YEIE - ECOLI - GREMLIN Contacts

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YEIE - Uncharacterized HTH-type transcriptional regulator YeiE

UniProt:	P0ACR4	Sequences: MHITLRQLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKRLVVNEHGRLLYPRALALLEQAVEIEQLFREDNGAIRIYASSTIGNYILPAVIARYRHDYPQLPIELSVGNSQDVMQAVLDFRVDIGFIEGPCHSTEIISEPWLEDELVVFAAPTSPLARGPVTLEQLAAAPWILRERGSGTREIVDYLLLSHLPKFEMAMELGNSEAIKHAVRHGLGISCLSRRVIEDQLQAGTLSEVAVPLPRLMRTLWRIHHRQKHLSNALRRFLDYCDPANVPR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12105
Length:	293 (281)
Sequences:	79675 (57934)
Seq/√Len:	3456.0

ECOLI - YEIE YBHD YAFC YNFL YFER OXYR LEUO YBDO YCAN NAC LYSR CYSB YDCI CYNR YEEY YBEF YFIE PGRR NHAR CBL AAER ABGR TDCA YIDZ YNEJ HCAR ILVY DSDC YHJC DMLR XAPR TTDR METR GCVA ICIA YAHB YIAU YDHB ALLS YGFI YHAJ YJIE HDFR PERR LRHA
BACSU - CYSL YWBI GLTC YCGK YYBE GLTR YWQM YUST ALSR CITR YTLI YVBU BSDA YOFA CZCR YXJO YKUM YOAU YRAN

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
72_A	76_Q	3.786	1.00
17_S	26_M	3.471	1.00
13_E	26_M	2.784	1.00
156_E	287_D	2.644	1.00
157_P	264_T	2.565	1.00
47_V	62_H	2.434	1.00
12_A	71_L	2.385	1.00
94_Y	139_V	2.381	1.00
164_V	239_R	2.305	1.00
157_P	160_E	2.290	1.00
160_E	264_T	2.277	1.00
12_A	16_K	2.270	1.00
90_A	121_E	2.268	1.00
10_V	37_A	2.212	1.00
13_E	17_S	2.202	1.00
69_R	76_Q	2.184	1.00
171_S	186_A	2.100	1.00
90_A	119_P	2.099	1.00
92_R	121_E	2.066	1.00
164_V	253_E	2.037	1.00
160_E	262_M	2.031	1.00
110_R	285_Y	2.031	1.00
73_L	77_A	2.009	1.00
228_V	235_S	2.009	1.00
15_L	59_V	2.003	1.00
162_E	239_R	1.998	1.00
179_T	182_Q	1.936	1.00
67_Y	71_L	1.934	1.00
10_V	34_V	1.912	1.00
13_E	16_K	1.906	1.00
15_L	67_Y	1.896	1.00
229_R	250_T	1.873	1.00
16_K	71_L	1.851	1.00
22_Q	25_V	1.847	1.00
12_A	67_Y	1.846	1.00
187_P	215_A	1.823	1.00
155_S	266_W	1.788	1.00
69_R	72_A	1.779	1.00
189_I	233_G	1.758	1.00
167_A	254_V	1.747	1.00
17_S	22_Q	1.733	1.00
19_S	22_Q	1.677	1.00
51_D	58_V	1.675	1.00
133_A	138_R	1.655	1.00
156_E	269_H	1.614	1.00
154_I	271_R	1.582	1.00
7_Q	44_Q	1.570	1.00
269_H	283_L	1.569	1.00
101_N	222_E	1.564	1.00
7_Q	40_D	1.561	1.00
53_V	58_V	1.554	1.00
12_A	70_A	1.551	1.00
114_D	285_Y	1.537	1.00
7_Q	37_A	1.516	1.00
76_Q	79_E	1.511	1.00
133_A	139_V	1.506	1.00
154_I	269_H	1.504	1.00
30_S	33_A	1.501	1.00
16_K	26_M	1.498	1.00
13_E	27_L	1.491	1.00
283_L	287_D	1.486	1.00
20_T	38_L	1.473	1.00
68_P	72_A	1.457	1.00
146_G	266_W	1.451	1.00
92_R	123_S	1.450	1.00
144_I	268_I	1.446	1.00
175_R	182_Q	1.444	1.00
132_Q	136_D	1.433	1.00
48_Q	51_D	1.414	1.00
111_Y	118_L	1.410	1.00
275_L	279_L	1.410	1.00
161_D	240_R	1.400	1.00
69_R	79_E	1.397	1.00
111_Y	282_F	1.390	1.00
157_P	266_W	1.390	1.00
134_V	142_G	1.373	1.00
267_R	283_L	1.369	1.00
29_L	33_A	1.360	1.00
