YIHL - ECOLI - GREMLIN Contacts

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YIHL - Uncharacterized HTH-type transcriptional regulator YihL

UniProt:	P0ACM9	Sequences: MAENQSTVENAKEKLDRWLKDGITTPGGKLPSERELGELLGIKRMTLRQALLNLEAESKIFRKDRKGWFVTQPRFNYSPELSASFQRAAIEQGREPSWGFTEKNRTSDIPETLAPLIAVTPSTELYRITGWGALEGHKVFYHETYINPEVAPGFIEQLENHSFSAVWEKCYQKETVVKKLIFKPVRMPGDISKYLGGSAGMPAILIEKHRADQQGNIVQIDIEYWRFEAVDLIINL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11838
Length:	236 (195)
Sequences:	22604 (18104)
Seq/√Len:	1296.4

ECOLI - YIHL MNGR YIDP PHNF FRLR YEGW
BACSU - YYDK GMUR YURK YBGA TRER YVOA YMFC

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
18_W	23_I	4.140	1.00
25_T	28_G	4.037	1.00
16_D	57_E	3.477	1.00
18_W	39_L	3.321	1.00
12_K	53_N	3.288	1.00
61_F	71_T	2.986	1.00
183_K	186_R	2.676	1.00
11_A	42_I	2.633	1.00
14_K	18_W	2.583	1.00
62_R	68_W	2.569	1.00
33_E	44_R	2.550	1.00
63_K	66_K	2.411	1.00
11_A	40_L	2.295	1.00
29_K	69_F	2.250	1.00
12_K	57_E	2.216	1.00
17_R	21_D	2.138	1.00
123_T	180_L	2.111	1.00
102_E	188_P	2.058	1.00
12_K	16_D	2.016	1.00
66_K	69_F	1.990	1.00
110_P	113_L	1.956	1.00
55_E	62_R	1.956	1.00
5_Q	13_E	1.950	1.00
49_Q	52_L	1.919	1.00
14_K	40_L	1.910	1.00
130_G	173_K	1.909	1.00
109_I	113_L	1.846	1.00
188_P	191_I	1.770	1.00
16_D	20_K	1.766	1.00
16_D	59_K	1.691	1.00
7_T	10_N	1.655	1.00
18_W	24_T	1.645	1.00
34_R	38_E	1.644	1.00
52_L	62_R	1.627	1.00
35_E	39_L	1.627	1.00
14_K	17_R	1.599	1.00
10_N	14_K	1.595	1.00
51_L	60_I	1.584	1.00
32_S	35_E	1.560	1.00
188_P	192_S	1.555	1.00
36_L	47_L	1.554	1.00
113_L	145_Y	1.554	1.00
97_S	133_A	1.541	1.00
55_E	60_I	1.538	1.00
95_E	99_G	1.532	1.00
60_I	68_W	1.532	1.00
127_R	143_E	1.517	1.00
129_T	143_E	1.467	1.00
8_V	53_N	1.444	1.00
42_I	47_L	1.437	1.00
18_W	22_G	1.436	1.00
33_E	48_R	1.418	1.00
186_R	190_D	1.395	1.00
26_P	72_Q	1.381	1.00
24_T	70_V	1.377	1.00
63_K	69_F	1.368	1.00
149_E	152_P	1.337	1.00
61_F	69_F	1.333	1.00
19_L	70_V	1.332	1.00
35_E	38_E	1.322	1.00
52_L	56_A	1.310	1.00
6_S	9_E	1.306	1.00
109_I	116_L	1.290	1.00
99_G	133_A	1.265	1.00
53_N	56_A	1.260	1.00
178_K	186_R	1.244	1.00
52_L	55_E	1.240	1.00
5_Q	10_N	1.238	1.00
88_A	157_Q	1.235	1.00
120_T	123_T	1.231	1.00
173_K	177_V	1.225	1.00
135_E	138_K	1.216	1.00
189_G	193_K	1.214	1.00
20_K	59_K	1.210	1.00
63_K	67_G	1.194	1.00
113_L	117_I	1.192	1.00
141_Y	191_I	1.191	1.00
148_P	152_P	1.180	1.00
162_S	166_V	1.178	1.00
176_V	180_L	1.167	1.00
7_T	46_T	1.147	1.00
51_L	68_W	1.145	1.00
53_N	57_E	1.138	1.00
117_I	180_L	1.124	1.00
184_P	188_P	1.094	1.00
93_G	97_S	1.071	1.00
170_C	197_G	1.063	1.00
