YEEY - ECOLI - GREMLIN Contacts

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YEEY - Uncharacterized HTH-type transcriptional regulator YeeY

UniProt:	P76369	Sequences: MKPLLDVLMILDALEKEGSFAAASAKLYKTPSALSYTVHKLESDLNIQLLDRSGHRAKFTRTGKMLLEKGREVLHTVRELEKQAIKLHEGWENELVIGVDDTFPFSLLAPLIEAFYQHHSVTRLKFINGVLGGSWDALTQGRADIIVGAMHEPPSSSEFGFSRLGDLEQVFAVAPHHPLALEEEPLNRRIIKRYRAIVVGDTAQAGASTASQLLDEQEAITVFDFKTKLELQISGLGCGYLPRYLAQRFLDSGALIEKKVVAQTLFEPVWIGWNEQTAGLASGWWRDEILANSAIAGVYAKSDDGKSAI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13392
Length:	309 (282)
Sequences:	79766 (57785)
Seq/√Len:	3441.0

ECOLI - YEEY YAHB YDHB YBHD YCAN ALLS YAFC OXYR YFER CYSB LYSR YNFL LEUO AAER CBL CYNR TTDR YEIE ABGR NAC ILVY YHAJ PGRR HCAR DMLR YDCI TDCA GCVA XAPR YBDO NHAR YHJC YNEJ YIAU YFIE DSDC METR YIDZ YBEF ICIA LRHA YJIE YGFI PERR HDFR
BACSU - YCGK CYSL YWBI ALSR YTLI YVBU GLTR CITR YYBE GLTC BSDA YWQM YXJO YOFA YOAU YUST YKUM CZCR 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_E	76_T	3.562	1.00
17_E	26_K	3.288	1.00
162_S	290_L	2.597	1.00
69_K	83_Q	2.432	1.00
13_A	26_K	2.408	1.00
98_G	143_A	2.360	1.00
163_R	268_P	2.215	1.00
166_D	268_P	2.193	1.00
163_R	166_D	2.188	1.00
94_E	125_K	2.179	1.00
177_H	194_Y	2.162	1.00
114_A	292_N	2.135	1.00
47_I	62_T	2.126	1.00
232_Q	239_G	2.110	1.00
10_I	37_T	2.058	1.00
12_D	71_R	2.055	1.00
94_E	123_R	2.029	1.00
168_E	243_R	2.019	1.00
166_D	266_F	2.018	1.00
12_D	16_K	1.983	1.00
114_A	288_E	1.982	1.00
69_K	76_T	1.979	1.00
233_I	254_A	1.973	1.00
170_V	243_R	1.972	1.00
187_N	190_I	1.972	1.00
22_A	25_A	1.930	1.00
13_A	17_E	1.928	1.00
96_V	125_K	1.913	1.00
13_A	16_K	1.872	1.00
229_L	249_F	1.853	1.00
12_D	67_L	1.847	1.00
15_E	59_F	1.818	1.00
16_K	71_R	1.811	1.00
173_V	258_K	1.799	1.00
73_V	77_V	1.798	1.00
10_I	34_L	1.791	1.00
67_L	71_R	1.781	1.00
197_I	237_G	1.775	1.00
170_V	257_E	1.752	1.00
233_I	249_F	1.720	1.00
161_F	270_W	1.689	1.00
195_R	219_A	1.689	1.00
51_D	58_K	1.669	1.00
65_M	83_Q	1.663	1.00
15_E	67_L	1.646	1.00
137_A	142_R	1.639	1.00
66_L	80_L	1.608	1.00
17_E	22_A	1.594	1.00
134_S	146_I	1.556	1.00
160_G	275_E	1.547	1.00
69_K	72_E	1.543	1.00
20_F	38_V	1.533	1.00
12_D	70_G	1.532	1.00
162_S	273_W	1.505	1.00