5_L	77_A	1.358	1.00
281_R	284_D	1.351	1.00
21_T	31_Q	1.349	1.00
198_R	202_D	1.348	1.00
224_I	235_S	1.338	1.00
226_H	229_R	1.336	1.00
11_F	67_Y	1.331	1.00
169_P	252_S	1.327	1.00
141_I	267_R	1.325	1.00
110_R	114_D	1.323	1.00
4_T	7_Q	1.319	1.00
12_A	74_L	1.313	1.00
109_A	230_H	1.307	1.00
36_A	40_D	1.303	1.00
61_E	64_R	1.295	1.00
135_L	152_E	1.287	1.00
186_A	234_I	1.276	1.00
112_R	215_A	1.275	1.00
10_V	29_L	1.260	1.00
177_P	257_P	1.252	1.00
141_I	279_L	1.252	1.00
112_R	187_P	1.252	1.00
109_A	113_H	1.244	1.00
125_G	133_A	1.243	1.00
167_A	234_I	1.241	1.00
239_R	253_E	1.236	1.00
88_N	117_Q	1.234	1.00
172_P	186_A	1.225	1.00
106_A	230_H	1.222	1.00
155_S	268_I	1.214	1.00
72_A	79_E	1.207	1.00
253_E	256_V	1.206	1.00
169_P	250_T	1.203	1.00
11_F	15_L	1.201	1.00
8_L	70_A	1.195	1.00
65_L	69_R	1.183	1.00
36_A	39_T	1.170	1.00
65_L	68_P	1.170	1.00
226_H	230_H	1.168	1.00
11_F	50_F	1.163	1.00
239_R	243_E	1.161	1.00
156_E	283_L	1.156	1.00
64_R	68_P	1.155	1.00
123_S	133_A	1.145	1.00
13_E	23_A	1.145	1.00
73_L	76_Q	1.145	1.00
115_Y	281_R	1.141	1.00
178_V	182_Q	1.137	1.00
187_P	213_E	1.132	1.00
37_A	40_D	1.127	1.00
176_G	252_S	1.093	1.00
20_T	57_L	1.092	1.00
121_E	217_E	1.091	1.00
39_T	43_G	1.085	1.00
162_E	262_M	1.076	1.00
190_L	214_M	1.075	1.00
135_L	150_S	1.074	1.00
166_F	253_E	1.062	1.00
168_A	231_G	1.061	1.00
91_I	282_F	1.058	1.00
285_Y	288_P	1.045	1.00
280_R	284_D	1.044	1.00
62_H	65_L	1.043	1.00
66_L	70_A	1.036	1.00
75_E	79_E	1.035	1.00
35_S	39_T	1.033	1.00
100_G	124_V	1.031	1.00
244_D	248_A	1.028	1.00
66_L	80_I	1.026	1.00
111_Y	285_Y	1.012	1.00
284_D	287_D	1.008	1.00
72_A	75_E	1.006	1.00
111_Y	115_Y	1.000	1.00
107_V	286_C	1.000	1.00
110_R	113_H	0.997	1.00
14_V	23_A	0.993	1.00
6_R	9_E	0.993	1.00
243_E	247_Q	0.991	1.00
23_A	34_V	0.988	1.00
189_I	224_I	0.987	1.00
199_E	202_D	0.984	1.00
40_D	43_G	0.979	1.00
14_V	20_T	0.978	1.00
109_A	232_L	0.973	1.00
18_G	58_V	0.973	1.00
9_E	78_V	0.970	1.00
166_F	242_I	0.969	1.00
199_E	203_Y	0.968	1.00
225_K	229_R	0.967	1.00
59_V	63_G	0.959	1.00
11_F	49_L	0.956	1.00
15_L	50_F	0.953	1.00
22_Q	26_M	0.952	1.00
154_I	157_P	0.949	1.00
277_N	281_R	0.949	1.00
204_L	208_H	0.941	1.00
11_F	41_L	0.938	1.00
276_S	279_L	0.935	1.00
218_L	224_I	0.932	1.00
165_V	234_I	0.929	1.00
114_D	288_P	0.924	1.00
6_R	37_A	0.922	1.00
29_L	34_V	0.915	1.00
107_V	285_Y	0.908	1.00
10_V	27_L	0.906	1.00
133_A	136_D	0.906	1.00
17_S	23_A	0.904	1.00
146_G	264_T	0.904	1.00
167_A	171_S	0.903	1.00
9_E	13_E	0.901	1.00
112_R	232_L	0.900	1.00
171_S	174_A	0.896	1.00
89_G	278_A	0.895	1.00
15_L	18_G	0.893	1.00
97_S	220_N	0.892	1.00
21_T	25_V	0.892	1.00
9_E	12_A	0.889	1.00
68_P	71_L	0.888	1.00
18_G	56_R	0.888	1.00
64_R	67_Y	0.884	1.00
173_L	186_A	0.881	1.00
53_V	56_R	0.879	1.00
11_F	59_V	0.873	1.00