198_S	201_M	1.052	1.00
9_E	13_E	1.032	1.00
29_K	67_G	1.029	1.00
24_T	28_G	1.024	1.00
94_R	98_W	1.021	1.00
145_Y	149_E	1.015	1.00
18_W	40_L	1.007	1.00
13_E	16_D	0.997	1.00
9_E	53_N	0.993	1.00
104_N	107_S	0.989	1.00
143_E	147_N	0.983	1.00
109_I	114_A	0.980	1.00
187_M	197_G	0.973	1.00
49_Q	53_N	0.971	1.00
192_S	196_G	0.969	1.00
108_D	113_L	0.955	1.00
15_L	36_L	0.945	1.00
149_E	153_G	0.942	1.00
27_G	61_F	0.940	1.00
85_F	88_A	0.922	1.00
8_V	12_K	0.909	1.00
43_K	46_T	0.909	1.00
128_I	132_G	0.908	1.00
98_W	102_E	0.907	1.00
107_S	113_L	0.896	1.00
147_N	150_V	0.893	1.00
65_R	68_W	0.889	1.00
99_G	103_K	0.888	1.00
177_V	181_I	0.884	1.00
128_I	145_Y	0.879	1.00
164_S	168_E	0.877	1.00
174_E	190_D	0.876	1.00
138_K	141_Y	0.876	1.00
29_K	32_S	0.867	1.00
108_D	124_E	0.866	1.00
5_Q	9_E	0.866	1.00
132_G	142_H	0.858	1.00
181_I	186_R	0.820	1.00
163_F	166_V	0.813	1.00
127_R	130_G	0.810	1.00
103_K	155_I	0.810	1.00
51_L	55_E	0.809	1.00
185_V	191_I	0.805	1.00
26_P	71_T	0.801	1.00
129_T	190_D	0.800	1.00
141_Y	145_Y	0.788	1.00
94_R	196_G	0.788	1.00
37_G	47_L	0.787	1.00
177_V	180_L	0.786	1.00
146_I	176_V	0.785	1.00
33_E	62_R	0.784	1.00
124_E	128_I	0.781	1.00
109_I	112_T	0.781	1.00
99_G	102_E	0.778	1.00
106_T	109_I	0.773	1.00
87_R	90_I	0.773	1.00
119_V	123_T	0.772	1.00
125_L	142_H	0.766	1.00
150_V	179_K	0.762	1.00
8_V	49_Q	0.759	1.00
84_S	88_A	0.757	1.00
125_L	145_Y	0.749	1.00
162_S	167_W	0.749	1.00
98_W	101_T	0.745	1.00
123_T	127_R	0.745	1.00
15_L	24_T	0.740	1.00
112_T	116_L	0.739	1.00
114_A	118_A	0.737	1.00
13_E	17_R	0.734	1.00
11_A	47_L	0.732	1.00
126_Y	176_V	0.732	1.00
186_R	189_G	0.731	1.00
142_H	145_Y	0.731	1.00
123_T	149_E	0.729	1.00
190_D	193_K	0.728	1.00
165_A	169_K	0.723	1.00
163_F	167_W	0.723	1.00
126_Y	130_G	0.722	1.00
127_R	131_W	0.718	1.00
91_E	103_K	0.717	1.00
98_W	188_P	0.716	1.00
115_P	118_A	0.716	1.00
30_L	60_I	0.714	1.00
27_G	72_Q	0.712	1.00
97_S	101_T	0.711	1.00
85_F	89_A	0.709	1.00
18_W	21_D	0.707	1.00
166_V	170_C	0.706	1.00
14_K	39_L	0.705	1.00
104_N	127_R	0.704	1.00
125_L	128_I	0.702	1.00
11_A	14_K	0.702	1.00
102_E	184_P	0.701	1.00
147_N	172_Q	0.696	1.00
197_G	201_M	0.694	1.00
185_V	189_G	0.692	1.00
133_A	136_G	0.691	1.00
38_E	41_G	0.690	1.00
36_L	40_L	0.687	1.00
36_L	51_L	0.683	1.00
94_R	192_S	0.682	1.00
86_Q	90_I	0.681	1.00
40_L	47_L	0.679	1.00
113_L	116_L	0.678	1.00
112_T	115_P	0.675	1.00
114_A	119_V	0.674	1.00
90_I	93_G	0.666	1.00
127_R	145_Y	0.665	1.00
161_H	164_S	0.665	1.00
24_T	30_L	0.664	1.00
83_A	91_E	0.662	1.00
191_I	194_Y	0.661	1.00
31_P	39_L	0.655	1.00
98_W	192_S	0.650	1.00