136_D	140_Q	1.504	1.00
16_K	26_K	1.482	1.00
19_S	22_A	1.477	1.00
7_V	44_D	1.474	1.00
7_V	37_T	1.455	1.00
7_V	40_K	1.444	1.00
286_R	290_L	1.437	1.00
90_G	121_V	1.433	1.00
48_Q	51_D	1.417	1.00
273_W	286_R	1.417	1.00
115_F	285_W	1.415	1.00
10_I	29_K	1.413	1.00
160_G	273_W	1.408	1.00
13_A	27_L	1.402	1.00
11_L	67_L	1.400	1.00
69_K	79_E	1.394	1.00
148_G	272_G	1.393	1.00
53_S	58_K	1.388	1.00
105_F	226_K	1.387	1.00
30_T	33_A	1.387	1.00
182_E	190_I	1.386	1.00
209_T	213_L	1.383	1.00
150_M	270_W	1.369	1.00
278_A	282_S	1.364	1.00
21_A	31_P	1.363	1.00
137_A	143_A	1.363	1.00
118_H	288_E	1.360	1.00
115_F	122_T	1.351	1.00
76_T	79_E	1.351	1.00
4_L	7_V	1.340	1.00
284_W	287_D	1.339	1.00
96_V	127_I	1.338	1.00
92_E	121_V	1.330	1.00
206_G	213_L	1.327	1.00
138_L	146_I	1.325	1.00
73_V	80_L	1.318	1.00
61_R	64_K	1.308	1.00
12_D	74_L	1.296	1.00
167_L	244_Y	1.293	1.00
114_A	118_H	1.292	1.00
271_I	286_R	1.283	1.00
68_E	72_E	1.278	1.00
175_P	254_A	1.277	1.00
66_L	81_E	1.276	1.00
139_T	158_E	1.267	1.00
5_L	77_V	1.265	1.00
145_I	271_I	1.260	1.00
69_K	80_L	1.246	1.00
175_P	256_I	1.246	1.00
194_Y	238_C	1.237	1.00
228_K	239_G	1.229	1.00
163_R	270_W	1.224	1.00
173_V	238_C	1.223	1.00
206_G	210_A	1.221	1.00
116_Y	219_A	1.220	1.00
230_E	233_I	1.219	1.00
243_R	257_E	1.209	1.00
29_K	33_A	1.202	1.00
65_M	68_E	1.199	1.00
116_Y	195_R	1.191	1.00
113_E	117_Q	1.174	1.00
145_I	282_S	1.174	1.00
113_E	234_S	1.173	1.00
36_Y	40_K	1.168	1.00
249_F	254_A	1.166	1.00
44_D	81_E	1.164	1.00
11_L	50_L	1.160	1.00
243_R	247_Q	1.147	1.00
161_F	272_G	1.144	1.00
11_L	15_E	1.144	1.00
65_M	69_K	1.142	1.00
185_P	261_V	1.138	1.00
110_P	234_S	1.105	1.00
195_R	217_Q	1.105	1.00
36_Y	39_H	1.093	1.00
173_V	177_H	1.093	1.00
177_H	180_A	1.092	1.00
64_K	68_E	1.091	1.00
39_H	43_S	1.086	1.00
72_E	79_E	1.085	1.00
119_H	284_W	1.084	1.00
288_E	292_N	1.083	1.00
162_S	286_R	1.079	1.00
247_Q	251_D	1.078	1.00
257_E	260_V	1.076	1.00
125_K	221_T	1.073	1.00
186_L	190_I	1.071	1.00
287_D	290_L	1.070	1.00
8_L	70_G	1.066	1.00
172_A	257_E	1.058	1.00
139_T	156_S	1.057	1.00
13_A	23_A	1.057	1.00
114_A	117_Q	1.053	1.00
274_N	277_T	1.047	1.00
230_E	234_S	1.044	1.00
20_F	57_A	1.041	1.00
73_V	76_T	1.041	1.00
283_G	287_D	1.035	1.00