218_L	227_A	0.872	1.00
16_K	67_Y	0.869	1.00
131_M	135_L	0.867	1.00
14_V	50_F	0.865	1.00
170_T	231_G	0.864	1.00
174_A	252_S	0.857	1.00
50_F	57_L	0.855	1.00
66_L	81_E	0.846	1.00
69_R	73_L	0.842	1.00
205_L	210_P	0.841	1.00
229_R	248_A	0.841	1.00
227_A	232_L	0.841	1.00
70_A	73_L	0.841	1.00
187_P	214_M	0.838	1.00
123_S	139_V	0.837	1.00
93_I	141_I	0.834	1.00
14_V	34_V	0.829	1.00
275_L	280_R	0.828	1.00
270_H	273_K	0.828	1.00
94_Y	142_G	0.827	1.00
31_Q	35_S	0.825	1.00
71_L	75_E	0.824	1.00
139_V	142_G	0.821	1.00
14_V	38_L	0.819	1.00
27_L	34_V	0.816	1.00
94_Y	144_I	0.815	1.00
220_N	223_A	0.814	1.00
281_R	285_Y	0.813	1.00
204_L	207_S	0.807	1.00
137_F	270_H	0.800	1.00
182_Q	185_A	0.798	1.00
162_E	260_R	0.798	1.00
181_E	184_A	0.796	1.00
200_I	204_L	0.793	1.00
119_P	213_E	0.788	1.00
172_P	176_G	0.786	1.00
118_L	278_A	0.782	1.00
101_N	226_H	0.781	1.00
95_A	100_G	0.780	1.00
179_T	257_P	0.776	1.00
167_A	172_P	0.775	1.00
5_L	74_L	0.774	1.00
20_T	34_V	0.774	1.00
44_Q	81_E	0.771	1.00
192_E	217_E	0.769	1.00
7_Q	10_V	0.768	1.00
111_Y	281_R	0.767	1.00
153_I	268_I	0.766	1.00
168_A	171_S	0.765	1.00
170_T	174_A	0.764	1.00
11_F	63_G	0.763	1.00
246_L	249_G	0.763	1.00
9_E	74_L	0.762	1.00
61_E	65_L	0.761	1.00
203_Y	207_S	0.757	1.00
59_V	64_R	0.756	1.00
168_A	232_L	0.756	1.00
11_F	66_L	0.754	1.00
106_A	109_A	0.753	1.00
167_A	252_S	0.752	1.00
184_A	210_P	0.750	1.00
39_T	48_Q	0.748	1.00
51_D	60_N	0.745	1.00
166_F	237_L	0.745	1.00
201_V	205_L	0.742	1.00
89_G	118_L	0.741	1.00
87_D	115_Y	0.736	1.00
135_L	153_I	0.736	1.00
15_L	64_R	0.734	1.00
18_G	64_R	0.733	1.00
140_D	279_L	0.729	1.00
188_W	212_F	0.727	1.00
141_I	282_F	0.725	1.00
15_L	63_G	0.722	1.00
177_P	255_A	0.722	1.00
165_V	236_C	0.721	1.00
200_I	203_Y	0.716	1.00
92_R	140_D	0.714	1.00
162_E	255_A	0.713	1.00
6_R	40_D	0.705	1.00
25_V	28_A	0.703	1.00
166_F	235_S	0.702	1.00
78_V	81_E	0.701	1.00
202_D	206_L	0.700	1.00
33_A	37_A	0.698	1.00
73_L	80_I	0.696	1.00
62_H	66_L	0.695	1.00
273_K	276_S	0.694	1.00
74_L	78_V	0.691	1.00
191_R	224_I	0.689	1.00
284_D	288_P	0.688	1.00
114_D	281_R	0.688	1.00
188_W	234_I	0.682	1.00
45_L	66_L	0.675	1.00
166_F	246_L	0.674	1.00
58_V	64_R	0.673	1.00
246_L	253_E	0.672	1.00
277_N	280_R	0.672	1.00
180_L	258_L	0.671	1.00
152_E	271_R	0.670	1.00
145_E	263_R	0.669	1.00
170_T	173_L	0.666	1.00
201_V	204_L	0.666	1.00
238_S	241_V	0.662	1.00
119_P	217_E	0.657	1.00
124_V	219_G	0.657	1.00
104_L	107_V	0.656	1.00
192_E	219_G	0.656	1.00
51_D	56_R	0.656	1.00
242_I	246_L	0.648	1.00
92_R	139_V	0.643	1.00
167_A	173_L	0.643	1.00
203_Y	206_L	0.633	1.00
218_L	223_A	0.633	1.00
134_V	153_I	0.630	1.00
47_V	51_D	0.629	1.00
216_M	227_A	0.625	1.00
77_A	80_I	0.620	1.00
135_L	138_R	0.620	1.00
141_I	283_L	0.620	1.00
169_P	249_G	0.618	1.00
278_A	281_R	0.616	1.00