189_G	192_S	0.649	1.00
23_I	39_L	0.647	1.00
107_S	127_R	0.647	1.00
109_I	117_I	0.645	1.00
175_T	191_I	0.643	1.00
117_I	122_S	0.642	1.00
34_R	37_G	0.641	1.00
138_K	142_H	0.639	1.00
190_D	194_Y	0.634	1.00
89_A	134_L	0.633	1.00
111_E	121_P	0.625	1.00
100_F	104_N	0.625	1.00
95_E	159_E	0.624	1.00
186_R	201_M	0.620	1.00
185_V	188_P	0.619	1.00
143_E	191_I	0.619	1.00
97_S	104_N	0.618	1.00
128_I	131_W	0.610	1.00
107_S	110_P	0.602	1.00
90_I	96_P	0.600	1.00
155_I	158_L	0.598	1.00
110_P	117_I	0.596	1.00
17_R	20_K	0.594	1.00
116_L	122_S	0.592	1.00
12_K	50_A	0.592	1.00
173_K	176_V	0.586	1.00
100_F	151_A	0.586	1.00
151_A	167_W	0.585	1.00
92_Q	97_S	0.584	1.00
11_A	15_L	0.582	1.00
187_M	191_I	0.580	1.00
191_I	195_L	0.578	1.00
85_F	90_I	0.576	1.00
46_T	49_Q	0.574	1.00
37_G	40_L	0.573	1.00
29_K	66_K	0.572	1.00
92_Q	96_P	0.571	1.00
24_T	31_P	0.571	1.00
123_T	176_V	0.568	1.00
46_T	50_A	0.567	1.00
129_T	141_Y	0.567	1.00
102_E	127_R	0.566	1.00
111_E	115_P	0.564	1.00
84_S	87_R	0.564	1.00
187_M	201_M	0.561	1.00
45_M	49_Q	0.560	1.00
88_A	92_Q	0.558	1.00
32_S	65_R	0.557	1.00
111_E	114_A	0.556	1.00
47_L	60_I	0.555	1.00
106_T	184_P	0.553	1.00
193_K	197_G	0.552	1.00
175_T	190_D	0.551	1.00
131_W	138_K	0.550	1.00
51_L	62_R	0.541	1.00
123_T	173_K	0.541	1.00
101_T	106_T	0.540	1.00
162_S	165_A	0.540	1.00
187_M	200_G	0.539	1.00
126_Y	129_T	0.538	1.00
109_I	119_V	0.535	1.00
117_I	123_T	0.534	1.00
37_G	44_R	0.534	1.00
103_K	107_S	0.533	1.00
101_T	104_N	0.532	1.00
187_M	192_S	0.530	1.00
55_E	68_W	0.529	1.00
97_S	136_G	0.527	1.00
125_L	149_E	0.526	1.00
118_A	122_S	0.524	1.00
87_R	91_E	0.524	1.00
37_G	45_M	0.521	1.00
100_F	103_K	0.520	1.00
160_N	164_S	0.519	1.00
156_E	159_E	0.519	1.00
107_S	184_P	0.519	1.00
91_E	107_S	0.517	1.00
101_T	131_W	0.517	1.00
33_E	68_W	0.516	1.00
9_E	12_K	0.516	1.00
101_T	191_I	0.515	1.00
109_I	125_L	0.509	1.00
83_A	87_R	0.508	1.00
144_T	148_P	0.506	1.00
102_E	185_V	0.506	1.00
103_K	156_E	0.506	1.00
119_V	125_L	0.505	1.00
172_Q	194_Y	0.505	1.00
145_Y	148_P	0.502	1.00
174_E	186_R	0.501	1.00
108_D	112_T	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
4u0wA	2	0.9958	100	0.093	Contact Map
3edpA	2	0.9322	100	0.128	Contact Map
2ra5A	2	0.6102	100	0.129	Contact Map
3f8mA	2	0.9534	100	0.13	Contact Map
3eetA	2	0.9619	100	0.151	Contact Map
3bwgA	2	0.9576	100	0.156	Contact Map
3f8lA	2	0.678	100	0.424	Contact Map
1hw1A	2	0.8178	99.9	0.469	Contact Map
4p96A	2	0.8941	99.9	0.485	Contact Map
2di3A	2	0.8305	99.9	0.5	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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