	0.815	1.00
113_A	158_A	0.815	1.00
130_Q	134_R	0.814	1.00
153_L	172_W	0.814	1.00
55_I	58_E	0.807	1.00
148_D	201_H	0.807	1.00
121_D	124_K	0.807	1.00
38_E	41_E	0.807	1.00
119_R	123_V	0.804	1.00
10_P	13_E	0.803	1.00
203_Q	207_A	0.801	1.00
204_I	219_A	0.797	1.00
46_T	49_V	0.793	1.00
125_M	154_A	0.789	1.00
119_R	211_K	0.787	1.00
163_M	167_L	0.785	1.00
132_E	144_S	0.780	1.00
114_A	216_A	0.777	1.00
35_P	38_E	0.775	1.00
54_L	63_V	0.774	1.00
117_A	208_L	0.769	1.00
163_M	166_E	0.768	1.00
12_Q	56_M	0.767	1.00
9_R	12_Q	0.767	1.00
207_A	219_A	0.759	1.00
55_I	65_V	0.754	1.00
112_F	115_L	0.754	1.00
100_Q	228_K	0.751	1.00
10_P	49_V	0.747	1.00
195_K	199_G	0.745	1.00
111_E	115_L	0.741	1.00
125_M	205_L	0.735	1.00
100_Q	116_Q	0.732	1.00
225_E	229_Q	0.732	1.00
101_A	164_L	0.731	1.00
130_Q	202_K	0.729	1.00
39_I	54_L	0.729	1.00
219_A	222_Q	0.722	1.00
99_L	227_V	0.721	1.00
112_F	161_N	0.716	1.00
204_I	216_A	0.715	1.00
133_E	137_A	0.711	1.00
149_M	176_E	0.704	1.00
45_V	50_V	0.702	1.00
131_L	143_S	0.702	1.00
101_A	109_I	0.700	1.00
123_V	209_I	0.688	1.00
127_Q	130_Q	0.684	1.00
34_P	38_E	0.684	1.00
218_L	221_W	0.684	1.00
122_I	208_L	0.682	1.00
113_A	117_A	0.682	1.00
222_Q	226_N	0.681	1.00
123_V	126_R	0.679	1.00
11_Y	15_G	0.677	1.00
56_M	60_K	0.676	1.00
225_E	228_K	0.675	1.00
143_S	147_G	0.672	1.00
135_E	147_G	0.669	1.00
26_P	42_M	0.669	1.00
129_L	198_L	0.666	1.00
153_L	165_V	0.662	1.00
204_I	223_H	0.659	1.00
8_Q	12_Q	0.658	1.00
124_K	150_Q	0.655	1.00
226_N	230_R	0.655	1.00
149_M	172_W	0.650	1.00
131_L	135_E	0.649	1.00
150_Q	153_L	0.640	1.00
27_Y	31_E	0.640	1.00
100_Q	108_N	0.637	1.00
121_D	154_A	0.637	1.00
94_G	162_S	0.634	1.00
49_V	53_A	0.632	1.00
121_D	157_E	0.631	1.00
200_D	203_Q	0.628	1.00
113_A	159_T	0.626	1.00
104_L	164_L	0.624	1.00
180_M	183_Q	0.621	1.00
68_G	71_I	0.618	1.00
77_S	94_G	0.614	1.00
135_E	140_A	0.613	1.00
21_L	25_T	0.610	1.00
109_I	159_T	0.610	1.00
29_P	75_D	0.609	1.00
110_A	213_A	0.605	1.00
103_Q	224_L	0.598	1.00
107_S	220_M	0.598	1.00
144_S	197_W	0.595	1.00
101_A	105_L	0.594	1.00
107_S	213_A	0.580	1.00
132_E	198_L	0.578	1.00
43_L	50_V	0.576	1.00
109_I	164_L	0.574	1.00
166_E	174_W	0.574	1.00
30_G	75_D	0.571	1.00
11_Y	52_E	0.567	1.00
72_Y	75_D	0.566	1.00
106_E	201_H	0.565	1.00
33_L	63_V	0.562	1.00
125_M	158_A	0.562	1.00
37_R	40_A	0.559	1.00
134_R	137_A	0.558	1.00
120_E	124_K	0.557	1.00
113_A	155_I	0.557	1.00
93_A	162_S	0.554	1.00
96_F	100_Q	0.553	1.00
111_E	221_W	0.553	1.00
110_A	155_I	0.552	1.00
55_I	59_I	0.549	1.00
229_Q	232_L	0.547	1.00
104_L	107_S	0.547	1.00
18_I	39_I	0.547	1.00
156_A	172_W	0.540	1.00
108_N	164_L	0.539	1.00
204_I	207_A	0.538	1.00
112_F	159_T	0.537	1.00
106_E	224_L	0.536	1.00
125_M	128_A	0.533	1.00
226_N	229_Q	0.533	1.00
229_Q	233_E	0.531	1.00
23_I	62_L	0.530	1.00
222_Q	225_E	0.530	1.00
21_L	24_K	0.527	1.00
166_E	169_R	0.524	1.00
149_M	153_L	0.521	1.00
193_Y	196_E	0.521	1.00
41_E	44_D	0.516	1.00
199_G	202_K	0.516	1.00
119_R	122_I	0.516	1.00
105_L	168_F	0.515	1.00
27_Y	33_L	0.513	1.00
133_E	199_G	0.512	1.00
208_L	216_A	0.511	1.00
27_Y	42_M	0.510	1.00
94_G	97_E	0.510	1.00
100_Q	103_Q	0.510	1.00
162_S	165_V	0.508	1.00
107_S	110_A	0.506	1.00
119_R	209_I	0.506	1.00
192_L	195_K	0.505	1.00
34_P	37_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
2hs5A	1	0.8054	100	0.213	Contact Map
4p96A	2	0.93	100	0.217	Contact Map
3c7jA	4	0.856	100	0.219	Contact Map
3ihuA	1	0.7938	100	0.223	Contact Map
4p9fA	1	0.821	100	0.224	Contact Map
3sxyA	2	0.7782	100	0.225	Contact Map
2di3A	2	0.8716	100	0.24	Contact Map
1hw1A	2	0.8599	100	0.259	Contact Map
3ic7A	2	0.4319	99.9	0.546	Contact Map
3by6A	2	0.4708	99.9	0.557	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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