111_L	289_I	1.031	1.00
248_R	252_S	1.024	1.00
229_L	233_I	1.020	1.00
37_T	40_K	1.020	1.00
6_D	9_M	1.019	1.00
11_L	49_L	1.016	1.00
35_S	39_H	1.016	1.00
168_E	266_F	1.015	1.00
127_I	137_A	1.013	1.00
81_E	85_I	1.008	1.00
188_R	262_A	1.007	1.00
75_H	79_E	0.996	1.00
288_E	291_A	0.994	1.00
222_V	228_K	0.987	1.00
115_F	288_E	0.983	1.00
174_A	235_G	0.981	1.00
14_L	23_A	0.980	1.00
197_I	228_K	0.952	1.00
95_L	285_W	0.950	1.00
14_L	20_F	0.948	1.00
66_L	70_G	0.945	1.00
172_A	246_A	0.945	1.00
40_K	43_S	0.942	1.00
115_F	119_H	0.941	1.00
29_K	34_L	0.940	1.00
78_R	81_E	0.932	1.00
9_M	78_R	0.931	1.00
207_A	210_A	0.931	1.00
208_S	212_Q	0.930	1.00
15_E	50_L	0.924	1.00
198_V	218_E	0.921	1.00
59_F	63_G	0.919	1.00
23_A	34_L	0.918	1.00
222_V	231_L	0.917	1.00
137_A	140_Q	0.916	1.00
22_A	26_K	0.915	1.00
210_A	213_L	0.914	1.00
10_I	27_L	0.913	1.00
171_F	238_C	0.912	1.00
207_A	211_S	0.911	1.00
11_L	41_L	0.910	1.00
78_R	82_K	0.909	1.00
72_E	75_H	0.907	1.00
11_L	59_F	0.898	1.00
101_D	224_D	0.895	1.00
65_M	87_L	0.894	1.00
279_G	282_S	0.888	1.00
118_H	291_A	0.882	1.00
209_T	214_L	0.879	1.00
18_G	58_K	0.874	1.00
173_V	179_L	0.873	1.00
77_V	81_E	0.872	1.00
150_M	268_P	0.867	1.00
68_E	71_R	0.860	1.00
111_L	288_E	0.859	1.00
160_G	163_R	0.859	1.00
143_A	146_I	0.853	1.00
180_A	256_I	0.851	1.00
50_L	57_A	0.847	1.00
47_I	84_A	0.846	1.00
62_T	65_M	0.843	1.00
205_A	208_S	0.841	1.00
6_D	37_T	0.841	1.00
21_A	25_A	0.837	1.00
98_G	148_G	0.833	1.00
135_W	139_T	0.830	1.00
196_A	216_E	0.829	1.00
190_I	193_R	0.829	1.00
192_K	214_L	0.827	1.00
205_A	209_T	0.826	1.00
113_E	236_L	0.824	1.00
98_G	134_S	0.823	1.00
123_R	217_Q	0.823	1.00
62_T	87_L	0.821	1.00
127_I	143_A	0.820	1.00
27_L	34_L	0.819	1.00
93_N	281_A	0.817	1.00
79_E	83_Q	0.817	1.00
116_Y	236_L	0.814	1.00
97_I	145_I	0.813	1.00
53_S	56_R	0.811	1.00
111_L	292_N	0.811	1.00
246_A	249_F	0.805	1.00
187_N	261_V	0.805	1.00
62_T	84_A	0.804	1.00
233_I	252_S	0.802	1.00
17_E	23_A	0.799	1.00
18_G	56_R	0.798	1.00
76_T	80_L	0.797	1.00
31_P	35_S	0.797	1.00
195_R	218_E	0.797	1.00
176_H	180_A	0.795	1.00
15_E	63_G	0.795	1.00
98_G	146_I	0.792	1.00
278_A	283_G	0.791	1.00
122_T	281_A	0.791	1.00
15_E	18_G	0.791	1.00
159_F	272_G	0.790	1.00