105_P	109_A	0.616	1.00
6_R	10_V	0.614	1.00
197_T	201_V	0.612	1.00
45_L	48_Q	0.609	1.00
115_Y	118_L	0.608	1.00
172_P	175_R	0.607	1.00
89_G	117_Q	0.606	1.00
91_I	141_I	0.604	1.00
80_I	84_F	0.599	1.00
14_V	19_S	0.599	1.00
146_G	155_S	0.599	1.00
23_A	27_L	0.597	1.00
42_E	52_R	0.597	1.00
109_A	112_R	0.593	1.00
20_T	31_Q	0.593	1.00
282_F	286_C	0.591	1.00
103_I	107_V	0.591	1.00
244_D	247_Q	0.588	1.00
198_R	217_E	0.586	1.00
106_A	110_R	0.586	1.00
250_T	253_E	0.585	1.00
94_Y	123_S	0.585	1.00
95_A	122_L	0.583	1.00
163_L	236_C	0.582	1.00
75_E	78_V	0.578	1.00
165_V	183_L	0.577	1.00
205_L	212_F	0.576	1.00
83_L	86_E	0.575	1.00
40_D	44_Q	0.575	1.00
171_S	234_I	0.574	1.00
18_G	57_L	0.574	1.00
199_E	204_L	0.573	1.00
88_N	119_P	0.573	1.00
158_W	267_R	0.572	1.00
269_H	275_L	0.572	1.00
48_Q	62_H	0.572	1.00
181_E	208_H	0.568	1.00
95_A	104_L	0.568	1.00
171_S	187_P	0.568	1.00
94_Y	125_G	0.567	1.00
134_V	268_I	0.565	1.00
173_L	178_V	0.565	1.00
97_S	126_N	0.564	1.00
280_R	283_L	0.560	1.00
50_F	59_V	0.559	1.00
185_A	213_E	0.559	1.00
8_L	66_L	0.555	1.00
197_T	200_I	0.553	1.00
33_A	36_A	0.553	1.00
106_A	226_H	0.552	1.00
110_R	288_P	0.552	1.00
269_H	280_R	0.552	1.00
222_E	226_H	0.551	1.00
12_A	78_V	0.551	1.00
202_D	205_L	0.548	1.00
279_L	283_L	0.548	1.00
119_P	215_A	0.547	1.00
161_D	263_R	0.545	1.00
99_I	103_I	0.545	1.00
179_T	258_L	0.544	1.00
4_T	40_D	0.542	1.00
77_A	81_E	0.541	1.00
191_R	221_S	0.541	1.00
29_L	37_A	0.539	1.00
38_L	42_E	0.539	1.00
70_A	74_L	0.537	1.00
198_R	204_L	0.534	1.00
170_T	252_S	0.534	1.00
181_E	210_P	0.533	1.00
101_N	220_N	0.532	1.00
69_R	80_I	0.531	1.00
224_I	228_V	0.530	1.00
167_A	174_A	0.529	1.00
69_R	83_L	0.528	1.00
113_H	232_L	0.528	1.00
32_S	35_S	0.527	1.00
165_V	188_W	0.527	1.00
94_Y	133_A	0.525	1.00
161_D	238_S	0.522	1.00
15_L	71_L	0.519	1.00
184_A	211_K	0.518	1.00
221_S	238_S	0.517	1.00
65_L	83_L	0.514	1.00
143_F	286_C	0.514	1.00
76_Q	80_I	0.513	1.00
237_L	242_I	0.512	1.00
119_P	214_M	0.512	1.00
32_S	36_A	0.511	1.00
247_Q	250_T	0.510	1.00
34_V	37_A	0.510	1.00
59_V	67_Y	0.506	1.00
97_S	124_V	0.506	1.00
10_V	38_L	0.505	1.00
20_T	52_R	0.502	1.00
242_I	253_E	0.501	1.00
96_S	99_I	0.501	1.00
166_F	251_L	0.501	1.00
275_L	278_A	0.500	1.00
134_V	270_H	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
2esnA	3	0.9932	100	0.08	Contact Map
1uthA	2	0.7509	100	0.09	Contact Map
3fxqA	3	0.9863	100	0.102	Contact Map
3fzvA	4	0.9693	100	0.105	Contact Map
1ixcA	4	0.9795	100	0.113	Contact Map
2h98A	2	0.6928	100	0.113	Contact Map
1al3A	1	0.7099	100	0.116	Contact Map
2h9bA	2	0.6928	100	0.119	Contact Map
4x6gA	4	0.9932	100	0.121	Contact Map
3hhgA	3	0.9863	100	0.13	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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