16_K	67_L	0.789	1.00
77_V	80_L	0.789	1.00
189_R	192_K	0.788	1.00
11_L	66_L	0.787	1.00
249_F	252_S	0.787	1.00
174_A	177_H	0.781	1.00
280_L	284_W	0.780	1.00
18_G	64_K	0.779	1.00
5_L	74_L	0.774	1.00
9_M	13_A	0.773	1.00
39_H	48_Q	0.772	1.00
172_A	239_G	0.769	1.00
287_D	291_A	0.765	1.00
174_A	236_L	0.760	1.00
71_R	75_H	0.760	1.00
168_E	264_T	0.757	1.00
168_E	259_K	0.754	1.00
14_L	50_L	0.753	1.00
20_F	34_L	0.749	1.00
99_V	104_P	0.748	1.00
7_V	10_I	0.748	1.00
133_G	136_D	0.745	1.00
231_L	236_L	0.743	1.00
80_L	84_A	0.742	1.00
64_K	67_L	0.740	1.00
250_L	253_G	0.736	1.00
139_T	159_F	0.735	1.00
158_E	275_E	0.731	1.00
208_S	211_S	0.731	1.00
118_H	284_W	0.727	1.00
141_G	274_N	0.726	1.00
145_I	285_W	0.726	1.00
51_D	60_T	0.726	1.00
284_W	288_E	0.726	1.00
70_G	73_V	0.723	1.00
115_F	284_W	0.719	1.00
93_N	122_T	0.717	1.00
14_L	34_L	0.716	1.00
172_A	241_L	0.715	1.00
61_R	65_M	0.706	1.00
173_V	256_I	0.705	1.00
144_D	282_S	0.703	1.00
242_P	245_L	0.702	1.00
176_H	235_G	0.700	1.00
9_M	12_D	0.697	1.00
114_A	291_A	0.697	1.00
224_D	227_T	0.693	1.00
172_A	250_L	0.693	1.00
85_I	88_H	0.688	1.00
14_L	38_V	0.686	1.00
62_T	66_L	0.682	1.00
151_H	154_P	0.679	1.00
179_L	194_Y	0.673	1.00
91_W	119_H	0.672	1.00
179_L	182_E	0.667	1.00
177_H	195_R	0.664	1.00
51_D	56_R	0.664	1.00
200_G	221_T	0.662	1.00
105_F	230_E	0.662	1.00
66_L	84_A	0.661	1.00
59_F	64_K	0.660	1.00
6_D	40_K	0.657	1.00
96_V	144_D	0.657	1.00
69_K	73_V	0.656	1.00
177_H	182_E	0.655	1.00
199_V	228_K	0.655	1.00
187_N	262_A	0.652	1.00
96_V	143_A	0.652	1.00
196_A	238_C	0.652	1.00
250_L	257_E	0.645	1.00
58_K	64_K	0.645	1.00
133_G	137_A	0.645	1.00
33_A	37_T	0.643	1.00
25_A	28_Y	0.640	1.00
9_M	74_L	0.640	1.00
220_I	231_L	0.638	1.00
171_F	240_Y	0.637	1.00
185_P	259_K	0.634	1.00
246_A	250_L	0.634	1.00
110_P	113_E	0.634	1.00
182_E	185_P	0.634	1.00
75_H	78_R	0.633	1.00
209_T	212_Q	0.631	1.00
79_E	82_K	0.630	1.00
11_L	63_G	0.627	1.00
248_R	251_D	0.625	1.00
123_R	221_T	0.624	1.00
280_L	283_G	0.623	1.00
42_E	52_R	0.620	1.00
182_E	195_R	0.619	1.00
176_H	256_I	0.614	1.00
193_R	217_Q	0.612	1.00
110_P	114_A	0.610	1.00
149_A	267_E	0.610	1.00
206_G	209_T	0.601	1.00
145_I	286_R	0.601	1.00
42_E	47_I	0.601	1.00
104_P	131_L	0.596	1.00
82_K	86_K	0.594	1.00
45_L	66_L	0.590	1.00
95_L	281_A	0.588	1.00
171_F	191_I	0.587	1.00
108_L	111_L	0.585	1.00
6_D	10_I	0.584	1.00
38_V	42_E	0.583	1.00
208_S	213_L	0.582	1.00
205_A	213_L	0.582	1.00
273_W	283_G	0.581	1.00
70_G	74_L	0.580	1.00
14_L	19_S	0.579	1.00
74_L	78_R	0.577	1.00
99_V	108_L	0.576	1.00
23_A	27_L	0.576	1.00
65_M	84_A	0.573	1.00
15_E	64_K	0.572	1.00
200_G	223_F	0.572	1.00
45_L	84_A	0.571	1.00
95_L	145_I	0.570	1.00
119_H	122_T	0.569	1.00
285_W	289_I	0.569	1.00
175_P	253_G	0.567	1.00
92_E	123_R	0.562	1.00
192_K	215_D	0.560	1.00
173_V	180_A	0.560	1.00
20_F	31_P	0.555	1.00
222_V	227_T	0.554	1.00
50_L	59_F	0.554	1.00
167_L	267_E	0.554	1.00
47_I	51_D	0.551	1.00
33_A	36_Y	0.550	1.00
164_L	271_I	0.549	1.00
169_Q	240_Y	0.549	1.00
177_H	238_C	0.548	1.00
150_M	161_F	0.546	1.00
228_K	232_Q	0.543	1.00
165_G	269_V	0.543	1.00
138_L	159_F	0.542	1.00
45_L	48_Q	0.540	1.00
241_L	246_A	0.539	1.00
32_S	36_Y	0.537	1.00
98_G	127_I	0.534	1.00
138_L	272_G	0.534	1.00
30_T	36_Y	0.532	1.00
93_N	121_V	0.530	1.00
231_L	237_G	0.529	1.00
110_P	230_E	0.529	1.00
201_D	221_T	0.528	1.00
82_K	85_I	0.525	1.00
86_K	91_W	0.523	1.00
59_F	67_L	0.522	1.00
109_A	113_E	0.522	1.00
83_Q	86_K	0.521	1.00
18_G	57_A	0.519	1.00
171_F	196_A	0.518	1.00
225_F	242_P	0.517	1.00
136_D	142_R	0.517	1.00
29_K	37_T	0.517	1.00
139_T	142_R	0.516	1.00
141_G	277_T	0.513	1.00
282_S	286_R	0.511	1.00
273_W	278_A	0.510	1.00
10_I	38_V	0.509	1.00
48_Q	62_T	0.509	1.00
107_L	111_L	0.509	1.00
160_G	276_Q	0.508	1.00
80_L	83_Q	0.508	1.00
99_V	126_F	0.508	1.00
103_F	107_L	0.507	1.00
112_I	124_L	0.505	1.00
20_F	56_R	0.504	1.00
147_V	289_I	0.501	1.00
134_S	141_G	0.501	1.00
105_F	224_D	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
3fzvA	4	0.9223	100	0.116	Contact Map
2esnA	3	0.9417	100	0.123	Contact Map
3fxqA	3	0.9385	100	0.131	Contact Map
1uthA	2	0.7184	100	0.131	Contact Map
1ixcA	4	0.932	100	0.131	Contact Map
4x6gA	4	0.9644	100	0.137	Contact Map
2h98A	2	0.6731	100	0.138	Contact Map
2h9bA	2	0.6764	100	0.141	Contact Map
1al3A	1	0.7055	100	0.142	Contact Map
3hhgA	3	0.9353	100	0.144	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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